From 2adcb11549ce0a4694e2375cb8d6282dc651f18b Mon Sep 17 00:00:00 2001 From: Susheel Varma Date: Wed, 25 Oct 2023 03:46:52 +0000 Subject: [PATCH] Commit new papers and preprints --- data/covid/preprints-summary.csv | 92 +- data/covid/preprints.csv | 336 +- data/covid/preprints.exact.csv | 178 +- data/covid/preprints.exact.json | 310 +- data/covid/preprints.json | 600 +- data/covid/raw-preprints.json | 106488 ++++++++++++++-------------- 6 files changed, 52278 insertions(+), 55726 deletions(-) diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 1db895d4..66c03727 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,46 +1,46 @@ -geriatric medicine,month,dermatology,oncology,allergy and immunology,public and global health,orthopedics,neurology,emergency medicine,ophthalmology,obstetrics and gynecology,immunology,health informatics,occupational and environmental health,respiratory medicine,biochemistry,microbiology,cardiovascular medicine,evolutionary biology,surgery,molecular biology,pharmacology and therapeutics,health economics,intensive care and critical care medicine,epidemiology,biophysics,genomics,bioinformatics,infectious diseases,scientific communication and education,primary care research,psychiatry and clinical psychology,pediatrics,radiology and imaging,dentistry and oral medicine,genetic and genomic medicine,pathology,hiv aids,Total,systems biology,health systems and quality improvement,health policy -,Oct-23,,,,,,,,,,,1,,1,,,,,,,,,,,,,,1,,,,,,,,,,3,,, -,Sep-23,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,1,,, -,Aug-23,,,,1,,,,,,,,1,,,,,,,,,,,4,,,,,,1,,,,,,,,7,,, -,Jul-23,,,,1,,,,,,,,,,,,,,,,,,,3,,,,,,,,,,,1,,,7,,2, -,Jun-23,,,,,1,,,,,,1,1,,,,,,,,,,,1,,,,2,1,,,,,,,,,7,,, -,May-23,,,,1,,,,,,1,,,1,,,,,,,,,,2,,,,1,,,,,,,,,,6,,, -,Apr-23,,,,2,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,3,,, -,Mar-23,,,,2,,,,,,,,1,,,,,,,,,,,2,,,,3,,,1,,,,,,,9,,, -,Feb-23,,,,2,,1,,,,,,,1,,,,,,,,,,3,,,,,,,,,,,,,,7,,, -,Jan-23,,,,,,,,,,,,,,,,,,,,,,,5,,,,1,,,,,,,,,,6,,, -,Dec-22,,,,1,,,,,,,,,2,,,,,,,,,,2,,,,4,,,,,,,,1,,11,,,1 -,Nov-22,,,,,,,,,,,,,,,,,,,,,,,,,,,4,,,,,,,,,,4,,, -,Oct-22,,,,2,,,,,,,,,,,,1,,,,,,,1,,,,2,,,,,,,,,,6,,, -,Sep-22,,,,1,,,,,,,,2,1,,1,,,,,,,,1,,,,2,,,,1,,,,,,9,,, -,Aug-22,,,,3,,,,,,,,,,,,,,,,,,,4,,,,3,,,,,,,,,,10,,, -,Jul-22,,,,,,,,,,1,1,,,,,,,,,,,,2,,,,2,,,,1,,,,,,7,,, -,Jun-22,,,,1,,,,,,,1,,,,,,,,,,,,6,,,,4,,,5,,,,1,,,18,,, -,May-22,,,,1,,,,,,,,,,,1,,,,,,1,,2,,,,5,,1,2,,,,,,,14,,1, -,Apr-22,,,,1,,,,,,,,1,1,,1,1,,,,,1,,4,,,,3,,,,,,,,,,15,,2, -,Mar-22,,,,,,,,,,,,,1,,,,1,,,,,,9,,,,5,,1,1,,,,,,,18,,, -,Feb-22,,,,1,,1,,,,,,,,,,,,,,,,,6,,,,4,,,,,,,,,,12,,, -,Jan-22,,,,1,,,,,,1,2,1,,,,1,,,,,,,5,,,,3,,,,,,,,,,14,,, -,Dec-21,,,,1,,1,,,,,,,,,1,1,,,,,,,9,,,,8,,1,,1,,,,,,23,,, -,Nov-21,,,,3,,1,,,,,,,,,,,,,,,,1,9,1,1,,5,,,1,,,,,,,24,,2, -1,Oct-21,,,,,,,,,,,,,,,,,,,,,,,4,,,,3,,,2,1,,,,,,11,,, -,Sep-21,,,,2,,,,,,,1,,,,,1,,,,1,,1,6,,,,5,,,,,,,,,,17,,, -,Aug-21,,,,3,,,,,,,1,1,1,,,1,,,,,,1,2,,,,3,,,,,,,,,,13,,, -,Jul-21,,1,,4,,,,,,,,,2,,,,,,,,,1,3,,,,12,,,,1,,,1,,,25,,, -,Jun-21,,,1,4,,1,,,,1,1,1,,,,,,,,,,1,6,,,,7,,1,1,1,,,,,,26,,, -,May-21,1,,,1,,,,,,,1,,,,,,,,,,,,11,,,,8,,,1,,,,1,,,24,,, -,Apr-21,,,1,1,,,,,,,1,2,,,,,,,,,,,4,,,,7,,1,1,,,,,,,19,,1, -1,Mar-21,,,,5,,1,,,,,1,,,1,,,,1,,,,,5,,,,17,,,1,1,1,,1,,,36,,, -,Feb-21,,,,1,,,,,,,1,,,,,1,,1,,,1,,8,,,,9,,,,,,,,,,23,,1, -1,Jan-21,,,,3,,,,,,1,,,,,,,,,,,,1,4,,,,8,,1,1,,,1,,,,23,,1,1 -,Dec-20,,,,2,,,,,,,3,,,,1,2,,,,,,,4,,2,,4,,1,2,,,,,,,22,,1, -,Nov-20,,,,5,,,,,,1,1,,,,,,,,,,,,6,,,1,12,,,,,,,,,,27,,,1 -1,Oct-20,,1,,,,,,,,1,1,,,,,,,,,,,1,6,,,1,11,,1,3,,,,,,,29,1,,1 -,Sep-20,,,,3,,,3,,,,1,,,,1,,,,,,,1,6,,,,7,,1,2,,,,,,1,26,,, -,Aug-20,,,,2,,,2,,1,,,1,,,,,,,1,,,,5,,,,11,,,,,,,1,,,25,,1, -,Jul-20,,,,4,,,,,,1,,,,,,1,,,,,,1,10,,1,,8,,,1,,,,,,,27,,, -1,Jun-20,,1,,3,,,,1,,1,1,,1,,,1,,,,,,3,6,,,1,9,,,4,,,,,,,35,,1,1 -1,May-20,,1,,9,,,,,,,1,1,1,,,2,,,,,1,1,8,,,1,10,,,,,,,,,,37,,, -,Apr-20,,,,1,,,,,,,,,,,,,,,,,,,7,,1,,7,,,,,,,2,,,19,,1, -,Mar-20,,,,3,,,,,,,,,,,,,,,,,,,4,,,,1,,,,,,,,,,8,,, -,Feb-20,,,,2,,,,,,,,,,,,,,,,,,,4,,,,1,,,,,,,,,,7,,, +oncology,systems biology,dentistry and oral medicine,hiv aids,health policy,primary care research,radiology and imaging,epidemiology,bioinformatics,pediatrics,Total,molecular biology,public and global health,biochemistry,scientific communication and education,health systems and quality improvement,genomics,intensive care and critical care medicine,pharmacology and therapeutics,respiratory medicine,evolutionary biology,orthopedics,geriatric medicine,month,genetic and genomic medicine,neurology,pathology,health economics,health informatics,microbiology,cardiovascular medicine,ophthalmology,biophysics,occupational and environmental health,allergy and immunology,obstetrics and gynecology,infectious diseases,immunology,psychiatry and clinical psychology,surgery,emergency medicine,dermatology +,,,,,,,,,,4,,,,,,,,,1,,,,Oct-23,,,,,1,,,,,,,,1,1,,,, +,,,,,,,,,,1,,,,,,,,,,,,,Sep-23,,,,,,,,,,,,,1,,,,, +,,,,,1,,4,,,7,,1,,,,,,,,,,,Aug-23,,,,,,,,,,1,,,,,,,, +,,,,,,,3,,,7,,1,,,2,,,,,,,,Jul-23,1,,,,,,,,,,,,,,,,, +,,,,,,,1,,,7,,,,1,,,,,,,1,,Jun-23,,,,,1,,,,,1,,,2,,,,, +,,,,,,,2,,,6,,1,,,,,,,1,,,,May-23,,,,,,,,,,,,,1,1,,,, +,,,,,,,,,,3,,2,,,,,,,,,,,Apr-23,,,,,,,,,,,,,1,,,,, +,,,,,,,2,,,8,,2,,,,,,,,,,,Mar-23,,,,,,,,,,,,,3,,1,,, +,,,,,,,4,,,8,,2,,,,,,,1,,,,Feb-23,,1,,,,,,,,,,,,,,,, +,,,,,,,5,,,6,,,,,,,,,,,,,Jan-23,,,,,,,,,,,,,1,,,,, +,,,,1,,,3,,,12,,1,,,,,,,2,,,,Dec-22,,,1,,,,,,,,,,4,,,,, +,,,,,,,,,,4,,,,,,,,,,,,,Nov-22,,,,,,,,,,,,,4,,,,, +,,,,,,,1,,,6,,2,,,,,,,,,,,Oct-22,,,,,,,1,,,,,,2,,,,, +,,,,,,,1,,1,9,,1,,,,,,,1,,,,Sep-22,,,,,,1,,,,2,,,2,,,,, +,,,,,,,4,,,9,,3,,,,,,,,,,,Aug-22,,,,,,,,,,,,,2,,,,, +,,,,,,,2,,1,8,,,,,,,,,,,,,Jul-22,,,,,1,,,,,,,,3,1,,,, +,,,,,,,5,,,16,,,,,,,,,,,,,Jun-22,1,,,,1,,,,,,,,4,,5,,, +,,,,,1,,2,,,14,,1,,,1,,,,,,,,May-22,,,,1,,1,,,,,,,5,,2,,, +,,,,,,,5,,,16,,1,,,2,,,,1,,,,Apr-22,,,,1,,1,1,,,1,,,3,,,,, +,,,,,1,,9,,,18,,,,,,,,,1,1,,,Mar-22,,,,,,,,,,,,,5,,1,,, +,,,,,,,6,,,12,,1,,,,,,,,,,,Feb-22,,1,,,,,,,,,,,4,,,,, +,,,,,,,5,,,14,,1,,,,,,,,,,,Jan-22,,,,,2,,1,,,1,,,3,1,,,, +,,,,,1,,10,,1,24,,1,,,,,,,,,,,Dec-21,,1,,,,1,1,,,,,,8,,,,, +,,,,,1,,9,,,25,,3,,,2,1,1,,,,,,Nov-21,,1,,,,,,,1,,,,5,,1,,, +,,,,,,,4,,1,11,,,,,,,,,,,,1,Oct-21,,,,,,,,,,,,,3,,2,,, +,,,,,,,6,,,16,,2,,,,,1,1,,,,,Sep-21,,,,,,,1,,,,,,5,,,,, +,,,,,,,2,,,13,,3,,,,,1,,1,,,,Aug-21,,,,,1,,1,,,1,,,3,,,,, +1,,,,,,,3,,1,25,,4,,,,,1,,2,,,,Jul-21,1,,,,,,,,,,,,11,,,,1, +,,,,,,,6,,1,26,,4,,,1,,1,,,,,,Jun-21,,1,,,1,,,,,1,1,,7,1,1,,, +,,,,,,,10,,,22,,1,,,,,,,,,,,May-21,1,,,,1,,,,,,,,7,,1,,,1 +,,,,,1,,4,,,18,,1,,,1,,,,,,,,Apr-21,,,,,1,1,,,,1,1,,6,,1,,, +,,,,,,1,6,,1,39,,5,1,,,,,,,,,2,Mar-21,1,1,,,2,,,,,,,,17,,1,1,, +,,,,,,,9,,,22,,1,,,1,,,,,,,,Feb-21,,,,1,,,1,,,,,,8,,,1,, +,,1,,1,1,,4,,,23,,3,,,1,,1,,,,,1,Jan-21,,,,,,,,,,,,,8,1,1,,, +,,,,,1,,4,,,22,,3,,,1,2,,,,,,,Dec-20,,,,,3,1,2,,,,,,3,,2,,, +,,,,1,,,6,1,,28,,5,,,,,,,,,,,Nov-20,,,,,1,,,,,,,,13,1,,,, +1,1,,,1,1,,6,1,,29,,,,,,,1,,,,,1,Oct-20,,,,,1,,,,,,,,11,1,3,,, +,,,1,,1,,6,,,26,,3,,,,,1,,,,,,Sep-20,,,,,1,1,,,,,,,7,,2,,3, +,,,,,,,6,,,26,1,2,,,1,,,,,,,,Aug-20,,,,,,,,,,1,,1,12,,,,2, +,,,,,,,9,,,26,,4,,,,1,1,,1,,,,Jul-20,,,,,,,1,,,,,,7,1,1,,, +1,,,,1,,,7,1,,36,,3,,,1,,2,,1,,,1,Jun-20,,,,,1,,1,1,,,,,10,1,4,,, +1,,,,,,,8,1,,37,,9,,,,,1,,1,,,1,May-20,,,,1,1,,2,,,1,,,10,,,,, +,,,,,,,7,,,19,,1,,,1,1,,,,,,,Apr-20,2,,,,,,,,,,,,7,,,,, +,,,,,,,4,,,8,,3,,,,,,,,,,,Mar-20,,,,,,,,,,,,,1,,,,, +,,,,,,,4,,,7,,2,,,,,,,,,,,Feb-20,,,,,,,,,,,,,1,,,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index faf94aa4..7fabeb69 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -1,4 +1,5 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity +bioRxiv,10.1101/2023.10.22.563481,2023-10-24,https://biorxiv.org/cgi/content/short/2023.10.22.563481,Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy,Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis,"Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D","Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.",immunology,fuzzy,100,100 medRxiv,10.1101/2023.10.12.23296948,2023-10-13,https://medrxiv.org/cgi/content/short/2023.10.12.23296948,"A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes",Johan H Thygesen; HUAYU ZHANG; Hanane Issa; Jinge Wu; Tuankasfee Hama; Ana-Catarina Pinho-Gomes; Tudor Groza; Sara Khalid; Richard Lumbers; Mevhibe Hocaoglu; Kamlesh Khunti; Rouven Priedon; Amitava Banerjee; Nikolas Pontikos; Christopher Tomlinson; Ana Torralbo; Paul Taylor; Cathie Sudlow; Spiros Denaxas; Harry Hemingway; Honghan Wu,"Institute of Health Informatics, University College London, London, UK; Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK.; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK; College of Life Sciences, University of Leicester, Leicester, UK; Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK","BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic. MethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2. @@ -265,15 +266,6 @@ MethodsWe included UK COVID-19 Infection Survey participants who tested positive ResultsOverall, Long Covid was reported by those [≥]16 years after 4.0% and 2.4% of first and second infections, respectively; the corresponding estimates among those <16 years were 1.0% and 0.6%. The aOR for Long Covid after second compared to first infections was 0.72 (95% confidence interval: 0.63-0.81) for those [≥]16 years and 0.93 (0.57-1.53) for those <16 years. ConclusionsThe risk of new-onset Long Covid after a second SARS-CoV-2 infection is lower than that after a first infection for those [≥]16 years, though there is no evidence of a difference in risk for those <16 years. However, there remains some risk of new-onset Long Covid after a second infection, with around 1 in 40 of those [≥]16 years and 1 in 165 of those <16 years reporting Long Covid after a second infection.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -358,6 +350,13 @@ MethodsThe study included five prospective cohorts from four countries (Iceland, Results162,237 and 168,783 individuals were included in the analysis of depression and anxiety, respectively, of whom 24,718 and 27,003 reported a significant person with COVID-19. Overall, the PR was 1.07 (95% CI: 1.05-1.10) for depression and 1.08 (95% CI: 1.03-1.13) for anxiety among significant others of COVID-19 patients. The respective PRs for depression and anxiety were 1.04 (95% CI: 1.01-1.07) and 1.03 (95% CI: 0.98-1.07) if the significant person was never hospitalized, 1.15 (95% CI: 1.08-1.23) and 1.24 (95% CI: 1.14-1.34) if the patient was hospitalized, 1.42 (95% CI: 1.27-1.57) and 1.45 (95% CI: 1.31-1.60) if admitted to the ICU, and 1.34 (95% CI: 1.22-1.46) and 1.36 (95% CI: 1.22-1.51) if the significant person died. Individuals of hospitalized, ICU admitted, or deceased patients showed higher prevalence of depression and anxiety during the entire 12 months after the COVID-19 diagnosis of the significant person. ConclusionsClose friends and family members of critically ill COVID-19 patients show elevated prevalence of depression and anxiety throughout the first year after the diagnosis.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2023.02.17.23286079,2023-02-23,https://medrxiv.org/cgi/content/short/2023.02.17.23286079,"Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.",Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson,UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency,"AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures. + +Methods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded. + +ConclusionsFew workplace surface samples were positive for SARS-CoV-2 RNA and positive samples typically contained low levels of nucleic acid. Although these data may infer a low probability of fomite transmission or other forms of transmission within the workplace, Ct values may have been lower at the time of contamination. Workplace environmental sampling identified lapses in COVID-control measures within individual sites and showed trends through the pandemic. + +Significance and Impact of the StudyPrior to this study, few published reports investigated SARS-CoV-2 RNA contamination within workplaces experiencing cases of COVID-19. This report provides extensive data on environmental sampling identifying trends across workplaces and through the pandemic.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.02.18.23286127,2023-02-19,https://medrxiv.org/cgi/content/short/2023.02.18.23286127,Antipsychotic prescribing and mortality in people with dementia before and during the COVID-19 pandemic: retrospective cohort study,Christian Schnier; Aoife McCarthy; Daniel R Morales; Ashley Akbari; Reecha Sofat; Caroline Dale; Rohan Takhar; Mamas Mamas; Kamlesh Khunti; Francesco Zaccardi; Cathie LM Sudlow; Tim Wilkinson,University of Edinburgh; University of Edinburgh; University of Dundee; Swansea University; University of Liverpool; University of Liverpool; University College London; Keele University; University of Leicester; University of Leicester; University of Edinburgh; University of Edinburgh,"BackgroundAntipsychotic drugs have been associated with increased mortality, stroke and myocardial infarction in people with dementia. Concerns have been raised that antipsychotic prescribing may have increased during the COVID-19 pandemic due to social restrictions imposed to limit the spread of the virus. We used multisource, routinely-collected healthcare data from Wales, UK, to investigate prescribing and mortality trends in people with dementia before and during the COVID-19 pandemic. MethodsWe used individual-level, anonymised, population-scale linked health data to identify adults aged [≥]60 years with a diagnosis of dementia in Wales, UK. We explored antipsychotic prescribing trends over 67 months between 1st January 2016 and 1st August 2021, overall and stratified by age and dementia subtype. We used time series analyses to examine all-cause, myocardial infarction (MI) and stroke mortality over the study period and identified the leading causes of death in people with dementia. @@ -495,7 +494,18 @@ Key pointsO_ST_ABSQuestionC_ST_ABSIs there an association between prescription o FindingsIn this retrospective cohort study of mental health outpatients with a recent (1-3 months) antidepressant prescription, there was a statistically significant 40% decrease in positive COVID-19 tests. This association was specifically observed for the most commonly prescribed antidepressant class, Selective Serotonin Reuptake Inhibitors, and remained when adjusted for socioeconomic parameters and physical health. MeaningAntidepressant prescription was associated with lower incidence of COVID-19 in the community, warranting further investigation as prophylactics in prospective clinical studies.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.12.19.22283660,2022-12-19,https://medrxiv.org/cgi/content/short/2022.12.19.22283660,"Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan",Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford,"Background The COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. Objectives A. To determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. B. To estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. C. To assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. Methods This population-based study uses the QResearch database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of severe COVID-19 outcomes after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and dissemination QResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.12.19.22283660,2022-12-19,https://medrxiv.org/cgi/content/short/2022.12.19.22283660,"Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan",Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford,"BackgroundThe COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. + +ObjectivesO_LITo determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. +C_LIO_LITo estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. +C_LIO_LITo assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. +C_LI + +MethodsThis population-based study uses the QResearch(R) database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. + +We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. + +Ethics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.12.16.22283578,2022-12-17,https://medrxiv.org/cgi/content/short/2022.12.16.22283578,"Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Jonathan R Emberson; Buddha Basnyat; Mark Campbell; Leon Peto; Guilherme Pessoa-Amorim; Natalie Staplin; Raph L Hamers; John Amuasi; Jeremy Nel; Evelyne Kestelyn; Manisha Rawal; Roshan Kumar Jha; Nguyen Thanh Phong; Uun Samardi; Damodar Paudel; Pham Ngoc Thach; Nasronudin Nasronudin; Emma Stratton; Louise Mew; Rahuldeb Sarkar; J Kenneth Baillie; Maya H Buch; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Marian Knight; Wei Shen Lim; Marion Mafham; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; OUCRU-Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Kumasi Center for Collaborative Research in Tropic Medicine, Kumasi, Ghana; Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal; Medicine Department, Nepal Armed Police Force Hospital, Chandragiri, Kathmandu, Nepal; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; RSUP Dr Hasan Sadikin Hospital, Bandung, West Java, Indonesia; Department of Medicine, Nepal Police Hospital, Maharajgunj, Kathmandu, Nepal; National Hospital for Tropical Diseases, Hanoi, Vietnam; University of Airlangga Teaching Hospital, Surabaya, Indonesia; University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Faculty of Life Sciences and Medicine, King's College, London, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundLow-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group. MethodsThis randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). @@ -505,6 +515,13 @@ FindingsBetween 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia InterpretationIn patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation. FundingUK Research and Innovation (Medical Research Council) and National Institute of Health and Care Research (Grant ref: MC_PC_19056), and Wellcome Trust (Grant Ref: 222406/Z/20/Z).",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.12.12.22283200,2022-12-14,https://medrxiv.org/cgi/content/short/2022.12.12.22283200,"COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK",Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Mike Seaborne; Michael Parker; Natasha Kennedy; Ashley Akbari; Luisa Zuccolo; Amaya Azcoaga-Lorenzo; Alisha Davies; Krishnarajah Nirantharakumar; Sinead Brophy,"National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, UK; Health Data Science Centre, Fondazione Human Technopole, Milan, Italy; School of Medicine, University of St Andrews, Scotland, UK and Hospital Rey Juan Carlos. Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz. Madrid. Sp; Research and Evaluation Division, Public Health Wales, UK.; Institute of Applied Health Research, Birmingham University, Birmingham, UK.; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U","BackgroundMultimorbidity and pregnancy are two risk factors for more severe outcomes after a SARS-CoV-2 infection, thus vaccination uptake is important for pregnant women living with multimorbidity. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage. + +MethodsThis cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy by multimorbidity and smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. Variation in uptake by; multimorbidity, smoking status, and demographics was examined jointly and separately for the independent conditions using hazard ratios (HR) from the Cox regression model. A bootstrapping internal validation was conducted to assess the performance of the models. + +ResultsWithin the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.02). Women living with multimorbidity (> 1 health condition) were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002). The validated model had similar performance and revealed that multimorbidity, smoking status, age, and deprivation level together have a significant impact on vaccine hesitancy (p < 0.05 for all). + +ConclusionYounger women, living without multimorbidity (zero or only one health condition), current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Women living with multimorbidity are slightly but significantly less likely to be hesitant about COVID-19 vaccination when pregnant.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.12.14.22283458,2022-12-14,https://medrxiv.org/cgi/content/short/2022.12.14.22283458,Trends in inequalities in avoidable hospitalisations across the COVID-19 pandemic: A cohort study of 23.5 million people in England,Mark A Green; Martin McKee; Jon Massey; Brain MacKenna; Amir Mehrkar; Sebastian Bacon; John Macleod; Syed Ahmar Shah; Aziz Sheikh; - The OpenSAFELY Consortium; - The LH&W NCS Collaborative; Srinivasa Vittal Katikireddi,University of Liverpool; London School of Hygiene and Tropical Medicine; University of Oxford; NHS England; University of Oxford; University of Oxford; University of Bristol; University of Edinburgh; University of Edinburgh; ; ; University of Glasgow,"BackgroundThe COVID-19 pandemic and associated national lockdowns created unprecedented disruption to healthcare, with reduced access to services and planned clinical encounters postponed or cancelled. It was widely anticipated that failure to obtain timely treatment would cause progression of illness and increased hospital admissions. Additional concerns were that social and spatial inequalities would widen given the disproportionate impacts of COVID-19 directly. The aim of our study is to determine whether this was observable in England. MethodsWith the approval of NHS England we utilised individual-level electronic health records from OpenSAFELY, which covered [~]40% of general practices in England (mean monthly population size 23.5 million people). We estimated crude and directly age-standardised rates for potentially preventable unplanned hospital admissions: ambulatory care sensitive conditions and urgent emergency sensitive conditions. We considered how trends in these outcomes varied by three measures of social and spatial inequality: neighbourhood socioeconomic deprivation, ethnicity, and geographical region. @@ -808,15 +825,6 @@ What this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron w C_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions. C_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group. C_LI",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.08.08.22278532,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278532,Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI),Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England. - -MethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence. - -Results14175 residents and 19973 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-83 days after first booster, but no protection was apparent after 84 days. Additional protection following booster vaccination waned, but was still present at 84+ days for COVID-associated hospitalisation (aHR: 0.47, 0.24-0.89) and death (aHR: 0.37, 0.21-0.62). Most residents (64.4%) had received primary course of AstraZeneca, but this did not impact on pre- or post-booster risks. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalisations and no deaths. - -ConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial. - -SummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.08.07.22278510,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.07.22278510,Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.,Marc F Österdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves,King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London,"Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. We examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration. @@ -917,14 +925,16 @@ MethodsWe performed a Mendelian randomisation analysis using single nucleotide p ResultsIn the UK Biobank cohort (N=485,825, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of sepsis (OR=0.80; 95% CI 0.66-0.96, per unit of natural log transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR=0.74; 95% CI 0.38-0.70); critical care admission with sepsis (OR=0.48, 95% CI 0.30-0.78) and critical care death with sepsis (OR=0.37, 95% CI 0.14 - 0.98) Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 - 0.97) and for sepsis survival in critical care (OR=0.22; 95% CI 0.04- 1.31) in the GainS and GenOSept consortium. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR=0.69, 95% 0.57 - 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results. ConclusionsIL6R blockade is causally associated with reduced incidence of sepsis, sepsis related critical care admission, and sepsis related mortality. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. This data suggests a randomised trial of IL-6 receptor antagonists in sepsis should be considered.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.06.15.22276446,2022-06-21,https://medrxiv.org/cgi/content/short/2022.06.15.22276446,Experiences of mental health and wellbeing support for NHS staff during the COVID-19 pandemic: a reflexive thematic analysis,Corinne Clarkson; Hannah Scott; Siobhan Hegarty; Emilia Soulios; Rupa Bhundia; Sam Gnanapragasam; Mary Jane Docherty; Rosalind Raine; Sharon Stevelink; Neil Greenberg; Matthew Hotopf; Simon Wessely; Ira Madan; Anne Marie Rafferty; Danielle Lamb,University College London; King's College London; King's College London; King's College London; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; University College London; King's College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; King's College London; UCL,"Staff in the National Health Service (NHS) have been placed under considerable strain during the COVID-19 pandemic; whilst NHS Trusts provide a variety of health and wellbeing support services, there has been little research investigating staff perceptions of these services. Moreover, the research that does exist typically includes only clinical staff, despite a large proportion of patient-facing NHS workers being in non-clinical roles. We interviewed forty-eight clinical and non-clinical healthcare workers from eighteen NHS Trusts in England about their experiences of workplace health and wellbeing support during the pandemic. Reflexive thematic analysis identified that perceived stigma around help-seeking, and staffing shortages due to wider socio-political contexts such as austerity, were barriers to using support services. Visible, caring leadership at all levels (CEO to line managers), peer support, easily accessible services, and clear communication about support offers were enablers. Our evidence suggests Trusts should have active strategies to improve help-seeking. This could involve providing all staff with regular reminders about support options, in a variety of formats (e.g. email, posters, mentioned in meetings), and easily remembered single points of access, delivered by a mix of in-house and externally-provided services, to cater for those more and less concerned about stigma and confidentiality. In addition, managers at all levels should be trained and supported to feel confident to speak about mental health with staff, with formal peer support facilitated by building in time for this during working hours. As others have pointed out, this will require long-term strategic planning to address workforce shortages.",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2022.06.20.22276205,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22276205,Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK),Hayley Holt; Clare Relton; Mohammad Talaei; Jane Symons; Molly R Davies; David A Jolliffe; Giulia Vivaldi; Florence Tydeman; Anne Williamson; Paul E Pfeffer; Christopher Orton; David Ford; Gwyneth A Davies; Ronan A Lyons; Chris J Griffiths; Frank Kee; Aziz Sheikh; Gerome Breen; Seif Shaheen; Adrian R Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; King's College London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Blizard Institute; Barts Health NHS Trust; Swansea University; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; University of Edinburgh; King's College London; Queen Mary University of London; Queen Mary University of London,"BackgroundCoronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is estimated to have caused more than 18 million deaths worldwide as of end-May 2022. +medRxiv,10.1101/2022.07.07.22277367,2022-07-10,https://medrxiv.org/cgi/content/short/2022.07.07.22277367,"Non-hospitalised, vaccinated adults with COVID-19 caused by Omicron BA.1 and BA.2 present with changing symptom profiles compared to those with Delta despite similar viral kinetics",Hermaleigh Townsley; Joshua Gahir; Timothy W Russell; Edward J Carr; Matala Dyke; Murad Miah; Bobbi Clayton; Callie Smith; Mauro Miranda; Nicola O'Reilly; Lorin Adams; Harriet V Mears; Christopher Bailey; James RM Black; Ashley S Fowler; Katalin Wilkinson; Matthew Hutchinson; Ruth Harvey; Bobbi Clayton; Gavin Kelly; Rupert Beale; Padmasayee Papineni; Tumena Corrah; Simon Caidan; Jerome Nicod; Steve Gamblin; George Kassiotis; Vincenzo Libri; Bryan Williams; Sonia Gandhi; Adam J Kucharski; Charles Swanton; David LV Bauer; Emma C Wall,"Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); London Northwest University Healthcare NHS Trust, London; London Northwest University Healthcare NHS Trust, London; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Department of Infectious Disease, St Mary's Hospital, Imperial College London, London; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; Francis Crick Institute, University College London, Gower Street, London; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute, University College London, Gower Street, London; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini","BackgroundSARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). + +MethodsIn a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive PCR or lateral flow test, self-swabbed on alternate days until day 10. We compared symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 and BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR Ct value as a proxy for viral load. -MethodsCOVIDENCE UK is a longitudinal population-based study that investigates risk factors for, and impacts of, COVID-19 in UK residents aged [≥]16 years. A unique feature is the capacity to support trial-within-cohort studies to evaluate interventions for prevention of COVID-19 and other acute respiratory illnesses. Participants complete a detailed online baseline questionnaire capturing self-reported information relating to their socio-demographic characteristics, occupation, lifestyle, quality of life, weight, height, longstanding medical conditions, medication use, vaccination status, diet and supplemental micronutrient intake. Follow-up on-line questionnaires capturing incident symptoms of COVID-19 and other acute respiratory infections, incident swab test-confirmed COVID-19, doses of SARS-CoV-2 vaccine received, and quality of life are completed at monthly intervals. +Results555 infection episodes were reported among 483 participants. Across VOCs, symptom burden and duration were similar, however symptom profiles differed among infections caused by Delta compared to Omicron sub-variants; symptoms of all Omicron sub-variants BA.1, BA.2 and BA.4/5 were very similar. Anosmia was reported in 7-13% of participants with Omicron sub-variants, compared to 25/60 (42%) with Delta infection (P= 1.31e-08 or 1.03e-05 or 5.63e-05; {chi}2 test d2+Delta vs. Omicron BA.1 or vs. BA.2, or BA.5, respectively), fever was more common with Omicron BA.5 (30/55, 55%) than Delta (20/60, 33%) (p 0.03). Amongst infections with all Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. Ct values were negatively associated with time since vaccination in participants infected with BA.1; however, this trend was not observed in BA.2/BA.4/5 infections. -ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. +ConclusionOur study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. -ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,fuzzy,100,100 +Trial registrationNCT04750356",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.06.15.22276446,2022-06-21,https://medrxiv.org/cgi/content/short/2022.06.15.22276446,Experiences of mental health and wellbeing support for NHS staff during the COVID-19 pandemic: a reflexive thematic analysis,Corinne Clarkson; Hannah Scott; Siobhan Hegarty; Emilia Soulios; Rupa Bhundia; Sam Gnanapragasam; Mary Jane Docherty; Rosalind Raine; Sharon Stevelink; Neil Greenberg; Matthew Hotopf; Simon Wessely; Ira Madan; Anne Marie Rafferty; Danielle Lamb,University College London; King's College London; King's College London; King's College London; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; University College London; King's College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; King's College London; UCL,"Staff in the National Health Service (NHS) have been placed under considerable strain during the COVID-19 pandemic; whilst NHS Trusts provide a variety of health and wellbeing support services, there has been little research investigating staff perceptions of these services. Moreover, the research that does exist typically includes only clinical staff, despite a large proportion of patient-facing NHS workers being in non-clinical roles. We interviewed forty-eight clinical and non-clinical healthcare workers from eighteen NHS Trusts in England about their experiences of workplace health and wellbeing support during the pandemic. Reflexive thematic analysis identified that perceived stigma around help-seeking, and staffing shortages due to wider socio-political contexts such as austerity, were barriers to using support services. Visible, caring leadership at all levels (CEO to line managers), peer support, easily accessible services, and clear communication about support offers were enablers. Our evidence suggests Trusts should have active strategies to improve help-seeking. This could involve providing all staff with regular reminders about support options, in a variety of formats (e.g. email, posters, mentioned in meetings), and easily remembered single points of access, delivered by a mix of in-house and externally-provided services, to cater for those more and less concerned about stigma and confidentiality. In addition, managers at all levels should be trained and supported to feel confident to speak about mental health with staff, with formal peer support facilitated by building in time for this during working hours. As others have pointed out, this will require long-term strategic planning to address workforce shortages.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. @@ -1005,13 +1015,6 @@ ResultsThree main themes emerged: (i) Implementing NEWS2 challenges and supports ConclusionWhether in specialist or general medical settings, the health professionals implementing EWS in healthcare face cultural and systems related challenges to adopting NEWS2 and digital solutions. The validity of NEWS2 in specialised settings and complex conditions is not yet apparent and requires comprehensive validation. EHRs integration and automation are powerful tools to facilitate NEWS2 if its principles are reviewed and rectified, and resources and training are accessible. Further examination of implementation from the cultural and automation domains are needed.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.06.13.22276316,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.13.22276316,Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England,Matt J Keeling,University of Warwick,"One of the key features of any infectious disease is whether infection generates long-lasting immunity or whether repeated reinfection is common. In the former, the long-term dynamics are driven by the birth of susceptible individuals while in the latter the dynamics are governed by the speed of waning immunity. Between these two extremes a range of scenarios is possible. During the early waves of SARS-CoV-2, the underlying paradigm was for long-lasting immunity, but more recent data and in particular the 2022 Omicron waves have shown that reinfection can be relatively common. Here we investigate reported SARS-CoV-2 cases in England, partitioning the data into four main waves, and consider the temporal distribution of first and second reports of infection. We show that a simple low-dimensional statistical model of random (but scaled) reinfection captures much of the observed dynamics, with the value of this scaling, k, providing information of underlying epidemiological patterns. We conclude that there is considerable heterogeneity in risk of reporting reinfection by wave, age-group and location. The high levels of reinfection in the Omicron wave (we estimate that 18% of all Omicron cases had been previously infected, although not necessarily previously reported infection) point to reinfection events dominating future COVID-19 dynamics.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.06.12.22276307,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.12.22276307,"Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study",Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status. - -MethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure. - -FindingsVaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses). - -InterpretationDifferential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.",public and global health,fuzzy,100,100 medRxiv,10.1101/2022.06.08.22276154,2022-06-09,https://medrxiv.org/cgi/content/short/2022.06.08.22276154,Validity of self-testing at home with rapid SARS-CoV-2 antibody detection by lateral flow immunoassay,Christina J Atchison; Maya Moshe; Jonathan C Brown; Matthew Whitaker; Nathan C K Wong; Anil A Bharath; Rachel A McKendry; Ara Darzi; Deborah Ashby; Christl A. Donnelly; Steven Riley; Paul Elliott; Wendy S Barclay; Graham Cooke; Helen Ward,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London School of Public Health; Imperial College London; Imperial College; Imperial College London","BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassays (LFIA) can be carried out in the home and have been used as an affordable and practical approach to large-scale antibody prevalence studies. However, assay performance differs from that of high-throughput laboratory-based assays which can be highly sensitive. We explore LFIA performance under field conditions compared to laboratory-based ELISA and assess the potential of LFIAs to identify people who lack functional antibodies following infection or vaccination. MethodsField evaluation of a self-administered LFIA test (Fortress, NI) among 3758 participants from the REal-time Assessment of Community Transmission-2 (REACT-2) study in England selected based on vaccination history and previous LFIA result to ensure a range of antibody titres. In July 2021, participants performed, at home, a self-administered LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample (Tasso-SST) for serological assessment of IgG antibodies to the spike protein using the Roche Elecsys(R) Anti-SARS-CoV-2 assay. We compared the self-administered and reported LFIA result to the quantitative Roche assay and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralisation. @@ -1165,6 +1168,15 @@ MethodsWe applied a two-stage Bayesian model to quantify inequalities in excess ResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. ConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.04.21.22274152,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.21.22274152,"Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.",Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy,"Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University","BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls. + +MethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis. + +ResultsCompared to matched individuals testing negative, surviving positive community-tested patients had a higher risk of post-viral illness (HR: 4.57, 95%CI: 1.77-11.80, p=0.002), fatigue (HR: 1.47, 95%CI: 1.24-1.75, p<0.001) and embolism (HR: 1.51, 95%CI: 1.13-2.02, p=0.005) at 5-24 weeks post-diagnosis. In the four weeks after COVID-19 higher rates of sick notes were being issued for community-tested (HR: 3.04, 95%CI: 0.88 to 10.50, p<0.079); the risk was reduced after four weeks, compared to controls. Overall healthcare attendance for anxiety, depression was less likely in those with COVID-19 in the first four weeks (HR: 0.83, 95%CI: 0.73-1.06, p=0.007). After four weeks, anxiety, depression is less likely to occur for the positive community-tested individuals (HR: 0.87, 95%CI: 0.77-1.00, p=0.048), but more likely for positive hospital-tested individuals (HR: 1.16, 95%CI: 1.00-1.45, p=0.053). Although statistical associations between positive infection and post-infection healthcare use are clear, the absolute use of healthcare is very. + +ConclusionsCommunity COVID-19 disease is associated with increased risks of post-viral illness, fatigue, embolism, depression, anxiety and respiratory conditions. Despite these elevated risks, the absolute healthcare burden is low. Either very small proportions of people experience adverse outcomes following COVID-19 or they are not presenting to healthcare. + +Trial registrationData held in SAIL databank are anonymised and therefore, no ethical approval is required. All data in SAIL has the permission from the relevant Caldicott Guardian or Data Protection Officer and SAIL-related projects are required to obtain Information Governance Review Panel (IGRP) approval. The IGRP approval number for this study is 1259.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.04.21.22274150,2022-04-22,https://medrxiv.org/cgi/content/short/2022.04.21.22274150,Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya,Stacey Orangi; John Ojal; Samuel P.C. Brand; Cameline Orlendo; Angela Kairu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Edward Otieno; Lynette I Ochola-Oyier; Charles N Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Ifedayo M. O Adetifa; J Anthony G Scott; Philip Bejon; Matt J. Keeling; Stefan Flasche; D. James Nokes; Edwine Barasa,"Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya","BackgroundFew studies have assessed the benefits of COVID-19 vaccines in settings where most of the population had been exposed to SARS-CoV-2 infection. MethodsWe conducted a cost-effectiveness analysis of COVID-19 vaccine in Kenya from a societal perspective over a 1.5-year time frame. An age-structured transmission model assumed at least 80% of the population to have prior natural immunity when an immune escape variant was introduced. We examine the effect of slow (18 months) or rapid (6 months) vaccine roll-out with vaccine coverage of 30%, 50% or 70% of the adult (> 18 years) population prioritizing roll-out in over 50-year olds (80% uptake in all scenarios). Cost data were obtained from primary analyses. We assumed vaccine procurement at $7 per dose and vaccine delivery costs of $3.90-$6.11 per dose. The cost-effectiveness threshold was USD 919. @@ -1816,6 +1828,13 @@ MethodsData from 15,190 employed/self-employed participants in the Virus Watch p FindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves. InterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.12.13.21267723,2021-12-14,https://medrxiv.org/cgi/content/short/2021.12.13.21267723,"Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom",Emma Rezel-Potts; Abdel Douiri; Xiaohui Sun; Phillip J Chowienczyk; Ajay M Shah; Martin C Gulliford,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"ObjectiveThis study aimed to estimate the incidence of new diabetes mellitus (DM) and cardiovascular diseases (CVD) up to one year after Covid-19 compared with matched controls. + +MethodsA cohort study was conducted using electronic records for 1,473 family practices with a population of 14.9 million. Covid-19 patients without DM or CVD were individually matched with controls and followed up to October 2021. A difference-in-difference analysis estimated the net effect of Covid-19 allowing for baseline differences and covariates. + +ResultsThere were 372,816 Covid-19 patients, with 2,935 CVD and 3,139 DM events, and 372,816 matched controls with 1,193 CVD and 1,861 DM events following the index date. Net incidence of DM increased in acute Covid-19 up to four weeks from index date (adjusted rate ratio, RR 1.71, 1.40 to 2.10) and remained elevated in post-acute (five to 12 weeks from index date; RR 1.17, 1.01 to 1.36) and long-Covid-19 (13 to 52 weeks, 1.20, 1.09 to 1.31). Acute Covid-19 was associated with net increased CVD incidence (RR 6.02, 95% confidence interval 4.84 to 7.47) including pulmonary embolism (RR 14.5, 7.72 to 27.4), atrial arrythmias (6.58, 3.78 to 11.4) and venous thromboses (5.44, 3.22 to 9.17). CVD incidence declined in post-acute Covid-19 (1.68, 1.41 to 2.01) and showed no net increase in long Covid-19 (0.95, 0.85 to 1.06). + +ConclusionsDM incidence remains elevated up to one year following Covid-19. CVD is increased early after Covid-19 mainly from pulmonary embolism, atrial arrhythmias and venous thromboses.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.12.09.21267516,2021-12-09,https://medrxiv.org/cgi/content/short/2021.12.09.21267516,Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study,Daniel Ayoubkhani; Charlotte Bermingham; Koen B Pouwels; Myer Glickman; Vahe Nafilyan; Francesco Zaccardi; Kamlesh Khunti; Nisreen A Alwan; Ann Sarah Walker,Office for National Statistics; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; University of Leicester; University of Leicester; University of Southampton; University of Oxford,"ObjectiveTo estimate associations between COVID-19 vaccination and Long Covid symptoms in adults who were infected with SARS-CoV-2 prior to vaccination. DesignObservational cohort study using individual-level interrupted time series analysis. @@ -1954,6 +1973,7 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSIn a recent systema What this paper addsIn unvaccinated individuals the protection against hospitalised COVID-19 conferred by previous infection is similar to that induced by vaccination. In those with previous infection, vaccination reduces the rates of reinfection and hospitalised COVID-19 by about 70%. Implications of all the available evidenceThe combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.11.19.21266529,2021-11-19,https://medrxiv.org/cgi/content/short/2021.11.19.21266529,Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England,Aleksandra J Borek; Katherine Maitland; Monsey Mcleod; Anne Campbell; Benedict Hayhoe; Christopher C Butler; Liz Morrell; Laurence Roope; Alison Holmes; Ann Sarah Walker; Sarah Tonkin-Crine; - the STEP-UP study team,University of Oxford; University of Oxford; Imperial College London; Imperia College London; Imperial College London; University of Oxford; University of Oxford; University of Oxford; Imperial College London; University of Oxford; University of Oxford; ,"The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners (GPs) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.",primary care research,fuzzy,100,100 medRxiv,10.1101/2021.11.15.21266264,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266264,Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies,Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis,University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London,"BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic. MethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis. @@ -2182,15 +2202,6 @@ MethodsWe performed a retrospective observational cohort study of adult contacts Results54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination. ConclusionsVaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.09.28.21264240,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.28.21264240,Predicting hospital-onset COVID-19 infections using dynamic networks of patient contacts: an observational study,Ashlegh C Myall; James Richard Price; Robert L Peach; Mohamed Abbas; Siddharth Mookerjee; Nina Zhu; Isa Ahmad; Damien Keng Yen Ming; Farzan Ramzan; Daniel Teixeira; Christophe Graf; Andrea Y Wiesse; Stephan Harbarth; Alison Holmes; Mauricio Barahona,Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; Imperial College London NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; University Hospital of Geneva; The University of Edinburgh; University Hospital of Geneva; Imperial College London; Imperial College London,"BackgroundReal-time prediction is key to prevention and control of healthcare-associated infections. Contacts between individuals drive infections, yet most prediction frameworks fail to capture the dynamics of contact. We develop a real-time machine learning framework that incorporates dynamic patient contact networks to predict patient-level hospital-onset COVID-19 infections (HOCIs), which we test and validate on international multi-site datasets spanning epidemic and endemic periods. - -MethodsOur framework extracts dynamic contact networks from routinely collected hospital data and combines them with patient clinical attributes and background contextual hospital data to forecast the infection status of individual patients. We train and test the HOCI prediction framework using 51,157 hospital patients admitted to a UK (London) National Health Service (NHS) Trust from 01 April 2020 to 01 April 2021, spanning UK COVID-19 surges 1 and 2. We then validate the framework by applying it to data from a non-UK (Geneva) hospital site during an epidemic surge (40,057 total inpatients) and to data from the same London Trust from a subsequent period post surge 2, when COVID-19 had become endemic (43,375 total inpatients). - -FindingsBased on the training data (London data spanning surges 1 and 2), the framework achieved high predictive performance using all variables (AUC-ROC 0{middle dot}89 [0{middle dot}88-0{middle dot}90]) but was almost as predictive using only contact network variables (AUC-ROC 0{middle dot}88 [0{middle dot}86-0{middle dot}90]), and more so than using only hospital contextual (AUC-ROC 0{middle dot}82 [0{middle dot}80-0{middle dot}84]) or patient clinical (AUC-ROC 0{middle dot}64 [0{middle dot}62-0{middle dot}66]) variables. The top three risk factors we identified consisted of one hospital contextual variable (background hospital COVID-19 prevalence) and two contact network variables (network closeness, and number of direct contacts to infectious patients), and together achieved AUC-ROC 0{middle dot}85 [0{middle dot}82-0{middle dot}88]. Furthermore, the addition of contact network variables improved performance relative to hospital contextual variables on both the non-UK (AUC-ROC increased from 0{middle dot}84 [0{middle dot}82-0{middle dot}86] to 0{middle dot}88 [0{middle dot}86-0{middle dot}90]) and the UK validation datasets (AUC-ROC increased from 0{middle dot}52 [0{middle dot}49-0{middle dot}53] to 0{middle dot}68 [0{middle dot}64-0{middle dot}70]). - -InterpretationOur results suggest that dynamic patient contact networks can be a robust predictor of respiratory viral infections spreading in hospitals. Their integration in clinical care has the potential to enhance individualised infection prevention and early diagnosis. - -FundingMedical Research Foundation, World Health Organisation, Engineering and Physical Sciences Research Council, National Institute for Health Research, Swiss National Science Foundation, German Research Foundation.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.09.27.21264166,2021-09-29,https://medrxiv.org/cgi/content/short/2021.09.27.21264166,Prevalence and duration of detectable SARS-CoV-2 nucleocapsid antibody in staff and residents of long-term care facilities over the first year of the pandemic (VIVALDI study): prospective cohort study,Maria Krutikov; Tom Palmer; Gokhan Tut; Christopher Fuller; Borscha Azmi; Rebecca Giddings; Madhumita Shrotri; Nayandeep Kaur; Panagiota Sylla; Tara Lancaster; Aidan Irwin-Singer; Andrew Hayward; Paul Moss; Andrew Copas; Laura Shallcross,"University College London; University College London; University of Birmingham, Medical School; University College London; University College London; University College London; University College London; University of Birmingham; University of Birmingham; University of Birmingham; Department of Health & Social Care; UCL; University of Birmingham; University College London; UCL","BackgroundLong Term Care Facilities (LTCF) have reported high SARS-CoV-2 infection rates and related mortality, but the proportion infected amongst survivors and duration of the antibody response to natural infection is unknown. We determined the prevalence and stability of nucleocapsid antibodies - the standard assay for detection of prior infection - in staff and residents from 201 LTCFs. MethodsProspective cohort study of residents aged >65 years and staff of LTCFs in England (11 June 2020-7 May 2021). Serial blood samples were tested for IgG antibodies against SARS-CoV-2 nucleocapsid protein. Prevalence and cumulative incidence of antibody-positivity were weighted to the LTCF population. Cumulative incidence of sero-reversion was estimated from Kaplan-Meier curves. @@ -2447,6 +2458,13 @@ MethodsProspective, multi-centre, trans-thoracic echocardiographic, cohort study ResultsOne hundred and twenty-one patients were recruited to COVID-RV, 118 underwent imaging and it was possible to determine the primary outcome in 112. RVD was present in seven (6.2% [95%CI; 2.5%, 12.5%]) patients. Thirty-day mortality was 85.7% in those with RVD, compared to 44.8% in those without (p=0.051). Patients with RVD were more likely to have; pulmonary thromboembolism (p<0.001), higher plateau pressure (p=0.048), lower dynamic compliance (p=0.031), higher NT-proBNP (p<0.006) and more frequent abnormal troponin (p=0.048). Abnormal NT-proBNP (OR 4.77 [1.22, 21.32], p=0.03) and abnormal Troponin (16.54 [4.98, 67.12], p<0.001) independently predicted 30-day mortality. ConclusionCOVID-RV demonstrates a prevalence of RVD in ventilated patients with COVID-19 of 6.2% and is associated with a mortality of 85.7%. Association is observed between RVD and each of the aetiological domains of; ARDS, ventilation, micro/macro thrombi and myocardial injury.",intensive care and critical care medicine,fuzzy,100,100 +medRxiv,10.1101/2021.07.27.21261031,2021-07-29,https://medrxiv.org/cgi/content/short/2021.07.27.21261031,Prognostic accuracy of triage tools for adults with suspected COVID-19 in a pre-hospital setting: an observational cohort study,Carl Marincowitz; Laura Sutton; Tony Stone; Richard Pilbery; Richard Campbell; Ben Thomas; Janette Turner; Peter Bath; Fiona Bell; Katie Biggs; Madina Hasan; Frank Hopfgartner; Suvodeep Mazumdar; Jennifer Petrie; Steve Goodacre,"(CURE), Health Services Research School of Health and Related Research, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Yorkshire Ambulance Service NHS Trust; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Information School, University of Sheffield; Yorkshire Ambulance Service NHS Trust; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; Information School, University of Sheffield; Information School, University of Sheffield; Information School, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield","Study ObjectiveTools proposed to triage patient acuity in COVID-19 infection have only been validated in hospital populations. We estimated the accuracy of five risk-stratification tools recommended to predict severe illness and compare accuracy to existing clinical decision-making in a pre-hospital setting. + +MethodsAn observational cohort study using linked ambulance service data for patients attended by EMS crews in the Yorkshire and Humber region of England between 18th March 2020 and 29th June 2020 was conducted to assess performance of the PRIEST tool, NEWS2, the WHO algorithm, CRB-65 and PMEWS in patients with suspected COVID-19 infection. The primary outcome was death or need for organ support. + +ResultsOf 7549 patients in our cohort, 17.6% (95% CI:16.8% to 18.5%) experienced the primary outcome. The NEWS2, PMEWS, PRIEST tool and WHO algorithm identified patients at risk of adverse outcomes with a high sensitivity (>0.95) and specificity ranging from 0.3 (NEWS2) to 0.41 (PRIEST tool). The high sensitivity of NEWS2 and PMEWS was achieved by using lower thresholds than previously recommended. On index assessment, 65% of patients were transported to hospital and EMS decision to transfer patients achieved a sensitivity of 0.84 (95% CI 0.83 to 0.85) and specificity of 0.39 (95% CI 0.39 to 0.40). + +ConclusionUse of NEWS2, PMEWS, PRIEST tool and WHO algorithm could improve sensitivity of EMS triage of patients with suspected COVID-19 infection. Use of the PRIEST tool would improve sensitivity of triage without increasing the number of patients conveyed to hospital.",emergency medicine,fuzzy,100,100 medRxiv,10.1101/2021.07.26.21261140,2021-07-28,https://medrxiv.org/cgi/content/short/2021.07.26.21261140,Higher serological responses and increased vaccine effectiveness demonstrate the value of extended vaccine schedules in combatting COVID-19 in England,Gayatri Amirthalingam; Jamie Lopez Bernal; Nick J Andrews; Heather Whitaker; Charlotte Gower; Julia Stowe; Elise Tessier; Sathyavani Subbarao; Georgina Ireland; Frances Baawuah; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corinne Whillock; Paul Moss; Shamez N Ladhani; Kevin E Brown; Mary E Ramsay,Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Brondesbury Medical Centre; Public Health England; University of Birmingham; Public Health England; Public Health England; Public Health England,"IntroductionIn January 2021, the UK decided to prioritise the delivery of the first dose of BNT162b2 (Pfizer/BioNTech) and AZD1222 (AstraZeneca) vaccines by extending the interval until the second dose up to 12 weeks. MethodsSerological responses were compared after BNT162b2 and AZD1222 vaccination with varying intervals in uninfected and previously-infected adults aged 50-89 years. These findings are evaluated against real-world national vaccine effectiveness (VE) estimates against COVID-19 in England. @@ -2456,15 +2474,6 @@ ResultsWe recruited 750 participants aged 50-89 years, including 126 (16.8%) wit ConclusionOur findings support the UK approach of prioritising the first dose of COVID-19 vaccines, with evidence of higher protection following extended schedules. Given global vaccine constraints, these results are relevant to policymakers, especially with highly transmissible variants and rising incidence in many countries. FundingPublic Health England",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.07.23.21260992,2021-07-25,https://medrxiv.org/cgi/content/short/2021.07.23.21260992,A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges,Bernadette C Young; David W Eyre; Saroj Kendrick; Chris White; Sylvester Smith; George Beveridge; Toby Nonnenmacher; Fegor Ichofu; Joseph Hillier; Ian Diamond; Emma Rourke; Fiona Dawe; Ieuan Day; Lisa Davies; Paul Staite; Andrea Lacey; James McCrae; Ffion Jones; Joseph Kelly; Urszula Bankiewicz; Sarah Tunkel; Richard Ovens; David Chapman; Peter Marks; Nick Hicks; Tom Fowler; Susan Hopkins; Lucy Yardley; Tim EA Peto,"University of Oxford; University of Oxford; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Department of Health and Social Care, UK Government; Deloitte MCS limited; Deloitte MCS limited; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Public Health England; University of Bristol; University of Oxford","BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools. - -MethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation. - -Co-primary outcomes in all students and staff were symptomatic COVID-19, adjusted for community case rates, to estimate within-school transmission (non-inferiority margin: <50% relative increase), and COVID-19-related school absence. Analyses were performed on an intention to treat (ITT) basis using quasi-Poisson regression, also estimating complier average causal effects (CACE). Secondary outcomes included participation rates, PCR results in contacts and performance characteristics of LFDs vs. PCR. - -FindingsOf 99 control and 102 intervention schools, 76 and 86 actively participated (19-April-2021 to 27-June-2021); additional national data allowed most non-participating schools to be included in the co-primary outcomes. 2432/5763(42.4%) intervention arm contacts participated. There were 657 symptomatic PCR-confirmed infections during 7,782,537 days-at-risk (59.1/100k/week) and 740 during 8,379,749 days-at-risk (61.8/100k/week) in the control and intervention arms respectively (ITT adjusted incidence rate ratio, aIRR=0.96 [95%CI 0.75-1.22;p=0.72]) (CACE-aIRR=0.86 [0.55-1.34]). There were 55,718 COVID-related absences during 3,092,515 person-school-days (1.8%) and 48,609 during 3,305,403 person-school-days(1.5%) in the control and intervention arms (ITT-aIRR=0.80 [95%CI 0.53-1.21;p=0.29]) (CACE-aIRR 0.61 [0.30-1.23]). 14/886(1.6%) control contacts providing an asymptomatic PCR sample tested positive compared to 44/2981(1.5%) intervention contacts (adjusted odds ratio, aOR=0.73 [95%CI 0.33-1.61;p=0.44]). Rates of symptomatic infection in contacts were 44/4665(0.9%) and 79/5955(1.3%), respectively (aOR=1.21 [0.82-1.79;p=0.34]). - -InterpretationDaily contact testing of school-based contacts was non-inferior to self-isolation for control of COVID-19 transmission. COVID-19 rates in school-based contacts in both intervention and control groups were <2%. Daily contact testing is a safe alternative to home isolation following school-based exposures.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.07.22.21260416,2021-07-23,https://medrxiv.org/cgi/content/short/2021.07.22.21260416,"Obesity, Ethnicity, and Covid-19 Mortality: A population-based cohort study of 12.6 Million Adults in England",Thomas Yates; Annabel Summerfield; Cameron Razieh; Amitava Banerjee; Yogini Chudasama; Melanie J Davies; Clare Gillies; Nazrul Islam; Claire Lawson; Evgeny Mirkes; Francesco Zaccardi; Kamlesh Khunti; Vahe Nafilyan,University of Leicester; Office for National Statistics; University of Leicester; University College London; University of Leicester; University of Leicester; University of Leicester; University of Oxford; University of Leicester; University of Leicester; University of Leicester; University of Leicester; Office for National Statistics,"ImportanceObesity and ethnicity are well characterised risk factors for severe COVID-19 outcomes, but the differential effects of obesity on COVID-19 outcomes by race/ethnicity has not been examined robustly in the general population. ObjectiveTo investigate the association between body mass index (BMI) and COVID-19 mortality across different ethnic groups. @@ -2670,15 +2679,6 @@ Clustering identified two distinct groups of individuals with different symptom Implications of available evidenceThere is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.",infectious diseases,fuzzy,96,100 medRxiv,10.1101/2021.06.28.21259529,2021-07-01,https://medrxiv.org/cgi/content/short/2021.06.28.21259529,Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection,Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff,"University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania","We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",genetic and genomic medicine,fuzzy,100,100 -medRxiv,10.1101/2021.06.23.21259400,2021-06-30,https://medrxiv.org/cgi/content/short/2021.06.23.21259400,Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record,Sarah Steeg; Lana Bojanić; George Tilston; Richard Williams; David A Jenkins; Matthew J Carr; Niels Peek; Darren M Ashcroft; Nav Kapur; Jennifer Voorhees; Roger T Webb,University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester,"BackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021. - -MethodsWe conducted a descriptive time series analysis utilising data from the Greater Manchester Care Record, which contains de-identified, primary care health records of 2.8 million patients. Counts of incident and all episodes of self-harm recorded between 1st January 2019 and 31st May 2021 were made for all patients, with stratification by sex, age group, ethnicity, and index of multiple deprivation (IMD) quintile and examination of overall differences by national and regional restriction phases. - -FindingsBetween 1st January 2019 and 31st May 2021, 33,444 episodes of self-harm by 13,148 individuals were recorded. Frequency ratios of incident and all episodes of self-harm were 0.59 (95% CI 0.51 to 0.69) and 0.69 (CI 0.63 to 0.75) respectively in April 2020 compared to February 2020. Between August 2020 and May 2021 frequency ratios were 0.92 (CI 0.88 to 0.96) for incident episodes and 0.86 (CI 0.84 to 0.88) for all episodes compared to the same months in 2019. Reductions were largest among men and people living in the most deprived neighbourhoods. An increase in all-episode self-harm (frequency ratio 1.09, CI 1.03 to 1.16) was observed for adolescents aged 10-17 between August 2020 and May 2021. - -InterpretationThe COVID-19 pandemic has had a sustained impact on help seeking for self-harm. Reductions in primary care recorded self-harm have implications for clinicians ability to assess the needs and risks of individuals. Some patients may be experiencing prolonged untreated deterioration in their mental health while other groups are presenting in higher numbers. Our findings have important implications for primary care and mental health services in manging ongoing demand. - -FundingUKRI COVID-19 Rapid Response Initiative (grant reference COV0499), University of Manchester Presidential Fellowship (SS), and NIHR Greater Manchester Patient Safety Translational Research Centre.",primary care research,fuzzy,100,100 medRxiv,10.1101/2021.06.21.21259145,2021-06-28,https://medrxiv.org/cgi/content/short/2021.06.21.21259145,Development and validation of blood-based prognostic biomarkers for severity of COVID disease outcome using EpiSwitch 3D genomic regulatory immuno-genetic profiling.,Ewan Hunter; Christina Koutsothanasi; Adam Wilson; Francisco Coroado Santos; Matthew Salter; Jurjen Westra; Ryan Powell; Ann Dring; Paulina Brajer; Benedict Egan; Parnall Matthew; Williams Catriona; Katzinski Aemilia; Lavin Thomas; Aroul Ramadass; William Messner; Amanda Brunton; Zoe Lyski; Peter Robbins; Jane Mellor; Rama Vancheeswaran; Andrew Barlow; Dmitri Pchejetski; Alexandre Akoulitchev,"Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK and The Queen's College, University of Oxford, Oxford, UK; Department of Biochemistry, University of Oxford, Oxford, UK and The Queen's College, University of Oxford, Oxford, UK; West Hertfordshire NHS Trust, Watford, UK; West Hertfordshire NHS Trust, Watford, UK; Norwich Medical School, University of East Anglia; Oxford BioDynamics Plc, Oxford UK","The COVID-19 pandemic has raised several global public health challenges to which the international medical community have responded. Diagnostic testing and the development of vaccines against the SARS-CoV-2 virus have made remarkable progress to date. As the population is now faced with the complex lifestyle and medical decisions that come with living in a pandemic, a forward-looking understanding of how a COVID-19 diagnosis may affect the health of an individual represents a pressing need. Previously we used whole genome microarray to identify 200 3D genomic marker leads that could predict mild or severe COVID-19 disease outcomes from blood samples in a multinational cohort of COVID-19 patients. Here, we focus on the development and validation of a qPCR assay to accurately predict severe COVID-19 disease requiring intensive care unit (ICU) support and/or mechanical ventilation. From 200 original biomarker leads we established a classification model containing six markers. The markers were qualified and validated on 38 COVID-19 patients from an independent cohort. Overall, the six-marker model obtained a positive predictive value of 93% and balanced accuracy of 88% across 116 patients for the prognosis of COVID-19 severity requiring ICU care/ventilation support. The six-marker signature identifies individuals at the highest risk of developing severe complications in COVID-19 with high predictive accuracy and can assist in patient prognosis and clinical management decisions.",infectious diseases,fuzzy,92,100 medRxiv,10.1101/2021.06.21.21259237,2021-06-28,https://medrxiv.org/cgi/content/short/2021.06.21.21259237,Changes in mobility pre and post first SARS-CoV-2 vaccination: findings from a prospective community cohort study including GPS movement tracking in England and Wales (Virus Watch),Vincent Nguyen; Yunzhe Liu; Richard Mumford; Ben Flanagan; Parth Patel; Isobel Braithwaite; Madhumita Shrotri; Thomas Edward Byrne; Sarah Beale; Anna Aryee; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Annalan M D Navaratnam; Pia Hardelid; Jana Kovar; Addy Pope; Tao Cheng; Andrew Hayward; Robert W Aldridge; - The Virus watch Collaborative,"Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; SpaceTimeLab, Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK; Esri UK; Esri UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Esri UK; SpaceTimeLab, Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; ","BackgroundSome evidence suggests that individuals may change adherence to public health policies aimed at reducing contact, transmission and spread of the SARS-CoV-2 virus after they receive their first SARS-CoV-2 vaccination. In this study, we aim to estimate the rate of change in average daily travel distance from a participants registered address before and after SARS-CoV-2 vaccination. @@ -2711,13 +2711,6 @@ MethodsIn June 2020, current and former members of the UK Police forces and Fire ResultsIn this cohort of non-healthcare key workers, 7.4% (396/5,348; 95% CI, 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (6.9-11.4) in those under 40 years, 11.5% (8.8-15.0) in those of non-white British ethnicity and 7.8% (7.1-8.7) in those currently working. The self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 0.77-0.83). The LFIAs (self-test and nurse-performed) had a similar performance: compared to ELISA, sensitivity was 82.1% (77.7-86.0) self-test and 76.4% (71.9-80.5) nurse-performed with specificity of 97.8% (97.3-98.2) and 98.5% (98.1-98.8) respectively. ConclusionA greater proportion of the non-healthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (5.8-6.1) following the first wave in England. The high acceptability and usability reported by participants and the similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home-testing in occupational and community prevalence studies.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.06.24.21259277,2021-06-25,https://medrxiv.org/cgi/content/short/2021.06.24.21259277,Risk factors for long COVID: analyses of 10 longitudinal studies and electronic health records in the UK,Ellen J. Thompson; Dylan M. Williams; Alex J. Walker; Ruth E. Mitchell; Claire L. Niedzwiedz; Tiffany C. Yang; Charlotte Huggins; Alex S. F. Kwong; Richard Silverwood; Giorgio Di Gessa; Ruth C. E. Bowyer; Kate Northstone; Bo Hou; Michael J. Green; Brian Dodgeon; Katie J. Doores; Emma Duncan; Frances M. K. Williams; - OpenSAFELY Collaborative; Andrew Steptoe; David J. Porteous; Rosemary R. C. McEachan; Laurie Tomlinson; Ben Goldacre; Praveetha Patalay; George B. Ploubidis; Srinivasa Vittal Katikireddi; Kate Tilling; Christopher T. Rentsch; Nicholas J. Timpson; Nishi Chaturvedi; Claire J. Steves,King's College London; University College London; University of Oxford; University of Bristol; University of Glasgow; Bradford Teaching Hospitals NHS Foundation Trust; University of Edinburgh; University of Bristol; University College London; University College London; King's College London; University of Bristol; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University College London; King's College London; King's College London; King's College London; ; University College London; University of Edinburgh; Bradford Teaching Hospitals NHS Foundation Trust; London School of Hygiene and Tropical Medicine; University of Oxford; University College London; University College London; University of Glasgow; University of Bristol; London School of Hygiene and Tropical Medicine; University of Bristol; University College London; King's College London,"BackgroundThe impact of long COVID is considerable, but risk factors are poorly characterised. We analysed symptom duration and risk factor from 10 longitudinal study (LS) samples and electronic healthcare records (EHR). - -MethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 participants in the UK LS, and 3,327 adults with COVID-19, were assigned a long COVID code from 1,199,812 individuals in primary care EHR. Outcomes for LS included symptom duration lasting 4+ weeks (long COVID) and 12+ weeks. Association with of age, sex, ethnicity, socioeconomic factors, smoking, general and mental health, overweight/obesity, diabetes, hypertension, hypercholesterolaemia, and asthma was assessed. - -ResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%). - -ConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.22.21259336,2021-06-24,https://medrxiv.org/cgi/content/short/2021.06.22.21259336,Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic,Hamish Gibbs; Naomi R Waterlow; James Cheshire; Leon Danon; Yang Liu; Chris Grundy; Adam J Kucharski; - LSHTM CMMID COVID-19 Working Group; Rosalind M Eggo,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; Department of Engineering Mathematics, University of Bristol, UK.; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine","Mobility data have demonstrated major changes in human movement patterns in response to COVID-19 and associated interventions in many countries. This can involve sub-national redistribution, short-term relocations as well as international migration. In this paper, we combine detailed location data from Facebook measuring the location of approximately 6 million daily active Facebook users in 5km2 tiles in the UK with census-derived population estimates to measure population mobility and redistribution. We provide time-varying population estimates and assess spatial population changes with respect to population density and four key reference dates in 2020 (First lockdown, End of term, Beginning of term, Christmas). We also show how population estimates derived from the distribution of Facebook users vary compared to mid-2020 small area population estimates by the UK national statistics agencies. We estimate that between March 2020 and March 2021, the total population of the UK declined and we identify important spatial variations in this population change, showing that low-density areas have experienced lower population decreases than urban areas. We estimate that, for the top 10% highest population tiles, the population has decreased by 6.6%. Further, we provide evidence that geographic redistributions of population within the UK coincide with dates of non-pharmaceutical interventions including lockdowns and movement restrictions, as well as seasonal patterns of migration around holiday dates. The methods used in this study reveal significant changes in population distribution at high spatial and temporal resolutions that have not previously been quantified by available demographic surveys in the UK. We found early indicators of potential longer-term changes in the population distribution of the UK although it is not clear if these changes may persist after the COVID-19 pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.06.16.21258691,2021-06-21,https://medrxiv.org/cgi/content/short/2021.06.16.21258691,App-based COVID-19 surveillance and prediction: The COVID Symptom Study Sweden,Beatrice Kennedy; Hugo Fitipaldi; Ulf Hammar; Marlena Maziarz; Neli Tsereteli; Nikolay Oskolkov; Georgios Varotsis; Camilla A Franks; Diem T Nguyen; Lampros Spiliopoulos; Hans-Olov Adami; Jonas Björk; Stefan Engblom; Katja Fall; Anna Grimby-Ekman; Jan-Eric Litton; Mats Martinell; Anna Oudin; Torbjörn Sjöström; Toomas Timpka; Carole H Sudre; Mark S Graham; Julien Lavigne du Cadet; Andrew T. Chan; Richard Davies; Sajaysurya Ganesh; Anna May; Sébastien Ourselin; Joan Capdevila Pujol; Somesh Selvachandran; Jonathan Wolf; Tim D Spector; Claire J Steves; Maria F Gomez; Paul W Franks; Tove Fall,"Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Skåne University Hospital, Malmö, Sweden; Clinical Effectiveness Group, Institute of Health and Society, University of Oslo, Oslo, Norway; Dept of Medical Epidemiology and Biostatistics, Karolinska Inst; Division of Occupational and Environmental Medicine, Lund University, Sweden; Clinical Studies Sweden, Forum South, Skåne University Hospital, Lund, Sweden; Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden; Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Örebro, Sweden; Integrative Epidemiology, Institute of Environmental Med; Biostatistics, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden; Department of Public Health and Caring Sciences, Uppsala University, Sweden; Primary Care and Health, Region Uppsala, Sweden; Division for Occupational and environmental medicine, Lund University, Sweden; Department of Public Health and Clinical Medicine, Section of Sustainable Health,; Novus International Group AB, Sweden; Department of Medical and Health Sciences, Linkoping University, Sweden; MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK; Centre for Medical Image Computing, University College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; ZOE Limited; ZOE Limited; ZOE Limited; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited; ZOE Limited; ZOE Limited; Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden","The app-based COVID Symptom Study was launched in Sweden in April 2020 to contribute to real-time COVID-19 surveillance. We enrolled 143,531 study participants ([≥]18 years) who contributed 10.6 million daily symptom reports between April 29, 2020 and February 10, 2021. Data from 19,161 self-reported PCR tests were used to create a symptom-based model to estimate the individual probability of symptomatic COVID-19, with an AUC of 0.78 (95% CI 0.74-0.83) in an external dataset. These individual probabilities were used to estimate daily regional COVID-19 prevalence, which were in turn used together with current hospital data to predict next week COVID-19 hospital admissions. We found that this hospital prediction model demonstrated a lower median absolute percentage error (MdAPE: 25.9%) across the five most populated regions in Sweden during the first pandemic wave than a model based on case notifications (MdAPE: 30.3%). During the second wave, the error rates were similar. When applying the same model to an English dataset, not including local COVID-19 test data, we observed MdAPEs of 22.3% and 19.0%, respectively, highlighting the transferability of the prediction model.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.06.17.21259103,2021-06-21,https://medrxiv.org/cgi/content/short/2021.06.17.21259103,REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant,Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Andrew J. Page; Sophie J. Prosolek; Alexander J. Trotter; Le Viet Thanh; Nabil-Fareed Alikhan; Leigh M Jackson; Catherine Ludden; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Medical School, University of Exeter, UK; Department of Medicine, University of Cambridge, UK; -; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021. @@ -2730,6 +2723,9 @@ DiscussionThe extent to which exponential growth continues, or slows down as a c bioRxiv,10.1101/2021.06.21.449178,2021-06-21,https://biorxiv.org/cgi/content/short/2021.06.21.449178,Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury,Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa,"University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford","Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies. One Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.",immunology,fuzzy,100,100 +medRxiv,10.1101/2021.06.17.21259100,2021-06-20,https://medrxiv.org/cgi/content/short/2021.06.17.21259100,COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya,Samuel P C Brand; John Ojal; Rabia Aziza; Vincent Were; Emelda Okiro; Ivy Kombe; Caroline Mburu; Morris Ogero; Ambrose Agweyu; George M Warimwe; James Nyagwange; Henry Karanja; John Gitonga; Daisy Mugo; Sophie Uyoga; Ifedayo M O Adetifa; J Anthony G Scott; Edward Otieno; Nickson Murunga; Mark Otiende; Lynette I Ochola-Oyier; Charles N Agoti; George Githinji; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Matt J Keeling; D James Nokes; Edwine Barasa,"University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya","Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya ([~]75% June 1st) have implications for a fourth wave and future control strategies. + +One Sentence SummaryCOVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.15.21258542,2021-06-16,https://medrxiv.org/cgi/content/short/2021.06.15.21258542,"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Marion Mafham; Leon Peto; Mark Campbell; Guilherme Pessoa-Amorim; Enti Spata; Natalie Staplin; Jonathan R Emberson; Benjamin Prudon; Paul Hine; Thomas Brown; Christopher A Green; Rahuldeb Sarkar; Purav Desai; Bryan Yates; Tom Bewick; Simon Tiberi; Tim Felton; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; David M Weinreich; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Liverpool University Hospitals NHS Foundation Trust; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; University Hospitals Birmingham NHS Foundation Trust; Medway NHS Foundation Trust; Calderdale and Huddersfield NHS Foundation Trust; Northumbria Healthcare NHS Foundation Trust; University Hospitals Of Derby and Burton NHS Foundation Trust; Barts Health NHS Trust; Manchester University NHS Foundation Trust; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundREGEN-COV is a combination of 2 monoclonal antibodies (casirivimab and imdevimab) that bind to two different sites on the receptor binding domain of the SARS-CoV-2 spike protein. We aimed to evaluate the efficacy and safety of REGEN-COV in patients admitted to hospital with COVID-19. MethodsIn this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting patients were randomly allocated (1:1) to either usual standard of care alone (usual care group) or usual care plus a single dose of REGEN-COV 8g (casirivimab 4g and imdevimab 4g) by intravenous infusion (REGEN-COV group). The primary outcome was 28-day mortality assessed first among patients without detectable antibodies to SARS-CoV-2 at randomisation (seronegative) and then in the overall population. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). @@ -2798,6 +2794,13 @@ ResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an ConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance. SummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.06.08.21258546,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258546,Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies,Jane Maddock; Sam Parsons; Giorgio Di Gessa; Michael J Green; Ellen J Thompson; Anna J Stevenson; Alex S.F. Kwong; Eoin McElroy; Gillian Santorelli; Richard J Silverwood; Gabriella Captur; Nish Chaturvedi; Claire J Steves; Andrew Steptoe; Praveetha Patalay; George B Ploubidis; Srinivasa Vittal Katikireddi,University College London; University College London; University College London; University of Glasgow; King's College London; University of Edinburgh; University of Bristol; University of Leicester; Bradford Institute for Health Research; University College London; University College London; University College London; King's College London; University College London; University College London; University College London; University of Glasgow,"BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies. + +MethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates. + +ResultsPrevalence of disruption varied across studies; between 6.4% (TwinsUK) and 31.8 % (Understanding Society) of study participants reported any disruption. Females (Odd Ratio (OR): 1.27 [95%CI: 1.15,1.40]; I2=53%), older persons (e.g. OR: 1.39 [1.13,1.72]; I2=77% for 65-75y vs 45-54y), and Ethnic minorities (excluding White minorities) (OR: 1.19 [1.05,1.35]; I2=0% vs White) were more likely to report healthcare disruptions. Those in a more disadvantaged social class (e.g. OR: 1.17 [1.08, 1.27]; I2=0% for manual/routine vs managerial/professional) were also more likely to report healthcare disruptions, but no clear differences were observed by education levels. + +ConclusionThe COVID-19 pandemic has led to unequal healthcare disruptions, which, if unaddressed, could contribute to the maintenance or widening of existing health inequalities.",health systems and quality improvement,fuzzy,97,100 medRxiv,10.1101/2021.06.07.21258476,2021-06-10,https://medrxiv.org/cgi/content/short/2021.06.07.21258476,Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics,Louise Dyson; Edward M Hill; Sam Moore; Jacob Curran-Sebastian; Michael J Tildesley; Katrina A Lythgoe; Thomas House; Lorenzo Pellis; Matt J Keeling,"The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, C; The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, C; The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, C; Department of Mathematics, University of Manchester, Manchester, United Kingdom; The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, C; Big Data Institute, Old Road Campus, University of Oxford, United Kingdom.; Department of Mathematics, University of Manchester, Manchester, United Kingdom.; Department of Mathematics, University of Manchester, Manchester, United Kingdom.; The Zeeman Institute for Systems Biology \& Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, ","Viral reproduction of SARS-CoV-2 provides opportunities for the acquisition of advantageous mutations, altering viral transmissibility, disease severity, and/or allowing escape from natural or vaccine-derived immunity. We use three mathematical models: a parsimonious deterministic model with homogeneous mixing; an age-structured model; and a stochastic importation model to investigate the effect of potential variants of concern (VOCs). Calibrating to the situation in England in May 2021, we find epidemiological trajectories for putative VOCs are wide-ranging and dependent on their transmissibility, immune escape capability, and the introduction timing of a postulated VOC-targeted vaccine. We demonstrate that a VOC with a substantial transmission advantage over resident variants, or with immune escape properties, can generate a wave of infections and hospitalisations comparable to the winter 2020-2021 wave. Moreover, a variant that is less transmissible, but shows partial immune-escape could provoke a wave of infection that would not be revealed until control measures are further relaxed.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258535,2021-06-08,https://medrxiv.org/cgi/content/short/2021.06.08.21258535,Altered neutrophil phenotype and function in non-ICU COVID-19 patients correlated with disease severity,Kylie BR Belchamber; Onn S Thein; Jon Hazeldine; Frances S Grudzinska; Michael J Hughes; Alice E Jasper; Kay Por Yip; Elizabeth Sapey; Dhruv Parekh; David R Thickett; Aaron Scott,"Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; 2National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham; Institute of Inflammation and Ageing, University of Birmingham","RationalInfection with the SARS-CoV2 virus is associated with elevated neutrophil counts. Evidence of neutrophil dysfunction in COVID-19 is based predominantly on transcriptomics or single functional assays. Cell functions are interwoven pathways, and so understanding the effect of COVID-19 across the spectrum of neutrophil function may identify tractable therapeutic targets. @@ -2863,7 +2866,6 @@ Implications of all the available evidenceThe significant, long-lasting health a medRxiv,10.1101/2021.05.27.21257032,2021-05-31,https://medrxiv.org/cgi/content/short/2021.05.27.21257032,How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology,Naomi R Waterlow; Edwin Van Leeuwen; Nicholas G Davies; - CMMID COVID-19 working group; Stefan Flasche; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; Public Health England; London School of Hygiene and Tropical Medicine; ; LSHTM; London School of Hygiene & Tropical Medicine,"We hypothesised that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected SARS-CoV-2 transmission, including generating reduced susceptibility in children. To determine what the pre-pandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 years of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.3 years (95%CI 6.8 - 7.9) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission. Significance statementCross-protection from seasonal epidemics of human coronaviruses (HCoVs) has been hypothesised to contribute to the relative sparing of children during the early phase of the pandemic. Testing this relies on understanding the pre-pandemic age-distribution of recent HCoV infections, but little is known about their dynamics. Using England and Wales as a case study, we use a transmission model to estimate the duration of immunity to seasonal coronaviruses, and show how cross-protection could have affected the age distribution of susceptibility during the first wave, and alter SARS-CoV-2 transmission patterns over the coming decade.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.05.22.21257633,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.22.21257633,Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021,Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung,"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany","The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.05.24.21257738,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.24.21257738,"Post-vaccination SARS-CoV-2 infection: risk factors and illness profile in a prospective, observational community-based case-control study",Michela Antonelli; Rose S Penfold; Jordi Merino; Carole H Sudre; Erika Molteni; Sarah Berry; Liane S Canas; Mark S Graham; Kerstin Klaser; Marc Modat; Benjamin Murray; Eric Kerfoot; Liyuan Chen; Jie Deng; Marc F Österdahl; Nathan J Cheetham; David Alden Drew; Long Alden Nguyen; Joan Capdeila; Christina Hu; Somesh Selvachandran; Lorenzo Polidori; Anna May; Jonathan Wolf; Andrew T Chan; Alexander Hammers; Emma Duncan; Timothy Spector; Sebastien Ourselin; Claire J Steves,"King's College London; King's College London; Department of Medicine, Harvard Medical School, Boston, MA, USA; Centre for Medical Image Computing, University College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; King's College London; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Zoe Global, London, UK; Zoe Global, London, UK; Zoe Global, London, UK; Lorenzo Polidori; Zoe Global, London, UK; Zoe Global, London, UK; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; King's College London; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK","BackgroundCOVID-19 vaccines show excellent efficacy in clinical trials and real-world data, but some people still contract SARS-CoV-2 despite vaccination. This study sought to identify risk factors associated with SARS-CoV-2 infection post-vaccination and describe characteristics of post-vaccination illness. MethodsAmongst 1,102,192 vaccinated UK adults from the COVID Symptom Study, 2394 (0.2%) cases of post-vaccination SARS-CoV-2 infection were identified between 8th December 2020 and 1st May 2021. Using a control group of vaccinated individuals testing negative, we assessed the associations of age, frailty, comorbidity, area-level deprivation and lifestyle factors with infection. Illness profile post-vaccination was assessed using a second control group of unvaccinated cases. @@ -2973,13 +2975,6 @@ Strengths and limitations of this studyO_LIUsing nationwide linked population-le C_LIO_LIMost demographic and socio-economic characteristics are derived from the 2011 Census and therefore are 10 years old. However, we focus primarily on characteristics that are unlikely to change over time, such as ethnicity or religion, or likely to be stable for our population C_LIO_LIBecause the data are based on the 2011 Census, it excluded people living in England in 2011 but not taking part in the 2011 Census; respondents who could not be linked to the 2011-2013 NHS patients register; recent migrants. Consequently, we excluded 5.4% of vaccinated people who could not be linked C_LI",public and global health,fuzzy,100,100 -medRxiv,10.1101/2021.05.12.21257102,2021-05-15,https://medrxiv.org/cgi/content/short/2021.05.12.21257102,"Spike-antibody responses following first and second doses of ChAdOx1 and BNT162b2 vaccines by age, gender, and clinical factors - a prospective community cohort study (Virus Watch)",Madhumita Shrotri; Ellen Fragaszy; Cyril Geismar; Vincent Nguyen; Sarah Beale; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Anna Aryee; Jamie Lopez Bernal; Anne M Johnson; Alison Rodger; Andrew C Hayward; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; University College London; University College London; University College London,"BackgroundVaccination constitutes the best long-term solution against Coronavirus Disease 2019 (COVID-19). Real-world immunogenicity data are sparse, particularly for ChAdOx1 and in populations with chronic conditions; and given the UKs extended dosing interval, it is also important to understand antibody responses in SARS-CoV-2-naive individuals following a single dose. - -MethodsAdults aged [≥]18 years from households enrolled in Virus Watch, a prospective community cohort study in England and Wales, provided capillary blood samples and self-reported vaccination status. Primary outcome variables were quantitative Spike total antibody levels (U/ml) and seropositivity to Spike ([≥]0.8 U/ml), as per Roches Elecsys Anti-SARS-CoV-2 S assay. Samples seropositive for Nucleocapsid, and samples taken prior to vaccination, were excluded. Outcomes were analysed by days since vaccination, vaccine type (BNT162b2 and ChAdOx1), and a range of self-reported demographic and clinical factors. - -Results8,517 vaccinated participants (median age 65 years [IQR: 58, 71]), contributed 13,232 samples (8,115 following ChAdOx1, 5,008 following BNT162b2). Seropositivity to Spike was 96.42% (95%CI 96, 96.79) at 28-34 days following a single dose, reaching 99.08% (97.8, 99.62) at 7-14 days after a second dose. Seropositivity rates, and Spike-antibody levels rose more quickly following the first dose of BNT162b2, however, were equivalent for both vaccines by 4 and 8 weeks, respectively. There was evidence of lower S-antibody levels with increasing age (p=0.0001). In partially vaccinated 65-79 year-olds, lower S-antibody levels were observed in men (25.9 vs 42.3 U/ml, p<0.0001), those with a chronic condition (33.0 vs 41.2 U/ml, p<0.0001), diabetes (22.32 vs 36.01 U/ml, p<0.0001), cardiovascular disease (32.1 vs 36.7 U/ml, p=0.0002), or history of cancer (30.1 vs 35.7 U/ml, p=0.0001), particularly those with haematological rather than solid organ cancer (7.48 vs 31.68 U/ml, p<0.0001), and those currently on immunosuppressive therapy (21.7 vs 35.6 U/ml, p<0.0001). Following a second dose, high S-antibody titres ([≥]250U/ml) were observed for nearly all individuals. - -InterpretationA single dose of either BNT162b2 or ChAdOx1 leads to high Spike seropositivity rates in SARS-CoV-2-naive individuals. However, observed disparities in antibody levels after the first dose by vaccine type, age, and comorbidities highlight the importance of ongoing non-pharmaceutical preventative measures such as social distancing, for partially vaccinated adults, particularly those who are older and more clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.06.21256757,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.06.21256757,COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study,Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw,"Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK","BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission. ObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector. @@ -3154,21 +3149,7 @@ MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study augm ResultsDuring round 10, we estimated an R number of 1.00 (95% confidence interval 0.81, 1.21). Between rounds 9 and 10 we estimated national prevalence has dropped by [~]60% from 0.49% (0.44%, 0.55%) in February to 0.20% (0.17%, 0.23%) in March. There were substantial falls in weighted regional prevalence: in South East from 0.36% (0.29%, 0.44%) in round 9 to 0.07% (0.04%, 0.12%) in round 10; London from 0.60% (0.48%, 0.76%) to 0.16% (0.10%, 0.26%); East of England from 0.47% (0.36%, 0.60%) to 0.15% (0.10%, 0.24%); East Midlands from 0.59% (0.45%, 0.77%) to 0.19% (0.13%, 0.28%); and North West from 0.69% (0.54%, 0.88%) to 0.31% (0.21%, 0.45%). Areas of apparent higher prevalence remain in parts of the North West, and Yorkshire and The Humber. The highest prevalence in March was found among school-aged children 5 to 12 years at 0.41% (0.27%, 0.62%), compared with the lowest in those aged 65 to 74 and 75 and over at 0.09% (0.05%, 0.16%). The close approximation between prevalence of infections and deaths (suitably lagged) is diverging, suggesting that infections may have resulted in fewer hospitalisations and deaths since the start of widespread vaccination. ConclusionWe report a sharp decline in prevalence of infections between February and March 2021. We did not observe an increase in the prevalence of SARS-CoV-2 following the reopening of schools in England, although the decline of prevalence appears to have stopped. Future rounds of REACT-1 will be able to measure the rate of growth or decline from this current plateau and hence help assess the effectiveness of the vaccination roll-out on transmission of the virus as well as the potential size of any third wave during the ensuing months.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.04.08.21255099,2021-04-14,https://medrxiv.org/cgi/content/short/2021.04.08.21255099,Occupational risks of COVID-19 in NHS workers in England,Diana van der Plaat; Ira Madan; David Coggon; Martie van Tongeren; Rhiannon Edge; Rupert Muiry; Vaughan Parsons; Paul Cullinan,Imperial College London; Guy's and St Thomas' NHS Foundation Trust; Southampton General Hospital; University of Manchester; Lancaster University; Guy's and St Thomas NHS Foundation Trust; Guy's and St Thomas NHS Foundation Trust; Imperial College London,"ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England - -MethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression. - -ResultsWith adjustment for employing trust, demographic characteristics, and previous frequency of sickness absence, risk relative to administrative/clerical occupations was highest in additional clinical services (including care assistants) (OR 2.31 [2.25-2.37]), registered nursing and midwifery professionals (OR 2.28 [2.23-2.34]) and allied health professionals (OR 1.94 [1.88-2.01]), and intermediate in doctors and dentists (OR 1.55 [1.50-1.61]). Differences in risk were higher after the employing trust had started to care for documented Covid-19 patients, and were reduced, but not eliminated, following additional adjustment for exposure to infected patients or materials, assessed by a job-exposure matrix. For prolonged Covid-19 sickness absence (episodes lasting >14 days), the variation in risk by staff group was somewhat greater. - -ConclusionsAfter allowance for possible bias and confounding by non-occupational exposures, we estimated that relative risks for Covid-19 among most patient-facing occupations were between 1.5 and 2.5. The highest risks were in those working in additional clinical services, nursing and midwifery and in allied health professions. Better protective measures for these staff groups should be a priority. Covid-19 may meet criteria for compensation as an occupational disease in some healthcare occupations. - -Key messagesO_LIWhat is already known about this subject? -Healthcare workers and other keyworkers (workers whose job was considered essential to societal functioning) had a higher likelihood of testing positive for COVID-19 than other workers during the first lockdown in England. Amongst healthcare workers, those working in inpatient settings had the highest rate of infection. -C_LIO_LIWhat are the new findings? -Between March and July 2000, the overall risk of COVID-19 sickness absence in National Health Service staff in England was lower at older ages, higher in non-white staff, and (in comparison with administrative and clerical staff) more than doubled in registered nurses and among workers such as healthcare assistants providing support to health professionals. Risk in health care scientists was little different from that in administrative and clerical occupations -C_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future? -Our results suggest that the risk reduction strategies that were in place for healthcare scientists were effective. However, the protection for nursing and supporting health professionals was insufficient. In the event of a further wave of infections resulting in high hospital admissions, attention should be paid to ensuring that risk reduction strategies for nurses and supporting health professionals are improved. -C_LI",occupational and environmental health,fuzzy,100,100 +bioRxiv,10.1101/2021.04.13.439482,2021-04-13,https://biorxiv.org/cgi/content/short/2021.04.13.439482,Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice,Kai Wu; Angela Choi; Matthew Koch; Sayda Elbashir; LingZhi Ma; Diana Lee; Angela Woods; Carole Henry; Charis Palandjian; Anna Hill; Hardik Jani; Julian Quinones; Naveen Nunna; Adrian B McDermott; Samantha Falcone; Elisabeth Narayanan; Tonya Colpitts; Hamilton Bennett; Kizzmekia Corbett; Robert Seder; Barney S Graham; Guillaume BE Stewart-Jones; Andrea Carfi; Darin K Edwards,"Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Moderna, Inc; Moderna, Inc; Moderna, Inc","Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.",microbiology,fuzzy,96,94 medRxiv,10.1101/2021.04.10.21254672,2021-04-12,https://medrxiv.org/cgi/content/short/2021.04.10.21254672,Inhaled budesonide for COVID-19 in people at higher risk of adverse outcomes in the community: interim analyses from the PRINCIPLE trial,- The PRINCIPLE Trial Collaborative Group; Ly-Mee Yu; Mona Bafadhel; Jienchi Dorward; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Nicholas Berry; Michelle A Detry; Christina T Saunders; Mark Fitzgerald; Victoria Harris; Simon de Lusignan; Monique I Andersson; Peter J Barnes; Richard EK Russell; Dan V Nicolau Jr.; Sanjay Ramakrishnan; FD Richard Hobbs; Christopher C Butler,"; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; National Heart and Lung Institute, Imperial College, London, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom; UQ Centre for Clinical Research, University of Queensland, Brisbane, Australia and Nuffield Department of Clinical Medicine, University of Oxford, United Kingdo; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom","BACKGROUNDInhaled budesonide has shown efficacy for treating COVID-19 in the community but has not yet been tested in effectiveness trials. METHODSWe performed a multicenter, open-label, multi-arm, adaptive platform randomized controlled trial involving people aged [≥]65 years, or [≥]50 years with comorbidities, and unwell [≤]14 days with suspected COVID-19 in the community (PRINCIPLE). Participants were randomized to usual care, usual care plus inhaled budesonide (800{micro}g twice daily for 14 days), or usual care plus other interventions. The co-primary endpoints are time to first self-reported recovery, and hospitalization/death related to COVID-19, both measured over 28 days from randomisation and analysed using Bayesian models. @@ -3236,15 +3217,6 @@ ResultsAcross the analysed datasets, one to two-thirds of participants experienc ConclusionPeople experiencing psychological distress pre-pandemic have been more likely to experience healthcare and economic disruptions, and clusters of disruptions across multiple domains during the pandemic. Failing to address these disruptions risks further widening the existing inequalities in mental health.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2021.04.01.21254789,2021-04-07,https://medrxiv.org/cgi/content/short/2021.04.01.21254789,Mendelian randomisation identifies alternative splicing of the FAS death receptor as a mediator of severe COVID-19,Lucija Klaric; Jack S Gisby; Artemis Papadaki; Marisa D Muckian; Erin Macdonald-Dunlop; Jing Hua Zhao; Alex Tokolyi; Elodie Persyn; Erola Pairo-Castineira; Andrew P Morris; Anette Kalnapenkis; Anne Richmond; Arianna Landini; Åsa K Hedman; Bram Prins; Daniela Zanetti; Eleanor Wheeler; Charles Kooperberg; Chen Yao; John R Petrie; Jingyuan Fu; Lasse Folkersen; Mark Walker; Martin Magnusson; Niclas Eriksson; Niklas Mattsson-Carlgren; Paul RHJ Timmers; Shih-Jen Hwang; Stefan Enroth; Stefan Gustafsson; Urmo Vosa; Yan Chen; Agneta Siegbahn; Alexander Reiner; Åsa Johansson; Barbara Thorand; Bruna Gigante; Caroline Hayward; Christian Herder; Christian Gieger; Claudia Langenberg; Daniel Levy; Daria V Zhernakova; J Gustav Smith; Harry Campbell; Johan Sundstrom; John Danesh; Karl Michaëlsson; Karsten Suhre; Lars Lind; Lars Wallentin; Leonid Padyukov; Mikael Landén; Nicholas J Wareham; Andreas Göteson; Oskar Hansson; Per Eriksson; Rona J Strawbridge; Themistocles L Assimes; Tõnu Esko; Ulf Gyllensten; J Kenneth Baillie; Dirk S Paul; Peter K Joshi; Adam S Butterworth; Anders Mälarstig; Nicola Pirastu; James F Wilson; James E Peters,"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK; Institute of Genomics, University of Tartu, Tartu, Estonia; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Medicine, Karolinska Institute, Stockholm, Sweden; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; Danish National Genome Center, Copenhagen, Denmark.; Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Department of Clinical Sciences, Lund University, Malmö, Sweden; Uppsala Clinical Research Center (UCR), Uppsala University, Uppsala, Sweden; Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Institute of Genomics, University of Tartu, Tartu, Estonia; Department of Medicine Solna, Karolinska Institutet; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany; Division of Cardiovascular Medicine, Dept of Medicine, Karolinska Institutet, Stockholm, Sweden; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Surgcial Sciences, Unit of Medical Epidemiology, Uppsala University, Uppsala, Sweden; Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden; Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden; Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden; Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Institute of Health and Wellbeing, College of Medicine, Veterinary and Life Sciences, University of Glasgow, UK; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Institute of Genomics, University of Tartu, Tartu, Estonia; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Karolinska Institute, Stockholm, Sweden; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK","Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify proteins that mediate severe COVID-19. Using protein quantitative trait loci (pQTL) data from the SCALLOP consortium, involving meta-analysis of up to 26,494 individuals, and COVID-19 genome-wide association data from the Host Genetics Initiative, we performed MR for 157 COVID-19 severity protein biomarkers. We identified significant MR results for five proteins: FAS, TNFRSF10A, CCL2, EPHB4 and LGALS9. Further evaluation of these candidates using sensitivity analyses and colocalization testing provided strong evidence to implicate the apoptosis-associated cytokine receptor FAS as a causal mediator of severe COVID-19. This effect was specific to severe disease. Using RNA-seq data from 4,778 individuals, we demonstrate that the pQTL at the FAS locus results from genetically influenced alternate splicing causing skipping of exon 6. We show that the risk allele for very severe COVID-19 increases the proportion of transcripts lacking exon 6, and thereby increases soluble FAS. Soluble FAS acts as a decoy receptor for FAS-ligand, inhibiting apoptosis induced through membrane-bound FAS. In summary, we demonstrate a novel genetic mechanism that contributes to risk of severe of COVID-19, highlighting a pathway that may be a promising therapeutic target.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.03.31.21254687,2021-04-05,https://medrxiv.org/cgi/content/short/2021.03.31.21254687,"SARS-CoV-2 infectivity by viral load, S gene variants and demographic factors and the utility of lateral flow devices to prevent transmission",Lennard YW Lee; Stefan Rozmanowski; Matthew Pang; Andre Charlett; Charlotte Anderson; Gareth J Hughes; Matthew Barnard; Leon Peto; Richard Vipond; Alex Sienkiewicz; Susan Hopkins; John Bell; Derrick W Crook; Nick Gent; A Sarah Walker; Tim EA Peto; David W Eyre,University of Oxford; UK Government Department of Health and Social Care; UK Government Department of Health and Social Care; Public Health England; Public Health England; Public Health England; UK Government Department of Health and Social Care; University of Oxford; Public Health England; Public Health England; Public Health England; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford,"BackgroundHow SARS-CoV-2 infectivity varies with viral load is incompletely understood. Whether rapid point-of-care antigen lateral flow devices (LFDs) detect most potential transmission sources despite imperfect sensitivity is unknown. - -MethodsWe combined SARS-CoV-2 testing and contact tracing data from England between 01-September-2020 and 28-February-2021. We used multivariable logistic regression to investigate relationships between PCR-confirmed infection in contacts of community-diagnosed cases and index case viral load, S gene target failure (proxy for B.1.1.7 infection), demographics, SARS-CoV-2 incidence, social deprivation, and contact event type. We used LFD performance to simulate the proportion of cases with a PCR-positive contact expected to be detected using one of four LFDs. - -Results231,498/2,474,066 (9%) contacts of 1,064,004 index cases tested PCR-positive. PCR-positive results in contacts independently increased with higher case viral loads (lower Ct values) e.g., 11.7%(95%CI 11.5-12.0%) at Ct=15 and 4.5%(4.4-4.6%) at Ct=30. B.1.1.7 infection increased PCR-positive results by [~]50%, (e.g. 1.55-fold, 95%CI 1.49-1.61, at Ct=20). PCR-positive results were most common in household contacts (at Ct=20.1, 8.7%[95%CI 8.6-8.9%]), followed by household visitors (7.1%[6.8-7.3%]), contacts at events/activities (5.2%[4.9-5.4%]), work/education (4.6%[4.4-4.8%]), and least common after outdoor contact (2.9%[2.3-3.8%]). Contacts of children were the least likely to test positive, particularly following contact outdoors or at work/education. The most and least sensitive LFDs would detect 89.5%(89.4-89.6%) and 83.0%(82.8-83.1%) of cases with PCR-positive contacts respectively. - -ConclusionsSARS-CoV-2 infectivity varies by case viral load, contact event type, and age. Those with high viral loads are the most infectious. B.1.1.7 increased transmission by [~]50%. The best performing LFDs detect most infectious cases. - -Key pointsIn 2,474,066 contacts of 1,064,004 SARS-CoV-2 cases, PCR-positive tests in contacts increased with higher index case viral loads, the B.1.1.7 variant and household contact. Children were less infectious. Lateral flow devices can detect 83.0-89.5% of infections leading to onward transmission.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.27.21254452,2021-03-29,https://medrxiv.org/cgi/content/short/2021.03.27.21254452,Risk factors for developing COVID-19: a population-based longitudinal study (COVIDENCE UK),Hayley Holt; Mohammad Talaei; Matthew Greenig; Dominik Zenner; Jane Symons; Clare Relton; Katherine S Young; Molly R Davies; Katherine N Thompson; Jed Ashman; Sultan Saeed Rajpoot; Ahmed Ali Kayyale; Sarah El Rifai; Philippa J Lloyd; David A Jolliffe; Sarah Finer; Stamatina Iliodromiti; Alec Miners; Nicholas S Hopkinson; Bodrul Alam; Paul E Pfeffer; David McCoy; Gwyneth A Davies; Ronan A Lyons; Chris J Griffiths; Frank Kee; Aziz Sheikh; Gerome Breen; Seif O Shaheen; Adrian R Martineau,"Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Queen Mary University of London; King's College London; King's College London; King's College London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; London School of Hygiene and Tropical Medicine; Imperial College London; Edenfield Road Surgery, Rochdale, UK; Queen Mary University of London; Quen Mary University London; Swansea University Medical School; Swansea University Medical School; Queen Mary University of London; Queen's University Belfast; Edinburgh University; King's College London; Queen Mary University of London; Queen Mary University of London","BackgroundRisk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain. MethodsWe undertook a prospective, population-based cohort study (COVIDENCE UK) from 1st May 2020 to 5th February 2021. Baseline information on potential risk factors was captured by online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19. @@ -3283,6 +3255,7 @@ Main outcome measuresVaccination intention was measured by individual participan ResultsSurvey response rate was 56% (20,792/36,998) in December 2020 and 52% (20,284/38,727) in February 2021, with 14,713 adults reporting across both time points. Of participants reporting across both timepoints, 13,281 (90%) answered Yes and 1,432 (10%) responded No or Unsure in December 2020. Of those answering No or Unsure in December 2020, 1,233 (86%) went on to answer Yes or Already had a COVID-19 vaccine in February 2021. The magnitude of this shift was consistent across all ethnic groups measured and all levels of social deprivation. Age was most strongly associated with vaccination intention, with 16-24-year-olds more likely to respond ""No"" or ""Unsure"" than those aged 75+ in December 2020 (RR: 4.32, 95% CI: 2.40-7.78 &2.93 95% CI: 2.19-3.92, respectively) and February 2021 (RR: 5.30 95% CI: 1.39-20.20 &20.21 95%CI: 7.19-56.78). The association between ethnicity and vaccination intention has weakened, but not disappeared, over time. Both vaccine- and illness-related psychological factors were shown to influence vaccination intention. ConclusionsOver four in five adults (86%) who were reluctant or intending to refuse a COVID-19 vaccine in December 2020 had changed their mind in February 2021 and planned on accepting, or had already accepted, a vaccine.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2021.03.24.21254227,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.24.21254227,COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death,Darryl P Leong; Amitava Banerjee; Salim Yusuf,McMaster University; University College London; McMaster University,"The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.03.26.21254390,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254390,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study,Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen,Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital,"BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors. MethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration. @@ -3329,6 +3302,7 @@ MethodsWe used Cox proportional hazards models to estimate hazard ratios (HRs) f ResultsWe observed a small proportion of care home residents with positive PCR tests following vaccination 1.05% (N=148), with 90% of infections occurring within 28-days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30,0.95), and an increased HR for those receiving the Pfizer-BioNTECH vaccine compared to the Oxford-AstraZeneca; 3.83 (2.45,5.98). For the 21-day landmark analysis we observed high HRs for individuals with low and intermediate frailty compared to those without; 4.59 (1.23,17.12) and 4.85 (1.68,14.04) respectively. ConclusionsIncreased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",geriatric medicine,fuzzy,100,100 +medRxiv,10.1101/2021.03.16.21253371,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.16.21253371,Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes,Emma Whitfield; Claire Coffey; Huayu Zhang; Ting Shi; Xiaodong Wu; Qiang Li; Honghan Wu,"Institute of Health Informatics, UCL, London, United Kingdom; University of Cambridge, Cambridge, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Shanghai East Hospital, Tongji University, Shanghai, China; Shanghai East Hospital, Tongji University, Shanghai, China; Institute of Health Informatics, UCL, London, United Kingdom","COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering axes of prognosis. We propose two innovative clustering approaches - Layered Axes and Prognosis Space - to apply on patients outcome data. We then show how these clusters can help predict a patients deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients hospital admission. Moreover, our method could be used to explore subtypes of long COVID and other diseases with heterogeneous outcomes.",health informatics,fuzzy,100,92 medRxiv,10.1101/2021.03.16.21253377,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.16.21253377,First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant,Luke B Snell; Wenjuan Wang; Adela Alcolea-Medina; Themoula Charalampous; Gaia Nebbia; Rahul Batra; Leonardo de Jongh; Finola Higgins; Yanzhong Wang; Jonathan D Edgeworth; Vasa Curcin,"King's College London; School of Population Health and Environmental Sciences, King's College London, London, UK; Viapath, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; School of Population Health and Environmental Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; School of Population Health and Environmental Sciences, King's College London, London, UK","IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection. MethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants. @@ -3465,6 +3439,23 @@ Results13,109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 ConclusionNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant. SummaryNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provided [≥] 85% protection against symptomatic and asymptomatic SARS-CoV-2 infection in healthcare workers, including against the B.1.1.7 variant. Single dose vaccination reduced symptomatic infection by 67%.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.03.08.21253110,2021-03-10,https://medrxiv.org/cgi/content/short/2021.03.08.21253110,Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 Long Term Care Facilities (VIVALDI study),Maria Krutikov; Tom Palmer; Gokhan Tut; Chris Fuller; Madhumita Shrotri; Haydn Williams; Daniel Davies; Aidan Irwin-Singer; James Robson; Andrew Hayward; Paul Moss; Andrew Copas; Laura J Shallcross,UCL; UCL; University of Birmingham; UCL; UCL; Four Seasons Healthcare Group; Palantir Ltd; UK Department of Health and Social Care; Four Seasons Healthcare Group; UCL; University of Birmingham; UCL; UCL,"BackgroundSARS-CoV-2 infection represents a major challenge for Long Term Care Facilities (LTCFs) and many residents and staff are now sero-positive following persistent outbreaks. We investigated the relationship between the presence of SARS-CoV-2 specific antibodies and subsequent infection in this population. + +MethodsProspective cohort study of infection in staff and residents in 100 LTCFs in England between October 2020 and February 2021. Blood samples were collected at baseline (June 2020), 2 and 4 months and tested for IgG antibodies to nucleocapsid and spike protein. PCR testing for SARS-CoV-2 was undertaken weekly in staff and monthly in residents. The primary analysis estimated the relative hazard of a PCR-positive test by baseline antibody status, from Cox regression adjusted for age and gender, and stratified by LTCF. + +FindingsStudy inclusion criteria were met by 682 residents and 1429 staff. Baseline IgG antibodies to nucleocapsid were detected in 226 residents (33%) and 408 staff (29%). A total of 93 antibody-negative residents had a PCR-positive test (0.054 per month at risk) compared to 4 antibody-positive residents (0.007 per month at risk). There were 111 PCR-positive tests in antibody-negative staff (0.042 per month at risk) compared to 10 in antibody-positive staff (0.009 per month at risk). The adjusted hazard ratios for reinfection in staff and residents with a baseline positive versus negative antibody test were 0.13 (95% CI 0.05-0.40) and 0.39 ((95% CI: 0.19-0.77) respectively. Of 12 reinfected participants with data on symptoms, 11 were symptomatic. Antibody titres to spike and nucleocapsid were comparable in PCR-positive and PCR-negative cases. + +InterpretationThe presence of IgG antibodies to nucleocapsid was associated with substantially reduced risk of reinfection in staff and residents for up to 10 months after primary infection. + +FundingUK Government Department of Health and Social Care + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe performed a systematic search of MEDLINE (Ovid) and MedRxiv on 18 January 2021 for studies in LTCFs that described the risk of infection in individuals who were seropositive for SARS-CoV-2 compared to individuals who were seronegative. Search terms were deliberately broad to improve capture of relevant literature and included ""SARS-CoV-2""OR ""COVID-19"" OR ""coronavirus"" AND ""care home"" OR ""nursing home"" OR ""long term care facility"" with no date or language restrictions. We did not identify any publications that focussed on risk of reinfection in seropositive individuals, but subsequent to our search one study has been published using data from two LTCFs in London, UK. This study reported a 96% reduction in the odds of reinfection in individuals who were seropositive compared to those who were seronegative based on 4-month follow-up in 161 participants. We found 10 studies that performed seroprevalence surveys in either staff or staff and residents in LTCFs in 8 cohorts. Five of these were carried out in response to SARS-CoV-2 outbreaks within the care homes, either as part of the subsequent investigation or as post-infection surveillance. The largest of these, which enrolled both staff and residents, was performed in 6 LTCFs and performed longitudinal antibody testing. + +Added value of this studyWe undertook a cohort study in staff and residents from 100 LTCFs in England to investigate whether individuals with evidence of prior SARS-CoV-2 infection could be infected twice. Staff and residents were offered up to three rounds of antibody testing and antibody results were linked to PCR test results which were obtained weekly from staff and monthly from residents through the national SARS-CoV-2 testing programme. This study, which was conducted in >2000 staff and residents, suggests that antibodies provide high levels of protection against reinfection for up to 10 months. Almost all cases of reinfection were symptomatic, but no cases required hospital treatment. Amongst those with detectable baseline antibodies, quantitative antibody titres against spike protein and nucleocapsid were comparable between cases of reinfection and those who did not become reinfected. + +Implications of all available evidenceDespite high background rates of infection in LTCFs, the overall risk of reinfection was low in this population. This is broadly consistent with findings from large cohort studies of hospital staff, but, importantly, extends the evidence of substantial protection to frail elderly, who are vulnerable to severe outcomes of SARS-CoV-2 due to age-related changes in immunity (immune-senescence) and high levels of comorbidity. The low risk of reinfection in our study suggests identification of immune correlates of protection in this population will require pooling of data across multiple cohorts. + +As vaccination coverage in residents approaches 100% in England, it will be important to understand whether vaccination and natural infection provide comparable levels of protection against infection. Such insights will inform future policy decisions regarding re-vaccination schedules in LTCF, and the longer-term need for non-pharmaceutical interventions to prevent SARS-CoV-2 transmission, such as asymptomatic testing and visitor restrictions.",geriatric medicine,fuzzy,100,100 medRxiv,10.1101/2021.03.09.21252736,2021-03-10,https://medrxiv.org/cgi/content/short/2021.03.09.21252736,"Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Lise Estcourt; Leon Peto; Jonathan R Emberson; Natalie Staplin; Enti Spata; Guilherme Pessoa-Amorim; Mark Campbell; Alistair Roddick; Nigel E Brunskill; Tina George; Daniel Zehnder; Simon Tiberi; Ni Ni Aung; Alison Uriel; John Widdrington; George Koshy; Thomas Brown; Steven Scott; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; David Roberts; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; University of Leicester, Leicester, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; North Cumbria Integrated Care NHS Foundation Trust, Carlisle, United Kingdom; Barts Health NHS Foundation Trust, London, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; North Manchester General Hospital, Pennine Acute Hospitals NHS Trust, Bury, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Portsmouth Hospitals NHS Foundation Trust, Portsmouth, United Kingdom; Countess of Chester Hospital, Chester, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundTreatment of COVID-19 patients with plasma containing anti-SARS-CoV-2 antibodies may have a beneficial effect on clinical outcomes. We aimed to evaluate the safety and efficacy of convalescent plasma in patients admitted to hospital with COVID-19. MethodsIn this randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) several possible treatments are being compared with usual care in patients hospitalised with COVID-19 in the UK. Eligible and consenting patients were randomly allocated to receive either usual care plus high titre convalescent plasma or usual care alone. The primary outcome was 28-day mortality. @@ -3622,6 +3613,13 @@ What Did the Researchers Do and Find?- We combined epidemiological and economic What Do These Findings Mean?- Lower- and middle-income countries (LMICs) and international bodies providing guidance for LMICs need to consider evidence specific to these settings when making recommendations about COVID-19 vaccination. - Further data and model-based analyses in such settings are urgently needed in order to ensure that vaccination decisions are appropriate to these contexts.",health economics,fuzzy,100,100 +medRxiv,10.1101/2021.02.23.21252276,2021-02-24,https://medrxiv.org/cgi/content/short/2021.02.23.21252276,Inequalities in the decline and recovery of pathological cancer diagnoses during the first six months of the COVID-19 pandemic: a population-based study,Ashleigh C. Hamilton; David W. Donnelly; Maurice B. Loughrey; Richard C. Turkington; Colin Fox; Deirdre Fitzpatrick; Ciaran E. O'Neill; Anna T. Gavin; Helen G. Coleman,"Centre for Public Health, Queen's University Belfast; Northern Ireland Cancer Registry; Department of Pathology, Belfast Health and Social Care Trust, Northern Ireland; Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Centre for Public Health, Queen's University Belfast","BackgroundThe restructuring of healthcare systems to cope with the demands of the COVID-19 pandemic has led to a reduction in clinical services such as cancer screening and diagnostics. + +MethodsData from the four Northern Ireland pathology labs was used to assess trends in pathological cancer diagnoses from 1st March to 12th September 2020 overall and by cancer site, gender and age. These trends were compared to the same timeframe from 2017-2019. + +ResultsBetween 1st March and 12th September 2020 there was a 23% reduction in cancer diagnoses compared to the same time period in the preceding three years. Although some recovery occurred in August and September 2020, this revealed inequalities across certain patient groups. Pathological diagnoses of lung, prostate and gynaecological malignancies remained well below pre-pandemic levels. Males and younger/middle-aged adults, particularly the 50-59 year old patient group, also lagged behind other population demographic groups in terms of returning to expected numbers of pathological cancer diagnoses. + +ConclusionsThere is a critical need to protect cancer diagnostic services in the ongoing pandemic to facilitate timely investigation of potential cancer cases. Targeted public health campaigns may be needed to reduce emerging inequalities in cancer diagnoses as the COVID-19 pandemic continues.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.02.18.21251973,2021-02-23,https://medrxiv.org/cgi/content/short/2021.02.18.21251973,REACT-1 round 9 interim report: downward trend of SARS-CoV-2 in England inFebruary 2021 but still at high prevalence,Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","Background and MethodsEngland entered its third national lockdown of the COVID-19 pandemic on 6th January 2021 with the aim of reducing the daily number of deaths and pressure on healthcare services. The real-time assessment of community transmission study (REACT-1) obtains throat and nose swabs from randomly selected people in England in order to describe patterns of SARS-CoV-2 prevalence. Here, we report data from round 9a of REACT-1 for swabs collected between 4th and 13th February 2021. ResultsOut of 85,473 tested-swabs, 378 were positive. Overall weighted prevalence of infection in the community in England was 0.51%, a fall of more than two thirds since our last report (round 8) in January 2021 when 1.57% of people tested positive. We estimate a halving time of 14.6 days and a reproduction number R of 0.72, based on the difference in prevalence between the end of round 8 and the beginning of round 9. Although prevalence fell in all nine regions of England over the same period, there was greater uncertainty in the trend for North West, North East, and Yorkshire and The Humber. Prevalence fell substantially across all age groups with highest prevalence among 18- to 24-year olds at 0.89% (0.47%, 1.67%) and those aged 5 to12 years at 0.86% (0.60%, 1.24%). Large household size, living in a deprived neighbourhood, and Asian ethnicity were all associated with increased prevalence. Healthcare and care home workers were more likely to test positive compared to other workers. @@ -3724,25 +3722,6 @@ This study provides evidence of any differences in the health and wellbeing of c What this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure. Overall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2021.02.04.21251087,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251087,Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach,Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing. - -MethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings. - -ResultsThe total number of cases in a school was not associated with a subsequent increase in the risk of testing positive (Staff OR per case 0.92, 95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst pupils, the number of recent cases within the same year group was significantly associated with subsequent increased risk of testing positive (OR per case 1.12, 95%CI 1.08 - 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 - 9.88). - -ConclusionsIn a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased risk, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment. - -O_TEXTBOXWhat is knownO_LIEvidence of the role schools play in the transmission of SARS-CoV-2 is limited -C_LIO_LIHigher positivity rates are observed in school staff compared to pupils -C_LIO_LILack of evidence on transmission pathways transmission into and within schools -C_LI - -What this study addsO_LIFirst UK national level study of transmission between pupils and staff in a school environment during the SARS-CoV-2 pandemic. -C_LIO_LISchools opening September-December 2020 was not associated with an increased subsequent risk of testing positive in staff -C_LIO_LIPupils were found to be at increased risk of testing positive, following cases appearing within their own year group -C_LI - -C_TEXTBOX",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.02.07.21251297,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.07.21251297,The changing characteristics of COVID-19 presentations: A regional comparison of SARS-CoV-2 hospitalised patients during the first and second wave.,Catherine Atkin; Vicky Kamwa; Vinay Reddy-Kolanu; Dhruv Parekh; Felicity Evison; Peter Nightingale; Suzy Gallier; Simon Ball; Elizabeth Sapey,"Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham; Acute Medicine, University Hospitals Birmingham NHS Foundation Trust; A. Intensive Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, B15 2GW, UK. B. Birmingham Acute Care Research Grou; Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; NIHR Clinical Research Facility Statistician, University Hospitals Birmingham NHS Foundation Trust; PIONEER Technical Director, Lead for Research Analytics Department of Health Informatics, University Hospitals Birmingham NHS Foundation Trust; A. Chief Medical Officer, University Hospitals Birmingham NHS Foundation Trust B. HDR-UK Midlands Site and Better Care Programme, University Hospitals Birmingh; A. Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care B. Birmingham Acute Care Research Group, Institute of Inflammat","BackgroundThis study assesses COVID-19 hospitalised patient demography and outcomes during wave 1 and wave 2, prior to new variants of the virus. MethodsAll patients with a positive SARS-CoV-2 swab between 10th March 2020 and 5th July 2020 (wave 1) and 1st September 2020 and 16th November 2020 (wave 2) admitted to University Hospitals Birmingham NHS Foundation Trust were included (n=4856), followed for 28 days. @@ -3791,12 +3770,6 @@ Research In ContextO_ST_ABSEvidence before the studyC_ST_ABSIn January 2020, we Added value of the studyWe report findings from a population representative, household survey of SARS-CoV-2 infection amongst a UK strictly Orthodox Jewish population. We demonstrate an extremely high seroprevalence rate of SARS-CoV-2 in this population which is more than five times the estimated seroprevalence nationally and five times the estimated seroprevalence in London. In addition the large number of children in our survey, reflective of the underlying population structure, allows us to demonstrate that in this setting there is a significant burden of disease in all age groups with secondary school aged children having an equivalent seroprevalence to adults. Implications of the available evidenceOur data provide clear evidence of the markedly disproportionate impact of SARS-CoV-2 in minority populations. In this setting infection occurs at high rates across all age groups including pre-school, primary school and secondary school-age children. Contextually appropriate measures to specifically reduce the impact of SARS-CoV-2 amongst minority populations are urgently required.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.02.02.21250989,2021-02-03,https://medrxiv.org/cgi/content/short/2021.02.02.21250989,Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020,Krishnan Bhaskaran; Rohini Mathur; Christopher T Rentsch; Caroline E Morton; William J Hulme; Anna Schultze; Brian McKenna; Rosalind M Eggo; Angel YS Wong; Elizabeth J Williamson; Harriet J Forbes; Kevin Wing; Helen I McDonald; Chris J Bates; Sebastian CJ Bacon; Alex J Walker; David Evans; Peter Inglesby; Amir Mehrkar; Helen J Curtis; Nichola J DeVito; Richard Croker; Henry Drysdale; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Laurie Tomlinson; Stephen JW Evans; Richard Grieve; Liam Smeeth; Ben Goldacre,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP, TPP House, Horsforth, Leeds; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford","Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent ""second wave"" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England. - -O_TBL View this table: -org.highwire.dtl.DTLVardef@987a5org.highwire.dtl.DTLVardef@1a8a141org.highwire.dtl.DTLVardef@1f2de56org.highwire.dtl.DTLVardef@1e2f9b8org.highwire.dtl.DTLVardef@78bfcc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONAssociation between ethnicity and COVID-19 death 1st Sept - 9th Nov 2020 - -C_TABLECAPTION C_TBL",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.01.30.21250777,2021-02-01,https://medrxiv.org/cgi/content/short/2021.01.30.21250777,Accuracy of four lateral flow immunoassays for anti SARS-CoV-2 antibodies: a head-to-head comparative study,Hayley E Jones; Ranya Mulchandani; Sian Taylor-Phillips; A E Ades; Justin Shute; Keith Perry; Nastassya Chandra; Tim Brooks; Andre Charlett; Matthew Hickman; Isabel Oliver; Stephen Kaptoge; John Danesh; Emanuele Di Angelantonio; - COMPARE Study investigators; - EDSAB-HOME investigators; David H WYLLIE,University of Bristol; Public Health England; University of Warwick; University of Bristol; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; University of Bristol; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; ; ; Public Health England,"BackgroundSARS-CoV-2 antibody tests are used for population surveillance and might have a future role in individual risk assessment. Lateral flow immunoassays (LFIAs) can deliver results rapidly and at scale, but have widely varying accuracy. MethodsIn a laboratory setting, we performed head-to-head comparisons of four LFIAs: the Rapid Test Consortiums AbC-19 Rapid Test, OrientGene COVID IgG/IgM Rapid Test Cassette, SureScreen COVID-19 Rapid Test Cassette, and Biomerica COVID-19 IgG/IgM Rapid Test. We analysed blood samples from 2,847 key workers and 1,995 pre-pandemic blood donors with all four devices. @@ -4129,21 +4102,6 @@ C_LIO_LIReal-time data sources such as online health forums are essential for mo C_LIO_LIIt is not yet possible to establish COVID-19 status or whether concerned posters have pre-existing mental or physical health issues, are recovered, or have become unwell for the first time. C_LIO_LIOnline health forums are help-seeking forums, which introduces self-selection bias. C_LI",health informatics,fuzzy,100,100 -medRxiv,10.1101/2020.12.15.20248096,2020-12-16,https://medrxiv.org/cgi/content/short/2020.12.15.20248096,"Anosmia and other SARS-CoV-2 positive test-associated symptoms, across three national, digital surveillance platforms as the COVID-19 pandemic and response unfolded: an observation study",Carole Helene Sudre; Ayya Keshet; Mark S Graham; Amit D Joshi; Smadar Shilo; Hagai Rossman; Benjamin Murray; Erika Molteni; Kerstin Klaser; Liane S Canas; Michela Antonelli; Marc Modat; Joan Capdevila Pujol; Sajaysurya Ganesh; Jonathan Wolf; Tomer Meir; Andrew T Chan; Claire Steves; Timothy Spector; John S Brownstein; Eran Segal; Sebastien Ourselin; Christina Astley,University College London; Weizmann Institute of Science; King's College London; Massachusetts General Hospital; Weizmann Institute of Science; Weizmann Institute of Science; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Weizmann Institute of Science; Massachusetts General Hospital; King's College London; King's College London; Boston Children's Hospital; Weizmann Institute of Science; King's College London; Boston Children's Hospital,"BackgroundMultiple participatory surveillance platforms were developed across the world in response to the COVID-19 pandemic, providing a real-time understanding of community-wide COVID-19 epidemiology. During this time, testing criteria broadened and healthcare policies matured. We sought to test whether there were consistent associations of symptoms with SARS-CoV-2 test status across three national surveillance platforms, during periods of testing and policy changes, and whether inconsistencies could better inform our understanding and future studies as the COVID-19 pandemic progresses. - -MethodsFour months (1st April 2020 to 31st July 2020) of observation through three volunteer COVID-19 digital surveillance platforms targeting communities in three countries (Israel, United Kingdom, and United States). Logistic regression of self-reported symptom on self-reported SARS-CoV-2 test status (or test access), adjusted for age and sex, in each of the study cohorts. Odds ratios over time were compared to known changes in testing policies and fluctuations in COVID-19 incidence. - -FindingsAnosmia/ageusia was the strongest, most consistent symptom associated with a positive COVID-19 test, based on 658,325 tests (5% positive) from over 10 million respondents in three digital surveillance platforms using longitudinal and cross-sectional survey methodologies. During higher-incidence periods with broader testing criteria, core COVID-19 symptoms were more strongly associated with test status. Lower incidence periods had, overall, larger confidence intervals. - -InterpretationThe strong association of anosmia/ageusia with self-reported SARS-CoV-2 test positivity is omnipresent, supporting its validity as a reliable COVID-19 signal, regardless of the participatory surveillance platform or testing policy. This analysis highlights that precise effect estimates, as well as an understanding of test access patterns to interpret differences, are best done only when incidence is high. These findings strongly support the need for testing access to be as open as possible both for real-time epidemiologic investigation and public health utility. - -FundingNIH, NIHR, Alzheimers Society, Wellcome Trust - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAs the COVID-19 pandemic has evolved, testing capacity expanded and governmental guidelines adapted, generally encouraging testing with a broader set of symptoms, not just fever with respiratory symptoms. In parallel, multiple large-scale citizen science digital surveillance platforms launched to complement knowledge from laboratory and somewhat smaller clinical studies. Symptoms such as loss of sense of smell have been identified as strongly predictive of COVID-19 infection in both clinical and syndromic surveillance analyses, and have therefore been used to inform these testing policy changes and access expansion. - -Added value of this studyThis study identifies symptoms that are or are not consistently associated with SARS-CoV-2 test positivity over time and across three country-based COVID-19 surveillance platforms in the United States, United Kingdom and Israel. These platforms are website and smartphone based, as well as cross-sectional and longitudinal. The study period of 4 months covers fluctuating COVID-19 prevalence during the fall of the first wave and, in some areas, rise of the second wave. In addition, the study period overlaps expansion of test access and test seeking. Importantly, these analyses track and highlight the value of individual symptoms to predict SARS-CoV-2 test positivity under a range of conditions. - -Implications of all the available evidenceDespite differences in surveillance methodology, access to SARS-CoV-2 testing and disease prevalence, loss of sense of smell or taste was consistently the strongest predictor of COVID-19 infection across all platforms over time. As access to testing broadened, the relevance of COVID-like symptoms and consistency of their predictive ability became apparent. However, confidence bounds generally widened with a fall in COVID-19 incidence. Therefore, for the most robust symptom-based COVID-19 prediction models should consider surveillance data during periods of higher incidence and improved test access, and effect estimates that replicate across different epidemiologic conditions and platforms.",infectious diseases,fuzzy,94,100 medRxiv,10.1101/2020.12.15.20248244,2020-12-16,https://medrxiv.org/cgi/content/short/2020.12.15.20248244,REACT-1 round 7 updated report: regional heterogeneity in changes in prevalence of SARS-CoV-2 infection during the second national COVID-19 lockdown in England,Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland exited a four-week second national lockdown on 2nd December 2020 initiated in response to the COVID-19 pandemic. Prior results showed that prevalence dropped during the first half of lockdown, with greater reductions in higher-prevalence northern regions. MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England, designed to monitor the spread of the epidemic and thus increase situational awareness. Round 7 of REACT-1 commenced swab-collection on 13th November 2020. A prior interim report included data from 13th to 24th November 2020 for 105,122 participants. Here, we report data for the entire round with swab results obtained up to 3rd December 2020. @@ -4226,6 +4184,21 @@ C_LIO_LIAdoption of POCT in care homes can be considered with appropriate prepar C_LIO_LIRepetitive errors and test malfunctioning can be mitigated with bespoke training for care home staff. C_LIO_LIIntegrated care pathways should be investigated to test the high variability of the context of use. C_LI",health systems and quality improvement,fuzzy,90,100 +medRxiv,10.1101/2020.12.01.20241729,2020-12-03,https://medrxiv.org/cgi/content/short/2020.12.01.20241729,International estimates of intended uptake and refusal of COVID-19 vaccines: A rapid systematic review and meta-analysis of large nationally representative samples,Eric Robinson; Andrew Jones; India Lesser; Michael Daly,University of Liverpool; University of Liverpool; University of Liverpool; Maynooth University,"BackgroundWidespread uptake of COVID-19 vaccines will be essential to extinguishing the COVID-19 pandemic. Vaccines have been developed in unprecedented time and hesitancy towards vaccination among the general population is unclear. + +MethodsSystematic review and meta-analysis of studies using large nationally representative samples (n[≥]1000) to examine the percentage of the population intending to vaccinate, unsure, or intending to refuse a COVID-19 vaccine when available. Generic inverse meta-analysis and meta-regression were used to pool estimates and examine time trends. PubMed, Scopus and pre-printer servers were searched from January-November, 2020. Registered on PROSPERO (CRD42020223132). + +FindingsTwenty-eight nationally representative samples (n = 58,656) from 13 countries indicate that as the pandemic has progressed, the percentage of people intending to vaccinate and refuse vaccination have been decreasing and increasing respectively. Pooled data from surveys conducted during June-October suggest that 60% (95% CI: 49% to 69%) intend to vaccinate and 20% (95% CI: 13% to 29%) intend to refuse vaccination, although intentions vary substantially between samples and countries (I2 > 90%). Being female, younger, of lower income or education level and belonging to an ethnic minority group were consistently associated with being less likely to intend to vaccinate. Findings were consistent across higher vs. lower quality studies. + +InterpretationIntentions to be vaccinated when a COVID-19 vaccine becomes available have been declining globally and there is an urgent need to address social inequalities in vaccine hesitancy and promote widespread uptake of vaccines as they become available. + +FundingN/A + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Scopus and pre-print servers for manuscripts from January to November, 2020, reporting on studies examining intentions to be vaccinated against COVID-19 in large nationally representative samples (N[≥]1000). No language restrictions were applied. Search terms were [(COVID OR coronavirus OR SARS-COV-2) AND (Vaccine OR Vaccination) AND (Inten* OR willing* OR attitud* OR hypothetical)]. From 792 articles, we identified 20 eligible articles reporting on 28 nationally representative samples. + +Added value of this studyThis is the first systematic study and meta-analysis to estimate the proportion of the global population willing to be vaccinated against vs. intending to refuse a vaccine when COVID-19 vaccines become available and how this trend has changed over time, using large and nationally representative samples. Results indicate that COVID-19 vaccination intentions vary substantially across countries, the percentage of the population intending to be vaccinated has declined across countries as the pandemic has progressed (March-May estimate: 79%, June-October estimate: 60%) and a growing number report intending to refuse a vaccine, when available (March-May estimate: 12%, June-October estimate: 20%). There is consistent socio-demographic patterning of vaccination intentions; being female, younger, of lower income or education level and belonging to an ethnic minority group are associated with a reduced likelihood of intending to be vaccinated when a vaccine become available. + +Implications of all the available evidenceIntentions to vaccinate against COVID-19 among the general public when a vaccine becomes available have been declining and this will limit the effectiveness of COVID-19 vaccination programmes. Findings highlight the need to improve public acceptability, trust and concern over the safety and benefit of COVID-19 vaccines and target vaccine uptake in disadvantaged groups who have already been disproportionately affected by the pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.27.20238147,2020-12-02,https://medrxiv.org/cgi/content/short/2020.11.27.20238147,"Ethnicity, Household Composition and COVID-19 Mortality: A National Linked Data Study",Vahe Nafilyan; Nazrul Islam; Daniel Ayoubkhani; Clare Gilles; Srinivasa Vittal Katikireddi; Rohini Mathur; Annabel Summerfield; Karen Tingay; Miqdad Asaria; Ann John; Peter Goldblatt; Amitava Banerjee; Myer Glickman; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; Office for National Statistics; Diabetes Research Centre, University of Leicester; University of Glasgow; London School of Hygiene and Tropical Medicine; Office for National Statistics; Office for National Statistics; London School of Economics and Political Sciences; Swansea University; UCL Institute of Health Equity, University College London; University College London; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates. We estimated associations between household composition and COVID-19 mortality in older adults ([≥] 65 years) using a newly linked census-based dataset, and investigated whether living in a multi-generational household explained some of the elevated COVID-19 mortality amongst ethnic minority groups. MethodsUsing retrospective data from the 2011 Census linked to Hospital Episode Statistics (2017-2019) and death registration data (up to 27th July 2020), we followed adults aged 65 years or over living in private households in England from 2 March 2020 until 27 July 2020 (n=10,078,568). We estimated hazard ratios (HRs) for COVID-19 death for people living in a multi-generational household compared with people living with another older adult, adjusting for geographical factors, socio-economic characteristics and pre-pandemic health. We conducted a causal mediation analysis to estimate the proportion of ethnic inequalities explained by living in a multi-generational household. @@ -4397,6 +4370,13 @@ ConclusionMild to moderate degrees of mobility restriction in most countries wer WHAT IS ALREADY KNOWN ON THIS TOPICSince SARS-CoV-2 became a pandemic, restrictions on mobility such as limitations on travel and closure of offices, restaurants, and shops have been imposed in an unprecedented way in both scale and scope to prevent the spread of COVID-19 in the absence of effective treatment options or a vaccine. Although mobility restriction has also brought about tremendous costs such as negative economic growth and other collateral impacts on health such as increased morbidity and mortality from lack of access to other essential health services, little evidence exists on the effectiveness of mobility restriction for the prevention of disease transmission. A search of PUBMED and Google Scholar for publications on this topic through Sep 20, 2020 revealed that most of the evidence on the effectiveness of physical distancing comes from mathematical modeling studies using a variety of assumptions. One study investigated only the combined effect of several interventions, including physical distancing, among SARS-CoV-2 infected patients. WHAT THIS STUDY ADDSThis is the first study to investigate the association between change in mobility and incidence of COVID-19 globally using real-time measures of mobility at the population level. For this, we used Google Global Mobility data and the daily incidence of COVID-19 for 36 countries from the day of 100th case detection through August 31, 2020. Our findings from LOESS regression show that in two-thirds of countries, reductions of up to 40% in commuting mobility were associated with decreased COVID-19 incidence, more so early in the pandemic. This decrease, however, plateaued as mobility decreased further. We found that associations between mobility restriction and incidence became smaller or negligible in the late phase of the pandemic in most countries. The reduced incidence rate of COVID-19 cases with a mild to moderate degree of mobility restriction in most countries suggests some value to limited mobility restriction in early phases of epidemic mitigation. The lack of impact in some others, however, suggests further research is needed to confirm these findings and determine the distinguishing factors for when mobility restrictions are helpful in decreasing viral transmission. Governments should carefully consider the level and period of mobility restriction necessary to achieve the desired benefits and minimize harm.",health policy,fuzzy,100,100 +medRxiv,10.1101/2020.10.30.20223123,2020-11-03,https://medrxiv.org/cgi/content/short/2020.10.30.20223123,High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundREACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive. + +MethodsREACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive. + +ResultsOverall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%). + +ConclusionThe co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.01.20222315,2020-11-02,https://medrxiv.org/cgi/content/short/2020.11.01.20222315,Association between living with children and outcomes from COVID-19: an OpenSAFELY cohort study of 12 million adults in England,Harriet Forbes; Caroline E Morton; Seb Bacon; Helen I McDonald; Caroline Minassian; Jeremy Brown; Christopher T. Rentsch; Rohini T. Mathur; Anna Schultze; Nicholas J DeVito; Brian MacKenna; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Henry Drysdale; Angel Wong; Jonathan Cockburn; Robert Mcmanus; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Liam Smeeth; Stephen JW Evans; Krishnan Bhaskaran; Rosalind M Eggo; Ben Goldacre; Laurie Tomlinson,"London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine","BackgroundClose contact with children may provide cross-reactive immunity to SARs-CoV-2 due to more frequent prior coryzal infections from seasonal coronaviruses. Alternatively, close contact with children may increase risk of SARs-CoV-2 infection. We investigated whether risk of infection with SARs-CoV-2 and severe outcomes differed between adults living with and without children. MethodsWorking on behalf of NHS England, we conducted a population-based cohort study using primary care data and pseudonymously-linked hospital and intensive care admissions, and death records, from patients registered in general practices representing 40% of England. Using multivariable Cox regression, we calculated fully-adjusted hazard ratios (HR) of outcomes from 1st February-3rd August 2020 comparing adults living with and without children in the household. @@ -4566,7 +4546,6 @@ medRxiv,10.1101/2020.10.13.20211813,2020-10-14,https://medrxiv.org/cgi/content/s Controlling any rise in infection is a compromise between public health and societal costs, with more stringent NPIs reducing cases but damaging the economy and restricting freedoms. Currently, NPI imposition is made in response to the epidemiological state, are of indefinite length and are often imposed at short notice, greatly increasing the negative impact. An alternative approach is to consider planned, limited duration periods of strict NPIs aiming to purposefully reduce prevalence before such emergency NPIs are required. These ""precautionary breaks"" may offer a means of keeping control of the epidemic, while their fixed duration and the forewarning may limit their society impact. Here, using simple analysis and age-structured models matched to the unfolding UK epidemic, we investigate the action of precautionary breaks. In particular we consider their impact on the prevalence of infection, as well as the total number of predicted hospitalisations and deaths. We find that precautionary breaks provide the biggest gains when the growth rate is low, but offer a much needed brake on increasing infection when the growth rate is higher, potentially allowing other measures (such as contact tracing) to regain control.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.10.11.20210625,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.11.20210625,Mental health service activity during COVID-19 lockdown among individuals with learning disabilities: South London and Maudsley data on services and mortality from January to July 2020,Evangelia Martin; Eleanor Nuzum; Matthew Broadbent; Robert Stewart,King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have had a widespread impact on mental healthcare service provision and use. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to quantify this for individuals with particular vulnerabilities, including those with learning disabilities and other neurodevelopmental disorders. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with potential neurodevelopmental disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st July 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with potential neurodevelopmental disorders. In addition, daily deaths are described for all current and previous SLaM service users with potential neurodevelopmental disorders over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. The largest declines in caseloads and total contacts were seen in Home Treatment Team, Liaison/A&E and Older Adult teams. Reduced accepted referrals and inpatient admissions were observed and there was an 103% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March (or a 282% increase if the 2-month period from 16th March to 15th May was considered alone).",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.10.08.20209411,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.08.20209411,"Elevated antiviral, myeloid and endothelial inflammatory markers in severe COVID-19",Ryan Thwaites; Ashley Sanchez Sevilla Uruchurtu; Matthew Siggins; Felicity Liew; Clark D Russell; Shona Moore; Edwin Carter; Simon Abrams; Charlotte-Eve Short; Thilipan Thaventhiran; Emma Bergstrom; Zoe Gardener; Stephanie Ascough; Christopher Chiu; Annemarie B Docherty; David Hunt; Yanick Crow; Tom Solomon; Graham Taylor; Lance Turtle; Ewen M Harrison; Malcolm Gracie Semple; J Kenneth Baillie; Peter JM Openshaw,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Edinburgh; University of Liverpool; University of Edinburgh; University of Liverpool; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Liverpool; Imperial College London; University ofLiverpool; University of Edinburgh; University of Liverpool; Roslin Institute, University of Edinburgh; Imperial College London","Introductory paragraphThe mechanisms that underpin COVID-19 disease severity, and determine the outcome of infection, are only beginning to be unraveled. The host inflammatory response contributes to lung injury, but circulating mediators levels fall below those in classical cytokine storms. We analyzed serial plasma samples from 619 patients hospitalized with COVID-19 recruited through the prospective multicenter ISARIC clinical characterization protocol U.K. study and 39 milder community cases not requiring hospitalization. Elevated levels of numerous mediators including angiopoietin-2, CXCL10, and GM-CSF were seen at recruitment in patients who later died. Markers of endothelial injury (angiopoietin-2 and von-Willebrand factor A2) were detected early in some patients, while inflammatory cytokines and markers of lung injury persisted for several weeks in fatal COVID-19 despite decreasing antiviral cytokine levels. Overall, markers of myeloid or endothelial cell activation were associated with severe, progressive, and fatal disease indicating a central role for innate immune activation and vascular inflammation in COVID-19.",infectious diseases,fuzzy,91,100 -medRxiv,10.1101/2020.10.09.20209957,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.09.20209957,Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19,Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi,"University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT","Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.08.20209304,2020-10-12,https://medrxiv.org/cgi/content/short/2020.10.08.20209304,Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data,Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses. MethodsWe included survivors ([≥]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities. @@ -4632,6 +4611,13 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID-19 outbreaks Added value of this studyWe conducted a national telephone survey with managers of all LTCFs in England which provided dementia care or care to residents aged > 65 years to collect data on the number of staff and residents in each facility, confirmed SARS-CoV-2 infections, characteristics of the facility e.g.size, staffing (use of temporary staff, staffing ratios, sickness pay) and disease control measures such as cohorting and isolation. We identified risk factors for infection in residents and staff, outbreaks (defined as [≥]1 case per LTCF) and large outbreaks using logistic regression. We also estimated the proportion of staff and residents who had been infected with SARS-CoV-2. Responses were obtained from 5126 of out 9081 (56%) of eligible LTCFs. To our knowledge, this is the largest and most detailed survey of risk factors for SARS-CoV-2 infection and outbreaks that has been conducted in LTCFs. Implications of all the available evidenceAlmost half of LTCFs surveyed in this study did not report any cases of infection, and remain vulnerable to infection and outbreaks, highlighting the need for effective control measures. Reducing transmission from staff requires adequate sick pay, minimal use of temporary staff, improved staffing ratios and staff cohorting. Transmission from residents is associated with the number of admissions to the facility and poor compliance with control measures such as isolation.",geriatric medicine,fuzzy,100,100 +medRxiv,10.1101/2020.09.30.20204727,2020-10-02,https://medrxiv.org/cgi/content/short/2020.09.30.20204727,High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020. + +MethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model. + +ResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants. + +ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.09.25.20201731,2020-09-27,https://medrxiv.org/cgi/content/short/2020.09.25.20201731,Antihypertensive Medications and COVID-19 Diagnosis and Mortality: Population-based Case-Control Analysis in the United Kingdom,Emma Rezel-Potts; Abdel Douiri; Phil J Chowienczyk; Martin C Gulliford,King's College London; King's College London; King's College London; King's College London,"ObjectivesTo evaluate antihypertensive medications and COVID-19 diagnosis and mortality, accounting for healthcare seeking behaviour. @@ -4702,19 +4688,7 @@ bioRxiv,10.1101/2020.09.16.297945,2020-09-16,https://biorxiv.org/cgi/content/sho medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.09.10.20191841,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.10.20191841,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample,Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ","We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.09.04.20187781,2020-09-09,https://medrxiv.org/cgi/content/short/2020.09.04.20187781,Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study,Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre,London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality. - -MethodsWe pre-specified and conducted an observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, representing 40% of the general population in England. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use prior to the COVID-19 outbreak in England and risk of COVID-19 mortality among people with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Model adjustment was informed by a directed acyclic graph. - -ResultsOf 194,637 patients with RA or SLE, 30,569 (15.7%) received [≥] 2 prescriptions of hydroxychloroquine in the six months prior to 1 March 2020. Between 1 March 2020 and 13 July 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0.23% (95% CI 0.18-0.29) among users and 0.22% (95% CI 0.20-0.25) among non-users; an absolute difference of 0.008% (95% CI -0.051-0.066). After accounting for age, sex, ethnicity, use of other immunuosuppressives, and geographic region, no association with COVID-19 mortality was observed (HR 1.03, 95% CI 0.80-1.33). We found no evidence of interactions with age or other immunosuppressives. Quantitative bias analyses indicated observed associations were robust to missing information regarding additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality. - -ConclusionWe found no evidence of a difference in COVID-19 mortality among patients who received hydroxychloroquine for treatment of rheumatological disease prior to the COVID-19 outbreak in England. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials and observational studies to date have shown no evidence of benefit of hydroxychloroquine as a treatment for hospitalised patients who already have COVID-19. A separate question remains: whether routine ongoing use of hydroxychloroquine in people without COVID-19 protects against new infections or severe outcomes. We searched MEDLINE/PubMed for pharmacoepidemiological studies evaluating hydroxychloroquine for prevention of severe COVID-19 outcomes. The keywords ""hydroxychloroquine AND (COVID OR coronavirus OR SARS-CoV-2) AND (prophyl* OR prevent*) AND (rate OR hazard OR odds OR risk)"" were used and results were filtered to articles from the last year with abstracts available. 109 papers were identified for screening; none investigated pre-exposure prophylactic use of hydroxychloroquine for prevention of severe COVID-19 outcomes. Clinical trials of prophylactic use of hydroxychloroquine are ongoing; however, the largest trial does not expect to meet recruitment targets due to ""...unjustified extrapolation and exaggerated safety concerns together with intense politicisation and negative publicity."" In the absence of reported clinical trials, evidence can be generated from real-world data to support the need for randomised clinical trials. - -Added value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data. - -Implications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.09.11.20192492,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.11.20192492,Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London","Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.05.20188821,2020-09-08,https://medrxiv.org/cgi/content/short/2020.09.05.20188821,Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis,Shirley Sze; Daniel Pan; Laura J Gray; Clareece R Nevill; Christopher A Martin; Joshua Nazareth; Jatinder S Minhas; Pip Divall; Kamlesh Khunti; Keith Abrams; Laura B Nellums; Manish Pareek,University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University Hospitals of Leicester NHS Trust; University of Leicester; University of Leicester; University of Nottingham; University of Leicester,"ImportanceThe association of ethnicity with outcomes in patients with COVID-19 is unclear. ObjectiveTo determine whether the risk of SARS-CoV-2 infection, COVID-19 intensive care unit (ICU) admission and mortality are associated with ethnicity. @@ -4832,7 +4806,7 @@ These national estimates broadly support the use of Global Burden of Disease mod bioRxiv,10.1101/2020.08.25.265074,2020-08-26,https://biorxiv.org/cgi/content/short/2020.08.25.265074,Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay,Manu Vanaerschot; Sabrina A Mann; James T Webber; Jack Kamm; Sidney M Bell; John Bell; Si Noon Hong; Minh Phuong Nguyen; Lienna Y Chan; Karan D Bhatt; Michelle Tan; Angela M Detweiler; Alex Espinosa; Wesley Wu; Joshua Batson; David Dynerman; - CLIAHUB Consortium; Debra A Wadford; Andreas Puschnik; Norma Neff; Vida Ahyong; Steve Miller; Patrick Ayscue; Cristina M Tato; Simon Paul; Amy Kistler; Joseph L DeRisi; Emily Dawn Crawford,Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Initiative; California Department of Public Health; Madera County Department of Public Health; Madera County Department of Public Health; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; California Department of Public Health; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; -; California Department of Public Health; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; University of California San Francisco; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub; Madera County Department of Public Health; Chan Zuckerberg Initiative; Chan Zuckerberg Biohub; Chan Zuckerberg Biohub,"We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.",molecular biology,fuzzy,92,100 -medRxiv,10.1101/2020.08.21.20177246,2020-08-24,https://medrxiv.org/cgi/content/short/2020.08.21.20177246,Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility,Irene V van Blokland; Pauline Lanting; Anil PS Ori; Judith M Vonk; Robert CA Warmerdam; Johanna C Herkert; Floranne Boulogne; Annique Claringbould; Esteban A Lopera-Maya; Meike Bartels; Jouke-Jan Hottenga; Andrea Ganna; Juha Karjalainen; - Lifelines COVID-19 cohort study; - The COVID-19 Host Genetics Initiative; Caroline Hayward; Chloe Fawns-Ritchie; Archie Campbell; David Porteous; Elizabeth T Cirulli; Kelly M Schiabor Barrett; Stephen Riffle; Alexandre Bolze; Simon White; Francisco Tanudjaja; Xueqing Wang; Jimmy M Ramirez III; Yan Wei Lim; James T Lu; Nicole L Washington; Eco JC de Geus; Patrick Deelen; H Marike Boezen; Lude H Franke,"University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Structural Computational Biology unit, EMB; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA and Analytic and Tra; ; ; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Department of Genetics, University Medical; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands","Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19, and this GWAS benefits from the larger sample size to provide new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, we recommend repeatedly collecting data of disease-related symptoms.",genetic and genomic medicine,fuzzy,100,100 +medRxiv,10.1101/2020.08.18.20177691,2020-08-22,https://medrxiv.org/cgi/content/short/2020.08.18.20177691,"Genetically-predicted vitamin D status, ambient UVB during the pandemic and COVID-19 risk in UK Biobank: Mendelian Randomisation study",Xue Li; Jos van Geffen; Michiel van Weele; Xiangrui Meng; XIAOMENG ZHANG; Yazhou He; Maria Timofeeva; Harry Campbell; Malcolm G Dunlop; Lina Zgaga; Evropi Theodoratou,"School of Public Health and the Second Affiliated Hospital, Zhejiang University; Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands; Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands; Vanke School of public Health,Tsinghua University; Usher Institute; Centre for Global Health, Usher Institute, University of Edinburgh; DIAS, Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark; Centre for Global Health, Usher Institute, University of Edinburgh; Institute of Genetics and Molecular Medicine; Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin; University of Edinburgh","A growing body of evidence shows that poor vitamin D status has been associated with an increased susceptibility to viral and bacterial respiratory infections. In this study, we aimed to examine the association between vitamin D and COVID-19 risk and outcomes, and to explore potential causal effects. We used logistic regression to identify associations between different vitamin D variables (25-hydroxyvitamin D concentration (25-OHD), ambient UVB and genetically-predicted 25-OHD concentrations) and COVID-19 (risk of infection, hospitalisation and death) in 495,780 participants from UK Biobank. We subsequently performed a Mendelian Randomisation (MR) study to test if there was any causal effect. In total, 1,746 COVID-19 cases and 399 COVID-19 deaths occurred between March and June 2020. We found significant inverse associations between COVID-19 infection and 25-OHD in univariable models, but these associations were non-significant after adjustment for confounders. Ambient UVB was strongly and inversely associated with hospitalization and death. Although the main MR analysis showed that genetically-predicted vitamin D levels were not causally associated with COVID-19 risk, MR sensitivity analysis using weighted mode method indicated a potential causal effect (OR=0.72, 95% CI:0.53-0.98; P=0.041). In conclusion, our study found suggestive evidence of association between vitamin D and the risk or severity of COVID-19 but further studies are needed.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.08.19.20178137,2020-08-22,https://medrxiv.org/cgi/content/short/2020.08.19.20178137,Testing for coronavirus (SARS-CoV-2) infection in populations with low infection prevalence: the largely ignored problem of false positives and the value of repeat testing,Cathie Sudlow; Peter Diggle; Oliver Warlow; David Seymour; Ben Gordon; Rhos Walker; Charles Warlow,"BHF Data Science Centre, Health Data Research UK; Usher Institute, University of Edinburgh; University of Lancaster; Health Data Research UK; Ventient Energy; Health Data Research UK; Health Data Research UK; Health Data Research UK; University of Edinburgh","BackgroundCalls are increasing for widespread SARS-CoV-2 infection testing of people from populations with a very low prevalence of infection. We quantified the impact of less than perfect diagnostic test accuracy on populations, and on individuals, in low prevalence settings, focusing on false positives and the role of confirmatory testing. MethodsWe developed a simple, interactive tool to assess the impact of different combinations of test sensitivity, specificity and infection prevalence in a notional population of 100,000. We derived numbers of true positives, true negatives, false positives and false negatives, positive predictive value (PPV - the percentage of test positives that are true positives) and overall test accuracy for three testing strategies: (1) single test for all; (2) add repeat testing in test positives; (3) add further repeat testing in those with discrepant results. We also assessed the impact on test results for individuals having one, two or three tests under these three strategies. @@ -4942,6 +4916,7 @@ MethodsWorking on behalf of NHS England, we used the OpenSAFELY platform to anal Results17.3 million adults were included, of whom 27,480 (0.16%) had HIV recorded. People living with HIV were more likely to be male, of black ethnicity, and from a more deprived geographical area than the general population. There were 14,882 COVID-19 deaths during the study period, with 25 among people with HIV. People living with HIV had nearly three-fold higher risk of COVID-19 death than those without HIV after adjusting for age and sex (HR=2.90, 95% CI 1.96-4.30). The association was attenuated but risk remained substantially raised, after adjustment for deprivation and ethnicity (adjusted HR=2.52, 1.70-3.73) and further adjustment for comorbidities (HR=2.30, 1.55-3.41). There was some evidence that the association was larger among people of black ethnicity (HR = 3.80, 2.15-6.74, compared to 1.64, 0.92-2.90 in non-black individuals, p-interaction=0.045) InterpretationHIV infection was associated with a markedly raised risk of COVID-19 death in a country with high levels of antiretroviral therapy coverage and viral suppression; the association was larger in people of black ethnicity.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.08.05.20169078,2020-08-06,https://medrxiv.org/cgi/content/short/2020.08.05.20169078,Transient dynamics of SARS-CoV-2 as England exited national lockdown,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health","Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.08.01.20166405,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.01.20166405,"Physical activity, BMI and COVID-19: an observational and Mendelian randomisation study",Xiaomeng Zhang; Xue Li; Ziwen Sun; Yazhou He; Wei Xu; Harry Campbell; Malcolm G Dunlop; Maria Timofeeva; Evropi Theodoratou,University of Edinburgh; Zhejiang University; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh,"Physical activity (PA) is known to be a protective lifestyle factor against several non-communicable diseases while its impact on infectious diseases, including Coronavirus Disease 2019 (COVID-19) is not as clear. We performed univariate and multivariate logistic regression to identify associations between body mass index (BMI) and both objectively and subjectively measured PA collected prospectively and COVID-19 related outcomes (Overall COVID-19, inpatient COVID-19, outpatient COVID-19, and COVID-19 death) in the UK Biobank (UKBB) cohort. Subsequently, we tested causality by using two-sample Mendelian randomisation (MR) analysis. In the multivariable model, the increased acceleration vector magnitude PA (AMPA) was associated with a decreased probability of overall and outpatient COVID-19. No association was found between self-reported moderate-to-vigorous PA (MVPA) or BMI and COVID-19 related outcomes. Although no causal association was found by MR analyses, this may be due to limited power and we conclude policies to encourage and facilitate exercise at a population level during the pandemic should be considered.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.08.03.20164897,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20164897,Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study,Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow,"ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood. @@ -5088,6 +5063,15 @@ C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.07.24.20161281,2020-07-24,https://medrxiv.org/cgi/content/short/2020.07.24.20161281,Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers,Samuel Clifford; Billy J Quilty; Timothy W Russell; Yang Liu; Yung-Wai Desmond Chan; Carl A B Pearson; Rosalind M Eggo; Akira Endo; - CMMID COVID-19 Working Group; Stefan Flasche; W John Edmunds,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. We used a simulation model of air travellers arriving to the UK from the EU or the USA and the timing of their stages of infection to evaluate the ability of these strategies to reduce the risk of seeding community transmission. We find that a quarantine period of 8 days on arrival with a PCR test on day 7 (with a 1-day delay for test results) can reduce the number of infectious arrivals released into the community by a median 94% compared to a no quarantine, no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median 99% reduction). Shorter quarantine periods still can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (the mean incubation period) in quarantine and have at least one negative test before release are highly effective (e.g. a test on day 5 with release on day 6 results in a median 88% reduction in transmission potential). Without intervention, the current high prevalence in the US (40 per 10,000) results in a higher expected number of infectious arrivals per week (up to 23) compared to the EU (up to 12), despite an estimated 8 times lower volume of travel in July 2020. Requiring a 14-day quarantine period likely results in less than 1 infectious traveller each entering the UK per week from the EU and the USA (97.5th percentile). We also find that on arrival the transmission risk is highest from pre-symptomatic travellers; quarantine policies will shift this risk increasingly towards asymptomatic infections if eventually-symptomatic individuals self-isolate after the onset of symptoms. As passenger numbers recover, strategies to reduce the risk of re-introduction should be evaluated in the context of domestic SARS-CoV-2 incidence, preparedness to manage new outbreaks, and the economic and psychological impacts of quarantine.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.07.15.20152967,2020-07-17,https://medrxiv.org/cgi/content/short/2020.07.15.20152967,Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.,Gisli Jenkins; Tom Drake; Annemarie B Docherty; Ewan Harrison; Jennifer Quint; Huzaifa Adamali; Sarah Agnew; Suresh Babu; Christopher Barber; Shaney Barratt; Elisabeth Bendstrup; Stephen Bianchi; Diego Castillo; Nazia Chaudhuri; Felix Chua; Robina Coker; William Chang; Anjali Cranshaw; Louise Crowley; Davinder Dosanjh; Christine Fiddler; Ian A Forrest; Peter George; Michael Gibbons; Katherine Groom; Sarah Haney; Simon Hart; Emily Heiden; Michael Henry; Ling-Pei Ho; Rachel Hoyles; John Hutchinson; Killian Hurley; Mark Jones; Steve Jones; Maria Kokosi; Michael Kreuter; Laura Mackay; Siva Mahendran; Georgios Margaritopoulos; Maria Molina-Molina; Philip Molyneaux; Aidan D O'Brien; Katherine O'Reilly; Alice Packham; Helen Parfrey; Venerino Poletti; Joanna Porter; Elisabetta Renzoni; Pilar Rivera-Ortega; Anne-Marie Russell; Gauri Saini; Lisa G Spencer; Giulia Stella; Helen Stone; Sharon Sturney; David Thickett; Muhunthan Thillai; Timothy Wallis; Katie Ward; Athol U Wells; Alex West; Melissa Wickremasinghe; Felix Woodhead; Glenn Herson; Lucy Howard; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Iain Stewart,"University of Nottingham; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX; University of Edinburgh; University of Edinburgh; Imperial College London; Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB.; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Queen Alexandra Hospital, Portsmouth, UK.; Northern General Hospital, Sheffield, S5 7AU, UK; Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB.; Centre for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99,8200 Aarhus N, Denmar; Northern General Hospital, Sheffield, S5 7AU, UK.; ILD Unit, Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Royal Brompton Hospital; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Nottingham University Hospital; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK.; Royal Brompton Hospital; South West Peninsula ILD Network, Royal Devon & Exeter Foundation NHS Trust Barrack Road, Exeter EX2 5DW, UK; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, UK, HU16 5JQ; University Hospitals Southampton NHS Foundation Trust, Southampton, UK; Cork University Hospital, Cork, Ireland; University of Oxford; Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK; University of Nottingham; Beaumont Hospital, Dublin, Ireland.; NIHR Southampton Biomedical Research Centre & Clinical and Experimental Sciences, University of Southampton, Southampton, UK; Action for Pulmonary Fibrosis; Guys and St Thomas' Hospital; Center for interstitial and rare lung diseases, Pneumology, Thoraxklinik, University of Heidelberg, Germany and German Center for Lung Research, 69126 Heidelber; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Kingston Hospital NHS Foundation Trust. Galsworthy Road, Kingston upon Thames, Surrey KT2 7QB, UK.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; ILD Unit, Respiratory Department, University Hospital of Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.; Imperial College London; University Hospital Limerick, Dooradoyle, Limerick, Ireland.; Department of Respiratory Medicine, Mater Misericordiae University Hospital, Dublin, Ireland.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Diseases of the Thorax, Morgagni Hospital, Forli, Italy.; University College London; Royal Brompton Hospital; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Imperial College London; Nottingham University Hospitals; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Laboratory of Biochemistry and Genetics, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.; University Hospital North Midlands NHS Trust, Royal Stoke University Hospital, Newcastle Road, Stoke-on-Trent, ST4 6QG, UK.; Royal United Hospitals Bath NHS Foundation Trust, Combe Park, Bath BA1 3NG, UK; University of Birmingham, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; University of Southampton; Imperial College London; Royal Brompton Hospital; Guys and St Thomas' Hospital; Imperial Healthcare NHS Trust, St Mary's Hospital, The Bays, S Wharf Rd, Paddington, London W2 1NY, UK.; Glenfield Hospital Leicester; Nottingham University Hospitals Trust; Nottingham University Hospitals Trust; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; University of Nottingham","RationaleThe impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established. + +ObjectivesTo assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population. + +MethodsAn international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death. + +Measurements and Main ResultsData from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC [≥]80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13-3.46). + +ConclusionsPatients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.",respiratory medicine,fuzzy,100,100 medRxiv,10.1101/2020.07.14.20153734,2020-07-16,https://medrxiv.org/cgi/content/short/2020.07.14.20153734,"Place and causes of acute cardiovascular mortality during the COVID19 pandemic: retrospective cohort study of 580,972 deaths in England and Wales, 2014 to 2020",Jianhua Wu; Mamas Mamas; Mohamed Mohamed; Chun Shing Kwok; Chris Roebuck; Ben Humberstone; Tom Denwood; Tom Luescher; Mark De Belder; John Deanfield; Chris Gale,University of Leeds; Keele University; Keele University; Keele University; NHS Digital; ONS; NHS Digital; Imperial College; Barts Health NHS Trust; UCL; University of Leeds,"ImportanceThe COVID-19 pandemic has resulted in a decline in admissions with cardiovascular (CV) emergencies. The fatal consequences of this are unknown. ObjectivesTo describe the place and causes of acute CV death during the COVID-19 pandemic. @@ -5105,15 +5089,6 @@ Main outcomesPlace (hospital, care home, home) and acute CV events directly cont ResultsAfter 2nd March 2020, there were 22,820 acute CV deaths of which 5.7% related to COVID-19, and an excess acute CV mortality of 1752 (+8%) compared with the expected daily deaths in the same period. Deaths in the community accounted for nearly half of all deaths during this period. Care homes had the greatest increase in excess acute CV deaths (1065, +40%), followed by deaths at home (1728, +34%) and in hospital (57, +0%). The most frequent cause of acute CV death during this period was stroke (8,290, 36.3%), followed by acute coronary syndrome (ACS) (5,532, 24.2%), heart failure (5,280, 23.1%), pulmonary embolism (2,067, 9.1%) and cardiac arrest (1,037, 4.5%). Deep vein thrombosis had the greatest increase in cause of excess acute CV death (18, +25%), followed pulmonary embolism (340, +19%) and stroke (782, +10%). The greatest cause of excess CV death in care homes was stroke (700, +48%), compared with cardiac arrest (80, +56%) at home, and pulmonary embolism (126, +14%) and cardiogenic shock (41, +14%) in hospital. Conclusions and relevanceThe COVID-19 pandemic has resulted in an inflation in acute CV deaths above that expected for the time of year, nearly half of which occurred in the community. The most common cause of acute CV death was stroke followed by acute coronary syndrome and heart failure. This is key information to optimise messaging to the public and enable health resource planning.",cardiovascular medicine,fuzzy,100,100 -medRxiv,10.1101/2020.07.14.20152629,2020-07-15,https://medrxiv.org/cgi/content/short/2020.07.14.20152629,Covid-19 infection and attributable mortality in UK Long Term Care Facilities: Cohort study using active surveillance and electronic records (March-June 2020),Peter F Dutey-Magni; Haydn Williams; Arnoupe Jhass; Greta Rait; Harry Hemingway; Andrew C Hayward; Laura Shallcross,University College London; Four Seasons Healthcare Group; UCL; University College London; University College London; University College London; UCL,"BackgroundEpidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic. - -MethodsCohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality. - -Results2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection. - -217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]). - -ConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.07.15.20151852,2020-07-15,https://medrxiv.org/cgi/content/short/2020.07.15.20151852,"Effect of Hydroxychloroquine in Hospitalized Patients with COVID-19: Preliminary results from a multi-centre, randomized, controlled trial.",Peter Horby; Marion Mafham; Louise Linsell; Jennifer L Bell; Natalie Staplin; Jonathan R Emberson; Martin Wiselka; Andrew Ustianowski; Einas Elmahi; Benjamin Prudon; Anthony Whitehouse; Timothy Felton; John Williams; Jakki Faccenda; Jonathan Underwood; J Kenneth Baillie; Lucy Chappell; Saul N Faust; Thomas Jaki; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Kathryn Rowan; Joel Tarning; James A Watson; Nicholas J White; Edmund Juszczak; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; University Hospitals fo Leicester NHS Trust and University of Leicester; Regional Infectious Diseases Unit, North Manchester General Hospital & University of Manchester, Manchester, UK; Research and Development Department, Northampton General Hospital, Northampton, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology & Infection, University of Birmingham, United Kingdom; Univeristy of Manchester and Manchester University NHS Foundation Trust, Manchester, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Department of Infectious Diseases, Cardiff and Vale University Health Board; Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; School of Life Sciences, King's College London, London, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; MRC Biostatistics Unit, University of Cambridge, Cambridge, United Ki; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Hea; Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Hea; Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Hea; Nuffield Department of Population Health, University of Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundHydroxychloroquine and chloroquine have been proposed as treatments for coronavirus disease 2019 (COVID-19) on the basis of in vitro activity, uncontrolled data, and small randomized studies. MethodsThe Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19. We report the preliminary results for the comparison of hydroxychloroquine vs. usual care alone. The primary outcome was 28-day mortality. @@ -5175,15 +5150,6 @@ ResultsThe 872 cases comprised 48.1% Black, 33.7% White, 12.6% Mixed/Other and 5 ConclusionsBlack and Mixed ethnicity are independently associated with greater admission risk with COVID-19 and may be risk factors for development of severe disease. Comorbidities and socioeconomic factors only partly account for this and additional ethnicity-related factors may play a large role. The impact of COVID-19 may be different in Asians. Funding sourcesBritish Heart Foundation (CH/1999001/11735 and RE/18/2/34213 to AMS); the National Institute for Health Research Biomedical Research Centre (NIHR BRC) at Guys & St Thomas NHS Foundation Trust and Kings College London (IS-BRC-1215-20006); and the NIHR BRC at South London and Maudsley NHS Foundation Trust and Kings College London (IS-BRC-1215-20018).",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.07.07.20148460,2020-07-08,https://medrxiv.org/cgi/content/short/2020.07.07.20148460,Reconstructing the global dynamics of under-ascertained COVID-19 cases and infections,Timothy W Russell; Nick Golding; Joel Hellewell; Sam Abbott; Lawrence Wright; Carl A B Pearson; Kevin van Zandvoort; Christopher I Jarvis; Hamish Gibbs; Yang Liu; Rosalind M Eggo; John W Edmunds; Adam J Kucharski,"London School of Hygiene and Tropical Medicine; Telethon Kids Institute and Curtin University; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Defence Science and Technology Laboratory/Sopra Steria, Fareham, United Kingdom; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine","BackgroundAsymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures. - -MethodsUsing reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever >= 37.5{degrees}C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the case fatality ratio (CFR) as an assumed baseline. We then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment. - -ResultsWe estimate that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.38% (Bangladesh) to 99.6% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 17.8 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. Despite low case detection in some countries, our results that adjust for this still suggest that all countries have had only a small fraction of their populations infected as of July 2020. - -ConclusionsWe found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each countrys population infected with SARS-CoV-2 worldwide is generally low. - -FundingWellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.07.06.20147348,2020-07-07,https://medrxiv.org/cgi/content/short/2020.07.06.20147348,Community prevalence of SARS-CoV-2 in England: Results from the ONS Coronavirus Infection Survey Pilot,Koen B Pouwels; Thomas House; Julie V Robotham; Paul Birrell; Andrew B Gelman; Nikola Bowers; Ian Boreham; Heledd Thomas; James Lewis; Iain Bell; John I Bell; John Newton; Jeremy Farrar; Ian Diamond; Pete Benton; Sarah Walker,University of Oxford; University of Manchester; Public Health England; Public Health England; Columbia University; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford,"ObjectiveTo estimate the percentage of individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) over time in the community in England and to quantify risk factors. DesignRepeated cross-sectional surveys of population-representative households with longitudinal follow-up if consent given. @@ -5236,6 +5202,16 @@ ResultsSurvival curves show an increased proportion of deaths between 23rd March ConclusionsThe survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2020.07.01.182709,2020-07-01,https://biorxiv.org/cgi/content/short/2020.07.01.182709,Genetic architecture of host proteins interacting with SARS-CoV-2,Maik Pietzner; Eleanor Wheeler; Julia Carrasco-Zanini; Johannes Raffler; Nicola D. Kerrison; Erin Oerton; Victoria P.W. Auyeung; Chris Finan; Juan P. Casas; Rachel Ostroff; Steve A. Williams; Gabi Kastenmüller; Markus Ralser; Eric G. Gamazon; Nicholas J. Wareham; Aroon Dinesh Hingorani; Claudia Langenberg,University of Cambridge; University of Cambridge; University of Cambridge; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); University of Cambridge; University of Cambridge; University of Cambridge; University College London; Harvard Medical School; SomaLogic Inc.; SomaLogic Inc.; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); The Francis Crick Institute; Vanderbilt University Medical Center; University of Cambridge; University College London; University of Cambridge,"Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification of genetic variants that influence the level or activity of these proteins in the host could enable rapid in silico assessment in human genetic studies of their causal relevance as molecular targets for new or repurposed drugs to treat COVID-19. We integrated large-scale genomic and aptamer-based plasma proteomic data from 10,708 individuals to characterize the genetic architecture of 179 host proteins reported to interact with SARS-CoV-2 proteins or to participate in the host response to COVID-19. We identified 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links, evidence that putative viral interaction partners such as MARK3 affect immune response, and establish the first link between a recently reported variant for respiratory failure of COVID-19 patients at the ABO locus and hypercoagulation, i.e. maladaptive host response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and dynamic and detailed interrogation of results is facilitated through an interactive webserver (https://omicscience.org/apps/covidpgwas/).",genomics,fuzzy,100,100 medRxiv,10.1101/2020.06.29.20142448,2020-06-30,https://medrxiv.org/cgi/content/short/2020.06.29.20142448,Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data,Robert Stewart; Matthew Broadbent,King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.",psychiatry and clinical psychology,fuzzy,100,100 +medRxiv,10.1101/2020.06.28.20141986,2020-06-29,https://medrxiv.org/cgi/content/short/2020.06.28.20141986,Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population,Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon,"University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton","IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases. + +Methods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available. + +Ethics and disseminationThe project has ethical approval and the results will be submitted for publication in a peer-reviewed journal. + +Strengths and limitations of the studyO_LIThe individual-level linkage of general practice, Public Health England testing, Hospital Episode Statistics and Office of National Statistics death register datasets enable a robust and accurate ascertainment of outcomes +C_LIO_LIThe models will be trained and evaluated in population-representative datasets of millions of individuals +C_LIO_LIShielding for clinically extremely vulnerable was advised and in place during the study period, therefore risk predictions influenced by the presence of some shielding conditions may require careful consideration +C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.06.26.20140921,2020-06-28,https://medrxiv.org/cgi/content/short/2020.06.26.20140921,Short Communication: Vitamin D and COVID-19 infection and mortality in UK Biobank,Claire E Hastie; Jill P Pell; Naveed Sattar,University of Glasgow; University of Glasgow; University of Glasgow,"PurposeVitamin D has been proposed as a potential causal factor in COVID-19 risk. We aimed to establish whether blood 25-hydroxyvitamin D (25(OH)D) concentration was associated with COVID-19 mortality, and inpatient confirmed COVID-19 infection, in UK Biobank participants. MethodsUK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including 25(OH)D concentration, were linked to COVID-19 mortality. Univariable and multivariable Cox proportional hazards regression analyses were performed for the association between 25(OH)D and COVID-19 death, and poisson regression analyses for the association between 25(OH)D and severe COVID-19 infection. @@ -5243,15 +5219,6 @@ MethodsUK Biobank recruited 502,624 participants aged 37-73 years between 2006 a ResultsComplete data were available for 341,484 UK Biobank participants, of which 656 had inpatient confirmed COVID-19 infection and 203 died of COVID-19 infection. Vitamin D was associated with severe COVID-19 infection and mortality univariably (mortality HR=0.99; 95% CI 0.98-0.998; p=0.016), but not after adjustment for confounders (mortality HR=0.998; 95% CI=0.99-1.01; p=0.696). ConclusionsOur findings do not support a potential link between vitamin D concentrations and risk of severe COVID-19 infection and mortality. Recommendations for vitamin D supplementation to lessen COVID-19 risks may provide false reassurance.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.06.26.20139873,2020-06-28,https://medrxiv.org/cgi/content/short/2020.06.26.20139873,Secondary pneumonia in critically ill ventilated patients with COVID-19,Mailis Maes; Ellen Higginson; Joana Pereira Dias; Martin D Curran; Surendra Parmar; Fahad Khokhar; Delphine Cuchet-Lourenço; Janine Lux; Sapna Sharma-Hajela; Benjamin Ravenhill; Razeen Mahroof; Amelia Solderholm; Sally Forrest; Sushmita Sridhar; Nicholas M Brown; Stephen Baker; Vilas Navapurkar; Gordon Dougan; Josefin Bartholdson Scott; Andrew Conway Morris,"Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Wellcome Sanger Insitute, Hinxton, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; University of Cambridge","BackgroundPandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive artificial ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP). - -ObjectivesTo study the incidence of VAP, as well as differences in secondary infections, and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients. - -MethodsIn this prospective observational study, we compared the incidence of VAP and secondary infections using a combination of a TaqMan multi-pathogen array and microbial culture. In addition, we determined the lung microbime composition using 16S RNA analyisis. The study involved eighteen COVID-19 and seven non-COVID-19 patients receiving invasive ventilation in three ICUs located in a single University teaching hospital between April 13th 2020 and May 7th 2020. - -ResultsWe observed a higher percentage of confirmed VAP in COVID-19 patients. However, there was no statistical difference in the detected organisms or pulmonary microbiome when compared to non-COVID-19 patients. - -ConclusionCOVID-19 makes people more susceptible to developing VAP, partly but not entirely due to the increased duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the array of secondary infections observed are similar to that seen in critically ill patients ventilated for other reasons.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2020.06.24.20139048,2020-06-25,https://medrxiv.org/cgi/content/short/2020.06.24.20139048,A geotemporal survey of hospital bed saturation across England during the first wave of the COVID-19 Pandemic,Bilal A Mateen; Harrison Wilde; John m Dennis; Andrew Duncan; Nicholas John Meyrick Thomas; Andrew P McGovern; Spiros Denaxas; Matt J Keeling; Sebastian J Vollmer,"The Alan Turing Institute; University of Warwick; Kings College Hospital NHS Foundation Trust; University of Warwick, Department of Statistics; University of Exeter Medical School; The Alan Turing Institute; Imperial College London, Faculty of Natural Sciences; University of Exeter Medical School; Royal Devon and Exeter NHS Foundation Trust, Diabetes and Endocrinology; University of Exeter Medical School; University College London; University of Warwick; The Alan Turing Institute; University of Warwick, Department of Statistics","BackgroundNon-pharmacological interventions were introduced based on modelling studies which suggested that the English National Health Service (NHS) would be overwhelmed by the COVID-19 pandemic. In this study, we describe the pattern of bed occupancy across England during the first wave of the pandemic, January 31st to June 5th 2020. MethodsBed availability and occupancy data was extracted from daily reports submitted by all English secondary care providers, between 27-Mar and 5-June. Two thresholds for safe occupancy were utilized (85% as per Royal College of Emergency Medicine and 92% as per NHS Improvement). @@ -5290,6 +5257,17 @@ Implications of all the available evidenceThese analyses support COVID-19 and no C_TEXTBOX",health policy,fuzzy,100,100 medRxiv,10.1101/2020.06.22.20137216,2020-06-23,https://medrxiv.org/cgi/content/short/2020.06.22.20137216,"Proteomic blood profiling in mild, severe and critical COVID-19 patients",Hamel Patel; Nicholas J Ashton; Richard J Dobson; Lars-magnus Anderson; Aylin Yilmaz; Kaj Blennow; Magnus Gisslen; Henrik Zetterberg,King's College London; University of Gothenburg; Kings College London; Sahlgrenska university hospital; University of Gothenburg; University of Gothenburg; University of Gothenburg; University of Gothenburg,"The recent SARS-CoV-2 pandemic manifests itself as a mild respiratory tract infection in the majority of individuals leading to COVID-19 disease. However, in some infected individuals, this can progress to severe pneumonia and acute respiratory distress syndrome (ARDS), leading to multi-organ failure and death. The purpose of this study is to explore the proteomic differences between mild, severe and critical COVID-19 positive patients. Blood protein profiling was performed on 59 COVID-19 mild (n=26), severe (n=9) or critical (n=24) cases and 28 controls using the OLINK inflammation, autoimmune, cardiovascular and neurology panels. Differential expression analysis was performed within and between disease groups to generate nine different analyses. From the 368 proteins measured per individual, more than 75% were observed to be significantly perturbed in COVID-19 cases. Six proteins (IL6, CKAP4, Gal-9, IL-1ra, LILRB4 and PD-L1) were identified to be associated with disease severity. The results have been made readily available through an interactive web-based application for instant data exploration and visualization, and can be accessed at https://phidatalab-shiny.rosalind.kcl.ac.uk/COVID19/. Our results demonstrate that dynamic changes in blood proteins that associate with disease severity can potentially be used as early biomarkers to monitor disease severity in COVID-19 and serve as potential therapeutic targets.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.06.22.20137273,2020-06-22,https://medrxiv.org/cgi/content/short/2020.06.22.20137273,Effect of Dexamethasone in Hospitalized Patients with COVID-19: Preliminary Report,Peter Horby; Wei Shen Lim; Jonathan Emberson; Marion Mafham; Jennifer Bell; Louise Linsell; Natalie Staplin; Christopher Brightling; Andrew Ustianowski; Einas Elmahi; Benjamin Prudon; Christopher Green; Timothy Felton; David Chadwick; Kanchan Rege; Christopher Fegan; Lucy C Chappell; Saul N Faust; Thomas Jaki; Katie Jeffery; Alan Montgomery; Kathryn Rowan; Edmund Juszczak; J Kenneth Baillie; Richard Haynes; Martin J Landray; - RECOVERY Collaborative Group,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Regional Infectious Diseases Unit, North Manchester General Hospital & University of Manchester, Manchester, United Kingdom; Research and Development Department, Northampton General Hospital, Northampton, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology & Infection, University of Birmingham, Birmingham, United Kingdom; University of Manchester and Manchester University NHS Foundation Trust, Manchester, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Department of Research and Development, Cardiff and Vale University Health Board, Cardiff, United Kingdom; School of Life Course Sciences, Kings College London, London, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; ","BackgroundCoronavirus disease 2019 (COVID-19) is associated with diffuse lung damage. Corticosteroids may modulate immune-mediated lung injury and reducing progression to respiratory failure and death. + +MethodsThe Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, adaptive, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19. We report the preliminary results for the comparison of dexamethasone 6 mg given once daily for up to ten days vs. usual care alone. The primary outcome was 28-day mortality. + +Results2104 patients randomly allocated to receive dexamethasone were compared with 4321 patients concurrently allocated to usual care. Overall, 454 (21.6%) patients allocated dexamethasone and 1065 (24.6%) patients allocated usual care died within 28 days (age-adjusted rate ratio [RR] 0.83; 95% confidence interval [CI] 0.74 to 0.92; P<0.001). The proportional and absolute mortality rate reductions varied significantly depending on level of respiratory support at randomization (test for trend p<0.001): Dexamethasone reduced deaths by one-third in patients receiving invasive mechanical ventilation (29.0% vs. 40.7%, RR 0.65 [95% CI 0.51 to 0.82]; p<0.001), by one-fifth in patients receiving oxygen without invasive mechanical ventilation (21.5% vs. 25.0%, RR 0.80 [95% CI 0.70 to 0.92]; p=0.002), but did not reduce mortality in patients not receiving respiratory support at randomization (17.0% vs. 13.2%, RR 1.22 [95% CI 0.93 to 1.61]; p=0.14). + +ConclusionsIn patients hospitalized with COVID-19, dexamethasone reduced 28-day mortality among those receiving invasive mechanical ventilation or oxygen at randomization, but not among patients not receiving respiratory support. + +Trial registrationsThe RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). + +FundingMedical Research Council and National Institute for Health Research (Grant ref: MC_PC_19056).",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.06.19.20135491,2020-06-20,https://medrxiv.org/cgi/content/short/2020.06.19.20135491,"Inhaled corticosteroid use and risk COVID-19 related death among 966,461 patients with COPD or asthma: an OpenSAFELY analysis",- The OpenSAFELY Collaborative; Anna Schultze; Alex J Walker; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Christopher T. Rentsch; Elizabeth J Williamson; Henry Drysdale; Richard Croker; Seb Bacon; William J Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Kevin Wing; Angel YS Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Jennifer Quint; Liam Smeeth; Ian J Douglas; Ben Goldacre,"; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine, NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; National Heart and Lung Institute, Imperial College; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford","BackgroundEarly descriptions of the coronavirus outbreak showed a lower prevalence of asthma and COPD than was expected for people diagnosed with COVID-19, leading to speculation that inhaled corticosteroids (ICS) may protect against infection with SARS-CoV-2, and development of serious sequelae. We evaluated the association between ICS and COVID-19 related death using linked electronic health records in the UK. MethodsWe conducted cohort studies on two groups of people (COPD and asthma) using the OpenSAFELY platform to analyse data from primary care practices linked to national death registrations. People receiving an ICS were compared to those receiving alternative respiratory medications. Our primary outcome was COVID-19 related death. diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index c963b46d..f1d82428 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -103,15 +103,6 @@ FindingsOverall, 276,840/800,000 (34.6%) of invited participants completed the q InterpretationAlthough COVID-19 is usually of short duration, some adults experience persistent and burdensome illness. FundingThis work is independent research funded by the National Institute for Health and Care Research (NIHR) (REACT Long COVID (REACT-LC) (COV-LT-0040)). This research is part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (UKRI) (MC_PC_20029). The views expressed in this publication are those of the author(s) and not necessarily those of NIHR or UKRI.",public and global health,exact,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,exact,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -182,6 +173,13 @@ ResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovas ConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events. Key MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.",epidemiology,exact,100,100 +medRxiv,10.1101/2023.02.17.23286079,2023-02-23,https://medrxiv.org/cgi/content/short/2023.02.17.23286079,"Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.",Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson,UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency,"AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures. + +Methods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded. + +ConclusionsFew workplace surface samples were positive for SARS-CoV-2 RNA and positive samples typically contained low levels of nucleic acid. Although these data may infer a low probability of fomite transmission or other forms of transmission within the workplace, Ct values may have been lower at the time of contamination. Workplace environmental sampling identified lapses in COVID-control measures within individual sites and showed trends through the pandemic. + +Significance and Impact of the StudyPrior to this study, few published reports investigated SARS-CoV-2 RNA contamination within workplaces experiencing cases of COVID-19. This report provides extensive data on environmental sampling identifying trends across workplaces and through the pandemic.",epidemiology,exact,100,100 medRxiv,10.1101/2023.02.18.23286127,2023-02-19,https://medrxiv.org/cgi/content/short/2023.02.18.23286127,Antipsychotic prescribing and mortality in people with dementia before and during the COVID-19 pandemic: retrospective cohort study,Christian Schnier; Aoife McCarthy; Daniel R Morales; Ashley Akbari; Reecha Sofat; Caroline Dale; Rohan Takhar; Mamas Mamas; Kamlesh Khunti; Francesco Zaccardi; Cathie LM Sudlow; Tim Wilkinson,University of Edinburgh; University of Edinburgh; University of Dundee; Swansea University; University of Liverpool; University of Liverpool; University College London; Keele University; University of Leicester; University of Leicester; University of Edinburgh; University of Edinburgh,"BackgroundAntipsychotic drugs have been associated with increased mortality, stroke and myocardial infarction in people with dementia. Concerns have been raised that antipsychotic prescribing may have increased during the COVID-19 pandemic due to social restrictions imposed to limit the spread of the virus. We used multisource, routinely-collected healthcare data from Wales, UK, to investigate prescribing and mortality trends in people with dementia before and during the COVID-19 pandemic. MethodsWe used individual-level, anonymised, population-scale linked health data to identify adults aged [≥]60 years with a diagnosis of dementia in Wales, UK. We explored antipsychotic prescribing trends over 67 months between 1st January 2016 and 1st August 2021, overall and stratified by age and dementia subtype. We used time series analyses to examine all-cause, myocardial infarction (MI) and stroke mortality over the study period and identified the leading causes of death in people with dementia. @@ -282,7 +280,18 @@ C_LI How this study might affect research, practice or policyO_LIOur findings highlight the role of household overcrowding in the disproportionate impact of SARS-CoV-2 infections on migrants. They also demonstrate the urgent need for policy interventions that improve housing conditions as part of efforts to reduce health inequalities. Further research investigating other causes of migrants over-representation in infection cases is also needed to inform further targeted policy interventions. C_LI",epidemiology,exact,100,100 -medRxiv,10.1101/2022.12.19.22283660,2022-12-19,https://medrxiv.org/cgi/content/short/2022.12.19.22283660,"Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan",Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford,"Background The COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. Objectives A. To determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. B. To estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. C. To assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. Methods This population-based study uses the QResearch database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of severe COVID-19 outcomes after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and dissemination QResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.",infectious diseases,exact,100,100 +medRxiv,10.1101/2022.12.19.22283660,2022-12-19,https://medrxiv.org/cgi/content/short/2022.12.19.22283660,"Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan",Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford,"BackgroundThe COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. + +ObjectivesO_LITo determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. +C_LIO_LITo estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. +C_LIO_LITo assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. +C_LI + +MethodsThis population-based study uses the QResearch(R) database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. + +We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. + +Ethics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.12.14.22283458,2022-12-14,https://medrxiv.org/cgi/content/short/2022.12.14.22283458,Trends in inequalities in avoidable hospitalisations across the COVID-19 pandemic: A cohort study of 23.5 million people in England,Mark A Green; Martin McKee; Jon Massey; Brain MacKenna; Amir Mehrkar; Sebastian Bacon; John Macleod; Syed Ahmar Shah; Aziz Sheikh; - The OpenSAFELY Consortium; - The LH&W NCS Collaborative; Srinivasa Vittal Katikireddi,University of Liverpool; London School of Hygiene and Tropical Medicine; University of Oxford; NHS England; University of Oxford; University of Oxford; University of Bristol; University of Edinburgh; University of Edinburgh; ; ; University of Glasgow,"BackgroundThe COVID-19 pandemic and associated national lockdowns created unprecedented disruption to healthcare, with reduced access to services and planned clinical encounters postponed or cancelled. It was widely anticipated that failure to obtain timely treatment would cause progression of illness and increased hospital admissions. Additional concerns were that social and spatial inequalities would widen given the disproportionate impacts of COVID-19 directly. The aim of our study is to determine whether this was observable in England. MethodsWith the approval of NHS England we utilised individual-level electronic health records from OpenSAFELY, which covered [~]40% of general practices in England (mean monthly population size 23.5 million people). We estimated crude and directly age-standardised rates for potentially preventable unplanned hospital admissions: ambulatory care sensitive conditions and urgent emergency sensitive conditions. We considered how trends in these outcomes varied by three measures of social and spatial inequality: neighbourhood socioeconomic deprivation, ethnicity, and geographical region. @@ -502,15 +511,6 @@ What this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron w C_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions. C_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group. C_LI",epidemiology,exact,100,100 -medRxiv,10.1101/2022.08.08.22278532,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278532,Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI),Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England. - -MethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence. - -Results14175 residents and 19973 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-83 days after first booster, but no protection was apparent after 84 days. Additional protection following booster vaccination waned, but was still present at 84+ days for COVID-associated hospitalisation (aHR: 0.47, 0.24-0.89) and death (aHR: 0.37, 0.21-0.62). Most residents (64.4%) had received primary course of AstraZeneca, but this did not impact on pre- or post-booster risks. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalisations and no deaths. - -ConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial. - -SummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.08.07.22278510,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.07.22278510,Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.,Marc F Österdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves,King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London,"Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. We examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration. @@ -545,13 +545,6 @@ Ethics and disseminationThe protocol was reviewed by South Central - Berkshire R Trial registration numberISRCTN10665760",infectious diseases,exact,100,100 medRxiv,10.1101/2022.06.15.22276446,2022-06-21,https://medrxiv.org/cgi/content/short/2022.06.15.22276446,Experiences of mental health and wellbeing support for NHS staff during the COVID-19 pandemic: a reflexive thematic analysis,Corinne Clarkson; Hannah Scott; Siobhan Hegarty; Emilia Soulios; Rupa Bhundia; Sam Gnanapragasam; Mary Jane Docherty; Rosalind Raine; Sharon Stevelink; Neil Greenberg; Matthew Hotopf; Simon Wessely; Ira Madan; Anne Marie Rafferty; Danielle Lamb,University College London; King's College London; King's College London; King's College London; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; University College London; King's College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; King's College London; UCL,"Staff in the National Health Service (NHS) have been placed under considerable strain during the COVID-19 pandemic; whilst NHS Trusts provide a variety of health and wellbeing support services, there has been little research investigating staff perceptions of these services. Moreover, the research that does exist typically includes only clinical staff, despite a large proportion of patient-facing NHS workers being in non-clinical roles. We interviewed forty-eight clinical and non-clinical healthcare workers from eighteen NHS Trusts in England about their experiences of workplace health and wellbeing support during the pandemic. Reflexive thematic analysis identified that perceived stigma around help-seeking, and staffing shortages due to wider socio-political contexts such as austerity, were barriers to using support services. Visible, caring leadership at all levels (CEO to line managers), peer support, easily accessible services, and clear communication about support offers were enablers. Our evidence suggests Trusts should have active strategies to improve help-seeking. This could involve providing all staff with regular reminders about support options, in a variety of formats (e.g. email, posters, mentioned in meetings), and easily remembered single points of access, delivered by a mix of in-house and externally-provided services, to cater for those more and less concerned about stigma and confidentiality. In addition, managers at all levels should be trained and supported to feel confident to speak about mental health with staff, with formal peer support facilitated by building in time for this during working hours. As others have pointed out, this will require long-term strategic planning to address workforce shortages.",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2022.06.20.22276205,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22276205,Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK),Hayley Holt; Clare Relton; Mohammad Talaei; Jane Symons; Molly R Davies; David A Jolliffe; Giulia Vivaldi; Florence Tydeman; Anne Williamson; Paul E Pfeffer; Christopher Orton; David Ford; Gwyneth A Davies; Ronan A Lyons; Chris J Griffiths; Frank Kee; Aziz Sheikh; Gerome Breen; Seif Shaheen; Adrian R Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; King's College London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Blizard Institute; Barts Health NHS Trust; Swansea University; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; University of Edinburgh; King's College London; Queen Mary University of London; Queen Mary University of London,"BackgroundCoronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is estimated to have caused more than 18 million deaths worldwide as of end-May 2022. - -MethodsCOVIDENCE UK is a longitudinal population-based study that investigates risk factors for, and impacts of, COVID-19 in UK residents aged [≥]16 years. A unique feature is the capacity to support trial-within-cohort studies to evaluate interventions for prevention of COVID-19 and other acute respiratory illnesses. Participants complete a detailed online baseline questionnaire capturing self-reported information relating to their socio-demographic characteristics, occupation, lifestyle, quality of life, weight, height, longstanding medical conditions, medication use, vaccination status, diet and supplemental micronutrient intake. Follow-up on-line questionnaires capturing incident symptoms of COVID-19 and other acute respiratory infections, incident swab test-confirmed COVID-19, doses of SARS-CoV-2 vaccine received, and quality of life are completed at monthly intervals. - -ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. - -ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,exact,100,100 medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,exact,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. @@ -603,13 +596,6 @@ Method12,965 healthcare staff (clinical and non-clinical) were recruited from 18 ResultsPMIEs were significantly associated with adverse mental health symptoms across healthcare staff. Specific work factors were significantly associated with experiences of moral injury, including being redeployed, lack of PPE, and having a colleague die of COVID-19. Nurses who reported symptoms of mental disorders were more likely to report all forms of PMIEs than those without symptoms (AOR 2.7; 95% CI 2.2, 3.3). Doctors who reported symptoms were only more likely to report betrayal events, such as breach of trust by colleagues (AOR 2.7, 95% CI 1.5, 4.9). ConclusionsA considerable proportion of NHS healthcare staff in both clinical and non-clinical roles report exposure to PMIEs during the COVID-19 pandemic. Prospective research is needed to identify the direction of causation between moral injury and mental disorder as well as continuing to monitor the longer term outcomes of exposure to PMIEs.",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2022.06.12.22276307,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.12.22276307,"Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study",Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status. - -MethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure. - -FindingsVaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses). - -InterpretationDifferential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.",public and global health,exact,100,100 medRxiv,10.1101/2022.06.08.22276154,2022-06-09,https://medrxiv.org/cgi/content/short/2022.06.08.22276154,Validity of self-testing at home with rapid SARS-CoV-2 antibody detection by lateral flow immunoassay,Christina J Atchison; Maya Moshe; Jonathan C Brown; Matthew Whitaker; Nathan C K Wong; Anil A Bharath; Rachel A McKendry; Ara Darzi; Deborah Ashby; Christl A. Donnelly; Steven Riley; Paul Elliott; Wendy S Barclay; Graham Cooke; Helen Ward,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London School of Public Health; Imperial College London; Imperial College; Imperial College London","BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassays (LFIA) can be carried out in the home and have been used as an affordable and practical approach to large-scale antibody prevalence studies. However, assay performance differs from that of high-throughput laboratory-based assays which can be highly sensitive. We explore LFIA performance under field conditions compared to laboratory-based ELISA and assess the potential of LFIAs to identify people who lack functional antibodies following infection or vaccination. MethodsField evaluation of a self-administered LFIA test (Fortress, NI) among 3758 participants from the REal-time Assessment of Community Transmission-2 (REACT-2) study in England selected based on vaccination history and previous LFIA result to ensure a range of antibody titres. In July 2021, participants performed, at home, a self-administered LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample (Tasso-SST) for serological assessment of IgG antibodies to the spike protein using the Roche Elecsys(R) Anti-SARS-CoV-2 assay. We compared the self-administered and reported LFIA result to the quantitative Roche assay and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralisation. @@ -668,6 +654,15 @@ MethodsWe applied a two-stage Bayesian model to quantify inequalities in excess ResultsWe found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100,000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. ConclusionThese results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.",epidemiology,exact,100,100 +medRxiv,10.1101/2022.04.21.22274152,2022-04-27,https://medrxiv.org/cgi/content/short/2022.04.21.22274152,"Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.",Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy,"Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University","BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls. + +MethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis. + +ResultsCompared to matched individuals testing negative, surviving positive community-tested patients had a higher risk of post-viral illness (HR: 4.57, 95%CI: 1.77-11.80, p=0.002), fatigue (HR: 1.47, 95%CI: 1.24-1.75, p<0.001) and embolism (HR: 1.51, 95%CI: 1.13-2.02, p=0.005) at 5-24 weeks post-diagnosis. In the four weeks after COVID-19 higher rates of sick notes were being issued for community-tested (HR: 3.04, 95%CI: 0.88 to 10.50, p<0.079); the risk was reduced after four weeks, compared to controls. Overall healthcare attendance for anxiety, depression was less likely in those with COVID-19 in the first four weeks (HR: 0.83, 95%CI: 0.73-1.06, p=0.007). After four weeks, anxiety, depression is less likely to occur for the positive community-tested individuals (HR: 0.87, 95%CI: 0.77-1.00, p=0.048), but more likely for positive hospital-tested individuals (HR: 1.16, 95%CI: 1.00-1.45, p=0.053). Although statistical associations between positive infection and post-infection healthcare use are clear, the absolute use of healthcare is very. + +ConclusionsCommunity COVID-19 disease is associated with increased risks of post-viral illness, fatigue, embolism, depression, anxiety and respiratory conditions. Despite these elevated risks, the absolute healthcare burden is low. Either very small proportions of people experience adverse outcomes following COVID-19 or they are not presenting to healthcare. + +Trial registrationData held in SAIL databank are anonymised and therefore, no ethical approval is required. All data in SAIL has the permission from the relevant Caldicott Guardian or Data Protection Officer and SAIL-related projects are required to obtain Information Governance Review Panel (IGRP) approval. The IGRP approval number for this study is 1259.",epidemiology,exact,100,100 medRxiv,10.1101/2022.04.22.22274176,2022-04-22,https://medrxiv.org/cgi/content/short/2022.04.22.22274176,Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform,Kevin Wing; Daniel J Grint; Rohini Mathur; Hamish Gibbs; George Hickman; Emily Nightingale; Anna Schultze; Harriet Forbes; Vahe Nafilyan; Krishnan Bhaskaran; Elizabeth Williamson; Thomas House; Lorenzo Pellis; Emily Herrett; Nileesa Gautam; Helen J Curtis; Christopher T. Rentsch; Angel Wong; Brian MacKenna; Amir Mehrkar; Seb Bacon; Ian J Douglas; Stephen Evans; Laurie Tomlinson; Ben Goldacre; Rosalind M Eggo,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Trop. Med.; University of Bristol; Office for National Statistics; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Manchester; The University of Manchester; London School of Hygiene & Tropical Medicine; Aetion Inc; University of Oxford; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene & Tropical Medicine","Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals. With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in wave 1 (01/02/2020-31/08/2020) and 2 731 427 in wave 2 (01/09/2020-31/01/2021). Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves (e.g. wave 2, 67+ living with 3 other generations vs 67+ year olds only: White HR 1{middle dot}61 95% CI 1{middle dot}38-1{middle dot}87, South Asian HR 1{middle dot}76 95% CI 1{middle dot}48-2{middle dot}10), with a trend for increased risks of severe COVID-19 with increasing generations in wave 2. Multigenerational living was associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics. FundingThis research was funded in part, by the Wellcome Trust. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.",epidemiology,exact,100,100 @@ -1309,15 +1304,6 @@ MethodsProspective, multi-centre, trans-thoracic echocardiographic, cohort study ResultsOne hundred and twenty-one patients were recruited to COVID-RV, 118 underwent imaging and it was possible to determine the primary outcome in 112. RVD was present in seven (6.2% [95%CI; 2.5%, 12.5%]) patients. Thirty-day mortality was 85.7% in those with RVD, compared to 44.8% in those without (p=0.051). Patients with RVD were more likely to have; pulmonary thromboembolism (p<0.001), higher plateau pressure (p=0.048), lower dynamic compliance (p=0.031), higher NT-proBNP (p<0.006) and more frequent abnormal troponin (p=0.048). Abnormal NT-proBNP (OR 4.77 [1.22, 21.32], p=0.03) and abnormal Troponin (16.54 [4.98, 67.12], p<0.001) independently predicted 30-day mortality. ConclusionCOVID-RV demonstrates a prevalence of RVD in ventilated patients with COVID-19 of 6.2% and is associated with a mortality of 85.7%. Association is observed between RVD and each of the aetiological domains of; ARDS, ventilation, micro/macro thrombi and myocardial injury.",intensive care and critical care medicine,exact,100,100 -medRxiv,10.1101/2021.07.23.21260992,2021-07-25,https://medrxiv.org/cgi/content/short/2021.07.23.21260992,A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges,Bernadette C Young; David W Eyre; Saroj Kendrick; Chris White; Sylvester Smith; George Beveridge; Toby Nonnenmacher; Fegor Ichofu; Joseph Hillier; Ian Diamond; Emma Rourke; Fiona Dawe; Ieuan Day; Lisa Davies; Paul Staite; Andrea Lacey; James McCrae; Ffion Jones; Joseph Kelly; Urszula Bankiewicz; Sarah Tunkel; Richard Ovens; David Chapman; Peter Marks; Nick Hicks; Tom Fowler; Susan Hopkins; Lucy Yardley; Tim EA Peto,"University of Oxford; University of Oxford; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Department of Health and Social Care, UK Government; Deloitte MCS limited; Deloitte MCS limited; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Public Health England; University of Bristol; University of Oxford","BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools. - -MethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation. - -Co-primary outcomes in all students and staff were symptomatic COVID-19, adjusted for community case rates, to estimate within-school transmission (non-inferiority margin: <50% relative increase), and COVID-19-related school absence. Analyses were performed on an intention to treat (ITT) basis using quasi-Poisson regression, also estimating complier average causal effects (CACE). Secondary outcomes included participation rates, PCR results in contacts and performance characteristics of LFDs vs. PCR. - -FindingsOf 99 control and 102 intervention schools, 76 and 86 actively participated (19-April-2021 to 27-June-2021); additional national data allowed most non-participating schools to be included in the co-primary outcomes. 2432/5763(42.4%) intervention arm contacts participated. There were 657 symptomatic PCR-confirmed infections during 7,782,537 days-at-risk (59.1/100k/week) and 740 during 8,379,749 days-at-risk (61.8/100k/week) in the control and intervention arms respectively (ITT adjusted incidence rate ratio, aIRR=0.96 [95%CI 0.75-1.22;p=0.72]) (CACE-aIRR=0.86 [0.55-1.34]). There were 55,718 COVID-related absences during 3,092,515 person-school-days (1.8%) and 48,609 during 3,305,403 person-school-days(1.5%) in the control and intervention arms (ITT-aIRR=0.80 [95%CI 0.53-1.21;p=0.29]) (CACE-aIRR 0.61 [0.30-1.23]). 14/886(1.6%) control contacts providing an asymptomatic PCR sample tested positive compared to 44/2981(1.5%) intervention contacts (adjusted odds ratio, aOR=0.73 [95%CI 0.33-1.61;p=0.44]). Rates of symptomatic infection in contacts were 44/4665(0.9%) and 79/5955(1.3%), respectively (aOR=1.21 [0.82-1.79;p=0.34]). - -InterpretationDaily contact testing of school-based contacts was non-inferior to self-isolation for control of COVID-19 transmission. COVID-19 rates in school-based contacts in both intervention and control groups were <2%. Daily contact testing is a safe alternative to home isolation following school-based exposures.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.07.22.21260416,2021-07-23,https://medrxiv.org/cgi/content/short/2021.07.22.21260416,"Obesity, Ethnicity, and Covid-19 Mortality: A population-based cohort study of 12.6 Million Adults in England",Thomas Yates; Annabel Summerfield; Cameron Razieh; Amitava Banerjee; Yogini Chudasama; Melanie J Davies; Clare Gillies; Nazrul Islam; Claire Lawson; Evgeny Mirkes; Francesco Zaccardi; Kamlesh Khunti; Vahe Nafilyan,University of Leicester; Office for National Statistics; University of Leicester; University College London; University of Leicester; University of Leicester; University of Leicester; University of Oxford; University of Leicester; University of Leicester; University of Leicester; University of Leicester; Office for National Statistics,"ImportanceObesity and ethnicity are well characterised risk factors for severe COVID-19 outcomes, but the differential effects of obesity on COVID-19 outcomes by race/ethnicity has not been examined robustly in the general population. ObjectiveTo investigate the association between body mass index (BMI) and COVID-19 mortality across different ethnic groups. @@ -1420,13 +1406,6 @@ MethodsIn June 2020, current and former members of the UK Police forces and Fire ResultsIn this cohort of non-healthcare key workers, 7.4% (396/5,348; 95% CI, 6.7-8.1) were antibody positive. Seroprevalence was 8.9% (6.9-11.4) in those under 40 years, 11.5% (8.8-15.0) in those of non-white British ethnicity and 7.8% (7.1-8.7) in those currently working. The self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 0.77-0.83). The LFIAs (self-test and nurse-performed) had a similar performance: compared to ELISA, sensitivity was 82.1% (77.7-86.0) self-test and 76.4% (71.9-80.5) nurse-performed with specificity of 97.8% (97.3-98.2) and 98.5% (98.1-98.8) respectively. ConclusionA greater proportion of the non-healthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (5.8-6.1) following the first wave in England. The high acceptability and usability reported by participants and the similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home-testing in occupational and community prevalence studies.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.06.24.21259277,2021-06-25,https://medrxiv.org/cgi/content/short/2021.06.24.21259277,Risk factors for long COVID: analyses of 10 longitudinal studies and electronic health records in the UK,Ellen J. Thompson; Dylan M. Williams; Alex J. Walker; Ruth E. Mitchell; Claire L. Niedzwiedz; Tiffany C. Yang; Charlotte Huggins; Alex S. F. Kwong; Richard Silverwood; Giorgio Di Gessa; Ruth C. E. Bowyer; Kate Northstone; Bo Hou; Michael J. Green; Brian Dodgeon; Katie J. Doores; Emma Duncan; Frances M. K. Williams; - OpenSAFELY Collaborative; Andrew Steptoe; David J. Porteous; Rosemary R. C. McEachan; Laurie Tomlinson; Ben Goldacre; Praveetha Patalay; George B. Ploubidis; Srinivasa Vittal Katikireddi; Kate Tilling; Christopher T. Rentsch; Nicholas J. Timpson; Nishi Chaturvedi; Claire J. Steves,King's College London; University College London; University of Oxford; University of Bristol; University of Glasgow; Bradford Teaching Hospitals NHS Foundation Trust; University of Edinburgh; University of Bristol; University College London; University College London; King's College London; University of Bristol; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University College London; King's College London; King's College London; King's College London; ; University College London; University of Edinburgh; Bradford Teaching Hospitals NHS Foundation Trust; London School of Hygiene and Tropical Medicine; University of Oxford; University College London; University College London; University of Glasgow; University of Bristol; London School of Hygiene and Tropical Medicine; University of Bristol; University College London; King's College London,"BackgroundThe impact of long COVID is considerable, but risk factors are poorly characterised. We analysed symptom duration and risk factor from 10 longitudinal study (LS) samples and electronic healthcare records (EHR). - -MethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 participants in the UK LS, and 3,327 adults with COVID-19, were assigned a long COVID code from 1,199,812 individuals in primary care EHR. Outcomes for LS included symptom duration lasting 4+ weeks (long COVID) and 12+ weeks. Association with of age, sex, ethnicity, socioeconomic factors, smoking, general and mental health, overweight/obesity, diabetes, hypertension, hypercholesterolaemia, and asthma was assessed. - -ResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%). - -ConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.",epidemiology,exact,100,100 bioRxiv,10.1101/2021.06.21.449178,2021-06-21,https://biorxiv.org/cgi/content/short/2021.06.21.449178,Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury,Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa,"University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford","Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies. One Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.",immunology,exact,100,100 @@ -1478,7 +1457,6 @@ Research in contextO_ST_ABSPrevious evidenceC_ST_ABSLong COVID and post-COVID sy Added value of this studyFor the first time, we report the baseline characteristics, investigation and outcomes of initial assessment of all eligible patients in a dedicated multi-professional post-COVID service, including 547 post-hospitalisation, 566 non-hospitalised and 212 patients discharged from emergency department. Despite relatively low comorbidity and risk factor burden in non-hospitalised patients, we show that both non-hospitalised and hospitalised patients presenting with persistent symptoms after SARS-CoV2 infection have high rates of functional impairment, specialist referral and rehabilitation, even 6-12 months after the acute infection. These real-world data will inform models of care during and beyond the pandemic. Implications of all the available evidenceThe significant, long-lasting health and social consequences of SARS-CoV-2 infection are not confined to those who required hospitalisation. As with other long-term conditions, care of patients experiencing Long COVID or specific end-organ effects require consistent, integrated, patient-centred approaches to investigation and management. At public health and policy level, burden of post-COVID morbidity demands renewed focus on effective infection suppression for all age groups.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.05.22.21257633,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.22.21257633,Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021,Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung,"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany","The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.14.21257229,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.14.21257229,Symptom profiles and accuracy of clinical definitions for COVID-19 in the community. Results of the Virus Watch community cohort.,Ellen Fragaszy; Madhumita Shrotri; Cyril Geismar; Anna Aryee; Sarah Beale; Isobel Braithwaite; Thomas Byrne; Wing Lam Erica Fong; Jo Gibbs; Pia Hardelid; Jana Kovar; Vasileios Edward Lampos; Eleni Nastouli; Annalan Mathew Dwight Navaratnam; Vincent Grigori Nguyen; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,"Centre for Public Health Data Science, Institute of Health Informatics, University College London; Department of Infectious Disease Epidemiology, London School ; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute for Global Health, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Institute of Epidemiology and Health Care, University College London; Department of Computer Science, University College London; Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health; Francis Crick Institute, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London; . Institute of Epidemiology and Health Care, University Colle; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Centre for Public Health Data Science, Institute of Health Informatics, University College London; Institute of Epidemiology and Health Care, University College London; ","BackgroundUnderstanding the symptomatology and accuracy of clinical case definitions for COVID-19 in the community is important for the initiation of Test, Trace and Isolate (TTI) and may, in future, be important for early prescription of antivirals. MethodsVirus Watch is a large community cohort with prospective daily recording of a wide range of symptoms and self-reporting of swab results (mainly undertaken through the UK TTI system). We compared frequency, severity, timing, and duration of symptoms in test positive and test negative cases. We compared the test performance of the current UK case definition used by TTI (any one of: new continuous cough, high temperature, or loss of or altered sense of smell or taste) with a wider definition that also included muscle aches, chills, headache, or loss of appetite. @@ -1605,21 +1583,6 @@ ResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0. ConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals. RegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.",infectious diseases,exact,100,100 -medRxiv,10.1101/2021.04.08.21255099,2021-04-14,https://medrxiv.org/cgi/content/short/2021.04.08.21255099,Occupational risks of COVID-19 in NHS workers in England,Diana van der Plaat; Ira Madan; David Coggon; Martie van Tongeren; Rhiannon Edge; Rupert Muiry; Vaughan Parsons; Paul Cullinan,Imperial College London; Guy's and St Thomas' NHS Foundation Trust; Southampton General Hospital; University of Manchester; Lancaster University; Guy's and St Thomas NHS Foundation Trust; Guy's and St Thomas NHS Foundation Trust; Imperial College London,"ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England - -MethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression. - -ResultsWith adjustment for employing trust, demographic characteristics, and previous frequency of sickness absence, risk relative to administrative/clerical occupations was highest in additional clinical services (including care assistants) (OR 2.31 [2.25-2.37]), registered nursing and midwifery professionals (OR 2.28 [2.23-2.34]) and allied health professionals (OR 1.94 [1.88-2.01]), and intermediate in doctors and dentists (OR 1.55 [1.50-1.61]). Differences in risk were higher after the employing trust had started to care for documented Covid-19 patients, and were reduced, but not eliminated, following additional adjustment for exposure to infected patients or materials, assessed by a job-exposure matrix. For prolonged Covid-19 sickness absence (episodes lasting >14 days), the variation in risk by staff group was somewhat greater. - -ConclusionsAfter allowance for possible bias and confounding by non-occupational exposures, we estimated that relative risks for Covid-19 among most patient-facing occupations were between 1.5 and 2.5. The highest risks were in those working in additional clinical services, nursing and midwifery and in allied health professions. Better protective measures for these staff groups should be a priority. Covid-19 may meet criteria for compensation as an occupational disease in some healthcare occupations. - -Key messagesO_LIWhat is already known about this subject? -Healthcare workers and other keyworkers (workers whose job was considered essential to societal functioning) had a higher likelihood of testing positive for COVID-19 than other workers during the first lockdown in England. Amongst healthcare workers, those working in inpatient settings had the highest rate of infection. -C_LIO_LIWhat are the new findings? -Between March and July 2000, the overall risk of COVID-19 sickness absence in National Health Service staff in England was lower at older ages, higher in non-white staff, and (in comparison with administrative and clerical staff) more than doubled in registered nurses and among workers such as healthcare assistants providing support to health professionals. Risk in health care scientists was little different from that in administrative and clerical occupations -C_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future? -Our results suggest that the risk reduction strategies that were in place for healthcare scientists were effective. However, the protection for nursing and supporting health professionals was insufficient. In the event of a further wave of infections resulting in high hospital admissions, attention should be paid to ensuring that risk reduction strategies for nurses and supporting health professionals are improved. -C_LI",occupational and environmental health,exact,100,100 medRxiv,10.1101/2021.04.10.21254672,2021-04-12,https://medrxiv.org/cgi/content/short/2021.04.10.21254672,Inhaled budesonide for COVID-19 in people at higher risk of adverse outcomes in the community: interim analyses from the PRINCIPLE trial,- The PRINCIPLE Trial Collaborative Group; Ly-Mee Yu; Mona Bafadhel; Jienchi Dorward; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Nicholas Berry; Michelle A Detry; Christina T Saunders; Mark Fitzgerald; Victoria Harris; Simon de Lusignan; Monique I Andersson; Peter J Barnes; Richard EK Russell; Dan V Nicolau Jr.; Sanjay Ramakrishnan; FD Richard Hobbs; Christopher C Butler,"; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; National Heart and Lung Institute, Imperial College, London, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom; UQ Centre for Clinical Research, University of Queensland, Brisbane, Australia and Nuffield Department of Clinical Medicine, University of Oxford, United Kingdo; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom","BACKGROUNDInhaled budesonide has shown efficacy for treating COVID-19 in the community but has not yet been tested in effectiveness trials. METHODSWe performed a multicenter, open-label, multi-arm, adaptive platform randomized controlled trial involving people aged [≥]65 years, or [≥]50 years with comorbidities, and unwell [≤]14 days with suspected COVID-19 in the community (PRINCIPLE). Participants were randomized to usual care, usual care plus inhaled budesonide (800{micro}g twice daily for 14 days), or usual care plus other interventions. The co-primary endpoints are time to first self-reported recovery, and hospitalization/death related to COVID-19, both measured over 28 days from randomisation and analysed using Bayesian models. @@ -1665,6 +1628,7 @@ Main outcome measuresVaccination intention was measured by individual participan ResultsSurvey response rate was 56% (20,792/36,998) in December 2020 and 52% (20,284/38,727) in February 2021, with 14,713 adults reporting across both time points. Of participants reporting across both timepoints, 13,281 (90%) answered Yes and 1,432 (10%) responded No or Unsure in December 2020. Of those answering No or Unsure in December 2020, 1,233 (86%) went on to answer Yes or Already had a COVID-19 vaccine in February 2021. The magnitude of this shift was consistent across all ethnic groups measured and all levels of social deprivation. Age was most strongly associated with vaccination intention, with 16-24-year-olds more likely to respond ""No"" or ""Unsure"" than those aged 75+ in December 2020 (RR: 4.32, 95% CI: 2.40-7.78 &2.93 95% CI: 2.19-3.92, respectively) and February 2021 (RR: 5.30 95% CI: 1.39-20.20 &20.21 95%CI: 7.19-56.78). The association between ethnicity and vaccination intention has weakened, but not disappeared, over time. Both vaccine- and illness-related psychological factors were shown to influence vaccination intention. ConclusionsOver four in five adults (86%) who were reluctant or intending to refuse a COVID-19 vaccine in December 2020 had changed their mind in February 2021 and planned on accepting, or had already accepted, a vaccine.",public and global health,exact,100,100 +medRxiv,10.1101/2021.03.24.21254227,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.24.21254227,COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death,Darryl P Leong; Amitava Banerjee; Salim Yusuf,McMaster University; University College London; McMaster University,"The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.",epidemiology,exact,100,100 medRxiv,10.1101/2021.03.26.21254390,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254390,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study,Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen,Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital,"BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors. MethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration. @@ -1808,25 +1772,6 @@ This study provides evidence of any differences in the health and wellbeing of c What this study adds?Improvements in physical activity levels, sleep time, happiness and general wellbeing were observed in general for children during school closures compared to previous years. However, children on FSM reported eating less fruit and vegetables and had lower self-assessed school competence compared to 2019. Compared to those not on FSM they also spent less time doing physical activity and consumed more takeaways during school closures. These trends are not evident among children not on FSM. All children reported improvements in wellbeing during lockdown especially on the happiness with family measure. Overall, findings suggest schools help to reduce inequalities in physical health for socio-economically deprived children. During school closures children from deprived backgrounds are likely to have poorer physical health (e.g. less time spent doing physical activities and poorer diet) and this is not observed in children who are not in receipt of FSM. This research suggests that school closures will result in widening health inequalities and when schools return measures will need to be in place to readdress the widened gap in physical health.",public and global health,exact,100,100 -medRxiv,10.1101/2021.02.04.21251087,2021-02-08,https://medrxiv.org/cgi/content/short/2021.02.04.21251087,Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach,Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing. - -MethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings. - -ResultsThe total number of cases in a school was not associated with a subsequent increase in the risk of testing positive (Staff OR per case 0.92, 95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst pupils, the number of recent cases within the same year group was significantly associated with subsequent increased risk of testing positive (OR per case 1.12, 95%CI 1.08 - 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 - 9.88). - -ConclusionsIn a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased risk, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment. - -O_TEXTBOXWhat is knownO_LIEvidence of the role schools play in the transmission of SARS-CoV-2 is limited -C_LIO_LIHigher positivity rates are observed in school staff compared to pupils -C_LIO_LILack of evidence on transmission pathways transmission into and within schools -C_LI - -What this study addsO_LIFirst UK national level study of transmission between pupils and staff in a school environment during the SARS-CoV-2 pandemic. -C_LIO_LISchools opening September-December 2020 was not associated with an increased subsequent risk of testing positive in staff -C_LIO_LIPupils were found to be at increased risk of testing positive, following cases appearing within their own year group -C_LI - -C_TEXTBOX",health informatics,exact,100,100 medRxiv,10.1101/2021.02.03.21251004,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. MethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. @@ -1842,12 +1787,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic Added value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves. Implications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.02.02.21250989,2021-02-03,https://medrxiv.org/cgi/content/short/2021.02.02.21250989,Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020,Krishnan Bhaskaran; Rohini Mathur; Christopher T Rentsch; Caroline E Morton; William J Hulme; Anna Schultze; Brian McKenna; Rosalind M Eggo; Angel YS Wong; Elizabeth J Williamson; Harriet J Forbes; Kevin Wing; Helen I McDonald; Chris J Bates; Sebastian CJ Bacon; Alex J Walker; David Evans; Peter Inglesby; Amir Mehrkar; Helen J Curtis; Nichola J DeVito; Richard Croker; Henry Drysdale; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Laurie Tomlinson; Stephen JW Evans; Richard Grieve; Liam Smeeth; Ben Goldacre,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP, TPP House, Horsforth, Leeds; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford","Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent ""second wave"" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England. - -O_TBL View this table: -org.highwire.dtl.DTLVardef@987a5org.highwire.dtl.DTLVardef@1a8a141org.highwire.dtl.DTLVardef@1f2de56org.highwire.dtl.DTLVardef@1e2f9b8org.highwire.dtl.DTLVardef@78bfcc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONAssociation between ethnicity and COVID-19 death 1st Sept - 9th Nov 2020 - -C_TABLECAPTION C_TBL",infectious diseases,exact,100,100 medRxiv,10.1101/2021.01.30.21250777,2021-02-01,https://medrxiv.org/cgi/content/short/2021.01.30.21250777,Accuracy of four lateral flow immunoassays for anti SARS-CoV-2 antibodies: a head-to-head comparative study,Hayley E Jones; Ranya Mulchandani; Sian Taylor-Phillips; A E Ades; Justin Shute; Keith Perry; Nastassya Chandra; Tim Brooks; Andre Charlett; Matthew Hickman; Isabel Oliver; Stephen Kaptoge; John Danesh; Emanuele Di Angelantonio; - COMPARE Study investigators; - EDSAB-HOME investigators; David H WYLLIE,University of Bristol; Public Health England; University of Warwick; University of Bristol; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; University of Bristol; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; ; ; Public Health England,"BackgroundSARS-CoV-2 antibody tests are used for population surveillance and might have a future role in individual risk assessment. Lateral flow immunoassays (LFIAs) can deliver results rapidly and at scale, but have widely varying accuracy. MethodsIn a laboratory setting, we performed head-to-head comparisons of four LFIAs: the Rapid Test Consortiums AbC-19 Rapid Test, OrientGene COVID IgG/IgM Rapid Test Cassette, SureScreen COVID-19 Rapid Test Cassette, and Biomerica COVID-19 IgG/IgM Rapid Test. We analysed blood samples from 2,847 key workers and 1,995 pre-pandemic blood donors with all four devices. @@ -2093,6 +2032,13 @@ ConclusionMild to moderate degrees of mobility restriction in most countries wer WHAT IS ALREADY KNOWN ON THIS TOPICSince SARS-CoV-2 became a pandemic, restrictions on mobility such as limitations on travel and closure of offices, restaurants, and shops have been imposed in an unprecedented way in both scale and scope to prevent the spread of COVID-19 in the absence of effective treatment options or a vaccine. Although mobility restriction has also brought about tremendous costs such as negative economic growth and other collateral impacts on health such as increased morbidity and mortality from lack of access to other essential health services, little evidence exists on the effectiveness of mobility restriction for the prevention of disease transmission. A search of PUBMED and Google Scholar for publications on this topic through Sep 20, 2020 revealed that most of the evidence on the effectiveness of physical distancing comes from mathematical modeling studies using a variety of assumptions. One study investigated only the combined effect of several interventions, including physical distancing, among SARS-CoV-2 infected patients. WHAT THIS STUDY ADDSThis is the first study to investigate the association between change in mobility and incidence of COVID-19 globally using real-time measures of mobility at the population level. For this, we used Google Global Mobility data and the daily incidence of COVID-19 for 36 countries from the day of 100th case detection through August 31, 2020. Our findings from LOESS regression show that in two-thirds of countries, reductions of up to 40% in commuting mobility were associated with decreased COVID-19 incidence, more so early in the pandemic. This decrease, however, plateaued as mobility decreased further. We found that associations between mobility restriction and incidence became smaller or negligible in the late phase of the pandemic in most countries. The reduced incidence rate of COVID-19 cases with a mild to moderate degree of mobility restriction in most countries suggests some value to limited mobility restriction in early phases of epidemic mitigation. The lack of impact in some others, however, suggests further research is needed to confirm these findings and determine the distinguishing factors for when mobility restrictions are helpful in decreasing viral transmission. Governments should carefully consider the level and period of mobility restriction necessary to achieve the desired benefits and minimize harm.",health policy,exact,100,100 +medRxiv,10.1101/2020.10.30.20223123,2020-11-03,https://medrxiv.org/cgi/content/short/2020.10.30.20223123,High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundREACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive. + +MethodsREACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive. + +ResultsOverall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%). + +ConclusionThe co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.11.01.20222315,2020-11-02,https://medrxiv.org/cgi/content/short/2020.11.01.20222315,Association between living with children and outcomes from COVID-19: an OpenSAFELY cohort study of 12 million adults in England,Harriet Forbes; Caroline E Morton; Seb Bacon; Helen I McDonald; Caroline Minassian; Jeremy Brown; Christopher T. Rentsch; Rohini T. Mathur; Anna Schultze; Nicholas J DeVito; Brian MacKenna; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Henry Drysdale; Angel Wong; Jonathan Cockburn; Robert Mcmanus; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Liam Smeeth; Stephen JW Evans; Krishnan Bhaskaran; Rosalind M Eggo; Ben Goldacre; Laurie Tomlinson,"London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine","BackgroundClose contact with children may provide cross-reactive immunity to SARs-CoV-2 due to more frequent prior coryzal infections from seasonal coronaviruses. Alternatively, close contact with children may increase risk of SARs-CoV-2 infection. We investigated whether risk of infection with SARs-CoV-2 and severe outcomes differed between adults living with and without children. MethodsWorking on behalf of NHS England, we conducted a population-based cohort study using primary care data and pseudonymously-linked hospital and intensive care admissions, and death records, from patients registered in general practices representing 40% of England. Using multivariable Cox regression, we calculated fully-adjusted hazard ratios (HR) of outcomes from 1st February-3rd August 2020 comparing adults living with and without children in the household. @@ -2185,7 +2131,6 @@ Results175,000 volunteers tested across England between 18th September and 5th O ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England, with highest rates in the North of England. Prevalence has increased in all age groups, including those at highest risk. Improved compliance with existing policy and, as necessary, additional interventions are required to control the spread of SARS-CoV-2 in the community and limit the numbers of hospital admissions and deaths from COVID-19.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.10.11.20210625,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.11.20210625,Mental health service activity during COVID-19 lockdown among individuals with learning disabilities: South London and Maudsley data on services and mortality from January to July 2020,Evangelia Martin; Eleanor Nuzum; Matthew Broadbent; Robert Stewart,King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have had a widespread impact on mental healthcare service provision and use. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to quantify this for individuals with particular vulnerabilities, including those with learning disabilities and other neurodevelopmental disorders. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with potential neurodevelopmental disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st July 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with potential neurodevelopmental disorders. In addition, daily deaths are described for all current and previous SLaM service users with potential neurodevelopmental disorders over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. The largest declines in caseloads and total contacts were seen in Home Treatment Team, Liaison/A&E and Older Adult teams. Reduced accepted referrals and inpatient admissions were observed and there was an 103% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March (or a 282% increase if the 2-month period from 16th March to 15th May was considered alone).",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2020.10.09.20209957,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.09.20209957,Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19,Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi,"University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT","Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.10.08.20209304,2020-10-12,https://medrxiv.org/cgi/content/short/2020.10.08.20209304,Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data,Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses. MethodsWe included survivors ([≥]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities. @@ -2221,6 +2166,13 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID-19 outbreaks Added value of this studyWe conducted a national telephone survey with managers of all LTCFs in England which provided dementia care or care to residents aged > 65 years to collect data on the number of staff and residents in each facility, confirmed SARS-CoV-2 infections, characteristics of the facility e.g.size, staffing (use of temporary staff, staffing ratios, sickness pay) and disease control measures such as cohorting and isolation. We identified risk factors for infection in residents and staff, outbreaks (defined as [≥]1 case per LTCF) and large outbreaks using logistic regression. We also estimated the proportion of staff and residents who had been infected with SARS-CoV-2. Responses were obtained from 5126 of out 9081 (56%) of eligible LTCFs. To our knowledge, this is the largest and most detailed survey of risk factors for SARS-CoV-2 infection and outbreaks that has been conducted in LTCFs. Implications of all the available evidenceAlmost half of LTCFs surveyed in this study did not report any cases of infection, and remain vulnerable to infection and outbreaks, highlighting the need for effective control measures. Reducing transmission from staff requires adequate sick pay, minimal use of temporary staff, improved staffing ratios and staff cohorting. Transmission from residents is associated with the number of admissions to the facility and poor compliance with control measures such as isolation.",geriatric medicine,exact,100,100 +medRxiv,10.1101/2020.09.30.20204727,2020-10-02,https://medrxiv.org/cgi/content/short/2020.09.30.20204727,High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020. + +MethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model. + +ResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants. + +ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.09.24.20200048,2020-09-25,https://medrxiv.org/cgi/content/short/2020.09.24.20200048,Genetic mechanisms of critical illness in Covid-19,Erola Pairo-Castineira; Sara Clohisey; Lucija Klaric; Andrew Bretherick; Konrad Rawlik; Nicholas Parkinson; Dorota Pasko; Susan Walker; Anne Richmond; Max Head Fourman; Andy Law; James Furniss; Elvina Gountouna; Nicola Wrobel; Clark D Russell; Loukas Moutsianas; Bo Wang; Alison Meynert; Zhijian Yang; Ranran Zhai; Chenqing Zheng; Fiona Griffith; Wilna Oosthuyzen; Barbara Shih; Seán Keating; Marie Zechner; Chris Haley; David J Porteous; Caroline Hayward; Julian Knight; Charlotte Summers; Manu Shankar-Hari; Lance Turtle; Antonia Ho; Charles Hinds; Peter Horby; Alistair Nichol; David Maslove; Lowell Ling; Paul Klenerman; Danny McAuley; Hugh Montgomery; Timothy Walsh; - The GenOMICC Investigators; - The ISARIC4C Investigators; - The Covid-19 Human Genetics Initiative; Xia Shen; Kathy Rowan; Angie Fawkes; Lee Murphy; Chris P Ponting; Albert Tenesa; Mark Caulfield; Richard Scott; Peter JM Openshaw; Malcolm G Semple; Veronique Vitart; James F Wilson; J Kenneth Baillie,"Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; The Roslin Institute; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; Genomics England; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK; Genomics England; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK; School of Immunology and Microbial Sciences, King's College London; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Univer; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland; Australian and New Zealand Intensive Care Research Cen; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.; University of Oxford; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; Department of Intensive Care Medicine, Royal Vi; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; -; -; -; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.; Intensive Care National Audit & Research Centre, London, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Genomics England; National Heart & Lung Institute, Imperial College London (St Mary's Campus), Norfolk Place, Paddington, London W2 1PG, UK.; University of Liverpool, Liverpool, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK; Ce; Roslin Institute, University of Edinburgh","The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases.2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19.3 @@ -2263,19 +2215,7 @@ ConclusionIn this large, single-centre study, there was a change in hospitalised medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,exact,100,100 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.09.10.20191841,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.10.20191841,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample,Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ","We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.09.04.20187781,2020-09-09,https://medrxiv.org/cgi/content/short/2020.09.04.20187781,Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study,Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre,London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality. - -MethodsWe pre-specified and conducted an observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, representing 40% of the general population in England. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use prior to the COVID-19 outbreak in England and risk of COVID-19 mortality among people with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Model adjustment was informed by a directed acyclic graph. - -ResultsOf 194,637 patients with RA or SLE, 30,569 (15.7%) received [≥] 2 prescriptions of hydroxychloroquine in the six months prior to 1 March 2020. Between 1 March 2020 and 13 July 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0.23% (95% CI 0.18-0.29) among users and 0.22% (95% CI 0.20-0.25) among non-users; an absolute difference of 0.008% (95% CI -0.051-0.066). After accounting for age, sex, ethnicity, use of other immunuosuppressives, and geographic region, no association with COVID-19 mortality was observed (HR 1.03, 95% CI 0.80-1.33). We found no evidence of interactions with age or other immunosuppressives. Quantitative bias analyses indicated observed associations were robust to missing information regarding additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality. - -ConclusionWe found no evidence of a difference in COVID-19 mortality among patients who received hydroxychloroquine for treatment of rheumatological disease prior to the COVID-19 outbreak in England. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials and observational studies to date have shown no evidence of benefit of hydroxychloroquine as a treatment for hospitalised patients who already have COVID-19. A separate question remains: whether routine ongoing use of hydroxychloroquine in people without COVID-19 protects against new infections or severe outcomes. We searched MEDLINE/PubMed for pharmacoepidemiological studies evaluating hydroxychloroquine for prevention of severe COVID-19 outcomes. The keywords ""hydroxychloroquine AND (COVID OR coronavirus OR SARS-CoV-2) AND (prophyl* OR prevent*) AND (rate OR hazard OR odds OR risk)"" were used and results were filtered to articles from the last year with abstracts available. 109 papers were identified for screening; none investigated pre-exposure prophylactic use of hydroxychloroquine for prevention of severe COVID-19 outcomes. Clinical trials of prophylactic use of hydroxychloroquine are ongoing; however, the largest trial does not expect to meet recruitment targets due to ""...unjustified extrapolation and exaggerated safety concerns together with intense politicisation and negative publicity."" In the absence of reported clinical trials, evidence can be generated from real-world data to support the need for randomised clinical trials. - -Added value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data. - -Implications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.",infectious diseases,exact,100,100 +medRxiv,10.1101/2020.09.11.20192492,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.11.20192492,Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London","Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.09.02.20185892,2020-09-07,https://medrxiv.org/cgi/content/short/2020.09.02.20185892,Prognostic accuracy of emergency department triage tools for adults with suspected COVID-19: The PRIEST observational cohort study,Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Amanda Loban; Simon Waterhouse; Richard Simmonds; Katie Biggs; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesThe World Health Organisation (WHO) and National Institute for Health and Care Excellence (NICE) recommend various triage tools to assist decision-making for patients with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in adults presenting to the emergency department (ED) with suspected COVID-19 infection. MethodsWe undertook a mixed prospective and retrospective observational cohort study in 70 EDs across the United Kingdom (UK). We collected data from people attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment with the following triage tools: the WHO algorithm, NEWS2, CURB-65, CRB-65, PMEWS and the swine flu adult hospital pathway (SFAHP). We used 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. @@ -2332,7 +2272,6 @@ The 8{middle dot}3% of school-aged children and 19{middle dot}6% of working-aged Among individuals aged [≥]70 years, 66{middle dot}2% had at least one underlying health condition, suggesting an age-targeted approach to vaccination may efficiently target individuals at risk of severe COVID-19. These national estimates broadly support the use of Global Burden of Disease modelled estimates and age-targeted vaccination strategies in other countries.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.08.21.20177246,2020-08-24,https://medrxiv.org/cgi/content/short/2020.08.21.20177246,Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility,Irene V van Blokland; Pauline Lanting; Anil PS Ori; Judith M Vonk; Robert CA Warmerdam; Johanna C Herkert; Floranne Boulogne; Annique Claringbould; Esteban A Lopera-Maya; Meike Bartels; Jouke-Jan Hottenga; Andrea Ganna; Juha Karjalainen; - Lifelines COVID-19 cohort study; - The COVID-19 Host Genetics Initiative; Caroline Hayward; Chloe Fawns-Ritchie; Archie Campbell; David Porteous; Elizabeth T Cirulli; Kelly M Schiabor Barrett; Stephen Riffle; Alexandre Bolze; Simon White; Francisco Tanudjaja; Xueqing Wang; Jimmy M Ramirez III; Yan Wei Lim; James T Lu; Nicole L Washington; Eco JC de Geus; Patrick Deelen; H Marike Boezen; Lude H Franke,"University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Structural Computational Biology unit, EMB; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA and Analytic and Tra; ; ; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Department of Genetics, University Medical; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands","Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19, and this GWAS benefits from the larger sample size to provide new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, we recommend repeatedly collecting data of disease-related symptoms.",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2020.08.19.20178137,2020-08-22,https://medrxiv.org/cgi/content/short/2020.08.19.20178137,Testing for coronavirus (SARS-CoV-2) infection in populations with low infection prevalence: the largely ignored problem of false positives and the value of repeat testing,Cathie Sudlow; Peter Diggle; Oliver Warlow; David Seymour; Ben Gordon; Rhos Walker; Charles Warlow,"BHF Data Science Centre, Health Data Research UK; Usher Institute, University of Edinburgh; University of Lancaster; Health Data Research UK; Ventient Energy; Health Data Research UK; Health Data Research UK; Health Data Research UK; University of Edinburgh","BackgroundCalls are increasing for widespread SARS-CoV-2 infection testing of people from populations with a very low prevalence of infection. We quantified the impact of less than perfect diagnostic test accuracy on populations, and on individuals, in low prevalence settings, focusing on false positives and the role of confirmatory testing. MethodsWe developed a simple, interactive tool to assess the impact of different combinations of test sensitivity, specificity and infection prevalence in a notional population of 100,000. We derived numbers of true positives, true negatives, false positives and false negatives, positive predictive value (PPV - the percentage of test positives that are true positives) and overall test accuracy for three testing strategies: (1) single test for all; (2) add repeat testing in test positives; (3) add further repeat testing in those with discrepant results. We also assessed the impact on test results for individuals having one, two or three tests under these three strategies. @@ -2410,6 +2349,7 @@ MethodsWorking on behalf of NHS England, we used the OpenSAFELY platform to anal Results17.3 million adults were included, of whom 27,480 (0.16%) had HIV recorded. People living with HIV were more likely to be male, of black ethnicity, and from a more deprived geographical area than the general population. There were 14,882 COVID-19 deaths during the study period, with 25 among people with HIV. People living with HIV had nearly three-fold higher risk of COVID-19 death than those without HIV after adjusting for age and sex (HR=2.90, 95% CI 1.96-4.30). The association was attenuated but risk remained substantially raised, after adjustment for deprivation and ethnicity (adjusted HR=2.52, 1.70-3.73) and further adjustment for comorbidities (HR=2.30, 1.55-3.41). There was some evidence that the association was larger among people of black ethnicity (HR = 3.80, 2.15-6.74, compared to 1.64, 0.92-2.90 in non-black individuals, p-interaction=0.045) InterpretationHIV infection was associated with a markedly raised risk of COVID-19 death in a country with high levels of antiretroviral therapy coverage and viral suppression; the association was larger in people of black ethnicity.",infectious diseases,exact,100,100 +medRxiv,10.1101/2020.08.05.20169078,2020-08-06,https://medrxiv.org/cgi/content/short/2020.08.05.20169078,Transient dynamics of SARS-CoV-2 as England exited national lockdown,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health","Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.08.03.20164897,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20164897,Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study,Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow,"ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood. Design and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population. @@ -2482,6 +2422,15 @@ C_LIO_LIThere is a strong geographical pattern, with 71.0% of the estimated exce C_LIO_LIThe impact was slightly higher is men compared to women, with 24,655 and 23,125 excess deaths respectively, and varied by age, with higher mortality in the group 70-79 years old and evidence of a lower but measurable risk even in people less than 60. C_LIO_LIThe analysis by week suggests differential trends, with more delayed impacts in women and elderly, and the risk limited to the early period in Central and Southern Italy, likely related to the implementation of lockdown policies and contributions from direct and indirect risk pathways. C_LI",epidemiology,exact,100,100 +medRxiv,10.1101/2020.07.15.20152967,2020-07-17,https://medrxiv.org/cgi/content/short/2020.07.15.20152967,Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.,Gisli Jenkins; Tom Drake; Annemarie B Docherty; Ewan Harrison; Jennifer Quint; Huzaifa Adamali; Sarah Agnew; Suresh Babu; Christopher Barber; Shaney Barratt; Elisabeth Bendstrup; Stephen Bianchi; Diego Castillo; Nazia Chaudhuri; Felix Chua; Robina Coker; William Chang; Anjali Cranshaw; Louise Crowley; Davinder Dosanjh; Christine Fiddler; Ian A Forrest; Peter George; Michael Gibbons; Katherine Groom; Sarah Haney; Simon Hart; Emily Heiden; Michael Henry; Ling-Pei Ho; Rachel Hoyles; John Hutchinson; Killian Hurley; Mark Jones; Steve Jones; Maria Kokosi; Michael Kreuter; Laura Mackay; Siva Mahendran; Georgios Margaritopoulos; Maria Molina-Molina; Philip Molyneaux; Aidan D O'Brien; Katherine O'Reilly; Alice Packham; Helen Parfrey; Venerino Poletti; Joanna Porter; Elisabetta Renzoni; Pilar Rivera-Ortega; Anne-Marie Russell; Gauri Saini; Lisa G Spencer; Giulia Stella; Helen Stone; Sharon Sturney; David Thickett; Muhunthan Thillai; Timothy Wallis; Katie Ward; Athol U Wells; Alex West; Melissa Wickremasinghe; Felix Woodhead; Glenn Herson; Lucy Howard; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Iain Stewart,"University of Nottingham; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX; University of Edinburgh; University of Edinburgh; Imperial College London; Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB.; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Queen Alexandra Hospital, Portsmouth, UK.; Northern General Hospital, Sheffield, S5 7AU, UK; Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB.; Centre for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99,8200 Aarhus N, Denmar; Northern General Hospital, Sheffield, S5 7AU, UK.; ILD Unit, Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Royal Brompton Hospital; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Nottingham University Hospital; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK.; Royal Brompton Hospital; South West Peninsula ILD Network, Royal Devon & Exeter Foundation NHS Trust Barrack Road, Exeter EX2 5DW, UK; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, UK, HU16 5JQ; University Hospitals Southampton NHS Foundation Trust, Southampton, UK; Cork University Hospital, Cork, Ireland; University of Oxford; Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK; University of Nottingham; Beaumont Hospital, Dublin, Ireland.; NIHR Southampton Biomedical Research Centre & Clinical and Experimental Sciences, University of Southampton, Southampton, UK; Action for Pulmonary Fibrosis; Guys and St Thomas' Hospital; Center for interstitial and rare lung diseases, Pneumology, Thoraxklinik, University of Heidelberg, Germany and German Center for Lung Research, 69126 Heidelber; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Kingston Hospital NHS Foundation Trust. Galsworthy Road, Kingston upon Thames, Surrey KT2 7QB, UK.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; ILD Unit, Respiratory Department, University Hospital of Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.; Imperial College London; University Hospital Limerick, Dooradoyle, Limerick, Ireland.; Department of Respiratory Medicine, Mater Misericordiae University Hospital, Dublin, Ireland.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Diseases of the Thorax, Morgagni Hospital, Forli, Italy.; University College London; Royal Brompton Hospital; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Imperial College London; Nottingham University Hospitals; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Laboratory of Biochemistry and Genetics, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.; University Hospital North Midlands NHS Trust, Royal Stoke University Hospital, Newcastle Road, Stoke-on-Trent, ST4 6QG, UK.; Royal United Hospitals Bath NHS Foundation Trust, Combe Park, Bath BA1 3NG, UK; University of Birmingham, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; University of Southampton; Imperial College London; Royal Brompton Hospital; Guys and St Thomas' Hospital; Imperial Healthcare NHS Trust, St Mary's Hospital, The Bays, S Wharf Rd, Paddington, London W2 1NY, UK.; Glenfield Hospital Leicester; Nottingham University Hospitals Trust; Nottingham University Hospitals Trust; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; University of Nottingham","RationaleThe impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established. + +ObjectivesTo assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population. + +MethodsAn international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death. + +Measurements and Main ResultsData from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC [≥]80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13-3.46). + +ConclusionsPatients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.",respiratory medicine,exact,100,100 medRxiv,10.1101/2020.07.14.20153734,2020-07-16,https://medrxiv.org/cgi/content/short/2020.07.14.20153734,"Place and causes of acute cardiovascular mortality during the COVID19 pandemic: retrospective cohort study of 580,972 deaths in England and Wales, 2014 to 2020",Jianhua Wu; Mamas Mamas; Mohamed Mohamed; Chun Shing Kwok; Chris Roebuck; Ben Humberstone; Tom Denwood; Tom Luescher; Mark De Belder; John Deanfield; Chris Gale,University of Leeds; Keele University; Keele University; Keele University; NHS Digital; ONS; NHS Digital; Imperial College; Barts Health NHS Trust; UCL; University of Leeds,"ImportanceThe COVID-19 pandemic has resulted in a decline in admissions with cardiovascular (CV) emergencies. The fatal consequences of this are unknown. ObjectivesTo describe the place and causes of acute CV death during the COVID-19 pandemic. @@ -2499,15 +2448,6 @@ Main outcomesPlace (hospital, care home, home) and acute CV events directly cont ResultsAfter 2nd March 2020, there were 22,820 acute CV deaths of which 5.7% related to COVID-19, and an excess acute CV mortality of 1752 (+8%) compared with the expected daily deaths in the same period. Deaths in the community accounted for nearly half of all deaths during this period. Care homes had the greatest increase in excess acute CV deaths (1065, +40%), followed by deaths at home (1728, +34%) and in hospital (57, +0%). The most frequent cause of acute CV death during this period was stroke (8,290, 36.3%), followed by acute coronary syndrome (ACS) (5,532, 24.2%), heart failure (5,280, 23.1%), pulmonary embolism (2,067, 9.1%) and cardiac arrest (1,037, 4.5%). Deep vein thrombosis had the greatest increase in cause of excess acute CV death (18, +25%), followed pulmonary embolism (340, +19%) and stroke (782, +10%). The greatest cause of excess CV death in care homes was stroke (700, +48%), compared with cardiac arrest (80, +56%) at home, and pulmonary embolism (126, +14%) and cardiogenic shock (41, +14%) in hospital. Conclusions and relevanceThe COVID-19 pandemic has resulted in an inflation in acute CV deaths above that expected for the time of year, nearly half of which occurred in the community. The most common cause of acute CV death was stroke followed by acute coronary syndrome and heart failure. This is key information to optimise messaging to the public and enable health resource planning.",cardiovascular medicine,exact,100,100 -medRxiv,10.1101/2020.07.14.20152629,2020-07-15,https://medrxiv.org/cgi/content/short/2020.07.14.20152629,Covid-19 infection and attributable mortality in UK Long Term Care Facilities: Cohort study using active surveillance and electronic records (March-June 2020),Peter F Dutey-Magni; Haydn Williams; Arnoupe Jhass; Greta Rait; Harry Hemingway; Andrew C Hayward; Laura Shallcross,University College London; Four Seasons Healthcare Group; UCL; University College London; University College London; University College London; UCL,"BackgroundEpidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic. - -MethodsCohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality. - -Results2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection. - -217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]). - -ConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.07.13.20152710,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.13.20152710,Excess mortality in mental health service users during the COVID-19 pandemic described by ethnic group: South London and Maudsley data,Robert Stewart; Matthew Broadbent; Jayati Das-Munshi,King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The COVID-19 pandemic in the UK was accompanied by excess all-cause mortality at a national level, only part of which was accounted for by known infections. Excess mortality has previously been described in people who had received care from the South London and Maudsley NHS Foundation Trust (SLaM), a large mental health service provider for 1.2m residents in south London. SLaMs Clinical Record Interactive Search (CRIS) data resource receives 24-hourly updates from its full electronic health record, including regularly sourced national mortality on all past and present SLaM service users. SLaMs urban catchment has high levels of deprivation and is ethnically diverse, so the objective of the descriptive analyses reported in this manuscript was to compare mortality in SLaM service users from 16th March to 15th May 2020 to that for the same period in 2019 within specific ethnic groups: i) White British, ii) Other White, iii) Black African/Caribbean, iv) South Asian, v) Other, and vi) missing/not stated. For Black African/Caribbean patients (the largest minority ethnic group) this ratio was 3.33, compared to 2.47 for White British patients. Considering premature mortality (restricting to deaths below age 70), these ratios were 2.74 and 1.96 respectively. Ratios were also high for those from Other ethnic groups (2.63 for all mortality, 3.07 for premature mortality).",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.07.12.20151753,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.12.20151753,"COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme",Michelle Kendall; Luke Milsom; Lucie Abeler-Dorner; Chris Wymant; Luca Ferretti; Mark Briers; Chris Holmes; David Bonsall; Johannes Abeler; Christophe Fraser,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Alan Turing Institute; University of Oxford; Alan Turing Institute; University of Oxford; University of Oxford; University of Oxford,"In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.",epidemiology,exact,100,100 medRxiv,10.1101/2020.07.10.20150524,2020-07-11,https://medrxiv.org/cgi/content/short/2020.07.10.20150524,Community prevalence of SARS-CoV-2 virus in England during May 2020: REACT study,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundEngland has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission. @@ -2570,6 +2510,16 @@ ResultsSurvival curves show an increased proportion of deaths between 23rd March ConclusionsThe survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",public and global health,exact,100,100 bioRxiv,10.1101/2020.07.01.182709,2020-07-01,https://biorxiv.org/cgi/content/short/2020.07.01.182709,Genetic architecture of host proteins interacting with SARS-CoV-2,Maik Pietzner; Eleanor Wheeler; Julia Carrasco-Zanini; Johannes Raffler; Nicola D. Kerrison; Erin Oerton; Victoria P.W. Auyeung; Chris Finan; Juan P. Casas; Rachel Ostroff; Steve A. Williams; Gabi Kastenmüller; Markus Ralser; Eric G. Gamazon; Nicholas J. Wareham; Aroon Dinesh Hingorani; Claudia Langenberg,University of Cambridge; University of Cambridge; University of Cambridge; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); University of Cambridge; University of Cambridge; University of Cambridge; University College London; Harvard Medical School; SomaLogic Inc.; SomaLogic Inc.; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); The Francis Crick Institute; Vanderbilt University Medical Center; University of Cambridge; University College London; University of Cambridge,"Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification of genetic variants that influence the level or activity of these proteins in the host could enable rapid in silico assessment in human genetic studies of their causal relevance as molecular targets for new or repurposed drugs to treat COVID-19. We integrated large-scale genomic and aptamer-based plasma proteomic data from 10,708 individuals to characterize the genetic architecture of 179 host proteins reported to interact with SARS-CoV-2 proteins or to participate in the host response to COVID-19. We identified 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links, evidence that putative viral interaction partners such as MARK3 affect immune response, and establish the first link between a recently reported variant for respiratory failure of COVID-19 patients at the ABO locus and hypercoagulation, i.e. maladaptive host response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and dynamic and detailed interrogation of results is facilitated through an interactive webserver (https://omicscience.org/apps/covidpgwas/).",genomics,exact,100,100 medRxiv,10.1101/2020.06.29.20142448,2020-06-30,https://medrxiv.org/cgi/content/short/2020.06.29.20142448,Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data,Robert Stewart; Matthew Broadbent,King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.06.28.20141986,2020-06-29,https://medrxiv.org/cgi/content/short/2020.06.28.20141986,Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population,Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon,"University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton","IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases. + +Methods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available. + +Ethics and disseminationThe project has ethical approval and the results will be submitted for publication in a peer-reviewed journal. + +Strengths and limitations of the studyO_LIThe individual-level linkage of general practice, Public Health England testing, Hospital Episode Statistics and Office of National Statistics death register datasets enable a robust and accurate ascertainment of outcomes +C_LIO_LIThe models will be trained and evaluated in population-representative datasets of millions of individuals +C_LIO_LIShielding for clinically extremely vulnerable was advised and in place during the study period, therefore risk predictions influenced by the presence of some shielding conditions may require careful consideration +C_LI",epidemiology,exact,100,100 medRxiv,10.1101/2020.06.24.20139048,2020-06-25,https://medrxiv.org/cgi/content/short/2020.06.24.20139048,A geotemporal survey of hospital bed saturation across England during the first wave of the COVID-19 Pandemic,Bilal A Mateen; Harrison Wilde; John m Dennis; Andrew Duncan; Nicholas John Meyrick Thomas; Andrew P McGovern; Spiros Denaxas; Matt J Keeling; Sebastian J Vollmer,"The Alan Turing Institute; University of Warwick; Kings College Hospital NHS Foundation Trust; University of Warwick, Department of Statistics; University of Exeter Medical School; The Alan Turing Institute; Imperial College London, Faculty of Natural Sciences; University of Exeter Medical School; Royal Devon and Exeter NHS Foundation Trust, Diabetes and Endocrinology; University of Exeter Medical School; University College London; University of Warwick; The Alan Turing Institute; University of Warwick, Department of Statistics","BackgroundNon-pharmacological interventions were introduced based on modelling studies which suggested that the English National Health Service (NHS) would be overwhelmed by the COVID-19 pandemic. In this study, we describe the pattern of bed occupancy across England during the first wave of the pandemic, January 31st to June 5th 2020. MethodsBed availability and occupancy data was extracted from daily reports submitted by all English secondary care providers, between 27-Mar and 5-June. Two thresholds for safe occupancy were utilized (85% as per Royal College of Emergency Medicine and 92% as per NHS Improvement). diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index 6b67c753..5c249862 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -223,20 +223,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -321,6 +307,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.02.17.23286079", + "date": "2023-02-23", + "link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286079", + "title": "Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.", + "authors": "Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson", + "affiliations": "UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency", + "abstract": "AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures.\n\nMethods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded.\n\nConclusionsFew workplace surface samples were positive for SARS-CoV-2 RNA and positive samples typically contained low levels of nucleic acid. Although these data may infer a low probability of fomite transmission or other forms of transmission within the workplace, Ct values may have been lower at the time of contamination. Workplace environmental sampling identified lapses in COVID-control measures within individual sites and showed trends through the pandemic.\n\nSignificance and Impact of the StudyPrior to this study, few published reports investigated SARS-CoV-2 RNA contamination within workplaces experiencing cases of COVID-19. This report provides extensive data on environmental sampling identifying trends across workplaces and through the pandemic.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.18.23286127", @@ -469,7 +469,7 @@ "title": "Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan", "authors": "Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox", "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford", - "abstract": "Background The COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. Objectives A. To determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. B. To estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. C. To assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. Methods This population-based study uses the QResearch database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of severe COVID-19 outcomes after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and dissemination QResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", + "abstract": "BackgroundThe COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England.\n\nObjectivesO_LITo determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations.\nC_LIO_LITo estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination.\nC_LIO_LITo assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations.\nC_LI\n\nMethodsThis population-based study uses the QResearch(R) database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible.\n\nWe will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals.\n\nEthics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", "category": "infectious diseases", "match_type": "exact", "author_similarity": 100, @@ -727,20 +727,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.08.08.22278532", - "date": "2022-08-09", - "link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278532", - "title": "Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI)", - "authors": "Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London", - "abstract": "BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England.\n\nMethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence.\n\nResults14175 residents and 19973 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-83 days after first booster, but no protection was apparent after 84 days. Additional protection following booster vaccination waned, but was still present at 84+ days for COVID-associated hospitalisation (aHR: 0.47, 0.24-0.89) and death (aHR: 0.37, 0.21-0.62). Most residents (64.4%) had received primary course of AstraZeneca, but this did not impact on pre- or post-booster risks. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalisations and no deaths.\n\nConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.\n\nSummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.08.07.22278510", @@ -797,20 +783,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22276205", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276205", - "title": "Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK)", - "authors": "Hayley Holt; Clare Relton; Mohammad Talaei; Jane Symons; Molly R Davies; David A Jolliffe; Giulia Vivaldi; Florence Tydeman; Anne Williamson; Paul E Pfeffer; Christopher Orton; David Ford; Gwyneth A Davies; Ronan A Lyons; Chris J Griffiths; Frank Kee; Aziz Sheikh; Gerome Breen; Seif Shaheen; Adrian R Martineau", - "affiliations": "Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; King's College London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Blizard Institute; Barts Health NHS Trust; Swansea University; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; University of Edinburgh; King's College London; Queen Mary University of London; Queen Mary University of London", - "abstract": "BackgroundCoronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is estimated to have caused more than 18 million deaths worldwide as of end-May 2022.\n\nMethodsCOVIDENCE UK is a longitudinal population-based study that investigates risk factors for, and impacts of, COVID-19 in UK residents aged [≥]16 years. A unique feature is the capacity to support trial-within-cohort studies to evaluate interventions for prevention of COVID-19 and other acute respiratory illnesses. Participants complete a detailed online baseline questionnaire capturing self-reported information relating to their socio-demographic characteristics, occupation, lifestyle, quality of life, weight, height, longstanding medical conditions, medication use, vaccination status, diet and supplemental micronutrient intake. Follow-up on-line questionnaires capturing incident symptoms of COVID-19 and other acute respiratory infections, incident swab test-confirmed COVID-19, doses of SARS-CoV-2 vaccine received, and quality of life are completed at monthly intervals.\n\nResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19.\n\nConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.20.22275994", @@ -895,20 +867,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.12.22276307", - "date": "2022-06-13", - "link": "https://medrxiv.org/cgi/content/short/2022.06.12.22276307", - "title": "Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study", - "authors": "Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London", - "abstract": "BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status.\n\nMethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure.\n\nFindingsVaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses).\n\nInterpretationDifferential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.08.22276154", @@ -1021,6 +979,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.04.21.22274152", + "date": "2022-04-27", + "link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274152", + "title": "Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.", + "authors": "Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University", + "abstract": "BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls.\n\nMethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis.\n\nResultsCompared to matched individuals testing negative, surviving positive community-tested patients had a higher risk of post-viral illness (HR: 4.57, 95%CI: 1.77-11.80, p=0.002), fatigue (HR: 1.47, 95%CI: 1.24-1.75, p<0.001) and embolism (HR: 1.51, 95%CI: 1.13-2.02, p=0.005) at 5-24 weeks post-diagnosis. In the four weeks after COVID-19 higher rates of sick notes were being issued for community-tested (HR: 3.04, 95%CI: 0.88 to 10.50, p<0.079); the risk was reduced after four weeks, compared to controls. Overall healthcare attendance for anxiety, depression was less likely in those with COVID-19 in the first four weeks (HR: 0.83, 95%CI: 0.73-1.06, p=0.007). After four weeks, anxiety, depression is less likely to occur for the positive community-tested individuals (HR: 0.87, 95%CI: 0.77-1.00, p=0.048), but more likely for positive hospital-tested individuals (HR: 1.16, 95%CI: 1.00-1.45, p=0.053). Although statistical associations between positive infection and post-infection healthcare use are clear, the absolute use of healthcare is very.\n\nConclusionsCommunity COVID-19 disease is associated with increased risks of post-viral illness, fatigue, embolism, depression, anxiety and respiratory conditions. Despite these elevated risks, the absolute healthcare burden is low. Either very small proportions of people experience adverse outcomes following COVID-19 or they are not presenting to healthcare.\n\nTrial registrationData held in SAIL databank are anonymised and therefore, no ethical approval is required. All data in SAIL has the permission from the relevant Caldicott Guardian or Data Protection Officer and SAIL-related projects are required to obtain Information Governance Review Panel (IGRP) approval. The IGRP approval number for this study is 1259.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.04.22.22274176", @@ -2029,20 +2001,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.23.21260992", - "date": "2021-07-25", - "link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260992", - "title": "A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges", - "authors": "Bernadette C Young; David W Eyre; Saroj Kendrick; Chris White; Sylvester Smith; George Beveridge; Toby Nonnenmacher; Fegor Ichofu; Joseph Hillier; Ian Diamond; Emma Rourke; Fiona Dawe; Ieuan Day; Lisa Davies; Paul Staite; Andrea Lacey; James McCrae; Ffion Jones; Joseph Kelly; Urszula Bankiewicz; Sarah Tunkel; Richard Ovens; David Chapman; Peter Marks; Nick Hicks; Tom Fowler; Susan Hopkins; Lucy Yardley; Tim EA Peto", - "affiliations": "University of Oxford; University of Oxford; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Department of Health and Social Care, UK Government; Deloitte MCS limited; Deloitte MCS limited; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Public Health England; University of Bristol; University of Oxford", - "abstract": "BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools.\n\nMethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation.\n\nCo-primary outcomes in all students and staff were symptomatic COVID-19, adjusted for community case rates, to estimate within-school transmission (non-inferiority margin: <50% relative increase), and COVID-19-related school absence. Analyses were performed on an intention to treat (ITT) basis using quasi-Poisson regression, also estimating complier average causal effects (CACE). Secondary outcomes included participation rates, PCR results in contacts and performance characteristics of LFDs vs. PCR.\n\nFindingsOf 99 control and 102 intervention schools, 76 and 86 actively participated (19-April-2021 to 27-June-2021); additional national data allowed most non-participating schools to be included in the co-primary outcomes. 2432/5763(42.4%) intervention arm contacts participated. There were 657 symptomatic PCR-confirmed infections during 7,782,537 days-at-risk (59.1/100k/week) and 740 during 8,379,749 days-at-risk (61.8/100k/week) in the control and intervention arms respectively (ITT adjusted incidence rate ratio, aIRR=0.96 [95%CI 0.75-1.22;p=0.72]) (CACE-aIRR=0.86 [0.55-1.34]). There were 55,718 COVID-related absences during 3,092,515 person-school-days (1.8%) and 48,609 during 3,305,403 person-school-days(1.5%) in the control and intervention arms (ITT-aIRR=0.80 [95%CI 0.53-1.21;p=0.29]) (CACE-aIRR 0.61 [0.30-1.23]). 14/886(1.6%) control contacts providing an asymptomatic PCR sample tested positive compared to 44/2981(1.5%) intervention contacts (adjusted odds ratio, aOR=0.73 [95%CI 0.33-1.61;p=0.44]). Rates of symptomatic infection in contacts were 44/4665(0.9%) and 79/5955(1.3%), respectively (aOR=1.21 [0.82-1.79;p=0.34]).\n\nInterpretationDaily contact testing of school-based contacts was non-inferior to self-isolation for control of COVID-19 transmission. COVID-19 rates in school-based contacts in both intervention and control groups were <2%. Daily contact testing is a safe alternative to home isolation following school-based exposures.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.22.21260416", @@ -2211,20 +2169,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.24.21259277", - "date": "2021-06-25", - "link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259277", - "title": "Risk factors for long COVID: analyses of 10 longitudinal studies and electronic health records in the UK", - "authors": "Ellen J. Thompson; Dylan M. Williams; Alex J. Walker; Ruth E. Mitchell; Claire L. Niedzwiedz; Tiffany C. Yang; Charlotte Huggins; Alex S. F. Kwong; Richard Silverwood; Giorgio Di Gessa; Ruth C. E. Bowyer; Kate Northstone; Bo Hou; Michael J. Green; Brian Dodgeon; Katie J. Doores; Emma Duncan; Frances M. K. Williams; - OpenSAFELY Collaborative; Andrew Steptoe; David J. Porteous; Rosemary R. C. McEachan; Laurie Tomlinson; Ben Goldacre; Praveetha Patalay; George B. Ploubidis; Srinivasa Vittal Katikireddi; Kate Tilling; Christopher T. Rentsch; Nicholas J. Timpson; Nishi Chaturvedi; Claire J. Steves", - "affiliations": "King's College London; University College London; University of Oxford; University of Bristol; University of Glasgow; Bradford Teaching Hospitals NHS Foundation Trust; University of Edinburgh; University of Bristol; University College London; University College London; King's College London; University of Bristol; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University College London; King's College London; King's College London; King's College London; ; University College London; University of Edinburgh; Bradford Teaching Hospitals NHS Foundation Trust; London School of Hygiene and Tropical Medicine; University of Oxford; University College London; University College London; University of Glasgow; University of Bristol; London School of Hygiene and Tropical Medicine; University of Bristol; University College London; King's College London", - "abstract": "BackgroundThe impact of long COVID is considerable, but risk factors are poorly characterised. We analysed symptom duration and risk factor from 10 longitudinal study (LS) samples and electronic healthcare records (EHR).\n\nMethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 participants in the UK LS, and 3,327 adults with COVID-19, were assigned a long COVID code from 1,199,812 individuals in primary care EHR. Outcomes for LS included symptom duration lasting 4+ weeks (long COVID) and 12+ weeks. Association with of age, sex, ethnicity, socioeconomic factors, smoking, general and mental health, overweight/obesity, diabetes, hypertension, hypercholesterolaemia, and asthma was assessed.\n\nResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%).\n\nConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2021.06.21.449178", @@ -2295,20 +2239,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.22.21257633", - "date": "2021-05-26", - "link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257633", - "title": "Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021", - "authors": "Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung", - "affiliations": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany", - "abstract": "The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.14.21257229", @@ -2519,20 +2449,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.04.08.21255099", - "date": "2021-04-14", - "link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255099", - "title": "Occupational risks of COVID-19 in NHS workers in England", - "authors": "Diana van der Plaat; Ira Madan; David Coggon; Martie van Tongeren; Rhiannon Edge; Rupert Muiry; Vaughan Parsons; Paul Cullinan", - "affiliations": "Imperial College London; Guy's and St Thomas' NHS Foundation Trust; Southampton General Hospital; University of Manchester; Lancaster University; Guy's and St Thomas NHS Foundation Trust; Guy's and St Thomas NHS Foundation Trust; Imperial College London", - "abstract": "ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England\n\nMethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression.\n\nResultsWith adjustment for employing trust, demographic characteristics, and previous frequency of sickness absence, risk relative to administrative/clerical occupations was highest in additional clinical services (including care assistants) (OR 2.31 [2.25-2.37]), registered nursing and midwifery professionals (OR 2.28 [2.23-2.34]) and allied health professionals (OR 1.94 [1.88-2.01]), and intermediate in doctors and dentists (OR 1.55 [1.50-1.61]). Differences in risk were higher after the employing trust had started to care for documented Covid-19 patients, and were reduced, but not eliminated, following additional adjustment for exposure to infected patients or materials, assessed by a job-exposure matrix. For prolonged Covid-19 sickness absence (episodes lasting >14 days), the variation in risk by staff group was somewhat greater.\n\nConclusionsAfter allowance for possible bias and confounding by non-occupational exposures, we estimated that relative risks for Covid-19 among most patient-facing occupations were between 1.5 and 2.5. The highest risks were in those working in additional clinical services, nursing and midwifery and in allied health professions. Better protective measures for these staff groups should be a priority. Covid-19 may meet criteria for compensation as an occupational disease in some healthcare occupations.\n\nKey messagesO_LIWhat is already known about this subject?\nHealthcare workers and other keyworkers (workers whose job was considered essential to societal functioning) had a higher likelihood of testing positive for COVID-19 than other workers during the first lockdown in England. Amongst healthcare workers, those working in inpatient settings had the highest rate of infection.\nC_LIO_LIWhat are the new findings?\nBetween March and July 2000, the overall risk of COVID-19 sickness absence in National Health Service staff in England was lower at older ages, higher in non-white staff, and (in comparison with administrative and clerical staff) more than doubled in registered nurses and among workers such as healthcare assistants providing support to health professionals. Risk in health care scientists was little different from that in administrative and clerical occupations\nC_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future?\nOur results suggest that the risk reduction strategies that were in place for healthcare scientists were effective. However, the protection for nursing and supporting health professionals was insufficient. In the event of a further wave of infections resulting in high hospital admissions, attention should be paid to ensuring that risk reduction strategies for nurses and supporting health professionals are improved.\nC_LI", - "category": "occupational and environmental health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.04.10.21254672", @@ -2603,6 +2519,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.24.21254227", + "date": "2021-03-26", + "link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254227", + "title": "COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death", + "authors": "Darryl P Leong; Amitava Banerjee; Salim Yusuf", + "affiliations": "McMaster University; University College London; McMaster University", + "abstract": "The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.26.21254390", @@ -2813,20 +2743,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.04.21251087", - "date": "2021-02-08", - "link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251087", - "title": "Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach", - "authors": "Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons", - "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", - "abstract": "BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing.\n\nMethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings.\n\nResultsThe total number of cases in a school was not associated with a subsequent increase in the risk of testing positive (Staff OR per case 0.92, 95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst pupils, the number of recent cases within the same year group was significantly associated with subsequent increased risk of testing positive (OR per case 1.12, 95%CI 1.08 - 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 - 9.88).\n\nConclusionsIn a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased risk, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment.\n\nO_TEXTBOXWhat is knownO_LIEvidence of the role schools play in the transmission of SARS-CoV-2 is limited\nC_LIO_LIHigher positivity rates are observed in school staff compared to pupils\nC_LIO_LILack of evidence on transmission pathways transmission into and within schools\nC_LI\n\nWhat this study addsO_LIFirst UK national level study of transmission between pupils and staff in a school environment during the SARS-CoV-2 pandemic.\nC_LIO_LISchools opening September-December 2020 was not associated with an increased subsequent risk of testing positive in staff\nC_LIO_LIPupils were found to be at increased risk of testing positive, following cases appearing within their own year group\nC_LI\n\nC_TEXTBOX", - "category": "health informatics", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.03.21251004", @@ -2841,20 +2757,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.02.21250989", - "date": "2021-02-03", - "link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250989", - "title": "Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020", - "authors": "Krishnan Bhaskaran; Rohini Mathur; Christopher T Rentsch; Caroline E Morton; William J Hulme; Anna Schultze; Brian McKenna; Rosalind M Eggo; Angel YS Wong; Elizabeth J Williamson; Harriet J Forbes; Kevin Wing; Helen I McDonald; Chris J Bates; Sebastian CJ Bacon; Alex J Walker; David Evans; Peter Inglesby; Amir Mehrkar; Helen J Curtis; Nichola J DeVito; Richard Croker; Henry Drysdale; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Laurie Tomlinson; Stephen JW Evans; Richard Grieve; Liam Smeeth; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP, TPP House, Horsforth, Leeds; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford", - "abstract": "Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent \"second wave\" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@987a5org.highwire.dtl.DTLVardef@1a8a141org.highwire.dtl.DTLVardef@1f2de56org.highwire.dtl.DTLVardef@1e2f9b8org.highwire.dtl.DTLVardef@78bfcc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONAssociation between ethnicity and COVID-19 death 1st Sept - 9th Nov 2020\n\nC_TABLECAPTION C_TBL", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.30.21250777", @@ -3247,6 +3149,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.30.20223123", + "date": "2020-11-03", + "link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223123", + "title": "High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", + "abstract": "BackgroundREACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive.\n\nMethodsREACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive.\n\nResultsOverall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%).\n\nConclusionThe co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.01.20222315", @@ -3387,20 +3303,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.10.09.20209957", - "date": "2020-10-13", - "link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209957", - "title": "Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19", - "authors": "Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi", - "affiliations": "University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT", - "abstract": "Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.10.08.20209304", @@ -3443,6 +3345,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.30.20204727", + "date": "2020-10-02", + "link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204727", + "title": "High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", + "abstract": "BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020.\n\nMethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model.\n\nResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants.\n\nConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.28.20202929", @@ -3585,13 +3501,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.09.04.20187781", - "date": "2020-09-09", - "link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187781", - "title": "Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study", - "authors": "Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality.\n\nMethodsWe pre-specified and conducted an observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, representing 40% of the general population in England. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use prior to the COVID-19 outbreak in England and risk of COVID-19 mortality among people with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Model adjustment was informed by a directed acyclic graph.\n\nResultsOf 194,637 patients with RA or SLE, 30,569 (15.7%) received [≥] 2 prescriptions of hydroxychloroquine in the six months prior to 1 March 2020. Between 1 March 2020 and 13 July 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0.23% (95% CI 0.18-0.29) among users and 0.22% (95% CI 0.20-0.25) among non-users; an absolute difference of 0.008% (95% CI -0.051-0.066). After accounting for age, sex, ethnicity, use of other immunuosuppressives, and geographic region, no association with COVID-19 mortality was observed (HR 1.03, 95% CI 0.80-1.33). We found no evidence of interactions with age or other immunosuppressives. Quantitative bias analyses indicated observed associations were robust to missing information regarding additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality.\n\nConclusionWe found no evidence of a difference in COVID-19 mortality among patients who received hydroxychloroquine for treatment of rheumatological disease prior to the COVID-19 outbreak in England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials and observational studies to date have shown no evidence of benefit of hydroxychloroquine as a treatment for hospitalised patients who already have COVID-19. A separate question remains: whether routine ongoing use of hydroxychloroquine in people without COVID-19 protects against new infections or severe outcomes. We searched MEDLINE/PubMed for pharmacoepidemiological studies evaluating hydroxychloroquine for prevention of severe COVID-19 outcomes. The keywords \"hydroxychloroquine AND (COVID OR coronavirus OR SARS-CoV-2) AND (prophyl* OR prevent*) AND (rate OR hazard OR odds OR risk)\" were used and results were filtered to articles from the last year with abstracts available. 109 papers were identified for screening; none investigated pre-exposure prophylactic use of hydroxychloroquine for prevention of severe COVID-19 outcomes. Clinical trials of prophylactic use of hydroxychloroquine are ongoing; however, the largest trial does not expect to meet recruitment targets due to \"...unjustified extrapolation and exaggerated safety concerns together with intense politicisation and negative publicity.\" In the absence of reported clinical trials, evidence can be generated from real-world data to support the need for randomised clinical trials.\n\nAdded value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data.\n\nImplications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.", + "doi": "10.1101/2020.09.11.20192492", + "date": "2020-09-11", + "link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192492", + "title": "Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.", "category": "infectious diseases", "match_type": "exact", "author_similarity": 100, @@ -3667,20 +3583,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.08.21.20177246", - "date": "2020-08-24", - "link": "https://medrxiv.org/cgi/content/short/2020.08.21.20177246", - "title": "Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility", - "authors": "Irene V van Blokland; Pauline Lanting; Anil PS Ori; Judith M Vonk; Robert CA Warmerdam; Johanna C Herkert; Floranne Boulogne; Annique Claringbould; Esteban A Lopera-Maya; Meike Bartels; Jouke-Jan Hottenga; Andrea Ganna; Juha Karjalainen; - Lifelines COVID-19 cohort study; - The COVID-19 Host Genetics Initiative; Caroline Hayward; Chloe Fawns-Ritchie; Archie Campbell; David Porteous; Elizabeth T Cirulli; Kelly M Schiabor Barrett; Stephen Riffle; Alexandre Bolze; Simon White; Francisco Tanudjaja; Xueqing Wang; Jimmy M Ramirez III; Yan Wei Lim; James T Lu; Nicole L Washington; Eco JC de Geus; Patrick Deelen; H Marike Boezen; Lude H Franke", - "affiliations": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Structural Computational Biology unit, EMB; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA and Analytic and Tra; ; ; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Department of Genetics, University Medical; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands", - "abstract": "Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19, and this GWAS benefits from the larger sample size to provide new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, we recommend repeatedly collecting data of disease-related symptoms.", - "category": "genetic and genomic medicine", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.08.19.20178137", @@ -3793,6 +3695,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.08.05.20169078", + "date": "2020-08-06", + "link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169078", + "title": "Transient dynamics of SARS-CoV-2 as England exited national lockdown", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health", + "abstract": "Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.03.20164897", @@ -3905,6 +3821,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.15.20152967", + "date": "2020-07-17", + "link": "https://medrxiv.org/cgi/content/short/2020.07.15.20152967", + "title": "Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.", + "authors": "Gisli Jenkins; Tom Drake; Annemarie B Docherty; Ewan Harrison; Jennifer Quint; Huzaifa Adamali; Sarah Agnew; Suresh Babu; Christopher Barber; Shaney Barratt; Elisabeth Bendstrup; Stephen Bianchi; Diego Castillo; Nazia Chaudhuri; Felix Chua; Robina Coker; William Chang; Anjali Cranshaw; Louise Crowley; Davinder Dosanjh; Christine Fiddler; Ian A Forrest; Peter George; Michael Gibbons; Katherine Groom; Sarah Haney; Simon Hart; Emily Heiden; Michael Henry; Ling-Pei Ho; Rachel Hoyles; John Hutchinson; Killian Hurley; Mark Jones; Steve Jones; Maria Kokosi; Michael Kreuter; Laura Mackay; Siva Mahendran; Georgios Margaritopoulos; Maria Molina-Molina; Philip Molyneaux; Aidan D O'Brien; Katherine O'Reilly; Alice Packham; Helen Parfrey; Venerino Poletti; Joanna Porter; Elisabetta Renzoni; Pilar Rivera-Ortega; Anne-Marie Russell; Gauri Saini; Lisa G Spencer; Giulia Stella; Helen Stone; Sharon Sturney; David Thickett; Muhunthan Thillai; Timothy Wallis; Katie Ward; Athol U Wells; Alex West; Melissa Wickremasinghe; Felix Woodhead; Glenn Herson; Lucy Howard; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Iain Stewart", + "affiliations": "University of Nottingham; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX; University of Edinburgh; University of Edinburgh; Imperial College London; Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB.; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Queen Alexandra Hospital, Portsmouth, UK.; Northern General Hospital, Sheffield, S5 7AU, UK; Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB.; Centre for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99,8200 Aarhus N, Denmar; Northern General Hospital, Sheffield, S5 7AU, UK.; ILD Unit, Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Royal Brompton Hospital; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Nottingham University Hospital; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK.; Royal Brompton Hospital; South West Peninsula ILD Network, Royal Devon & Exeter Foundation NHS Trust Barrack Road, Exeter EX2 5DW, UK; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, UK, HU16 5JQ; University Hospitals Southampton NHS Foundation Trust, Southampton, UK; Cork University Hospital, Cork, Ireland; University of Oxford; Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK; University of Nottingham; Beaumont Hospital, Dublin, Ireland.; NIHR Southampton Biomedical Research Centre & Clinical and Experimental Sciences, University of Southampton, Southampton, UK; Action for Pulmonary Fibrosis; Guys and St Thomas' Hospital; Center for interstitial and rare lung diseases, Pneumology, Thoraxklinik, University of Heidelberg, Germany and German Center for Lung Research, 69126 Heidelber; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Kingston Hospital NHS Foundation Trust. Galsworthy Road, Kingston upon Thames, Surrey KT2 7QB, UK.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; ILD Unit, Respiratory Department, University Hospital of Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.; Imperial College London; University Hospital Limerick, Dooradoyle, Limerick, Ireland.; Department of Respiratory Medicine, Mater Misericordiae University Hospital, Dublin, Ireland.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Diseases of the Thorax, Morgagni Hospital, Forli, Italy.; University College London; Royal Brompton Hospital; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Imperial College London; Nottingham University Hospitals; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Laboratory of Biochemistry and Genetics, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.; University Hospital North Midlands NHS Trust, Royal Stoke University Hospital, Newcastle Road, Stoke-on-Trent, ST4 6QG, UK.; Royal United Hospitals Bath NHS Foundation Trust, Combe Park, Bath BA1 3NG, UK; University of Birmingham, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; University of Southampton; Imperial College London; Royal Brompton Hospital; Guys and St Thomas' Hospital; Imperial Healthcare NHS Trust, St Mary's Hospital, The Bays, S Wharf Rd, Paddington, London W2 1NY, UK.; Glenfield Hospital Leicester; Nottingham University Hospitals Trust; Nottingham University Hospitals Trust; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; University of Nottingham", + "abstract": "RationaleThe impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established.\n\nObjectivesTo assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population.\n\nMethodsAn international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death.\n\nMeasurements and Main ResultsData from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC [≥]80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13-3.46).\n\nConclusionsPatients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.", + "category": "respiratory medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.14.20153734", @@ -3919,20 +3849,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.14.20152629", - "date": "2020-07-15", - "link": "https://medrxiv.org/cgi/content/short/2020.07.14.20152629", - "title": "Covid-19 infection and attributable mortality in UK Long Term Care Facilities: Cohort study using active surveillance and electronic records (March-June 2020)", - "authors": "Peter F Dutey-Magni; Haydn Williams; Arnoupe Jhass; Greta Rait; Harry Hemingway; Andrew C Hayward; Laura Shallcross", - "affiliations": "University College London; Four Seasons Healthcare Group; UCL; University College London; University College London; University College London; UCL", - "abstract": "BackgroundEpidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic.\n\nMethodsCohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality.\n\nResults2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection.\n\n217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]).\n\nConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.13.20152710", @@ -4059,6 +3975,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.28.20141986", + "date": "2020-06-29", + "link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141986", + "title": "Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population", + "authors": "Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon", + "affiliations": "University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton", + "abstract": "IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases.\n\nMethods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available.\n\nEthics and disseminationThe project has ethical approval and the results will be submitted for publication in a peer-reviewed journal.\n\nStrengths and limitations of the studyO_LIThe individual-level linkage of general practice, Public Health England testing, Hospital Episode Statistics and Office of National Statistics death register datasets enable a robust and accurate ascertainment of outcomes\nC_LIO_LIThe models will be trained and evaluated in population-representative datasets of millions of individuals\nC_LIO_LIShielding for clinically extremely vulnerable was advised and in place during the study period, therefore risk predictions influenced by the presence of some shielding conditions may require careful consideration\nC_LI", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.24.20139048", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 93cfa8bb..b7e77daa 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -1,4 +1,18 @@ [ + { + "site": "bioRxiv", + "doi": "10.1101/2023.10.22.563481", + "date": "2023-10-24", + "link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", + "title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", + "authors": "Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis", + "affiliations": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D", + "abstract": "Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.10.12.23296948", @@ -475,20 +489,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -601,6 +601,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.02.17.23286079", + "date": "2023-02-23", + "link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286079", + "title": "Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.", + "authors": "Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson", + "affiliations": "UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency", + "abstract": "AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures.\n\nMethods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded.\n\nConclusionsFew workplace surface samples were positive for SARS-CoV-2 RNA and positive samples typically contained low levels of nucleic acid. Although these data may infer a low probability of fomite transmission or other forms of transmission within the workplace, Ct values may have been lower at the time of contamination. Workplace environmental sampling identified lapses in COVID-control measures within individual sites and showed trends through the pandemic.\n\nSignificance and Impact of the StudyPrior to this study, few published reports investigated SARS-CoV-2 RNA contamination within workplaces experiencing cases of COVID-19. This report provides extensive data on environmental sampling identifying trends across workplaces and through the pandemic.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.02.18.23286127", @@ -819,7 +833,7 @@ "title": "Analysis of uptake, effectiveness and safety of COVID-19 vaccinations in pregnancy using the QResearch database: research protocol and statistical analysis plan", "authors": "Emma Copland; Jennifer A Hirst; Tom Ranger; Winnie Xue Mei; Sharon Dixon; Carol Coupland; Kenneth Hodson; Jonathan Luke Richardson; Anthony Harnden; Aziz Sheikh; Carol Dezateux; Brenda Kelly; Marian Knight; Jonathan Van Tam; Alessandra Morelli; Joanne Enstone; Julia Hippisley-Cox", "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Newcastle upon Tyne Hospitals NHS Foundation Trust; Newcastle upon Tyne Hospitals NHS Foundation Trust; University of Oxford; The University of Edinburgh College of Medicine and Veterinary Medicine; Queen Mary University of London; University of Oxford; University of Oxford; University of Nottingham; University of Oxford; Leicester City Clinical Commissioning Group; University of Oxford", - "abstract": "Background The COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. Objectives A. To determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. B. To estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. C. To assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. Methods This population-based study uses the QResearch database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of severe COVID-19 outcomes after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and dissemination QResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", + "abstract": "BackgroundThe COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England.\n\nObjectivesO_LITo determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations.\nC_LIO_LITo estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination.\nC_LIO_LITo assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations.\nC_LI\n\nMethodsThis population-based study uses the QResearch(R) database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible.\n\nWe will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals.\n\nEthics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, @@ -839,6 +853,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.12.12.22283200", + "date": "2022-12-14", + "link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283200", + "title": "COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK", + "authors": "Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Mike Seaborne; Michael Parker; Natasha Kennedy; Ashley Akbari; Luisa Zuccolo; Amaya Azcoaga-Lorenzo; Alisha Davies; Krishnarajah Nirantharakumar; Sinead Brophy", + "affiliations": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, UK; Health Data Science Centre, Fondazione Human Technopole, Milan, Italy; School of Medicine, University of St Andrews, Scotland, UK and Hospital Rey Juan Carlos. Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz. Madrid. Sp; Research and Evaluation Division, Public Health Wales, UK.; Institute of Applied Health Research, Birmingham University, Birmingham, UK.; National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U", + "abstract": "BackgroundMultimorbidity and pregnancy are two risk factors for more severe outcomes after a SARS-CoV-2 infection, thus vaccination uptake is important for pregnant women living with multimorbidity. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage.\n\nMethodsThis cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy by multimorbidity and smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. Variation in uptake by; multimorbidity, smoking status, and demographics was examined jointly and separately for the independent conditions using hazard ratios (HR) from the Cox regression model. A bootstrapping internal validation was conducted to assess the performance of the models.\n\nResultsWithin the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.02). Women living with multimorbidity (> 1 health condition) were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002). The validated model had similar performance and revealed that multimorbidity, smoking status, age, and deprivation level together have a significant impact on vaccine hesitancy (p < 0.05 for all).\n\nConclusionYounger women, living without multimorbidity (zero or only one health condition), current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Women living with multimorbidity are slightly but significantly less likely to be hesitant about COVID-19 vaccination when pregnant.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.12.14.22283458", @@ -1287,20 +1315,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.08.08.22278532", - "date": "2022-08-09", - "link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278532", - "title": "Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI)", - "authors": "Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London", - "abstract": "BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England.\n\nMethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence.\n\nResults14175 residents and 19973 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-83 days after first booster, but no protection was apparent after 84 days. Additional protection following booster vaccination waned, but was still present at 84+ days for COVID-associated hospitalisation (aHR: 0.47, 0.24-0.89) and death (aHR: 0.37, 0.21-0.62). Most residents (64.4%) had received primary course of AstraZeneca, but this did not impact on pre- or post-booster risks. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalisations and no deaths.\n\nConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.\n\nSummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.08.07.22278510", @@ -1441,6 +1455,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.07.07.22277367", + "date": "2022-07-10", + "link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277367", + "title": "Non-hospitalised, vaccinated adults with COVID-19 caused by Omicron BA.1 and BA.2 present with changing symptom profiles compared to those with Delta despite similar viral kinetics", + "authors": "Hermaleigh Townsley; Joshua Gahir; Timothy W Russell; Edward J Carr; Matala Dyke; Murad Miah; Bobbi Clayton; Callie Smith; Mauro Miranda; Nicola O'Reilly; Lorin Adams; Harriet V Mears; Christopher Bailey; James RM Black; Ashley S Fowler; Katalin Wilkinson; Matthew Hutchinson; Ruth Harvey; Bobbi Clayton; Gavin Kelly; Rupert Beale; Padmasayee Papineni; Tumena Corrah; Simon Caidan; Jerome Nicod; Steve Gamblin; George Kassiotis; Vincenzo Libri; Bryan Williams; Sonia Gandhi; Adam J Kucharski; Charles Swanton; David LV Bauer; Emma C Wall", + "affiliations": "Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute; Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); London Northwest University Healthcare NHS Trust, London; London Northwest University Healthcare NHS Trust, London; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute, Department of Infectious Disease, St Mary's Hospital, Imperial College London, London; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo; Francis Crick Institute, University College London, Gower Street, London; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Francis Crick Institute, University College London, Gower Street, London; Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK); Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini", + "abstract": "BackgroundSARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC).\n\nMethodsIn a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive PCR or lateral flow test, self-swabbed on alternate days until day 10. We compared symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 and BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR Ct value as a proxy for viral load.\n\nResults555 infection episodes were reported among 483 participants. Across VOCs, symptom burden and duration were similar, however symptom profiles differed among infections caused by Delta compared to Omicron sub-variants; symptoms of all Omicron sub-variants BA.1, BA.2 and BA.4/5 were very similar. Anosmia was reported in 7-13% of participants with Omicron sub-variants, compared to 25/60 (42%) with Delta infection (P= 1.31e-08 or 1.03e-05 or 5.63e-05; {chi}2 test d2+Delta vs. Omicron BA.1 or vs. BA.2, or BA.5, respectively), fever was more common with Omicron BA.5 (30/55, 55%) than Delta (20/60, 33%) (p 0.03). Amongst infections with all Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. Ct values were negatively associated with time since vaccination in participants infected with BA.1; however, this trend was not observed in BA.2/BA.4/5 infections.\n\nConclusionOur study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults.\n\nTrial registrationNCT04750356", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.06.15.22276446", @@ -1455,20 +1483,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22276205", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276205", - "title": "Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK)", - "authors": "Hayley Holt; Clare Relton; Mohammad Talaei; Jane Symons; Molly R Davies; David A Jolliffe; Giulia Vivaldi; Florence Tydeman; Anne Williamson; Paul E Pfeffer; Christopher Orton; David Ford; Gwyneth A Davies; Ronan A Lyons; Chris J Griffiths; Frank Kee; Aziz Sheikh; Gerome Breen; Seif Shaheen; Adrian R Martineau", - "affiliations": "Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; King's College London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Blizard Institute; Barts Health NHS Trust; Swansea University; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; University of Edinburgh; King's College London; Queen Mary University of London; Queen Mary University of London", - "abstract": "BackgroundCoronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is estimated to have caused more than 18 million deaths worldwide as of end-May 2022.\n\nMethodsCOVIDENCE UK is a longitudinal population-based study that investigates risk factors for, and impacts of, COVID-19 in UK residents aged [≥]16 years. A unique feature is the capacity to support trial-within-cohort studies to evaluate interventions for prevention of COVID-19 and other acute respiratory illnesses. Participants complete a detailed online baseline questionnaire capturing self-reported information relating to their socio-demographic characteristics, occupation, lifestyle, quality of life, weight, height, longstanding medical conditions, medication use, vaccination status, diet and supplemental micronutrient intake. Follow-up on-line questionnaires capturing incident symptoms of COVID-19 and other acute respiratory infections, incident swab test-confirmed COVID-19, doses of SARS-CoV-2 vaccine received, and quality of life are completed at monthly intervals.\n\nResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19.\n\nConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.20.22275994", @@ -1623,20 +1637,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.12.22276307", - "date": "2022-06-13", - "link": "https://medrxiv.org/cgi/content/short/2022.06.12.22276307", - "title": "Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study", - "authors": "Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London", - "abstract": "BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status.\n\nMethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure.\n\nFindingsVaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses).\n\nInterpretationDifferential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.08.22276154", @@ -1917,6 +1917,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.04.21.22274152", + "date": "2022-04-27", + "link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274152", + "title": "Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.", + "authors": "Jonathan Kennedy; Michael Parker; Michael Seaborne; Mohamed Mhereeg; Alex J Walker; Venexia Walker; Spiros Denaxas; Natasha Kennedy; Srinivasa Vittal Katikireddi; Sinead Brophy", + "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG.; University of Bristol; University College London; Swansea University; University of Glasgow; Swansea University", + "abstract": "BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls.\n\nMethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis.\n\nResultsCompared to matched individuals testing negative, surviving positive community-tested patients had a higher risk of post-viral illness (HR: 4.57, 95%CI: 1.77-11.80, p=0.002), fatigue (HR: 1.47, 95%CI: 1.24-1.75, p<0.001) and embolism (HR: 1.51, 95%CI: 1.13-2.02, p=0.005) at 5-24 weeks post-diagnosis. In the four weeks after COVID-19 higher rates of sick notes were being issued for community-tested (HR: 3.04, 95%CI: 0.88 to 10.50, p<0.079); the risk was reduced after four weeks, compared to controls. Overall healthcare attendance for anxiety, depression was less likely in those with COVID-19 in the first four weeks (HR: 0.83, 95%CI: 0.73-1.06, p=0.007). After four weeks, anxiety, depression is less likely to occur for the positive community-tested individuals (HR: 0.87, 95%CI: 0.77-1.00, p=0.048), but more likely for positive hospital-tested individuals (HR: 1.16, 95%CI: 1.00-1.45, p=0.053). Although statistical associations between positive infection and post-infection healthcare use are clear, the absolute use of healthcare is very.\n\nConclusionsCommunity COVID-19 disease is associated with increased risks of post-viral illness, fatigue, embolism, depression, anxiety and respiratory conditions. Despite these elevated risks, the absolute healthcare burden is low. Either very small proportions of people experience adverse outcomes following COVID-19 or they are not presenting to healthcare.\n\nTrial registrationData held in SAIL databank are anonymised and therefore, no ethical approval is required. All data in SAIL has the permission from the relevant Caldicott Guardian or Data Protection Officer and SAIL-related projects are required to obtain Information Governance Review Panel (IGRP) approval. The IGRP approval number for this study is 1259.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.04.21.22274150", @@ -2967,6 +2981,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.13.21267723", + "date": "2021-12-14", + "link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267723", + "title": "Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom", + "authors": "Emma Rezel-Potts; Abdel Douiri; Xiaohui Sun; Phillip J Chowienczyk; Ajay M Shah; Martin C Gulliford", + "affiliations": "King's College London; King's College London; King's College London; King's College London; King's College London; King's College London", + "abstract": "ObjectiveThis study aimed to estimate the incidence of new diabetes mellitus (DM) and cardiovascular diseases (CVD) up to one year after Covid-19 compared with matched controls.\n\nMethodsA cohort study was conducted using electronic records for 1,473 family practices with a population of 14.9 million. Covid-19 patients without DM or CVD were individually matched with controls and followed up to October 2021. A difference-in-difference analysis estimated the net effect of Covid-19 allowing for baseline differences and covariates.\n\nResultsThere were 372,816 Covid-19 patients, with 2,935 CVD and 3,139 DM events, and 372,816 matched controls with 1,193 CVD and 1,861 DM events following the index date. Net incidence of DM increased in acute Covid-19 up to four weeks from index date (adjusted rate ratio, RR 1.71, 1.40 to 2.10) and remained elevated in post-acute (five to 12 weeks from index date; RR 1.17, 1.01 to 1.36) and long-Covid-19 (13 to 52 weeks, 1.20, 1.09 to 1.31). Acute Covid-19 was associated with net increased CVD incidence (RR 6.02, 95% confidence interval 4.84 to 7.47) including pulmonary embolism (RR 14.5, 7.72 to 27.4), atrial arrythmias (6.58, 3.78 to 11.4) and venous thromboses (5.44, 3.22 to 9.17). CVD incidence declined in post-acute Covid-19 (1.68, 1.41 to 2.01) and showed no net increase in long Covid-19 (0.95, 0.85 to 1.06).\n\nConclusionsDM incidence remains elevated up to one year following Covid-19. CVD is increased early after Covid-19 mainly from pulmonary embolism, atrial arrhythmias and venous thromboses.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.09.21267516", @@ -3149,6 +3177,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.11.19.21266529", + "date": "2021-11-19", + "link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266529", + "title": "Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England", + "authors": "Aleksandra J Borek; Katherine Maitland; Monsey Mcleod; Anne Campbell; Benedict Hayhoe; Christopher C Butler; Liz Morrell; Laurence Roope; Alison Holmes; Ann Sarah Walker; Sarah Tonkin-Crine; - the STEP-UP study team", + "affiliations": "University of Oxford; University of Oxford; Imperial College London; Imperia College London; Imperial College London; University of Oxford; University of Oxford; University of Oxford; Imperial College London; University of Oxford; University of Oxford; ", + "abstract": "The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners (GPs) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.", + "category": "primary care research", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.15.21266264", @@ -3541,20 +3583,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.09.28.21264240", - "date": "2021-09-29", - "link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264240", - "title": "Predicting hospital-onset COVID-19 infections using dynamic networks of patient contacts: an observational study", - "authors": "Ashlegh C Myall; James Richard Price; Robert L Peach; Mohamed Abbas; Siddharth Mookerjee; Nina Zhu; Isa Ahmad; Damien Keng Yen Ming; Farzan Ramzan; Daniel Teixeira; Christophe Graf; Andrea Y Wiesse; Stephan Harbarth; Alison Holmes; Mauricio Barahona", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; Imperial College London NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University Hospital of Geneva; University Hospital of Geneva; The University of Edinburgh; University Hospital of Geneva; Imperial College London; Imperial College London", - "abstract": "BackgroundReal-time prediction is key to prevention and control of healthcare-associated infections. Contacts between individuals drive infections, yet most prediction frameworks fail to capture the dynamics of contact. We develop a real-time machine learning framework that incorporates dynamic patient contact networks to predict patient-level hospital-onset COVID-19 infections (HOCIs), which we test and validate on international multi-site datasets spanning epidemic and endemic periods.\n\nMethodsOur framework extracts dynamic contact networks from routinely collected hospital data and combines them with patient clinical attributes and background contextual hospital data to forecast the infection status of individual patients. We train and test the HOCI prediction framework using 51,157 hospital patients admitted to a UK (London) National Health Service (NHS) Trust from 01 April 2020 to 01 April 2021, spanning UK COVID-19 surges 1 and 2. We then validate the framework by applying it to data from a non-UK (Geneva) hospital site during an epidemic surge (40,057 total inpatients) and to data from the same London Trust from a subsequent period post surge 2, when COVID-19 had become endemic (43,375 total inpatients).\n\nFindingsBased on the training data (London data spanning surges 1 and 2), the framework achieved high predictive performance using all variables (AUC-ROC 0{middle dot}89 [0{middle dot}88-0{middle dot}90]) but was almost as predictive using only contact network variables (AUC-ROC 0{middle dot}88 [0{middle dot}86-0{middle dot}90]), and more so than using only hospital contextual (AUC-ROC 0{middle dot}82 [0{middle dot}80-0{middle dot}84]) or patient clinical (AUC-ROC 0{middle dot}64 [0{middle dot}62-0{middle dot}66]) variables. The top three risk factors we identified consisted of one hospital contextual variable (background hospital COVID-19 prevalence) and two contact network variables (network closeness, and number of direct contacts to infectious patients), and together achieved AUC-ROC 0{middle dot}85 [0{middle dot}82-0{middle dot}88]. Furthermore, the addition of contact network variables improved performance relative to hospital contextual variables on both the non-UK (AUC-ROC increased from 0{middle dot}84 [0{middle dot}82-0{middle dot}86] to 0{middle dot}88 [0{middle dot}86-0{middle dot}90]) and the UK validation datasets (AUC-ROC increased from 0{middle dot}52 [0{middle dot}49-0{middle dot}53] to 0{middle dot}68 [0{middle dot}64-0{middle dot}70]).\n\nInterpretationOur results suggest that dynamic patient contact networks can be a robust predictor of respiratory viral infections spreading in hospitals. Their integration in clinical care has the potential to enhance individualised infection prevention and early diagnosis.\n\nFundingMedical Research Foundation, World Health Organisation, Engineering and Physical Sciences Research Council, National Institute for Health Research, Swiss National Science Foundation, German Research Foundation.", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.09.27.21264166", @@ -3961,6 +3989,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.07.27.21261031", + "date": "2021-07-29", + "link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261031", + "title": "Prognostic accuracy of triage tools for adults with suspected COVID-19 in a pre-hospital setting: an observational cohort study", + "authors": "Carl Marincowitz; Laura Sutton; Tony Stone; Richard Pilbery; Richard Campbell; Ben Thomas; Janette Turner; Peter Bath; Fiona Bell; Katie Biggs; Madina Hasan; Frank Hopfgartner; Suvodeep Mazumdar; Jennifer Petrie; Steve Goodacre", + "affiliations": "(CURE), Health Services Research School of Health and Related Research, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Yorkshire Ambulance Service NHS Trust; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield; Information School, University of Sheffield; Yorkshire Ambulance Service NHS Trust; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; Information School, University of Sheffield; Information School, University of Sheffield; Information School, University of Sheffield; Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield; CURE, Health Services Research School of Health and Related Research, University of Sheffield", + "abstract": "Study ObjectiveTools proposed to triage patient acuity in COVID-19 infection have only been validated in hospital populations. We estimated the accuracy of five risk-stratification tools recommended to predict severe illness and compare accuracy to existing clinical decision-making in a pre-hospital setting.\n\nMethodsAn observational cohort study using linked ambulance service data for patients attended by EMS crews in the Yorkshire and Humber region of England between 18th March 2020 and 29th June 2020 was conducted to assess performance of the PRIEST tool, NEWS2, the WHO algorithm, CRB-65 and PMEWS in patients with suspected COVID-19 infection. The primary outcome was death or need for organ support.\n\nResultsOf 7549 patients in our cohort, 17.6% (95% CI:16.8% to 18.5%) experienced the primary outcome. The NEWS2, PMEWS, PRIEST tool and WHO algorithm identified patients at risk of adverse outcomes with a high sensitivity (>0.95) and specificity ranging from 0.3 (NEWS2) to 0.41 (PRIEST tool). The high sensitivity of NEWS2 and PMEWS was achieved by using lower thresholds than previously recommended. On index assessment, 65% of patients were transported to hospital and EMS decision to transfer patients achieved a sensitivity of 0.84 (95% CI 0.83 to 0.85) and specificity of 0.39 (95% CI 0.39 to 0.40).\n\nConclusionUse of NEWS2, PMEWS, PRIEST tool and WHO algorithm could improve sensitivity of EMS triage of patients with suspected COVID-19 infection. Use of the PRIEST tool would improve sensitivity of triage without increasing the number of patients conveyed to hospital.", + "category": "emergency medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.26.21261140", @@ -3975,20 +4017,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.23.21260992", - "date": "2021-07-25", - "link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260992", - "title": "A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges", - "authors": "Bernadette C Young; David W Eyre; Saroj Kendrick; Chris White; Sylvester Smith; George Beveridge; Toby Nonnenmacher; Fegor Ichofu; Joseph Hillier; Ian Diamond; Emma Rourke; Fiona Dawe; Ieuan Day; Lisa Davies; Paul Staite; Andrea Lacey; James McCrae; Ffion Jones; Joseph Kelly; Urszula Bankiewicz; Sarah Tunkel; Richard Ovens; David Chapman; Peter Marks; Nick Hicks; Tom Fowler; Susan Hopkins; Lucy Yardley; Tim EA Peto", - "affiliations": "University of Oxford; University of Oxford; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Department of Health and Social Care, UK Government; Deloitte MCS limited; Deloitte MCS limited; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Department of Health and Social Care, UK Government; Public Health England; University of Bristol; University of Oxford", - "abstract": "BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools.\n\nMethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation.\n\nCo-primary outcomes in all students and staff were symptomatic COVID-19, adjusted for community case rates, to estimate within-school transmission (non-inferiority margin: <50% relative increase), and COVID-19-related school absence. Analyses were performed on an intention to treat (ITT) basis using quasi-Poisson regression, also estimating complier average causal effects (CACE). Secondary outcomes included participation rates, PCR results in contacts and performance characteristics of LFDs vs. PCR.\n\nFindingsOf 99 control and 102 intervention schools, 76 and 86 actively participated (19-April-2021 to 27-June-2021); additional national data allowed most non-participating schools to be included in the co-primary outcomes. 2432/5763(42.4%) intervention arm contacts participated. There were 657 symptomatic PCR-confirmed infections during 7,782,537 days-at-risk (59.1/100k/week) and 740 during 8,379,749 days-at-risk (61.8/100k/week) in the control and intervention arms respectively (ITT adjusted incidence rate ratio, aIRR=0.96 [95%CI 0.75-1.22;p=0.72]) (CACE-aIRR=0.86 [0.55-1.34]). There were 55,718 COVID-related absences during 3,092,515 person-school-days (1.8%) and 48,609 during 3,305,403 person-school-days(1.5%) in the control and intervention arms (ITT-aIRR=0.80 [95%CI 0.53-1.21;p=0.29]) (CACE-aIRR 0.61 [0.30-1.23]). 14/886(1.6%) control contacts providing an asymptomatic PCR sample tested positive compared to 44/2981(1.5%) intervention contacts (adjusted odds ratio, aOR=0.73 [95%CI 0.33-1.61;p=0.44]). Rates of symptomatic infection in contacts were 44/4665(0.9%) and 79/5955(1.3%), respectively (aOR=1.21 [0.82-1.79;p=0.34]).\n\nInterpretationDaily contact testing of school-based contacts was non-inferior to self-isolation for control of COVID-19 transmission. COVID-19 rates in school-based contacts in both intervention and control groups were <2%. Daily contact testing is a safe alternative to home isolation following school-based exposures.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.22.21260416", @@ -4297,20 +4325,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.23.21259400", - "date": "2021-06-30", - "link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259400", - "title": "Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record", - "authors": "Sarah Steeg; Lana Bojani\u0107; George Tilston; Richard Williams; David A Jenkins; Matthew J Carr; Niels Peek; Darren M Ashcroft; Nav Kapur; Jennifer Voorhees; Roger T Webb", - "affiliations": "University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester", - "abstract": "BackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021.\n\nMethodsWe conducted a descriptive time series analysis utilising data from the Greater Manchester Care Record, which contains de-identified, primary care health records of 2.8 million patients. Counts of incident and all episodes of self-harm recorded between 1st January 2019 and 31st May 2021 were made for all patients, with stratification by sex, age group, ethnicity, and index of multiple deprivation (IMD) quintile and examination of overall differences by national and regional restriction phases.\n\nFindingsBetween 1st January 2019 and 31st May 2021, 33,444 episodes of self-harm by 13,148 individuals were recorded. Frequency ratios of incident and all episodes of self-harm were 0.59 (95% CI 0.51 to 0.69) and 0.69 (CI 0.63 to 0.75) respectively in April 2020 compared to February 2020. Between August 2020 and May 2021 frequency ratios were 0.92 (CI 0.88 to 0.96) for incident episodes and 0.86 (CI 0.84 to 0.88) for all episodes compared to the same months in 2019. Reductions were largest among men and people living in the most deprived neighbourhoods. An increase in all-episode self-harm (frequency ratio 1.09, CI 1.03 to 1.16) was observed for adolescents aged 10-17 between August 2020 and May 2021.\n\nInterpretationThe COVID-19 pandemic has had a sustained impact on help seeking for self-harm. Reductions in primary care recorded self-harm have implications for clinicians ability to assess the needs and risks of individuals. Some patients may be experiencing prolonged untreated deterioration in their mental health while other groups are presenting in higher numbers. Our findings have important implications for primary care and mental health services in manging ongoing demand.\n\nFundingUKRI COVID-19 Rapid Response Initiative (grant reference COV0499), University of Manchester Presidential Fellowship (SS), and NIHR Greater Manchester Patient Safety Translational Research Centre.", - "category": "primary care research", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.21.21259145", @@ -4395,20 +4409,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.24.21259277", - "date": "2021-06-25", - "link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259277", - "title": "Risk factors for long COVID: analyses of 10 longitudinal studies and electronic health records in the UK", - "authors": "Ellen J. Thompson; Dylan M. Williams; Alex J. Walker; Ruth E. Mitchell; Claire L. Niedzwiedz; Tiffany C. Yang; Charlotte Huggins; Alex S. F. Kwong; Richard Silverwood; Giorgio Di Gessa; Ruth C. E. Bowyer; Kate Northstone; Bo Hou; Michael J. Green; Brian Dodgeon; Katie J. Doores; Emma Duncan; Frances M. K. Williams; - OpenSAFELY Collaborative; Andrew Steptoe; David J. Porteous; Rosemary R. C. McEachan; Laurie Tomlinson; Ben Goldacre; Praveetha Patalay; George B. Ploubidis; Srinivasa Vittal Katikireddi; Kate Tilling; Christopher T. Rentsch; Nicholas J. Timpson; Nishi Chaturvedi; Claire J. Steves", - "affiliations": "King's College London; University College London; University of Oxford; University of Bristol; University of Glasgow; Bradford Teaching Hospitals NHS Foundation Trust; University of Edinburgh; University of Bristol; University College London; University College London; King's College London; University of Bristol; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University College London; King's College London; King's College London; King's College London; ; University College London; University of Edinburgh; Bradford Teaching Hospitals NHS Foundation Trust; London School of Hygiene and Tropical Medicine; University of Oxford; University College London; University College London; University of Glasgow; University of Bristol; London School of Hygiene and Tropical Medicine; University of Bristol; University College London; King's College London", - "abstract": "BackgroundThe impact of long COVID is considerable, but risk factors are poorly characterised. We analysed symptom duration and risk factor from 10 longitudinal study (LS) samples and electronic healthcare records (EHR).\n\nMethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 participants in the UK LS, and 3,327 adults with COVID-19, were assigned a long COVID code from 1,199,812 individuals in primary care EHR. Outcomes for LS included symptom duration lasting 4+ weeks (long COVID) and 12+ weeks. Association with of age, sex, ethnicity, socioeconomic factors, smoking, general and mental health, overweight/obesity, diabetes, hypertension, hypercholesterolaemia, and asthma was assessed.\n\nResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%).\n\nConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.22.21259336", @@ -4465,6 +4465,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.06.17.21259100", + "date": "2021-06-20", + "link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259100", + "title": "COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya", + "authors": "Samuel P C Brand; John Ojal; Rabia Aziza; Vincent Were; Emelda Okiro; Ivy Kombe; Caroline Mburu; Morris Ogero; Ambrose Agweyu; George M Warimwe; James Nyagwange; Henry Karanja; John Gitonga; Daisy Mugo; Sophie Uyoga; Ifedayo M O Adetifa; J Anthony G Scott; Edward Otieno; Nickson Murunga; Mark Otiende; Lynette I Ochola-Oyier; Charles N Agoti; George Githinji; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Matt J Keeling; D James Nokes; Edwine Barasa", + "affiliations": "University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya", + "abstract": "Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya ([~]75% June 1st) have implications for a fourth wave and future control strategies.\n\nOne Sentence SummaryCOVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.15.21258542", @@ -4563,6 +4577,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.06.08.21258546", + "date": "2021-06-12", + "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258546", + "title": "Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies", + "authors": "Jane Maddock; Sam Parsons; Giorgio Di Gessa; Michael J Green; Ellen J Thompson; Anna J Stevenson; Alex S.F. Kwong; Eoin McElroy; Gillian Santorelli; Richard J Silverwood; Gabriella Captur; Nish Chaturvedi; Claire J Steves; Andrew Steptoe; Praveetha Patalay; George B Ploubidis; Srinivasa Vittal Katikireddi", + "affiliations": "University College London; University College London; University College London; University of Glasgow; King's College London; University of Edinburgh; University of Bristol; University of Leicester; Bradford Institute for Health Research; University College London; University College London; University College London; King's College London; University College London; University College London; University College London; University of Glasgow", + "abstract": "BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies.\n\nMethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates.\n\nResultsPrevalence of disruption varied across studies; between 6.4% (TwinsUK) and 31.8 % (Understanding Society) of study participants reported any disruption. Females (Odd Ratio (OR): 1.27 [95%CI: 1.15,1.40]; I2=53%), older persons (e.g. OR: 1.39 [1.13,1.72]; I2=77% for 65-75y vs 45-54y), and Ethnic minorities (excluding White minorities) (OR: 1.19 [1.05,1.35]; I2=0% vs White) were more likely to report healthcare disruptions. Those in a more disadvantaged social class (e.g. OR: 1.17 [1.08, 1.27]; I2=0% for manual/routine vs managerial/professional) were also more likely to report healthcare disruptions, but no clear differences were observed by education levels.\n\nConclusionThe COVID-19 pandemic has led to unequal healthcare disruptions, which, if unaddressed, could contribute to the maintenance or widening of existing health inequalities.", + "category": "health systems and quality improvement", + "match_type": "fuzzy", + "author_similarity": 97, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.07.21258476", @@ -4675,20 +4703,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.22.21257633", - "date": "2021-05-26", - "link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257633", - "title": "Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021", - "authors": "Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung", - "affiliations": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany", - "abstract": "The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.24.21257738", @@ -4857,20 +4871,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.12.21257102", - "date": "2021-05-15", - "link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257102", - "title": "Spike-antibody responses following first and second doses of ChAdOx1 and BNT162b2 vaccines by age, gender, and clinical factors - a prospective community cohort study (Virus Watch)", - "authors": "Madhumita Shrotri; Ellen Fragaszy; Cyril Geismar; Vincent Nguyen; Sarah Beale; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Anna Aryee; Jamie Lopez Bernal; Anne M Johnson; Alison Rodger; Andrew C Hayward; Robert W Aldridge", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; University College London; University College London; University College London", - "abstract": "BackgroundVaccination constitutes the best long-term solution against Coronavirus Disease 2019 (COVID-19). Real-world immunogenicity data are sparse, particularly for ChAdOx1 and in populations with chronic conditions; and given the UKs extended dosing interval, it is also important to understand antibody responses in SARS-CoV-2-naive individuals following a single dose.\n\nMethodsAdults aged [≥]18 years from households enrolled in Virus Watch, a prospective community cohort study in England and Wales, provided capillary blood samples and self-reported vaccination status. Primary outcome variables were quantitative Spike total antibody levels (U/ml) and seropositivity to Spike ([≥]0.8 U/ml), as per Roches Elecsys Anti-SARS-CoV-2 S assay. Samples seropositive for Nucleocapsid, and samples taken prior to vaccination, were excluded. Outcomes were analysed by days since vaccination, vaccine type (BNT162b2 and ChAdOx1), and a range of self-reported demographic and clinical factors.\n\nResults8,517 vaccinated participants (median age 65 years [IQR: 58, 71]), contributed 13,232 samples (8,115 following ChAdOx1, 5,008 following BNT162b2). Seropositivity to Spike was 96.42% (95%CI 96, 96.79) at 28-34 days following a single dose, reaching 99.08% (97.8, 99.62) at 7-14 days after a second dose. Seropositivity rates, and Spike-antibody levels rose more quickly following the first dose of BNT162b2, however, were equivalent for both vaccines by 4 and 8 weeks, respectively. There was evidence of lower S-antibody levels with increasing age (p=0.0001). In partially vaccinated 65-79 year-olds, lower S-antibody levels were observed in men (25.9 vs 42.3 U/ml, p<0.0001), those with a chronic condition (33.0 vs 41.2 U/ml, p<0.0001), diabetes (22.32 vs 36.01 U/ml, p<0.0001), cardiovascular disease (32.1 vs 36.7 U/ml, p=0.0002), or history of cancer (30.1 vs 35.7 U/ml, p=0.0001), particularly those with haematological rather than solid organ cancer (7.48 vs 31.68 U/ml, p<0.0001), and those currently on immunosuppressive therapy (21.7 vs 35.6 U/ml, p<0.0001). Following a second dose, high S-antibody titres ([≥]250U/ml) were observed for nearly all individuals.\n\nInterpretationA single dose of either BNT162b2 or ChAdOx1 leads to high Spike seropositivity rates in SARS-CoV-2-naive individuals. However, observed disparities in antibody levels after the first dose by vaccine type, age, and comorbidities highlight the importance of ongoing non-pharmaceutical preventative measures such as social distancing, for partially vaccinated adults, particularly those who are older and more clinically vulnerable.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.06.21256757", @@ -5138,18 +5138,18 @@ "affiliation_similarity": 100 }, { - "site": "medRxiv", - "doi": "10.1101/2021.04.08.21255099", - "date": "2021-04-14", - "link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255099", - "title": "Occupational risks of COVID-19 in NHS workers in England", - "authors": "Diana van der Plaat; Ira Madan; David Coggon; Martie van Tongeren; Rhiannon Edge; Rupert Muiry; Vaughan Parsons; Paul Cullinan", - "affiliations": "Imperial College London; Guy's and St Thomas' NHS Foundation Trust; Southampton General Hospital; University of Manchester; Lancaster University; Guy's and St Thomas NHS Foundation Trust; Guy's and St Thomas NHS Foundation Trust; Imperial College London", - "abstract": "ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England\n\nMethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression.\n\nResultsWith adjustment for employing trust, demographic characteristics, and previous frequency of sickness absence, risk relative to administrative/clerical occupations was highest in additional clinical services (including care assistants) (OR 2.31 [2.25-2.37]), registered nursing and midwifery professionals (OR 2.28 [2.23-2.34]) and allied health professionals (OR 1.94 [1.88-2.01]), and intermediate in doctors and dentists (OR 1.55 [1.50-1.61]). Differences in risk were higher after the employing trust had started to care for documented Covid-19 patients, and were reduced, but not eliminated, following additional adjustment for exposure to infected patients or materials, assessed by a job-exposure matrix. For prolonged Covid-19 sickness absence (episodes lasting >14 days), the variation in risk by staff group was somewhat greater.\n\nConclusionsAfter allowance for possible bias and confounding by non-occupational exposures, we estimated that relative risks for Covid-19 among most patient-facing occupations were between 1.5 and 2.5. The highest risks were in those working in additional clinical services, nursing and midwifery and in allied health professions. Better protective measures for these staff groups should be a priority. Covid-19 may meet criteria for compensation as an occupational disease in some healthcare occupations.\n\nKey messagesO_LIWhat is already known about this subject?\nHealthcare workers and other keyworkers (workers whose job was considered essential to societal functioning) had a higher likelihood of testing positive for COVID-19 than other workers during the first lockdown in England. Amongst healthcare workers, those working in inpatient settings had the highest rate of infection.\nC_LIO_LIWhat are the new findings?\nBetween March and July 2000, the overall risk of COVID-19 sickness absence in National Health Service staff in England was lower at older ages, higher in non-white staff, and (in comparison with administrative and clerical staff) more than doubled in registered nurses and among workers such as healthcare assistants providing support to health professionals. Risk in health care scientists was little different from that in administrative and clerical occupations\nC_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future?\nOur results suggest that the risk reduction strategies that were in place for healthcare scientists were effective. However, the protection for nursing and supporting health professionals was insufficient. In the event of a further wave of infections resulting in high hospital admissions, attention should be paid to ensuring that risk reduction strategies for nurses and supporting health professionals are improved.\nC_LI", - "category": "occupational and environmental health", + "site": "bioRxiv", + "doi": "10.1101/2021.04.13.439482", + "date": "2021-04-13", + "link": "https://biorxiv.org/cgi/content/short/2021.04.13.439482", + "title": "Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice", + "authors": "Kai Wu; Angela Choi; Matthew Koch; Sayda Elbashir; LingZhi Ma; Diana Lee; Angela Woods; Carole Henry; Charis Palandjian; Anna Hill; Hardik Jani; Julian Quinones; Naveen Nunna; Adrian B McDermott; Samantha Falcone; Elisabeth Narayanan; Tonya Colpitts; Hamilton Bennett; Kizzmekia Corbett; Robert Seder; Barney S Graham; Guillaume BE Stewart-Jones; Andrea Carfi; Darin K Edwards", + "affiliations": "Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Moderna, Inc; Moderna, Inc; Moderna, Inc; Moderna, Inc; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Moderna, Inc; Moderna, Inc; Moderna, Inc", + "abstract": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.", + "category": "microbiology", "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 + "author_similarity": 96, + "affiliation_similarity": 94 }, { "site": "medRxiv", @@ -5249,20 +5249,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.31.21254687", - "date": "2021-04-05", - "link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254687", - "title": "SARS-CoV-2 infectivity by viral load, S gene variants and demographic factors and the utility of lateral flow devices to prevent transmission", - "authors": "Lennard YW Lee; Stefan Rozmanowski; Matthew Pang; Andre Charlett; Charlotte Anderson; Gareth J Hughes; Matthew Barnard; Leon Peto; Richard Vipond; Alex Sienkiewicz; Susan Hopkins; John Bell; Derrick W Crook; Nick Gent; A Sarah Walker; Tim EA Peto; David W Eyre", - "affiliations": "University of Oxford; UK Government Department of Health and Social Care; UK Government Department of Health and Social Care; Public Health England; Public Health England; Public Health England; UK Government Department of Health and Social Care; University of Oxford; Public Health England; Public Health England; Public Health England; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford", - "abstract": "BackgroundHow SARS-CoV-2 infectivity varies with viral load is incompletely understood. Whether rapid point-of-care antigen lateral flow devices (LFDs) detect most potential transmission sources despite imperfect sensitivity is unknown.\n\nMethodsWe combined SARS-CoV-2 testing and contact tracing data from England between 01-September-2020 and 28-February-2021. We used multivariable logistic regression to investigate relationships between PCR-confirmed infection in contacts of community-diagnosed cases and index case viral load, S gene target failure (proxy for B.1.1.7 infection), demographics, SARS-CoV-2 incidence, social deprivation, and contact event type. We used LFD performance to simulate the proportion of cases with a PCR-positive contact expected to be detected using one of four LFDs.\n\nResults231,498/2,474,066 (9%) contacts of 1,064,004 index cases tested PCR-positive. PCR-positive results in contacts independently increased with higher case viral loads (lower Ct values) e.g., 11.7%(95%CI 11.5-12.0%) at Ct=15 and 4.5%(4.4-4.6%) at Ct=30. B.1.1.7 infection increased PCR-positive results by [~]50%, (e.g. 1.55-fold, 95%CI 1.49-1.61, at Ct=20). PCR-positive results were most common in household contacts (at Ct=20.1, 8.7%[95%CI 8.6-8.9%]), followed by household visitors (7.1%[6.8-7.3%]), contacts at events/activities (5.2%[4.9-5.4%]), work/education (4.6%[4.4-4.8%]), and least common after outdoor contact (2.9%[2.3-3.8%]). Contacts of children were the least likely to test positive, particularly following contact outdoors or at work/education. The most and least sensitive LFDs would detect 89.5%(89.4-89.6%) and 83.0%(82.8-83.1%) of cases with PCR-positive contacts respectively.\n\nConclusionsSARS-CoV-2 infectivity varies by case viral load, contact event type, and age. Those with high viral loads are the most infectious. B.1.1.7 increased transmission by [~]50%. The best performing LFDs detect most infectious cases.\n\nKey pointsIn 2,474,066 contacts of 1,064,004 SARS-CoV-2 cases, PCR-positive tests in contacts increased with higher index case viral loads, the B.1.1.7 variant and household contact. Children were less infectious. Lateral flow devices can detect 83.0-89.5% of infections leading to onward transmission.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.27.21254452", @@ -5319,6 +5305,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.24.21254227", + "date": "2021-03-26", + "link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254227", + "title": "COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death", + "authors": "Darryl P Leong; Amitava Banerjee; Salim Yusuf", + "affiliations": "McMaster University; University College London; McMaster University", + "abstract": "The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.26.21254390", @@ -5375,6 +5375,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.16.21253371", + "date": "2021-03-24", + "link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253371", + "title": "Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes", + "authors": "Emma Whitfield; Claire Coffey; Huayu Zhang; Ting Shi; Xiaodong Wu; Qiang Li; Honghan Wu", + "affiliations": "Institute of Health Informatics, UCL, London, United Kingdom; University of Cambridge, Cambridge, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Shanghai East Hospital, Tongji University, Shanghai, China; Shanghai East Hospital, Tongji University, Shanghai, China; Institute of Health Informatics, UCL, London, United Kingdom", + "abstract": "COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering axes of prognosis. We propose two innovative clustering approaches - Layered Axes and Prognosis Space - to apply on patients outcome data. We then show how these clusters can help predict a patients deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients hospital admission. Moreover, our method could be used to explore subtypes of long COVID and other diseases with heterogeneous outcomes.", + "category": "health informatics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 92 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.16.21253377", @@ -5599,6 +5613,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.08.21253110", + "date": "2021-03-10", + "link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253110", + "title": "Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 Long Term Care Facilities (VIVALDI study)", + "authors": "Maria Krutikov; Tom Palmer; Gokhan Tut; Chris Fuller; Madhumita Shrotri; Haydn Williams; Daniel Davies; Aidan Irwin-Singer; James Robson; Andrew Hayward; Paul Moss; Andrew Copas; Laura J Shallcross", + "affiliations": "UCL; UCL; University of Birmingham; UCL; UCL; Four Seasons Healthcare Group; Palantir Ltd; UK Department of Health and Social Care; Four Seasons Healthcare Group; UCL; University of Birmingham; UCL; UCL", + "abstract": "BackgroundSARS-CoV-2 infection represents a major challenge for Long Term Care Facilities (LTCFs) and many residents and staff are now sero-positive following persistent outbreaks. We investigated the relationship between the presence of SARS-CoV-2 specific antibodies and subsequent infection in this population.\n\nMethodsProspective cohort study of infection in staff and residents in 100 LTCFs in England between October 2020 and February 2021. Blood samples were collected at baseline (June 2020), 2 and 4 months and tested for IgG antibodies to nucleocapsid and spike protein. PCR testing for SARS-CoV-2 was undertaken weekly in staff and monthly in residents. The primary analysis estimated the relative hazard of a PCR-positive test by baseline antibody status, from Cox regression adjusted for age and gender, and stratified by LTCF.\n\nFindingsStudy inclusion criteria were met by 682 residents and 1429 staff. Baseline IgG antibodies to nucleocapsid were detected in 226 residents (33%) and 408 staff (29%). A total of 93 antibody-negative residents had a PCR-positive test (0.054 per month at risk) compared to 4 antibody-positive residents (0.007 per month at risk). There were 111 PCR-positive tests in antibody-negative staff (0.042 per month at risk) compared to 10 in antibody-positive staff (0.009 per month at risk). The adjusted hazard ratios for reinfection in staff and residents with a baseline positive versus negative antibody test were 0.13 (95% CI 0.05-0.40) and 0.39 ((95% CI: 0.19-0.77) respectively. Of 12 reinfected participants with data on symptoms, 11 were symptomatic. Antibody titres to spike and nucleocapsid were comparable in PCR-positive and PCR-negative cases.\n\nInterpretationThe presence of IgG antibodies to nucleocapsid was associated with substantially reduced risk of reinfection in staff and residents for up to 10 months after primary infection.\n\nFundingUK Government Department of Health and Social Care\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe performed a systematic search of MEDLINE (Ovid) and MedRxiv on 18 January 2021 for studies in LTCFs that described the risk of infection in individuals who were seropositive for SARS-CoV-2 compared to individuals who were seronegative. Search terms were deliberately broad to improve capture of relevant literature and included \"SARS-CoV-2\"OR \"COVID-19\" OR \"coronavirus\" AND \"care home\" OR \"nursing home\" OR \"long term care facility\" with no date or language restrictions. We did not identify any publications that focussed on risk of reinfection in seropositive individuals, but subsequent to our search one study has been published using data from two LTCFs in London, UK. This study reported a 96% reduction in the odds of reinfection in individuals who were seropositive compared to those who were seronegative based on 4-month follow-up in 161 participants. We found 10 studies that performed seroprevalence surveys in either staff or staff and residents in LTCFs in 8 cohorts. Five of these were carried out in response to SARS-CoV-2 outbreaks within the care homes, either as part of the subsequent investigation or as post-infection surveillance. The largest of these, which enrolled both staff and residents, was performed in 6 LTCFs and performed longitudinal antibody testing.\n\nAdded value of this studyWe undertook a cohort study in staff and residents from 100 LTCFs in England to investigate whether individuals with evidence of prior SARS-CoV-2 infection could be infected twice. Staff and residents were offered up to three rounds of antibody testing and antibody results were linked to PCR test results which were obtained weekly from staff and monthly from residents through the national SARS-CoV-2 testing programme. This study, which was conducted in >2000 staff and residents, suggests that antibodies provide high levels of protection against reinfection for up to 10 months. Almost all cases of reinfection were symptomatic, but no cases required hospital treatment. Amongst those with detectable baseline antibodies, quantitative antibody titres against spike protein and nucleocapsid were comparable between cases of reinfection and those who did not become reinfected.\n\nImplications of all available evidenceDespite high background rates of infection in LTCFs, the overall risk of reinfection was low in this population. This is broadly consistent with findings from large cohort studies of hospital staff, but, importantly, extends the evidence of substantial protection to frail elderly, who are vulnerable to severe outcomes of SARS-CoV-2 due to age-related changes in immunity (immune-senescence) and high levels of comorbidity. The low risk of reinfection in our study suggests identification of immune correlates of protection in this population will require pooling of data across multiple cohorts.\n\nAs vaccination coverage in residents approaches 100% in England, it will be important to understand whether vaccination and natural infection provide comparable levels of protection against infection. Such insights will inform future policy decisions regarding re-vaccination schedules in LTCF, and the longer-term need for non-pharmaceutical interventions to prevent SARS-CoV-2 transmission, such as asymptomatic testing and visitor restrictions.", + "category": "geriatric medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.09.21252736", @@ -5809,6 +5837,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.02.23.21252276", + "date": "2021-02-24", + "link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252276", + "title": "Inequalities in the decline and recovery of pathological cancer diagnoses during the first six months of the COVID-19 pandemic: a population-based study", + "authors": "Ashleigh C. Hamilton; David W. Donnelly; Maurice B. Loughrey; Richard C. Turkington; Colin Fox; Deirdre Fitzpatrick; Ciaran E. O'Neill; Anna T. Gavin; Helen G. Coleman", + "affiliations": "Centre for Public Health, Queen's University Belfast; Northern Ireland Cancer Registry; Department of Pathology, Belfast Health and Social Care Trust, Northern Ireland; Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Northern Ireland Cancer Registry; Centre for Public Health, Queen's University Belfast", + "abstract": "BackgroundThe restructuring of healthcare systems to cope with the demands of the COVID-19 pandemic has led to a reduction in clinical services such as cancer screening and diagnostics.\n\nMethodsData from the four Northern Ireland pathology labs was used to assess trends in pathological cancer diagnoses from 1st March to 12th September 2020 overall and by cancer site, gender and age. These trends were compared to the same timeframe from 2017-2019.\n\nResultsBetween 1st March and 12th September 2020 there was a 23% reduction in cancer diagnoses compared to the same time period in the preceding three years. Although some recovery occurred in August and September 2020, this revealed inequalities across certain patient groups. Pathological diagnoses of lung, prostate and gynaecological malignancies remained well below pre-pandemic levels. Males and younger/middle-aged adults, particularly the 50-59 year old patient group, also lagged behind other population demographic groups in terms of returning to expected numbers of pathological cancer diagnoses.\n\nConclusionsThere is a critical need to protect cancer diagnostic services in the ongoing pandemic to facilitate timely investigation of potential cancer cases. Targeted public health campaigns may be needed to reduce emerging inequalities in cancer diagnoses as the COVID-19 pandemic continues.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.02.18.21251973", @@ -5963,20 +6005,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.04.21251087", - "date": "2021-02-08", - "link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251087", - "title": "Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach", - "authors": "Daniel A Thompson; Hoda Abbasizanjani; Richard Fry; Emily Marchant; Lucy J Griffiths; Ashley Akbari; Joseph Hollinghurst; Laura North; Jane Lyons; Fatemeh Torabi; Gareth Davies; Mike B Gravenor; Ronan A Lyons", - "affiliations": "Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", - "abstract": "BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing.\n\nMethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings.\n\nResultsThe total number of cases in a school was not associated with a subsequent increase in the risk of testing positive (Staff OR per case 0.92, 95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst pupils, the number of recent cases within the same year group was significantly associated with subsequent increased risk of testing positive (OR per case 1.12, 95%CI 1.08 - 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 - 9.88).\n\nConclusionsIn a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased risk, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment.\n\nO_TEXTBOXWhat is knownO_LIEvidence of the role schools play in the transmission of SARS-CoV-2 is limited\nC_LIO_LIHigher positivity rates are observed in school staff compared to pupils\nC_LIO_LILack of evidence on transmission pathways transmission into and within schools\nC_LI\n\nWhat this study addsO_LIFirst UK national level study of transmission between pupils and staff in a school environment during the SARS-CoV-2 pandemic.\nC_LIO_LISchools opening September-December 2020 was not associated with an increased subsequent risk of testing positive in staff\nC_LIO_LIPupils were found to be at increased risk of testing positive, following cases appearing within their own year group\nC_LI\n\nC_TEXTBOX", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.07.21251297", @@ -6061,20 +6089,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.02.21250989", - "date": "2021-02-03", - "link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250989", - "title": "Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020", - "authors": "Krishnan Bhaskaran; Rohini Mathur; Christopher T Rentsch; Caroline E Morton; William J Hulme; Anna Schultze; Brian McKenna; Rosalind M Eggo; Angel YS Wong; Elizabeth J Williamson; Harriet J Forbes; Kevin Wing; Helen I McDonald; Chris J Bates; Sebastian CJ Bacon; Alex J Walker; David Evans; Peter Inglesby; Amir Mehrkar; Helen J Curtis; Nichola J DeVito; Richard Croker; Henry Drysdale; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Laurie Tomlinson; Stephen JW Evans; Richard Grieve; Liam Smeeth; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP, TPP House, Horsforth, Leeds; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford", - "abstract": "Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent \"second wave\" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@987a5org.highwire.dtl.DTLVardef@1a8a141org.highwire.dtl.DTLVardef@1f2de56org.highwire.dtl.DTLVardef@1e2f9b8org.highwire.dtl.DTLVardef@78bfcc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONAssociation between ethnicity and COVID-19 death 1st Sept - 9th Nov 2020\n\nC_TABLECAPTION C_TBL", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.30.21250777", @@ -6523,20 +6537,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.15.20248096", - "date": "2020-12-16", - "link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248096", - "title": "Anosmia and other SARS-CoV-2 positive test-associated symptoms, across three national, digital surveillance platforms as the COVID-19 pandemic and response unfolded: an observation study", - "authors": "Carole Helene Sudre; Ayya Keshet; Mark S Graham; Amit D Joshi; Smadar Shilo; Hagai Rossman; Benjamin Murray; Erika Molteni; Kerstin Klaser; Liane S Canas; Michela Antonelli; Marc Modat; Joan Capdevila Pujol; Sajaysurya Ganesh; Jonathan Wolf; Tomer Meir; Andrew T Chan; Claire Steves; Timothy Spector; John S Brownstein; Eran Segal; Sebastien Ourselin; Christina Astley", - "affiliations": "University College London; Weizmann Institute of Science; King's College London; Massachusetts General Hospital; Weizmann Institute of Science; Weizmann Institute of Science; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Weizmann Institute of Science; Massachusetts General Hospital; King's College London; King's College London; Boston Children's Hospital; Weizmann Institute of Science; King's College London; Boston Children's Hospital", - "abstract": "BackgroundMultiple participatory surveillance platforms were developed across the world in response to the COVID-19 pandemic, providing a real-time understanding of community-wide COVID-19 epidemiology. During this time, testing criteria broadened and healthcare policies matured. We sought to test whether there were consistent associations of symptoms with SARS-CoV-2 test status across three national surveillance platforms, during periods of testing and policy changes, and whether inconsistencies could better inform our understanding and future studies as the COVID-19 pandemic progresses.\n\nMethodsFour months (1st April 2020 to 31st July 2020) of observation through three volunteer COVID-19 digital surveillance platforms targeting communities in three countries (Israel, United Kingdom, and United States). Logistic regression of self-reported symptom on self-reported SARS-CoV-2 test status (or test access), adjusted for age and sex, in each of the study cohorts. Odds ratios over time were compared to known changes in testing policies and fluctuations in COVID-19 incidence.\n\nFindingsAnosmia/ageusia was the strongest, most consistent symptom associated with a positive COVID-19 test, based on 658,325 tests (5% positive) from over 10 million respondents in three digital surveillance platforms using longitudinal and cross-sectional survey methodologies. During higher-incidence periods with broader testing criteria, core COVID-19 symptoms were more strongly associated with test status. Lower incidence periods had, overall, larger confidence intervals.\n\nInterpretationThe strong association of anosmia/ageusia with self-reported SARS-CoV-2 test positivity is omnipresent, supporting its validity as a reliable COVID-19 signal, regardless of the participatory surveillance platform or testing policy. This analysis highlights that precise effect estimates, as well as an understanding of test access patterns to interpret differences, are best done only when incidence is high. These findings strongly support the need for testing access to be as open as possible both for real-time epidemiologic investigation and public health utility.\n\nFundingNIH, NIHR, Alzheimers Society, Wellcome Trust\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAs the COVID-19 pandemic has evolved, testing capacity expanded and governmental guidelines adapted, generally encouraging testing with a broader set of symptoms, not just fever with respiratory symptoms. In parallel, multiple large-scale citizen science digital surveillance platforms launched to complement knowledge from laboratory and somewhat smaller clinical studies. Symptoms such as loss of sense of smell have been identified as strongly predictive of COVID-19 infection in both clinical and syndromic surveillance analyses, and have therefore been used to inform these testing policy changes and access expansion.\n\nAdded value of this studyThis study identifies symptoms that are or are not consistently associated with SARS-CoV-2 test positivity over time and across three country-based COVID-19 surveillance platforms in the United States, United Kingdom and Israel. These platforms are website and smartphone based, as well as cross-sectional and longitudinal. The study period of 4 months covers fluctuating COVID-19 prevalence during the fall of the first wave and, in some areas, rise of the second wave. In addition, the study period overlaps expansion of test access and test seeking. Importantly, these analyses track and highlight the value of individual symptoms to predict SARS-CoV-2 test positivity under a range of conditions.\n\nImplications of all the available evidenceDespite differences in surveillance methodology, access to SARS-CoV-2 testing and disease prevalence, loss of sense of smell or taste was consistently the strongest predictor of COVID-19 infection across all platforms over time. As access to testing broadened, the relevance of COVID-like symptoms and consistency of their predictive ability became apparent. However, confidence bounds generally widened with a fall in COVID-19 incidence. Therefore, for the most robust symptom-based COVID-19 prediction models should consider surveillance data during periods of higher incidence and improved test access, and effect estimates that replicate across different epidemiologic conditions and platforms.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.15.20248244", @@ -6691,6 +6691,20 @@ "author_similarity": 90, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.12.01.20241729", + "date": "2020-12-03", + "link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241729", + "title": "International estimates of intended uptake and refusal of COVID-19 vaccines: A rapid systematic review and meta-analysis of large nationally representative samples", + "authors": "Eric Robinson; Andrew Jones; India Lesser; Michael Daly", + "affiliations": "University of Liverpool; University of Liverpool; University of Liverpool; Maynooth University", + "abstract": "BackgroundWidespread uptake of COVID-19 vaccines will be essential to extinguishing the COVID-19 pandemic. Vaccines have been developed in unprecedented time and hesitancy towards vaccination among the general population is unclear.\n\nMethodsSystematic review and meta-analysis of studies using large nationally representative samples (n[≥]1000) to examine the percentage of the population intending to vaccinate, unsure, or intending to refuse a COVID-19 vaccine when available. Generic inverse meta-analysis and meta-regression were used to pool estimates and examine time trends. PubMed, Scopus and pre-printer servers were searched from January-November, 2020. Registered on PROSPERO (CRD42020223132).\n\nFindingsTwenty-eight nationally representative samples (n = 58,656) from 13 countries indicate that as the pandemic has progressed, the percentage of people intending to vaccinate and refuse vaccination have been decreasing and increasing respectively. Pooled data from surveys conducted during June-October suggest that 60% (95% CI: 49% to 69%) intend to vaccinate and 20% (95% CI: 13% to 29%) intend to refuse vaccination, although intentions vary substantially between samples and countries (I2 > 90%). Being female, younger, of lower income or education level and belonging to an ethnic minority group were consistently associated with being less likely to intend to vaccinate. Findings were consistent across higher vs. lower quality studies.\n\nInterpretationIntentions to be vaccinated when a COVID-19 vaccine becomes available have been declining globally and there is an urgent need to address social inequalities in vaccine hesitancy and promote widespread uptake of vaccines as they become available.\n\nFundingN/A\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Scopus and pre-print servers for manuscripts from January to November, 2020, reporting on studies examining intentions to be vaccinated against COVID-19 in large nationally representative samples (N[≥]1000). No language restrictions were applied. Search terms were [(COVID OR coronavirus OR SARS-COV-2) AND (Vaccine OR Vaccination) AND (Inten* OR willing* OR attitud* OR hypothetical)]. From 792 articles, we identified 20 eligible articles reporting on 28 nationally representative samples.\n\nAdded value of this studyThis is the first systematic study and meta-analysis to estimate the proportion of the global population willing to be vaccinated against vs. intending to refuse a vaccine when COVID-19 vaccines become available and how this trend has changed over time, using large and nationally representative samples. Results indicate that COVID-19 vaccination intentions vary substantially across countries, the percentage of the population intending to be vaccinated has declined across countries as the pandemic has progressed (March-May estimate: 79%, June-October estimate: 60%) and a growing number report intending to refuse a vaccine, when available (March-May estimate: 12%, June-October estimate: 20%). There is consistent socio-demographic patterning of vaccination intentions; being female, younger, of lower income or education level and belonging to an ethnic minority group are associated with a reduced likelihood of intending to be vaccinated when a vaccine become available.\n\nImplications of all the available evidenceIntentions to vaccinate against COVID-19 among the general public when a vaccine becomes available have been declining and this will limit the effectiveness of COVID-19 vaccination programmes. Findings highlight the need to improve public acceptability, trust and concern over the safety and benefit of COVID-19 vaccines and target vaccine uptake in disadvantaged groups who have already been disproportionately affected by the pandemic.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.27.20238147", @@ -7069,6 +7083,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.30.20223123", + "date": "2020-11-03", + "link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223123", + "title": "High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", + "abstract": "BackgroundREACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive.\n\nMethodsREACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive.\n\nResultsOverall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%).\n\nConclusionThe co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.01.20222315", @@ -7391,20 +7419,6 @@ "author_similarity": 91, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.10.09.20209957", - "date": "2020-10-13", - "link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209957", - "title": "Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19", - "authors": "Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi", - "affiliations": "University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT", - "abstract": "Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.10.08.20209304", @@ -7503,6 +7517,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.30.20204727", + "date": "2020-10-02", + "link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204727", + "title": "High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", + "abstract": "BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020.\n\nMethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model.\n\nResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants.\n\nConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.28.20202929", @@ -7729,13 +7757,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.09.04.20187781", - "date": "2020-09-09", - "link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187781", - "title": "Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study", - "authors": "Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre", - "affiliations": "London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality.\n\nMethodsWe pre-specified and conducted an observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, representing 40% of the general population in England. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use prior to the COVID-19 outbreak in England and risk of COVID-19 mortality among people with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Model adjustment was informed by a directed acyclic graph.\n\nResultsOf 194,637 patients with RA or SLE, 30,569 (15.7%) received [≥] 2 prescriptions of hydroxychloroquine in the six months prior to 1 March 2020. Between 1 March 2020 and 13 July 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0.23% (95% CI 0.18-0.29) among users and 0.22% (95% CI 0.20-0.25) among non-users; an absolute difference of 0.008% (95% CI -0.051-0.066). After accounting for age, sex, ethnicity, use of other immunuosuppressives, and geographic region, no association with COVID-19 mortality was observed (HR 1.03, 95% CI 0.80-1.33). We found no evidence of interactions with age or other immunosuppressives. Quantitative bias analyses indicated observed associations were robust to missing information regarding additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality.\n\nConclusionWe found no evidence of a difference in COVID-19 mortality among patients who received hydroxychloroquine for treatment of rheumatological disease prior to the COVID-19 outbreak in England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials and observational studies to date have shown no evidence of benefit of hydroxychloroquine as a treatment for hospitalised patients who already have COVID-19. A separate question remains: whether routine ongoing use of hydroxychloroquine in people without COVID-19 protects against new infections or severe outcomes. We searched MEDLINE/PubMed for pharmacoepidemiological studies evaluating hydroxychloroquine for prevention of severe COVID-19 outcomes. The keywords \"hydroxychloroquine AND (COVID OR coronavirus OR SARS-CoV-2) AND (prophyl* OR prevent*) AND (rate OR hazard OR odds OR risk)\" were used and results were filtered to articles from the last year with abstracts available. 109 papers were identified for screening; none investigated pre-exposure prophylactic use of hydroxychloroquine for prevention of severe COVID-19 outcomes. Clinical trials of prophylactic use of hydroxychloroquine are ongoing; however, the largest trial does not expect to meet recruitment targets due to \"...unjustified extrapolation and exaggerated safety concerns together with intense politicisation and negative publicity.\" In the absence of reported clinical trials, evidence can be generated from real-world data to support the need for randomised clinical trials.\n\nAdded value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data.\n\nImplications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.", + "doi": "10.1101/2020.09.11.20192492", + "date": "2020-09-11", + "link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192492", + "title": "Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.", "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, @@ -7939,14 +7967,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.08.21.20177246", - "date": "2020-08-24", - "link": "https://medrxiv.org/cgi/content/short/2020.08.21.20177246", - "title": "Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility", - "authors": "Irene V van Blokland; Pauline Lanting; Anil PS Ori; Judith M Vonk; Robert CA Warmerdam; Johanna C Herkert; Floranne Boulogne; Annique Claringbould; Esteban A Lopera-Maya; Meike Bartels; Jouke-Jan Hottenga; Andrea Ganna; Juha Karjalainen; - Lifelines COVID-19 cohort study; - The COVID-19 Host Genetics Initiative; Caroline Hayward; Chloe Fawns-Ritchie; Archie Campbell; David Porteous; Elizabeth T Cirulli; Kelly M Schiabor Barrett; Stephen Riffle; Alexandre Bolze; Simon White; Francisco Tanudjaja; Xueqing Wang; Jimmy M Ramirez III; Yan Wei Lim; James T Lu; Nicole L Washington; Eco JC de Geus; Patrick Deelen; H Marike Boezen; Lude H Franke", - "affiliations": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Structural Computational Biology unit, EMB; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA and Analytic and Tra; ; ; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA; Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Department of Genetics, University Medical; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands", - "abstract": "Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19, and this GWAS benefits from the larger sample size to provide new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, we recommend repeatedly collecting data of disease-related symptoms.", - "category": "genetic and genomic medicine", + "doi": "10.1101/2020.08.18.20177691", + "date": "2020-08-22", + "link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177691", + "title": "Genetically-predicted vitamin D status, ambient UVB during the pandemic and COVID-19 risk in UK Biobank: Mendelian Randomisation study", + "authors": "Xue Li; Jos van Geffen; Michiel van Weele; Xiangrui Meng; XIAOMENG ZHANG; Yazhou He; Maria Timofeeva; Harry Campbell; Malcolm G Dunlop; Lina Zgaga; Evropi Theodoratou", + "affiliations": "School of Public Health and the Second Affiliated Hospital, Zhejiang University; Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands; Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands; Vanke School of public Health,Tsinghua University; Usher Institute; Centre for Global Health, Usher Institute, University of Edinburgh; DIAS, Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark; Centre for Global Health, Usher Institute, University of Edinburgh; Institute of Genetics and Molecular Medicine; Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin; University of Edinburgh", + "abstract": "A growing body of evidence shows that poor vitamin D status has been associated with an increased susceptibility to viral and bacterial respiratory infections. In this study, we aimed to examine the association between vitamin D and COVID-19 risk and outcomes, and to explore potential causal effects. We used logistic regression to identify associations between different vitamin D variables (25-hydroxyvitamin D concentration (25-OHD), ambient UVB and genetically-predicted 25-OHD concentrations) and COVID-19 (risk of infection, hospitalisation and death) in 495,780 participants from UK Biobank. We subsequently performed a Mendelian Randomisation (MR) study to test if there was any causal effect. In total, 1,746 COVID-19 cases and 399 COVID-19 deaths occurred between March and June 2020. We found significant inverse associations between COVID-19 infection and 25-OHD in univariable models, but these associations were non-significant after adjustment for confounders. Ambient UVB was strongly and inversely associated with hospitalization and death. Although the main MR analysis showed that genetically-predicted vitamin D levels were not causally associated with COVID-19 risk, MR sensitivity analysis using weighted mode method indicated a potential causal effect (OR=0.72, 95% CI:0.53-0.98; P=0.041). In conclusion, our study found suggestive evidence of association between vitamin D and the risk or severity of COVID-19 but further studies are needed.", + "category": "epidemiology", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -8119,6 +8147,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.08.05.20169078", + "date": "2020-08-06", + "link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169078", + "title": "Transient dynamics of SARS-CoV-2 as England exited national lockdown", + "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health", + "abstract": "Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.01.20166405", @@ -8371,6 +8413,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.15.20152967", + "date": "2020-07-17", + "link": "https://medrxiv.org/cgi/content/short/2020.07.15.20152967", + "title": "Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.", + "authors": "Gisli Jenkins; Tom Drake; Annemarie B Docherty; Ewan Harrison; Jennifer Quint; Huzaifa Adamali; Sarah Agnew; Suresh Babu; Christopher Barber; Shaney Barratt; Elisabeth Bendstrup; Stephen Bianchi; Diego Castillo; Nazia Chaudhuri; Felix Chua; Robina Coker; William Chang; Anjali Cranshaw; Louise Crowley; Davinder Dosanjh; Christine Fiddler; Ian A Forrest; Peter George; Michael Gibbons; Katherine Groom; Sarah Haney; Simon Hart; Emily Heiden; Michael Henry; Ling-Pei Ho; Rachel Hoyles; John Hutchinson; Killian Hurley; Mark Jones; Steve Jones; Maria Kokosi; Michael Kreuter; Laura Mackay; Siva Mahendran; Georgios Margaritopoulos; Maria Molina-Molina; Philip Molyneaux; Aidan D O'Brien; Katherine O'Reilly; Alice Packham; Helen Parfrey; Venerino Poletti; Joanna Porter; Elisabetta Renzoni; Pilar Rivera-Ortega; Anne-Marie Russell; Gauri Saini; Lisa G Spencer; Giulia Stella; Helen Stone; Sharon Sturney; David Thickett; Muhunthan Thillai; Timothy Wallis; Katie Ward; Athol U Wells; Alex West; Melissa Wickremasinghe; Felix Woodhead; Glenn Herson; Lucy Howard; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Iain Stewart", + "affiliations": "University of Nottingham; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX; University of Edinburgh; University of Edinburgh; Imperial College London; Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB.; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Queen Alexandra Hospital, Portsmouth, UK.; Northern General Hospital, Sheffield, S5 7AU, UK; Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB.; Centre for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99,8200 Aarhus N, Denmar; Northern General Hospital, Sheffield, S5 7AU, UK.; ILD Unit, Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Royal Brompton Hospital; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Nottingham University Hospital; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK.; Royal Brompton Hospital; South West Peninsula ILD Network, Royal Devon & Exeter Foundation NHS Trust Barrack Road, Exeter EX2 5DW, UK; Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, UK, HU16 5JQ; University Hospitals Southampton NHS Foundation Trust, Southampton, UK; Cork University Hospital, Cork, Ireland; University of Oxford; Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK; University of Nottingham; Beaumont Hospital, Dublin, Ireland.; NIHR Southampton Biomedical Research Centre & Clinical and Experimental Sciences, University of Southampton, Southampton, UK; Action for Pulmonary Fibrosis; Guys and St Thomas' Hospital; Center for interstitial and rare lung diseases, Pneumology, Thoraxklinik, University of Heidelberg, Germany and German Center for Lung Research, 69126 Heidelber; Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ; Kingston Hospital NHS Foundation Trust. Galsworthy Road, Kingston upon Thames, Surrey KT2 7QB, UK.; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; ILD Unit, Respiratory Department, University Hospital of Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.; Imperial College London; University Hospital Limerick, Dooradoyle, Limerick, Ireland.; Department of Respiratory Medicine, Mater Misericordiae University Hospital, Dublin, Ireland.; Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; Department of Diseases of the Thorax, Morgagni Hospital, Forli, Italy.; University College London; Royal Brompton Hospital; ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK; Imperial College London; Nottingham University Hospitals; Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK.; Laboratory of Biochemistry and Genetics, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.; University Hospital North Midlands NHS Trust, Royal Stoke University Hospital, Newcastle Road, Stoke-on-Trent, ST4 6QG, UK.; Royal United Hospitals Bath NHS Foundation Trust, Combe Park, Bath BA1 3NG, UK; University of Birmingham, Birmingham, UK.; Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK; University of Southampton; Imperial College London; Royal Brompton Hospital; Guys and St Thomas' Hospital; Imperial Healthcare NHS Trust, St Mary's Hospital, The Bays, S Wharf Rd, Paddington, London W2 1NY, UK.; Glenfield Hospital Leicester; Nottingham University Hospitals Trust; Nottingham University Hospitals Trust; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; University of Nottingham", + "abstract": "RationaleThe impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established.\n\nObjectivesTo assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population.\n\nMethodsAn international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death.\n\nMeasurements and Main ResultsData from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC [≥]80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13-3.46).\n\nConclusionsPatients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.", + "category": "respiratory medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.14.20153734", @@ -8385,20 +8441,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.14.20152629", - "date": "2020-07-15", - "link": "https://medrxiv.org/cgi/content/short/2020.07.14.20152629", - "title": "Covid-19 infection and attributable mortality in UK Long Term Care Facilities: Cohort study using active surveillance and electronic records (March-June 2020)", - "authors": "Peter F Dutey-Magni; Haydn Williams; Arnoupe Jhass; Greta Rait; Harry Hemingway; Andrew C Hayward; Laura Shallcross", - "affiliations": "University College London; Four Seasons Healthcare Group; UCL; University College London; University College London; University College London; UCL", - "abstract": "BackgroundEpidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic.\n\nMethodsCohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality.\n\nResults2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection.\n\n217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]).\n\nConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.15.20151852", @@ -8525,20 +8567,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.07.20148460", - "date": "2020-07-08", - "link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148460", - "title": "Reconstructing the global dynamics of under-ascertained COVID-19 cases and infections", - "authors": "Timothy W Russell; Nick Golding; Joel Hellewell; Sam Abbott; Lawrence Wright; Carl A B Pearson; Kevin van Zandvoort; Christopher I Jarvis; Hamish Gibbs; Yang Liu; Rosalind M Eggo; John W Edmunds; Adam J Kucharski", - "affiliations": "London School of Hygiene and Tropical Medicine; Telethon Kids Institute and Curtin University; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Defence Science and Technology Laboratory/Sopra Steria, Fareham, United Kingdom; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundAsymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.\n\nMethodsUsing reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever >= 37.5{degrees}C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the case fatality ratio (CFR) as an assumed baseline. We then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.\n\nResultsWe estimate that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.38% (Bangladesh) to 99.6% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 17.8 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. Despite low case detection in some countries, our results that adjust for this still suggest that all countries have had only a small fraction of their populations infected as of July 2020.\n\nConclusionsWe found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each countrys population infected with SARS-CoV-2 worldwide is generally low.\n\nFundingWellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.06.20147348", @@ -8611,13 +8639,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.06.26.20140921", - "date": "2020-06-28", - "link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140921", - "title": "Short Communication: Vitamin D and COVID-19 infection and mortality in UK Biobank", - "authors": "Claire E Hastie; Jill P Pell; Naveed Sattar", - "affiliations": "University of Glasgow; University of Glasgow; University of Glasgow", - "abstract": "PurposeVitamin D has been proposed as a potential causal factor in COVID-19 risk. We aimed to establish whether blood 25-hydroxyvitamin D (25(OH)D) concentration was associated with COVID-19 mortality, and inpatient confirmed COVID-19 infection, in UK Biobank participants.\n\nMethodsUK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including 25(OH)D concentration, were linked to COVID-19 mortality. Univariable and multivariable Cox proportional hazards regression analyses were performed for the association between 25(OH)D and COVID-19 death, and poisson regression analyses for the association between 25(OH)D and severe COVID-19 infection.\n\nResultsComplete data were available for 341,484 UK Biobank participants, of which 656 had inpatient confirmed COVID-19 infection and 203 died of COVID-19 infection. Vitamin D was associated with severe COVID-19 infection and mortality univariably (mortality HR=0.99; 95% CI 0.98-0.998; p=0.016), but not after adjustment for confounders (mortality HR=0.998; 95% CI=0.99-1.01; p=0.696).\n\nConclusionsOur findings do not support a potential link between vitamin D concentrations and risk of severe COVID-19 infection and mortality. Recommendations for vitamin D supplementation to lessen COVID-19 risks may provide false reassurance.", + "doi": "10.1101/2020.06.28.20141986", + "date": "2020-06-29", + "link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141986", + "title": "Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population", + "authors": "Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon", + "affiliations": "University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton", + "abstract": "IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases.\n\nMethods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available.\n\nEthics and disseminationThe project has ethical approval and the results will be submitted for publication in a peer-reviewed journal.\n\nStrengths and limitations of the studyO_LIThe individual-level linkage of general practice, Public Health England testing, Hospital Episode Statistics and Office of National Statistics death register datasets enable a robust and accurate ascertainment of outcomes\nC_LIO_LIThe models will be trained and evaluated in population-representative datasets of millions of individuals\nC_LIO_LIShielding for clinically extremely vulnerable was advised and in place during the study period, therefore risk predictions influenced by the presence of some shielding conditions may require careful consideration\nC_LI", "category": "epidemiology", "match_type": "fuzzy", "author_similarity": 100, @@ -8625,14 +8653,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.06.26.20139873", + "doi": "10.1101/2020.06.26.20140921", "date": "2020-06-28", - "link": "https://medrxiv.org/cgi/content/short/2020.06.26.20139873", - "title": "Secondary pneumonia in critically ill ventilated patients with COVID-19", - "authors": "Mailis Maes; Ellen Higginson; Joana Pereira Dias; Martin D Curran; Surendra Parmar; Fahad Khokhar; Delphine Cuchet-Louren\u00e7o; Janine Lux; Sapna Sharma-Hajela; Benjamin Ravenhill; Razeen Mahroof; Amelia Solderholm; Sally Forrest; Sushmita Sridhar; Nicholas M Brown; Stephen Baker; Vilas Navapurkar; Gordon Dougan; Josefin Bartholdson Scott; Andrew Conway Morris", - "affiliations": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Wellcome Sanger Insitute, Hinxton, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom; University of Cambridge", - "abstract": "BackgroundPandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive artificial ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP).\n\nObjectivesTo study the incidence of VAP, as well as differences in secondary infections, and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients.\n\nMethodsIn this prospective observational study, we compared the incidence of VAP and secondary infections using a combination of a TaqMan multi-pathogen array and microbial culture. In addition, we determined the lung microbime composition using 16S RNA analyisis. The study involved eighteen COVID-19 and seven non-COVID-19 patients receiving invasive ventilation in three ICUs located in a single University teaching hospital between April 13th 2020 and May 7th 2020.\n\nResultsWe observed a higher percentage of confirmed VAP in COVID-19 patients. However, there was no statistical difference in the detected organisms or pulmonary microbiome when compared to non-COVID-19 patients.\n\nConclusionCOVID-19 makes people more susceptible to developing VAP, partly but not entirely due to the increased duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the array of secondary infections observed are similar to that seen in critically ill patients ventilated for other reasons.", - "category": "intensive care and critical care medicine", + "link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140921", + "title": "Short Communication: Vitamin D and COVID-19 infection and mortality in UK Biobank", + "authors": "Claire E Hastie; Jill P Pell; Naveed Sattar", + "affiliations": "University of Glasgow; University of Glasgow; University of Glasgow", + "abstract": "PurposeVitamin D has been proposed as a potential causal factor in COVID-19 risk. We aimed to establish whether blood 25-hydroxyvitamin D (25(OH)D) concentration was associated with COVID-19 mortality, and inpatient confirmed COVID-19 infection, in UK Biobank participants.\n\nMethodsUK Biobank recruited 502,624 participants aged 37-73 years between 2006 and 2010. Baseline exposure data, including 25(OH)D concentration, were linked to COVID-19 mortality. Univariable and multivariable Cox proportional hazards regression analyses were performed for the association between 25(OH)D and COVID-19 death, and poisson regression analyses for the association between 25(OH)D and severe COVID-19 infection.\n\nResultsComplete data were available for 341,484 UK Biobank participants, of which 656 had inpatient confirmed COVID-19 infection and 203 died of COVID-19 infection. Vitamin D was associated with severe COVID-19 infection and mortality univariably (mortality HR=0.99; 95% CI 0.98-0.998; p=0.016), but not after adjustment for confounders (mortality HR=0.998; 95% CI=0.99-1.01; p=0.696).\n\nConclusionsOur findings do not support a potential link between vitamin D concentrations and risk of severe COVID-19 infection and mortality. Recommendations for vitamin D supplementation to lessen COVID-19 risks may provide false reassurance.", + "category": "epidemiology", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -8693,6 +8721,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.22.20137273", + "date": "2020-06-22", + "link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137273", + "title": "Effect of Dexamethasone in Hospitalized Patients with COVID-19: Preliminary Report", + "authors": "Peter Horby; Wei Shen Lim; Jonathan Emberson; Marion Mafham; Jennifer Bell; Louise Linsell; Natalie Staplin; Christopher Brightling; Andrew Ustianowski; Einas Elmahi; Benjamin Prudon; Christopher Green; Timothy Felton; David Chadwick; Kanchan Rege; Christopher Fegan; Lucy C Chappell; Saul N Faust; Thomas Jaki; Katie Jeffery; Alan Montgomery; Kathryn Rowan; Edmund Juszczak; J Kenneth Baillie; Richard Haynes; Martin J Landray; - RECOVERY Collaborative Group", + "affiliations": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Regional Infectious Diseases Unit, North Manchester General Hospital & University of Manchester, Manchester, United Kingdom; Research and Development Department, Northampton General Hospital, Northampton, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology & Infection, University of Birmingham, Birmingham, United Kingdom; University of Manchester and Manchester University NHS Foundation Trust, Manchester, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Department of Research and Development, Cardiff and Vale University Health Board, Cardiff, United Kingdom; School of Life Course Sciences, Kings College London, London, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; ", + "abstract": "BackgroundCoronavirus disease 2019 (COVID-19) is associated with diffuse lung damage. Corticosteroids may modulate immune-mediated lung injury and reducing progression to respiratory failure and death.\n\nMethodsThe Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, adaptive, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19. We report the preliminary results for the comparison of dexamethasone 6 mg given once daily for up to ten days vs. usual care alone. The primary outcome was 28-day mortality.\n\nResults2104 patients randomly allocated to receive dexamethasone were compared with 4321 patients concurrently allocated to usual care. Overall, 454 (21.6%) patients allocated dexamethasone and 1065 (24.6%) patients allocated usual care died within 28 days (age-adjusted rate ratio [RR] 0.83; 95% confidence interval [CI] 0.74 to 0.92; P<0.001). The proportional and absolute mortality rate reductions varied significantly depending on level of respiratory support at randomization (test for trend p<0.001): Dexamethasone reduced deaths by one-third in patients receiving invasive mechanical ventilation (29.0% vs. 40.7%, RR 0.65 [95% CI 0.51 to 0.82]; p<0.001), by one-fifth in patients receiving oxygen without invasive mechanical ventilation (21.5% vs. 25.0%, RR 0.80 [95% CI 0.70 to 0.92]; p=0.002), but did not reduce mortality in patients not receiving respiratory support at randomization (17.0% vs. 13.2%, RR 1.22 [95% CI 0.93 to 1.61]; p=0.14).\n\nConclusionsIn patients hospitalized with COVID-19, dexamethasone reduced 28-day mortality among those receiving invasive mechanical ventilation or oxygen at randomization, but not among patients not receiving respiratory support.\n\nTrial registrationsThe RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFundingMedical Research Council and National Institute for Health Research (Grant ref: MC_PC_19056).", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.19.20135491", diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index 869aec5b..ebda9e2d 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,4 +1,716 @@ [ + { + "rel_doi": "10.1101/2023.10.22.563156", + "rel_title": "A 50-gene high-risk profile predictive of COVID-19 and Idiopathic Pulmonary Fibrosis mortality originates from a molecular imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563156", + "rel_abs": "Background: We aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality. Methods: Whole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon gamma;-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-beta) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fisher exact. Results: We identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGF{beta}-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF. Conclusion: A 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Bochra Tourki", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Minxue Jia", + "author_inst": "Department of Epidemiology, College of Public Health, and Health Professions, and College of Medicine, University of Florida, Gainesville, FL, USA." + }, + { + "author_name": "Theodoros Karampitsakos", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Iset M Vera", + "author_inst": "Division of infectious Disease, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA." + }, + { + "author_name": "Alyssa Arsenault", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Krystin Marlin", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Carole Y Perrot", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Dylan Allen", + "author_inst": "Division of infectious Disease, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA." + }, + { + "author_name": "Forouzandeh Farsaei", + "author_inst": "Division of infectious Disease, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA" + }, + { + "author_name": "David Rutenberg", + "author_inst": "Division of infectious Disease, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA" + }, + { + "author_name": "Debabrata Bandyopadhyay", + "author_inst": "Center for Advanced Lung Disease and Lung Transplant Program. Tampa General Hospital, FL, USA" + }, + { + "author_name": "Ricardo Restrepo", + "author_inst": "Center for Advanced Lung Disease and Lung Transplant Program. Tampa General Hospital, FL, USA" + }, + { + "author_name": "Muhammad R. Qureshi", + "author_inst": "Center for Advanced Lung Disease and Lung Transplant Program. Tampa General Hospital, FL, USA" + }, + { + "author_name": "Kapilkumar Patel", + "author_inst": "Center for Advanced Lung Disease and Lung Transplant Program. Tampa General Hospital, FL, USA" + }, + { + "author_name": "Argyrios Tzouvelekis", + "author_inst": "Department of Respiratory Medicine, University of Patras, Patras, Greece." + }, + { + "author_name": "Maria Kapetanaki", + "author_inst": "Department of Epidemiology, College of Public Health, and Health Professions, and College of Medicine, University of Florida, Gainesville, FL, USA." + }, + { + "author_name": "Brenda Juan-Guardela", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + }, + { + "author_name": "Kami Kim", + "author_inst": "Division of infectious Disease, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA." + }, + { + "author_name": "Panayiotis V Benos", + "author_inst": "Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA." + }, + { + "author_name": "Jose Herazo-Maya", + "author_inst": "Ubben Center for Pulmonary Fibrosis Research, Division of Pulmonary, Critical Care and Sleep Medicine. Department of Internal Medicine, Morsani College of Medic" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, + { + "rel_doi": "10.1101/2023.10.23.563139", + "rel_title": "Feasibility of intranasal delivery of thin-film freeze-dried monoclonal antibodies", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563139", + "rel_abs": "Monoclonal antibodies (mAbs) administered intranasally as dry powders can be potentially applied for the treatment or pre-exposure prevention of viral infections in the upper respiratory tract. However, a method to transform the mAbs from liquid to dry powders suitable for intranasal administration and a device that can spray the dry powders to the desired region of the nasal cavity are needed to fully realize the potentials of the mAbs. Herein, we report that thin-film freeze-drying can be applied to prepare aerosolizable mAb dry powders and that the dry powders can be sprayed into the posterior nasal cavity using the Unidose (UDS) Powder Nasal Spray System from Aptar Pharma. AUG-3387, a human-derived mAb that neutralizes the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was used in the present study. First, we prepared AUG-3387 thin-film freeze-dried powders (i.e., TFF AUG-3387 powders) from liquid formulations containing different levels of mAbs. The TFF AUG-3387 powder with the highest solid content (i.e., TFF AUG-3387C powder) was then chosen for further characterization, including the evaluation of the plume geometry, spray pattern, and particle size distribution after the powder was sprayed using the UDS Powder device. Finally, the deposition patterns of the TFF AUG-3387C powder sprayed using the UDS Powder device were studied using 3D-printed nasal replica casts based on an adult model and a child model. It is concluded that it is feasible to intranasally deliver mAbs as dry powders by transforming the mAbs into dry powders using thin-film freeze-drying and then spray the powder using the UDS Powder device.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yu-Sheng Yu", + "author_inst": "The University of Texas at Austin, College of Pharmacy" + }, + { + "author_name": "Haiyue Xu", + "author_inst": "The University of Texas at Austin, College of Pharmacy" + }, + { + "author_name": "Khaled AboulFotouh", + "author_inst": "The University of Texas at Austin, College of Pharmacy" + }, + { + "author_name": "Gerallt Williams", + "author_inst": "Aptar Pharma, Le Vaudreuil, France" + }, + { + "author_name": "Julie Suman", + "author_inst": "Aptar Pharma, Congers, NY, United States" + }, + { + "author_name": "Sawittree Sahakijpijarn", + "author_inst": "TFF Pharmaceuticals, Inc. Fort Worth, TX, United States" + }, + { + "author_name": "Chris Cano", + "author_inst": "TFF Pharmaceuticals, Inc. Fort Worth, TX, United States" + }, + { + "author_name": "Zachary Warnken", + "author_inst": "Via Therapeutics, Inc. Austin, Texas, United States" + }, + { + "author_name": "Kevin C.-W. Wu", + "author_inst": "National Taiwan University, Department of Chemical Engineering, Taipei, Taiwan" + }, + { + "author_name": "Robert O Williams III", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Zhengrong Cui", + "author_inst": "The University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, + { + "rel_doi": "10.1101/2023.10.23.563669", + "rel_title": "SARS-CoV-2 induces acute neurological signs while Calcitonin Gene-Related Peptide (CGRP) signaling blockade reduces interleukin 6 (IL-6) release and weight loss in mouse models", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563669", + "rel_abs": "COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. We evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS-CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. We determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that blockage of CGRP signaling protects against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shafaqat M Rahman", + "author_inst": "University of Rochester" + }, + { + "author_name": "David W Buchholz", + "author_inst": "Cornell University" + }, + { + "author_name": "Brian Imbiakha", + "author_inst": "Cornell University" + }, + { + "author_name": "Mason C Jaeger", + "author_inst": "Cornell University" + }, + { + "author_name": "Justin Leach", + "author_inst": "University of Rochester" + }, + { + "author_name": "Raven M Osborn", + "author_inst": "University of Rochester" + }, + { + "author_name": "Ann O Birmingham", + "author_inst": "University of Rochester" + }, + { + "author_name": "Stephen Dewhurst", + "author_inst": "University of Rochester" + }, + { + "author_name": "Hector C Aguilar", + "author_inst": "Cornell University" + }, + { + "author_name": "Anne E Luebke", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, + { + "rel_doi": "10.1101/2023.10.23.563621", + "rel_title": "Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563621", + "rel_abs": "Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David J Bean", + "author_inst": "Boston University Chobanian & Avedisian School of Medicine" + }, + { + "author_name": "Janet Monroe", + "author_inst": "Boston University Chobanian & Avedisian School of Medicine" + }, + { + "author_name": "Yan Mei Liang", + "author_inst": "Boston University Chobanian & Avedisian School of Medicine" + }, + { + "author_name": "Ella Borberg", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yasmeen Senussi", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Zoe Swank", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Sujata Chalise", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "David Walt", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Janice Weinberg", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Manish Sagar", + "author_inst": "Boston University Chobanian & Avedisian School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.22.563481", + "rel_title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", + "rel_abs": "Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ashley Priddey", + "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" + }, + { + "author_name": "Michael Xin Hua Chen-Xu", + "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" + }, + { + "author_name": "Daniel James Cooper", + "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" + }, + { + "author_name": "Serena MacMillan", + "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" + }, + { + "author_name": "Georg Meisl", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" + }, + { + "author_name": "Catherine K Xu", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" + }, + { + "author_name": "Myra Hosmillo", + "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Ian G Goodfellow", + "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Rafael Kollyfas", + "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" + }, + { + "author_name": "Rainer Doffinger", + "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK" + }, + { + "author_name": "John R Bradley", + "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" + }, + { + "author_name": "Irina I Mohorianu", + "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" + }, + { + "author_name": "Rachel Jones", + "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" + }, + { + "author_name": "Tuomas P.J. Knowles", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" + }, + { + "author_name": "Rona Smith", + "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" + }, + { + "author_name": "Vasilis Kosmoliaptsis", + "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.23.563088", + "rel_title": "Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity", + "rel_date": "2023-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563088", + "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Richard T Eastman", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Radda Rusinova", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Karl F Herold", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Xi-Ping Huang", + "author_inst": "University of North Carolina School of Medicine" + }, + { + "author_name": "Patricia Dranchak", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Ty C Voss", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Sandeep Rana", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Jonathan H Shrimp", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Alex D White", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Hugh C Hemmings Jr.", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Bryan L Roth", + "author_inst": "University of North Carolina School of Medicine" + }, + { + "author_name": "James Inglese", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + }, + { + "author_name": "Olaf S Andersen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jayme L Dahlin", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "pharmacology and toxicology" + }, + { + "rel_doi": "10.1101/2023.10.23.563427", + "rel_title": "A bioactive peptide from the pearl has dual roles in resisting SARS-CoV-2 infection and its complications", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563427", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is a critical receptor for the entry of the SARS-CoV-2 virus into cells. Moreover, a decrease in ACE2 level and its activity due to SARS-CoV-2 infection is considered a crucial reason for the development of Covid-19-associated complications. Here, we report a bioactive peptide derived from the seawater pearl oyster Pinctada fucata, named SCOL polypeptide, which binds strongly to ACE2 and effectively inhibits 65% of the binding of the SARS-CoV-2 S protein to ACE2; thus, this peptide can be used as a blocker to enable cells to resist SARS-CoV-2 infection. The SCOL polypeptide also increases ACE2 enzyme activity by 3.76 times. Previous studies have shown that ACE2 deficiency is associated with inflammation, pain, cardiovascular diseases, insulin resistance, and nervous system injury. Therefore, the SCOL polypeptide can be used to treat or alleviate complications such as lung inflammation, pain, diabetes, cardiovascular diseases, and loss of taste or smell caused by SARS-CoV-2 infection. Thus, the SCOL polypeptide can play a dual role in resisting SARS-CoV-2 infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xiaojun Liu", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Yayu Wang", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Zehui Yin", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Qin Wang", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Xinjiani Chen", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Bailei Li", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Liping Yao", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Zhen Zhang", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + }, + { + "author_name": "Rongqing Zhang", + "author_inst": "Yangtze Delta Region Institute of Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, + { + "rel_doi": "10.1101/2023.10.22.563490", + "rel_title": "Screening Peptide Drug Candidates to Neutralize Whole Viral Agents : A Case study with SARS-CoV-2 Virus", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563490", + "rel_abs": "Covid19 pandemic revealed the reality for the need of therapeutic and pharmaceutical molecule development in a short time with different approaches. Although the enhancement of immunological memory by vaccination was the quicker and robust strategy, still medication is required for immediate treatment for a patient. For this purpose, one of the approaches is developing new therapeutic molecule development like peptide-based drugs. Also, peptides can be used developing other molecules like nanobodies. Here, M13 phage display library was used for selecting SARS-CoV-2 interacting peptides for developing a neutralizing molecule for further use. Biopanning was applied with four iterative cycles to select phages displaying different 12-amino acid-long peptides. Then, the M13 phage genomic region where peptide sequences expressed were analyzed and sequences were obtained. Randomly selected peptide sequences were synthesized by solid-state peptide synthesis method. These peptides were analyzed by quartz crystal microbalance method in terms or peptide interaction capacity with specifically wild-type S protein. Next, QCM data was further validated by enzyme-linked immunosorbent assay (ELISA) in order to check peptides according to their neutralizing capacity rather than binding to S1 protein. The results showed that, phage display served an opportunity for selecting peptides which can be used and developed further as pharmaceutical molecules. More specifically, scpep3, scpep8 and scpep10 had both binding and neutralizing capacity for S1 protein as a candidate for therapeutic molecule.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Cemile Elif Ozcelik", + "author_inst": "Bilkent University" + }, + { + "author_name": "Cemre Zekiye Araz", + "author_inst": "Synbiotik Biotechnology and Biomedical Technology Bilkent Kumeevler, Cankaya, Ankara, 06800, Turkey." + }, + { + "author_name": "Ozgur Yilmaz", + "author_inst": "Material Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli, 41470, Turkey." + }, + { + "author_name": "Sevgi Gulyuz", + "author_inst": "Material Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli, 41470, Turkey." + }, + { + "author_name": "Aykut Ozkul", + "author_inst": "School of Veterinaty Medicine, Ankara University" + }, + { + "author_name": "Urartu Ozgur Safak Seker", + "author_inst": "BILKENT UNIVERSITY" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, + { + "rel_doi": "10.1101/2023.10.21.563433", + "rel_title": "Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.21.563433", + "rel_abs": "Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution. Results: We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2000 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment. Availability: The data underlying the article are available in the online Supplementary Material.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anze Bozic", + "author_inst": "Jozef Stefan Institute" + }, + { + "author_name": "Rudolf Podgornik", + "author_inst": "UCAS" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, + { + "rel_doi": "10.1101/2023.10.20.563308", + "rel_title": "Assessing nanobody interaction with SARS-CoV-2 Nsp9", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.20.563308", + "rel_abs": "The interaction between SARS-CoV-2 non-structural protein Nsp9 and the nanobody 2NSP90 was investigated by NMR spectroscopy using the paramagnetic perturbation methodology PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation). The Nsp9 monomer is an essential component of the replication and transcription complex (RTC) that reproduces the viral gRNA for subsequent propagation. Therefore preventing Nsp9 recruitment in RTC would represent an efficient antiviral strategy that could be applied to different coronaviruses, given the Nsp9 relative invariance. The NMR results were consistent with a previous characterization suggesting a 4:4 Nsp9-to-nanobody stoichiometry with the occurrence of two epitope pairs on each of the Nsp9 units that establish the inter-dimer contacts of Nsp9 tetramer. The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. However a different distribution of the mapped epitopes on the tetramer surface with respect to the former 4:4 complex could also be possible, as well as different stoichiometries of the Nsp9-nanobody assemblies such as the 2:2 stoichiometry suggested by the recent crystal structure of the Nsp9 complex with 2NSP23 (PDB ID: 8dqu), a nanobody exhibiting essentially the same affinity as 2NSP90. The experimental NMR evidence, however, ruled out the occurrence in liquid state of the relevant Nsp9 conformational change observed in the same crystal structure.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Gennaro Esposito", + "author_inst": "New York University Abu Dhabi" + }, + { + "author_name": "Yamanappa Hunashal", + "author_inst": "New York University Abu Dhabi" + }, + { + "author_name": "Mathias Percipalle", + "author_inst": "New York University Abu Dhabi" + }, + { + "author_name": "Federico Fogolari", + "author_inst": "University of Udine" + }, + { + "author_name": "Tomas Venit", + "author_inst": "New York University Abu Dhabi" + }, + { + "author_name": "Ainars Leonchiks", + "author_inst": "ASLA Biotech AB" + }, + { + "author_name": "Kristin C. Gunsalus", + "author_inst": "New York University" + }, + { + "author_name": "Fabio Piano", + "author_inst": "New York University" + }, + { + "author_name": "Piergiorgio Percipalle", + "author_inst": "New York University Abu Dhabi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, + { + "rel_doi": "10.1101/2023.10.23.563555", + "rel_title": "Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563555", + "rel_abs": "Enveloped viruses carry one or multiple proteins with receptor binding functionalities. Functional receptors can either be glycans, proteinaceous or both, recombinant protein approaches are instrumental to gain more insight into these binding properties. Visualizing and measuring receptor binding normally entails antibody detection or direct labelling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here we report a suite of different fluorescent fusions, both N- and/or C- terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained a total of three or six fluorescent protein barrels and were applied directly to cells to determine receptor binding properties.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ilhan Tomris", + "author_inst": "Utrecht Institute for Pharmaceutical Sciences, Utrecht University" + }, + { + "author_name": "Roosmarijn van der Woude", + "author_inst": "Utrecht Institute for Pharmaceutical Sciences, Utrecht University" + }, + { + "author_name": "Rebeca de Paiva Droes Rocha", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Alba Torrents de la Pena", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Andrew B. Ward", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Robert Paul de Vries", + "author_inst": "Utrecht Institute for Pharmaceutical Sciences, Utrecht University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, + { + "rel_doi": "10.1101/2023.10.21.563398", + "rel_title": "Evaluation of the neutralising antibody response in human and hamster sera against SARS-CoV-2 variants up to and including BA.2.86 using an authentic virus neutralisation assay", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.21.563398", + "rel_abs": "New vaccines, therapeutics and immunity elicited by natural infection create evolutionary pressure on SARS-CoV-2 to evolve and adapt to evade vaccine-induced and infection-elicited immunity. Vaccine and therapeutics developers thus find themselves in an \"arms race\" with the virus. The ongoing assessment of emerging SARS-CoV-2 variants remains essential as the global community transitions from an emergency response to a long-term management plan. Here, we describe how an authentic virus neutralisation assay using low passage clinical virus isolates has been employed to monitor resistance of emerging virus variants to neutralising antibodies from humans and experimentally infected hamsters. Sera and plasma from people who received three doses of a vaccine as well as those who received a bivalent booster were assessed against SARS-CoV-2 variants, up to and including BA.2.86. Contemporary or recent virus variants showed substantial resistance to neutralisation by antibodies from those who had received three vaccines but were still effectively neutralised by antibodies from individuals who had received a bivalent booster (ancestral/BA.1). Convalescent sera from hamsters that had been experimentally infected with one of seven virus variants (ancestral, BA.1, BA.4, BA.5.2.1, XBB.1.5, XBB.1.16, XBB.2.3) were also tested here. The most contemporary variant, BA.2.86, was effectively neutralised by sera from hamsters infected with XBB.1.5 and XBB.1.16 but it was not neutralised by sera from those infected with BA.5.2.1. These data support the recommendations given by the WHO that a new vaccine was required and should consist of an XBB sub-lineage antigen.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Naomi S Coombes", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Kevin R Bewley", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Yann Le Duff", + "author_inst": "Scientific Research and Innovation, Medicines and Healthcare products Regulatory Agency, South Mimms, United Kingdom" + }, + { + "author_name": "Nassim Alami-Rahmouni", + "author_inst": "Scientific Research and Innovation, Medicines and Healthcare products Regulatory Agency, South Mimms, United Kingdom" + }, + { + "author_name": "Kathryn A Ryan", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Sarah Kempster", + "author_inst": "Scientific Research and Innovation, Medicines and Healthcare products Regulatory Agency, South Mimms, United Kingdom" + }, + { + "author_name": "Deborah Ferguson", + "author_inst": "Scientific Research and Innovation, Medicines and Healthcare products Regulatory Agency, South Mimms, United Kingdom" + }, + { + "author_name": "Elizabeth R Davies", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Thomas M Weldon", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Eleanor S Cross", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Lauren Smith", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Conner Norris", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Karly Rai Rogers-Broadway", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Kuiama Lewandowski", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Samantha Treagus", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Steven T Pullan", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Bassam Hallis", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Sue Charlton", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Yper Hall", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + }, + { + "author_name": "Simon G. P. Funnell", + "author_inst": "UK Health Security Agency, Porton Down, Salisbury, Wiltshire, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.10.19.563209", "rel_title": "Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant", @@ -1043,7 +1755,7 @@ "rel_date": "2023-10-19", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.18.563016", - "rel_abs": "Vaccines have demonstrated remarkable effectiveness in protecting against COVID-19; however, concerns regarding vaccine-associated enhanced respiratory diseases (VAERD) following breakthrough infections have emerged. Spike protein subunit vaccines for SARS-CoV-2 induce VAERD in hamsters, where aluminum adjuvants promote a Th2-biased immune response, leading to increased type 2 pulmonary inflammation in animals with breakthrough infections. To gain a deeper understanding of the potential risks and the underlying mechanisms of VAERD, we immunized ACE2-humanized mice with SARS-CoV-2 Spike protein adjuvanted with aluminum and CpG-ODN. Subsequently, we exposed them to increasing doses of SARS-CoV-2 to establish a breakthrough infection. The vaccine elicited robust neutralizing antibody responses, reduced viral titers, and enhanced host survival. However, following a breakthrough infection, vaccinated animals exhibited severe pulmonary immunopathology, characterized by a significant perivascular infiltration of eosinophils and CD4+ T cells, along with increased expression of Th2/Th17 cytokines. Intracellular flow cytometric analysis revealed a systemic Th17 inflammatory response, particularly pronounced in the lungs. Our data demonstrate that aluminum/CpG adjuvants induce strong antibody and Th1-associated immunity against COVID-19 but also prime a robust Th2/Th17 inflammatory response, which may contribute to the rapid onset of T cell-mediated pulmonary immunopathology following a breakthrough infection. These findings underscore the necessity for further research to unravel the complexities of VAERD in COVID-19 and to enhance vaccine formulations for broad protection and maximum safety.", + "rel_abs": "Vaccines have demonstrated remarkable effectiveness in protecting against COVID-19; however, concerns regarding vaccine-associated enhanced respiratory diseases (VAERD) following breakthrough infections have emerged. Spike protein subunit vaccines for SARS-CoV-2 induce VAERD in hamsters, where aluminum adjuvants promote a Th2-biased immune response, leading to increased type 2 pulmonary inflammation in animals with breakthrough infections. To gain a deeper understanding of the potential risks and the underlying mechanisms of VAERD, we immunized ACE2-humanized mice with SARS-CoV-2 Spike protein adjuvanted with aluminum and CpG-ODN. Subsequently, we exposed them to increasing doses of SARS-CoV-2 to establish a breakthrough infection. The vaccine elicited robust neutralizing antibody responses, reduced viral titers, and enhanced host survival. However, following a breakthrough infection, vaccinated animals exhibited severe pulmonary immunopathology, characterized by a significant perivascular infiltration of eosinophils and CD4+ T cells, along with increased expression of Th2/Th17 cytokines. Intracellular flow cytometric analysis revealed a systemic Th17 inflammatory response, particularly pronounced in the lungs. Our data demonstrate that aluminum/CpG adjuvants induce strong antibody and Th1-associated immunity against COVID-19 but also prime a robust Th2/Th17 inflammatory response, which may contribute to the rapid onset of T cell-mediated pulmonary immunopathology following a breakthrough infection. These findings underscore the necessity for further research to unravel the complexities of VAERD in COVID-19 and to enhance vaccine formulations for broad protection and maximum safety.\n\nSignificance statementThis research investigates the safety and efficacy of a Spike protein subunit vaccine adjuvanted with Alum and CpG in an ACE2-humanized mouse model, simulating SARS-CoV-2 breakthrough infections. The study reveals that despite robust protection against severe COVID-19, vaccinated mice exhibit substantial pulmonary immunopathology, including eosinophilia and enhanced Th2 effector immunity, following breakthrough infections. Surprisingly, the study also uncovers a significant systemic Th17 inflammatory response in vaccinated mice. This research sheds light on the potential risks associated with COVID-19 vaccine breakthrough infections and the need for a comprehensive understanding of vaccine-induced immune responses, emphasizing the importance of ongoing research, surveillance, and careful vaccine development for both protection and safety in the fight against the COVID-19 pandemic.", "rel_num_authors": 8, "rel_authors": [ { @@ -1109,7 +1821,7 @@ "rel_date": "2023-10-19", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.19.23297194", - "rel_abs": "INTRODUCTION: Adverse events (AE) such as pain at injection site or fever are common after COVID-19 vaccination. We aimed to describe determinants of AE after COVID-19 vaccination and investigate the association between AE and pre- and post-vaccination antibody concentrations. METHODS: Participants of an ongoing prospective cohort study (VASCO) completed a questionnaire on AE within two months after COVID-19 vaccination and provided 6-monthly serum samples. Data from May 2021 to November 2022 were included. Logistic regression analyses were performed to investigate determinants of AE after mRNA vaccination, including pre-vaccination Ig antibody concentrations against the receptor binding domain. Multivariable linear regression was performed in SARS-CoV-2 naive participants to assess the association between AE and log-transformed antibody concentrations 3-8 weeks after mRNA vaccination. RESULTS: 47,947 AE questionnaires were completed by 28,032 participants. In 42% and 34% of questionnaires, injection site and systemic AE were reported, respectively. In 2.2% of questionnaires, participants sought medical attention due to AE. AE were reported significantly more frequently by women, younger participants (<60 years), participants with medical risk conditions and Spikevax recipients (versus Comirnaty). Higher pre-vaccination antibody concentrations were associated with higher incidence of systemic AE after the second and third dose, but not with injection site AE or AE for which medical attention was sought. Any AE after the third dose was associated with higher post-vaccination antibody concentrations (geometric mean concentration ratio: 1.38, 95%CI 1.23-1.54). CONCLUSION: Our study suggests that high pre-vaccination antibody levels induce AE, and that experiencing AE may be a marker for a good antibody response to vaccination.", + "rel_abs": "INTRODUCTIONAdverse events (AE) such as pain at injection site or fever are common after COVID-19 vaccination. We aimed to describe determinants of AE after COVID-19 vaccination and investigate the association between AE and pre- and post-vaccination antibody concentrations.\n\nMETHODSParticipants of an ongoing prospective cohort study (VASCO) completed a questionnaire on AE within two months after COVID-19 vaccination and provided 6-monthly serum samples. Data from May 2021 to November 2022 were included. Logistic regression analyses were performed to investigate determinants of AE after mRNA vaccination, including pre-vaccination Ig antibody concentrations against the receptor binding domain. Multivariable linear regression was performed in SARS-CoV-2 naive participants to assess the association between AE and log-transformed antibody concentrations 3-8 weeks after mRNA vaccination.\n\nRESULTS47,947 AE questionnaires were completed by 28,032 participants. In 42% and 34% of questionnaires, injection site and systemic AE were reported, respectively. In 2.2% of questionnaires, participants sought medical attention due to AE. AE were reported significantly more frequently by women, younger participants (<60 years), participants with medical risk conditions and Spikevax recipients (versus Comirnaty). Higher pre-vaccination antibody concentrations were associated with higher incidence of systemic AE after the second and third dose, but not with injection site AE or AE for which medical attention was sought. Any AE after the third dose was associated with higher post-vaccination antibody concentrations (geometric mean concentration ratio: 1.38, 95%CI 1.23-1.54).\n\nCONCLUSIONOur study suggests that high pre-vaccination antibody levels are associated with AE, and that experiencing AE may be a marker for a good antibody response to vaccination.", "rel_num_authors": 7, "rel_authors": [ { @@ -1201,41 +1913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.18.23297204", - "rel_title": "Excess deaths in China during SARS-CoV-2 viral waves in 2022-2023", - "rel_date": "2023-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.18.23297204", - "rel_abs": "Background The extent to which the Omicron variant of SARS-CoV-2 raised death rates in China during its viral wave of December 2022-January 2023 remains undocumented. Methods We worked with an established national survey organization to survey 8,004 adults in all 31 administrative areas of China to ask about deaths in families since January 2020. We examined age-specific death rates, focusing on deaths above age 60 years, and at 15-59 years. We compared these to the United Nations (UN) estimates of age-specific mortality in 2019. Findings The survey participants were broadly similar to the 2020 census and other national surveys in age, sex, region, and smoking status, but had lower SARS-CoV-2 vaccination rates and higher education levels. There were no differences between reporting of deaths during the Omicron period versus earlier. The survey captured 456 deaths, of which 329 occurred at ages 60+ years and 212 were women. At ages 60+ years, death rates per 1000 rose 242% (95%CI 128-398%) during December 2022-January 2023. Deaths at ages 15-59 years did not rise appreciably. The UN estimates approximately 675,000 deaths per month at ages 60+ years in 2019. If rates doubled nationally as in our survey, China had approximately 1.35 million excess deaths over the two months. Interpretation China experienced a sharp but short increase in excess deaths among its elderly during the Omicron wave. If death registry data corroborate our estimates of substantial excess deaths in China, the worldwide estimates of excess deaths to 2023 may need upward adjustment.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "University of Toronto" - }, - { - "author_name": "Teresa Lam", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Ed Morawski", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Angus Reid", - "author_inst": "Angus Reid Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.17.23297174", "rel_title": "Persistent high mortality rates for Diabetes Mellitus and Hypertension after excluding deaths associated with COVID-19 in Brazil, 2020-2022", @@ -1634,7 +2311,7 @@ "rel_date": "2023-10-16", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.13.562198", - "rel_abs": "This research offers a bioinformatics approach to forecasting both domestic and wild animals likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/562198v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@1c351d4org.highwire.dtl.DTLVardef@313633org.highwire.dtl.DTLVardef@dd6e2borg.highwire.dtl.DTLVardef@16bd1b3_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "This research offers a bioinformatics approach to forecasting both domestic and wild animals likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/562198v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@15bca85org.highwire.dtl.DTLVardef@14cfa0dorg.highwire.dtl.DTLVardef@b485cborg.highwire.dtl.DTLVardef@1bbd3d0_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 8, "rel_authors": [ { @@ -1729,6 +2406,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.10.11.23296868", + "rel_title": "Did long COVID increase road deaths in the U.S.?", + "rel_date": "2023-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296868", + "rel_abs": "ObjectiveTo examine data on COVID-19 disease associated with a 10 percent increase in U.S. road deaths from 2020 to 2021 that raises the question of the potential effect of pandemic stress and neurological damage from COVID-19 disease.\n\nMethodsPoisson regression was used to estimate the association of recent COVID-19 cases, accumulated cases, maximum temperatures, truck registrations, and gasoline prices with road deaths monthly among U.S. states in 2021. Using the regression coefficients, changes in each risk factor from 2020 to 2021 were used to calculate expected deaths in 2021 if each factor had remained the same as in 2020.\n\nResultsCorrected for the other risk factors, road deaths were associated with accumulated COVID-19 cases but not cases in the previous month. More than 20,700 road deaths were associated with the changes in accumulated COVID-19 cases but were substantially offset by about 19,100 less-than-expected deaths associated with increased gasoline prices.\n\nConclusionsWhile more research is needed, the data are sufficient to warn people with \"long COVID\" to minimize road use.\n\nWhat is already known about this topicPrevious short-term fluctuations in road deaths are related to changes in temperature, fuel prices, and truck registrations.\n\nWhat this study addsCorrected for other risk factors, the monthly changes in road deaths from 2020 to 2021 in U.S. states were associated with cumulative COVID-19 cases.\n\nHow this study might affect research, practice, or policyStudies are needed to distinguish the potential relative effects of neurological damage as well as the stress of coping with the pandemic on driving, walking, and bicyclist behavior. Warning people with \"long covid\" about road risk is warranted.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Leon S Robertson", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.11.561987", "rel_title": "Resolving the pharmacological redox-sensitivity of SARS-CoV-2 PLpro in drug repurposing screening enabled identification of the competitive GRL-0617 binding site inhibitor CPI-169", @@ -2280,7 +2976,7 @@ "rel_date": "2023-10-15", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.13.23296903", - "rel_abs": "ImportanceActive monitoring of health outcomes after COVID-19 vaccination provides early detection of rare outcomes that may not be identified in prelicensure trials.\n\nObjectiveTo conduct near real-time monitoring of health outcomes following COVID-19 vaccination in the United States (US) pediatric population aged 6 months to 17 years.\n\nDesignWe evaluated 21 pre-specified health outcomes; 15 were sequentially tested through near real-time surveillance, and 6 were monitored descriptively within a cohort of vaccinated children. We tested for increased rate of each outcome following vaccination compared to a historical comparator cohort.\n\nSettingThis population-based study was conducted under the US Food and Drug Administration public health surveillance mandate using three commercial claims databases.\n\nParticipantsChildren aged 6 months to 17 years were included if they received a monovalent COVID-19 vaccine dose before early 2023 and had continuous enrollment in a medical health insurance plan from the start of an outcome-specific clean window to the COVID-19 vaccination dose.\n\nExposureExposure was defined as receipt of a monovalent BNT162b2, mRNA-1273, or NVX-CoV2373 COVID-19 vaccine dose. The primary analysis evaluated dose 1 and dose 2 combined, and secondary analyses evaluated each dose separately. Follow-up time was censored at death, disenrollment, end of risk window, end of study period, or a subsequent dose administration.\n\nMain OutcomesTwenty-one prespecified health outcomes.\n\nResultsThe study included 4,102,016 enrollees aged 6 months to17 years. Thirteen of 15 outcomes sequentially tested did not meet the threshold for a statistical signal. In the primary analysis, myocarditis or pericarditis signals were detected following BNT162b2 vaccine in children aged 12-17 years old and seizures/convulsions signals were detected following vaccination with BNT162b2 and mRNA-1273 in children aged 2-4/5 years. However, in a post-hoc sensitivity analysis, the seizures/convulsions signal was sensitive to background rates selection and was not observed when 2022 background rates were selected instead of 2020 rates.\n\nConclusions and RelevanceOf the two signaled outcomes, the myocarditis or pericarditis signals are consistent with previously published reports. The new signal detected for seizures/convulsions among younger children should be further investigated in a robust epidemiological study with better confounding adjustment.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDid active monitoring detect statistical signals for health outcomes following monovalent COVID-19 vaccination in the US children aged 6 months to 17 years?\n\nFindingsIn this study including 4,102,106 vaccinated enrollees from three commercial claims databases, myocarditis or pericarditis signaled after BNT162b2 (12-17 years) and a new signal was detected for seizures/convulsions after BNT162b2 (2-4 years) and mRNA1273 COVID-19 vaccinations (2-5 years).\n\nMeaningNear real-time monitoring of vaccines can rapidly identify potential safety concerns. While the myocarditis or pericarditis signal is consistent with existing evidence, the new seizures/convulsions signal should be interpreted cautiously given study limitations.", + "rel_abs": "ImportanceActive monitoring of health outcomes after COVID-19 vaccination provides early detection of rare outcomes that may not be identified in prelicensure trials.\n\nObjectiveTo conduct near real-time monitoring of health outcomes following COVID-19 vaccination in the United States (US) pediatric population aged 6 months to 17 years.\n\nDesignWe evaluated 21 pre-specified health outcomes; 15 were sequentially tested through near real-time surveillance, and 6 were monitored descriptively within a cohort of vaccinated children. We tested for increased rate of each outcome following vaccination compared to a historical comparator cohort.\n\nSettingThis population-based study was conducted under the US Food and Drug Administration public health surveillance mandate using three commercial claims databases.\n\nParticipantsChildren aged 6 months to 17 years were included if they received a monovalent COVID-19 vaccine dose before early 2023 and had continuous enrollment in a medical health insurance plan from the start of an outcome-specific clean window to the COVID-19 vaccination dose.\n\nExposureExposure was defined as receipt of a monovalent BNT162b2, mRNA-1273, or NVX-CoV2373 COVID-19 vaccine dose. The primary analysis evaluated dose 1 and dose 2 combined, and secondary analyses evaluated each dose separately. Follow-up time was censored at death, disenrollment, end of risk window, end of study period, or a subsequent dose administration.\n\nMain OutcomesTwenty-one prespecified health outcomes.\n\nResultsThe study included 4,102,016 enrollees aged 6 months to17 years. Thirteen of 15 outcomes sequentially tested did not meet the threshold for a statistical signal. In the primary analysis, myocarditis or pericarditis signals were detected following BNT162b2 vaccine in children aged 12-17 years old and seizures/convulsions signals were detected following vaccination with BNT162b2 and mRNA-1273 in children aged 2-4/5 years. However, in a post-hoc sensitivity analysis, the seizures/convulsions signal was sensitive to background rates selection and was not observed when 2022 background rates were selected instead of 2020 rates.\n\nConclusions and RelevanceOf the two signaled outcomes, the myocarditis or pericarditis signals are consistent with previously published reports. The new signal detected for seizures/convulsions among younger children should be further investigated in a robust epidemiological study with better confounding adjustment.", "rel_num_authors": 26, "rel_authors": [ { @@ -3051,37 +3747,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.10.12.23296938", - "rel_title": "The impact of COVID-19 on non-communicable disease patients in sub-Saharan African countries: systematic review", - "rel_date": "2023-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296938", - "rel_abs": "BackgroundCOVID-19 and its prevention measures have had a significant impact on patients with non-communicable diseases (NCDs) by disrupting routine healthcare service and increasing risk factors. These challenges were expected to be more severe in sub-Saharan Africa due to the lack of physical infrastructure and inadequate resources. The quantity of studies conducted was limited, and there was a lack of published systematic reviews in the specified region. This systematic review aimed to comprehensively assess the impact of COVID-19 on NCD patients in sub-Saharan Countries.\n\nMethodThis systematic review adheres to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines and is registered with PROSPERO (ID CRD42023387755). Extensive searches were conducted in MEDLINE, EMBASE, and CINAHL databases in November 2022, supplemented by a manual search of references, grey literature, and the WHO COVID-19 database. Inclusion criteria encompassed studies that reported on the impact of COVID-19 on NCD patients in sub-Saharan African countries, focusing on access to care, health outcomes, and factors related to NCDs. Critical appraisal of study quality was performed using the Joanna Briggs Institute (JBI) analytical cross-sectional studies critical appraisal tool. Data were extracted and synthesized, highlighting the main findings and relevant limitations.\n\nFindingsThis review included 26 primary studies with a cumulative sample size of 15,722 participants, conducted in six sub-Saharan African countries. Findings of these studies identified that the COVID-19 pandemic caused a disruption of 76% to 80% of regular NCDs patient care provision. The studies also identified a reduction in patient health-seeking behavior and reduced medication adherence (39.0%-63%), leading to poor treatment outcome (35.66%-55.8%). Furthermore, the pandemic and related lockdowns have been implicated in the increased prevalence of substance use, decreased physical exercise, and increased mental health problems.\n\nConclusionThis systematic review identified the complex challenges faced by NCD patients in sub-Saharan Africa during the COVID-19 pandemic. It also underlines the need to consider the indirect impact on vulnerable populations while developing pandemic prevention and control strategies for the future. The current NCD management strategies should prioritize the restoration of access to essential healthcare services while considering the multifaceted risks posed by decreased physical activity, poor dietary practices, and increased substance use.\n\nThe main limitation of this review was the study design and setting. All of the studies included in this review employed a cross-sectional design, which may result in a low quality of evidence. This study identified research conducted in only six countries among the 46 UN-classified sub-Saharan nations, which may impair the generalizability of the result.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Muluken Bafa Basa", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Jan De Vries", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "David McDonagh", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Catherine Comiskey", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.11.23296808", "rel_title": "Safety of SARS-CoV-2 test-to-stay in daycare: a regression discontinuity in time analysis", @@ -3847,6 +4512,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.10.09.561498", + "rel_title": "SHIFTR enables the unbiased and multiplexed identification of proteins bound to specific RNA regions in live cells", + "rel_date": "2023-10-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.09.561498", + "rel_abs": "RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures close to zero background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5' and 3'- terminal regions of the authentic SARS-CoV-2 RNA genome in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jens Aydin", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" + }, + { + "author_name": "Alexander Gabel", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" + }, + { + "author_name": "Sebastian Zielinski", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" + }, + { + "author_name": "Sabina Ganskih", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" + }, + { + "author_name": "Nora Schmidt", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" + }, + { + "author_name": "Christina R Hartigan", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, USA" + }, + { + "author_name": "Monica Schenone", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, USA" + }, + { + "author_name": "Steven A Carr", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, USA" + }, + { + "author_name": "Mathias Munschauer", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), University of Wuerzburg Faculty of Medicine, Wuerzbu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.10.10.23296820", "rel_title": "Perceptions of access to harm reduction services during the COVID-19 pandemic among people who inject drugs in Chicago", @@ -5013,105 +5729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.04.560875", - "rel_title": "Unveiling the antiviral capabilities of targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2", - "rel_date": "2023-10-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.04.560875", - "rel_abs": "The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase (HsDHODH), one of the enzymes in charge of pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated quinone-based compounds, discovering potent HsDHODH inhibition (low nanomolar IC50) and promising in vitro anti-SARS-CoV-2 activity (low micromolar EC50). These compounds exhibited low toxicity, indicating potential for further development. Additionally, we employed computational tools like molecular docking and QSAR models to analyze protein-ligand interactions. These findings represent a significant step forward in the search for effective antiviral treatments and have great potential to impact the development of new broad-spectrum antiviral drugs.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Aline Purificacao", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - }, - { - "author_name": "Sabrina Silva-Mendonca", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Luiza Cruz", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Sacramento", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Jairo Temerozo", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Caroline Freitas", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Bruna Godoi", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Miguel Vaidergorn", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Juliana Leite", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Luis Alvarez", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Murillo Freitas", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Meryck Silva", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Bianca Martin", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Renata Lopez", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Bruno Neves", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Fabio Costa", - "author_inst": "h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Thiago Souza", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Flavio Emery", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Andrade", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Cristina Nonato", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.05.561047", "rel_title": "Fourth dose of Microneedle Array Patch of SARS-CoV-2 S1 Protein Subunit Vaccine Elicits Robust Long-lasting Humoral Responses in mice", @@ -5769,6 +6386,117 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.10.04.560777", + "rel_title": "mRNA vaccines encoding membrane-anchored receptor-binding domains of SARS-CoV-2 mutants induce strong humoral responses and can overcome immune imprinting", + "rel_date": "2023-10-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.04.560777", + "rel_abs": "To address the limitations of whole-spike COVID vaccines, we explored mRNA vaccines encoding membrane-anchored receptor-binding domain (RBD-TMs), each a fusion of a variant RBD, the transmembrane (TM) and cytoplasmic tail (CT) fragments of the SARS-CoV-2 spike protein. In naive mice, RBD-TM mRNA vaccines against ancestral SARS-CoV-2, Beta, Delta, Delta-plus, Kappa, Omicron BA.1 or BA.5, all induced strong humoral responses against the target RBD. Multiplex surrogate viral neutralization (sVNT) assays indicated broad neutralizing activity against a range of variant RBDs. In the setting of a heterologous boost, against the background of exposure to ancestral whole spike vaccines, sVNT studies suggested that RBD-TM vaccines were able to overcome the detrimental effects of immune imprinting. Omicron BA.1 and BA.5 RBD-TM booster vaccines induced serum antibodies with 12 and 22-fold higher neutralizing activity against the target RBD than their equivalent whole spike variants. Boosting with BA.1 or BA.5 RBD-TM provided good protection against more recent variants including XBB and XBB.1.5. Each RBD-TM mRNA is 28% of the length of its whole-spike equivalent. This advantage will enable tetravalent mRNA vaccines to be developed at well-tolerated doses of formulated mRNA.\n\nOne Sentence SummarymRNA vaccines encoding membrane-anchored RBDs of SARS-CoV-2 mutants are effective vaccines that can overcome immune imprinting in mice", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Hareth A Al-Wassiti", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Stewart A Fabb", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Samantha L Grimley", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Ruby Kochappan", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Joan K Ho", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Chinn Yi Wong", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Chee Wah Tan", + "author_inst": "Duke NUS Medical School, Singapore" + }, + { + "author_name": "Thomas J Payne", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Asuka Takanashi", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Horatio Sicilia", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Serena L.Y. Teo", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + }, + { + "author_name": "Julie L McAuley", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Paula Ellenberg", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "James P Cooney", + "author_inst": "Walter and Eliza Hall Institute of Medical Research, Melbourne" + }, + { + "author_name": "Kathryn C Davidson", + "author_inst": "Walter and Eliza Hall Institute of Medical Research, Melbourne" + }, + { + "author_name": "Richard Bowen", + "author_inst": "Biomedical Sciences, Colorado State University" + }, + { + "author_name": "Marc Pellegrini", + "author_inst": "Walter and Eliza Hall Institute of Medical Research, Melbourne" + }, + { + "author_name": "Steven Rockman", + "author_inst": "Seqirus" + }, + { + "author_name": "Dale I Godfrey", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Terry M Nolan", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Georgia Deliyannis", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Damian F.J. Purcell", + "author_inst": "Peter Doherty Institute for Infection and Immunity, and Department of Infectious Diseases, University of Melbourne" + }, + { + "author_name": "Colin W Pouton", + "author_inst": "Monash Institute of Pharmaceutical Sciences, Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.10.03.560426", "rel_title": "SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia", @@ -6811,33 +7539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.01.560357", - "rel_title": "The TMPRSS2 non-protease domains regulating SARS-CoV-2 Spike in mediated virus entry", - "rel_date": "2023-10-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.01.560357", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters cells by binding to the angiotensin-converting enzyme 2 (hACE2) receptor. This process is aided by the transmembrane protease serine 2 (TMPRSS2), which enhances entry efficiency and infectiousness by cleaving the SARS-CoV-2 surface glycoprotein (Spike). The cleavage primes the Spike protein, promoting membrane fusion instead of receptor-mediated endocytosis. Despite the pivotal role played by TMPRSS2, our understanding of its non-protease distinct domains remains limited. In this report, we present evidence indicating the potential phosphorylation of a minimum of six tyrosine residues within the cytosolic tail (CT) of TMPRSS2. Through the use of TMPRSS2 CT phospho-mimetic mutants, we observed a reduction in TMPRSS2 protease activity, accompanied by a decrease in SARS-CoV-2 pseudovirus infection, which was found to occur mainly via the endosomal pathway. We expanded our investigation beyond TMPRSS2 CT and discovered the involvement of other non-protease domains in regulating infection. Our co-immunoprecipitation experiments demonstrated a strong interaction between TMPRSS2 and Spike. We revealed a 21 amino acid long TMPRSS2-Spike-binding region (TSBR) within the TMPRSS2 scavenger receptor cysteine-rich (SRCR) domain that contributes to this interaction. Our study sheds light on novel functionalities associated with TMPRSS2s cytosolic tail and SRCR region. Both of these regions have the capability to regulate SARS-CoV-2 entry pathways. These findings contribute to a deeper understanding of the complex interplay between viral entry and host factors, opening new avenues for potential therapeutic interventions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Romano Strobelt", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Julia Adler", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yosef Shaul", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.10.01.560365", "rel_title": "Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination", @@ -7314,7 +8015,7 @@ "rel_date": "2023-09-29", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.28.560070", - "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potentials of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on the inhibition of SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE, then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding Spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE also reduced syncytia formation compared to control cells. Based on our study, both TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/560070v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@7400c6org.highwire.dtl.DTLVardef@1dedae3org.highwire.dtl.DTLVardef@1f47225org.highwire.dtl.DTLVardef@171de30_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potentials of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on the inhibition of SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE, then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding Spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE also reduced syncytia formation compared to control cells. Based on our study, both TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/560070v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@3ac364org.highwire.dtl.DTLVardef@1f1eac3org.highwire.dtl.DTLVardef@16be2a6org.highwire.dtl.DTLVardef@1ed21d8_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 7, "rel_authors": [ { @@ -7351,6 +8052,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2023.09.28.23296264", + "rel_title": "Endemic means change as SARS-CoV-2 evolves", + "rel_date": "2023-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.28.23296264", + "rel_abs": "COVID-19 has become endemic, with dynamics that reflect the waning of immunity and re-exposure, by contrast to the epidemic phase driven by exposure in immunologically naive populations. Endemic does not, however, mean constant. Further evolution of SARS-CoV-2, as well as changes in behaviour and public health policy, continue to play a major role in the endemic load of disease and mortality. In this paper, we analyse evolutionary models to explore the impact that newly arising variants can have on the short-term and longer-term endemic load, characterizing how these impacts depend on the transmission and immunological properties of variants. We describe how evolutionary changes in the virus will increase the endemic load most for persistently immune-escape variants, by an intermediate amount for more transmissible variants, and least for transiently immune-escape variants. Balancing the tendency for evolution to favour variants that increase the endemic load, we explore the impact of vaccination strategies and non-pharmaceutical interventions (NPIs) that can counter these increases in the impact of disease. We end with some open questions about the future of COVID-19 as an endemic disease.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sarah Otto", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Ailene MacPherson", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Caroline Colijn", + "author_inst": "Simon Fraser University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.09.29.23296352", "rel_title": "Prevalence of COVID-19 and long COVID - Results from the 2022 Behavioral Risk Factor Surveillance System, 50 states.", @@ -8433,29 +9161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.09.26.23295911", - "rel_title": "Analysis of Potential Risk Factors of COVID-19 Based on Variants: Omicron, Delta, and Alpha", - "rel_date": "2023-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.26.23295911", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has changed which affects the risk of COVID-19 infection for specific subgroups. We focused on the subgroups based on the factors (sex, age, and vaccination) and COVID-19 strains (Alpha, Delta, and Omicron). Past studies focused on analyzing these factors based on one geographic region or one COVID-19 strain. Therefore, there is a need to understand these factors association with risk of COVID-19 infection through analyzing data from various geographic regions and strains. The association between COVID-19 strains and the factors was assessed through chi-square test and odds ratio tests. Sex, vaccination, age had a significant association with testing positive for the COVID-19 strains of interest in most geographies. The biggest difference was unvaccinated individuals have 3.14 higher odds of getting Alpha than vaccinated individuals in Canada. These findings provide insights into the groups that are more susceptible to contracting specific strains of COVID-19.\n\nSummaryThis manuscript offers a broad examination of key factors that may impact the risk of COVID-19 infection across various geographic regions. Results provide evidence about potential risk factors for COVID-19 infection around the world for certain sub-groups as COVID-19 mutates.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dharshini Kannan", - "author_inst": "Innovation Academy" - }, - { - "author_name": "Sreenidhi Muppiri", - "author_inst": "Cambridge High School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.09.25.23289158", "rel_title": "Recruitment, Consent and DNA Sample Acquisition in a U.S. Precision Health Cohort During the COVID-19 Pandemic", @@ -9049,6 +9754,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.09.22.559030", + "rel_title": "Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses", + "rel_date": "2023-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.22.559030", + "rel_abs": "Diverse mammalian species display susceptibility to and infection with SARS-CoV-2. Potential SARS-CoV-2 spillback into rodents is understudied despite their host role for numerous zoonoses and human proximity. We assessed exposure and infection among white-footed mice (Peromyscus leucopus) in Connecticut, USA. We observed 1% (6/540) wild-type neutralizing antibody seroprevalence among 2020-2022 residential mice with no cross-neutralization of variants. We detected no SARS-CoV-2 infections via RT-qPCR, but identified non-SARS-CoV-2 betacoronavirus infections via pan-coronavirus PCR among 1% (5/468) of residential mice. Sequencing revealed two divergent betacoronaviruses, preliminarily named Peromyscus coronavirus-1 and -2. Both belong to the Betacoronavirus 1 species and are [~]90% identical to the closest known relative, Porcine hemagglutinating encephalomyelitis virus. Low SARS-CoV-2 seroprevalence suggests white-footed mice may not be sufficiently susceptible or exposed to SARS-CoV-2 to present a long-term human health risk. However, the discovery of divergent, non-SARS-CoV-2 betacoronaviruses expands the diversity of known rodent coronaviruses and further investigation is required to understand their transmission extent.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Rebecca Earnest", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Anne M. Hahn", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nicole M. Feriancek", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Matthew Brandt", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Renata B. Filler", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Zhe Zhao", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Mallery I. Breban", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nicholas F.G. Chen", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Robert T. Koch", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Abbey J. Porzucek", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Afeez Sodeinde", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Alexa Garbiel", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Claire Keanna", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Hannah Litwak", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Heidi R. Stuber", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Jamie L. Cantoni", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Virginia E. Pitzer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Ximena A. Olarte Castillo", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Laura B. Goodman", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Craig B. Wilen", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Megan A. Linske", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Scott C. Williams", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Nathan D. Grubaugh", + "author_inst": "Yale School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2023.09.22.558940", "rel_title": "Multi-modal profiling of biostabilized human skin modules reveals a coordinated ecosystem response to injected mRNA-1273 COVID-19 vaccine.", @@ -9539,7 +10355,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@1f28c5dorg.highwire.dtl.DTLVardef@dd6509org.highwire.dtl.DTLVardef@1143250org.highwire.dtl.DTLVardef@f346a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@99738corg.highwire.dtl.DTLVardef@710334org.highwire.dtl.DTLVardef@1895254org.highwire.dtl.DTLVardef@7c17f2_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -10251,61 +11067,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.20.23295832", - "rel_title": "Targeted MRM-analysis of plasma proteins in frozen whole blood samples from patients with COVID-19", - "rel_date": "2023-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.20.23295832", - "rel_abs": "The COVID-19 pandemic has exposed a number of key challenges that need to be urgently addressed. In particular, rapid identification and validation of prognostic markers is required. Mass spectrometric studies of blood plasma proteomics provide a deep understanding of the relationship between the severe course of infection and activation of specific pathophysiological pathways. Analysis of plasma proteins in whole blood may also be relevant for the pandemic as it requires minimal sample preparation. Here, for the first time, frozen whole blood samples were used to analyze 189 plasma proteins using multiple reaction monitoring (MRM) mass spectrometry and stable isotope-labeled peptide standards (SIS). A total of 128 samples (FRCC, Russia) from patients with mild (n=40), moderate (n=36) and severe (n=19) COVID-19 infection and healthy controls (n=33) were analyzed. Levels of 114 proteins were quantified and compared. Significant differences between all of the groups were revealed for 61 proteins. Changes in the levels of 30 reproducible COVID-19 markers (SERPING1, CRP, C9, ORM1, APOA1, SAA1/SAA2, LBP, AFM, IGFALS, etc.) were consistent with studies performed with serum/plasma samples. Levels of 70 proteins correlated between whole blood and plasma samples. The best-performing classifier built with 13 significantly different proteins achieved the best combination of ROC-AUC (0.93-0.95) and accuracy (0.87-0.93) metrics and distinguished patients from controls, as well as patients by severity and risk of mortality. Overall, the results support the use of frozen whole blood for MRM analysis of plasma proteins and assessment of the status of patients with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anna E. Bugrova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Polina A. Strelnikova", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Alexey S. Kononikhin", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Natalia V. Zakharova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Elizaveta O. Diyachkova", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Alexander G. Brzhozovskiy", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Maria I. Indeykina", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Ilya N. Kurochkin", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Alexander V. Averyanov", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Evgeny N. Nikolaev", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.19.23295768", "rel_title": "COVID-19 VACCINE ACCEPTANCE AND HESITANCY IN GHANA: A SYSTEMATIC REVIEW", @@ -10995,6 +11756,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.09.15.557929", + "rel_title": "Third dose COVID-19 mRNA vaccine enhances IgG4 isotype switching and recognition of Omicron subvariants by memory B cells after with mRNA but not adenovirus priming", + "rel_date": "2023-09-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.15.557929", + "rel_abs": "BackgroundBooster vaccinations are recommended to improve protection against severe disease from SARS-CoV-2 infection. With primary vaccinations involving various adenoviral vector and mRNA-based formulations, it remains unclear if these differentially affect the immune response to booster doses. We here examined the effects of homologous (mRNA/mRNA) and heterologous (adenoviral vector/mRNA) vaccination on antibody and memory B cell (Bmem) responses against ancestral and Omicron subvariants.\n\nMethodsHealthy adults who received primary BNT162b2 (mRNA) (n=18) or ChAdOx1 (vector) (n=25) vaccination were sampled 1-month and 6-months after their 2nd and 3rd dose (homologous or heterologous) vaccination. Recombinant spike receptor-binding domain (RBD) proteins from ancestral, Omicron BA.2 and BA.5 variants were produced for ELISA-based serology, and tetramerized for immunophenotyping of RBD-specific Bmem.\n\nResultsDose 3 boosters significantly increased ancestral RBD-specific plasma IgG and Bmem in both cohorts. Up to 80% of ancestral RBD-specific Bmem expressed IgG1+. IgG4+ Bmem were detectable after primary mRNA vaccination, and expanded significantly to 5-20% after dose 3, whereas heterologous boosting did not elicit IgG4+ Bmem. Recognition of Omicron BA.2 and BA.5 by ancestral RBD-specific plasma IgG increased from 20% to 60% after the 3rd dose in both cohorts. Reactivity of ancestral RBD-specific Bmem to Omicron BA.2 and BA.5 increased following a homologous booster from 40% to 60%, but not after a heterologous booster.\n\nConclusionA 3rd mRNA dose generates similarly robust serological and Bmem responses in homologous and heterologous vaccination groups. The expansion of IgG4+ Bmem after mRNA priming might result from the unique vaccine formulation or dosing schedule affecting the Bmem response duration and antibody maturation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Gemma E. Hartley", + "author_inst": "Monash University" + }, + { + "author_name": "Holly A. Fryer", + "author_inst": "Monash University" + }, + { + "author_name": "Paul A. Gill", + "author_inst": "Monash University" + }, + { + "author_name": "Irene Boo", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Scott J. Bornheimer", + "author_inst": "BD Biosciences" + }, + { + "author_name": "P. Mark Hogarth", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Heidi E. Drummer", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Robyn E. O'Hehir", + "author_inst": "Alfred Health" + }, + { + "author_name": "Emily S.J. Edwards", + "author_inst": "Monash University" + }, + { + "author_name": "Menno C. van Zelm", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.17.558185", "rel_title": "Evidence associating neutrophilia, lung damage, hyperlactatemia, blood acidosis, impaired oxygen transport, and mortality in critically ill COVID-19 patients", @@ -12009,61 +12825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.13.23295114", - "rel_title": "Assessing the impact of the Gamma variant on COVID-19 Patient admissions in a Southern Brazilian tertiary hospital - A comparison of dual pandemic phases", - "rel_date": "2023-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.13.23295114", - "rel_abs": "Since the first case of COVID-19, Brazil has undergone infection waves with distinct characteristics. The description of new variants has alerted the emergence of more contagious or virulent viruses. The variant of concern Gamma emerged in Brazil and caused an epidemic wave, but its spread outside the country was limited. We report the clinical-epidemiological profile of hospitalized patients with COVID-19 by comparing two periods. A retrospective cohort study was performed. The primary outcome was to assess individuals with COVID-19 admitted in wards and intensive care units at CHC-UFPR between March 2020 and July 2021, correlating demographic, clinical-epidemiologic, and survival data with the most prevalent viral variant found in each period. We used Kaplan-Meier analysis to estimate the probability of survival and receiver operating characteristic curves to evaluate laboratory tests to find a cutoff point for poor outcomes. Data from 2,887 individuals were analyzed, 1,495 and 1,392 from the first and second periods, respectively. Hospitalization predominated among males in both periods, and the median age was significantly lower in the second one. The frequency of comorbidities was similar. Various demographic factors, clinical assessments, and laboratory tests were examined in relation to greater severity. When comparing the two studied periods, we observed predominance of the Wild virus during the first wave and the Gamma variant during the second, with no significant difference in outcomes. The findings suggest that despite the association of many factors with increased severity, the temporal variation between the two periods did not result in a notable divergence in the measured outcomes. The COVID-19 pandemic has lasted for a long time, with periods marked by peaks of cases, often caused by the emergence of viral variants, resulting in higher infection rates and rapid dissemination but, for variant Gamma, no apparent greater virulence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Natalia R Domino", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Bruna A Lapinscki", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Felipe Zhen", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Guilherme Yamaguto", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Emmanueli C S Costa", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Vitor L Moriya", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Luciane A Pereira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Ricardo Petterle", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Meri B Nogueira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Sonia M Raboni", - "author_inst": "Universidade Federal do Parana Setor de Ciencias da Saude" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23294140", "rel_title": "Effectiveness of Canadian travel restrictions in reducing burden of SARS-CoV-2 variants of concern", @@ -12629,6 +13390,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.12.23295445", + "rel_title": "Determinants of SARS-CoV-2 IgG response and decay in Canadian healthcare workers: a prospective cohort study.", + "rel_date": "2023-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295445", + "rel_abs": "IntroductionHealthcare workers (HCWs) from an interprovincial Canadian cohort were asked to give serial blood samples to identify factors associated with anti-receptor binding domain (anti-RBD) IgG response to the SARS-CoV-2 virus.\n\nMethodsMembers of the HCW cohort donated blood samples four months after their first SARS-CoV-2 immunization and again at 7, 10 and 13 months. Date and type of immunizations and dates of SARS-CoV-2 infection were collected at each of four contacts, together with information on immunologically-compromising conditions and current therapies. Blood samples were analyzed centrally for anti-RBD IgG and anti-nucleocapsid IgG (Abbott Architect, Abbott Diagnostics). Records of immunization and SARS-CoV-2 testing from public health agencies were used to assess the impact of reporting errors on estimates from the random-effects multivariable model fitted to the data.\n\nResults2752 of 4567 vaccinated cohort participants agreed to donate at least one blood sample. Modelling of anti-RBD IgG titer from 8903 samples showed an increase in IgG with each vaccine dose and with first infection. A decrease in IgG titer was found with the number of months since vaccination or infection, with the sharpest decline after the third dose. An immunization regime that included mRNA1273 (Moderna) resulted in higher anti-RBD IgG. Participants reporting multiple sclerosis, rheumatoid arthritis or taking selective immunosuppressants, tumor necrosis factor inhibitors, calcineurin inhibitors and antineoplastic agents had lower anti-RBD IgG. Supplementary analyses showed higher anti-RBD IgG in those reporting side-effects of vaccination, no relation of anti-RBD IgG to obesity and lower titers in women immunized early in pregnancy. Sensitivity analysis results suggested no important bias in the self-report data.\n\nConclusionCreation of a prospective cohort was central to the credibility of results presented here. Serial serology assessments, with longitudinal analysis, provided effect estimates with enhanced accuracy and a clearer understanding of medical and other factors affecting response to vaccination.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nicola Cherry", + "author_inst": "University of Alberta" + }, + { + "author_name": "Igor Burstyn", + "author_inst": "Dornsife School of Public Health, Drexel University" + }, + { + "author_name": "Carmen Charlton", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Yan Chen", + "author_inst": "St Jude Children's Research Hospital, Memphis" + }, + { + "author_name": "Quentin Durand-Moreau", + "author_inst": "University of Alberta" + }, + { + "author_name": "France Labreche", + "author_inst": "IRSST Montreal" + }, + { + "author_name": "Shannon Ruzycki", + "author_inst": "University of Calgary" + }, + { + "author_name": "LeeAnn Turnbull", + "author_inst": "Alberta Precision Laboratories" + }, + { + "author_name": "Tanis Zadunayski", + "author_inst": "University of Alberta" + }, + { + "author_name": "Yutaka Yasui", + "author_inst": "St Jude Children's Research Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.13.23295489", "rel_title": "Towards mitigating health inequity via machine learning: a nationwide cohort study to develop and validate ethnicity-specific models for prediction of cardiovascular disease risk in COVID-19 patients", @@ -13415,89 +14231,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.12.23295441", - "rel_title": "Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings", - "rel_date": "2023-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295441", - "rel_abs": "PurposeThis study assessed the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) coronavirus disease 2019 (COVID-19) diagnostic code U07.1 against polymerase chain reaction (PCR) test results (Objective 1), and electronic medical record (EMR)-based codified algorithm for severe COVID-19 illness based on endpoints used in the Pfizer-BioNTech COVID-19 vaccine trial against chart review (Objective 2).\n\nMethodsThis retrospective, longitudinal cohort study used EMR data from the Mass General Brigham COVID-19 Data Mart (3/1/2020-11/19/2020) for adult patients with [≥]1 PCR test, antigen test, or code U07.1 (Objective 1) and adult patients with a positive PCR test hospitalized with COVID-19 (Objective 2).\n\nResultsAmong 354,124 patients in Objective 1, 96% had [≥]1 PCR test (including 6% with [≥]1 positive PCR test; 11% with [≥]1 code U07.1). Code U07.1 had low sensitivity (54%) and positive predictive value (PPV; 63%) but high specificity (97%) against the PCR test. Among 300 patients hospitalized for COVID-19 randomly sampled for chart review in Objective 2, the EMR-based case definition for severe COVID-19 illness had high PPV (>95%), showing better performance than severe/critical COVID-19 endpoints defined by the World Health Organization (PPV: 79%).\n\nConclusionsCOVID-19 diagnosis based on ICD-10-CM code U07.1 had inadequate sensitivity and requires confirmation by PCR testing. The EMR-based case definition showed high PPV and can be used to identify cases of severe COVID-19 illness in real-world datasets. These findings highlight the importance of validating outcomes in real-world data, and can guide researchers analyzing COVID-19 data when PCR tests are not readily available.\n\nKEY POINTSO_LIThis study evaluated the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) codes and an electronic medical record (EMR)-based algorithm for identifying coronavirus disease 2019 (COVID-19) diagnosis and severe COVID-19 illness in real-world data.\nC_LIO_LIICD-10-CM code U07.1 for COVID-19 had low sensitivity and positive predictive value (PPV) against PCR tests.\nC_LIO_LIThe EMR-based algorithm for severe COVID-19 illness developed from the Pfizer- BioNTech COVID-19 vaccine trial had high PPV against chart review, and may be used to identify severe cases in real-world data.\nC_LIO_LIThese results highlight the importance of validating outcomes when conducting analyses of real-world datasets.\nC_LI\n\nPLAIN LANGUAGE SUMMARYAs polymerase chain reaction (PCR) tests for coronavirus disease 2019 (COVID-19) diagnosis are becoming less frequently used and there is no standard definition of severe COVID-19 illness, it is important to have a way of correctly identifying COVID-19 diagnosis or severe COVID-19 illness in real-world data (e.g., electronic medical records [EMRs]). This study examined: 1) how a diagnosis code for COVID-19 used in EMRs (i.e., U07.1) compares to PCR test results in terms of accurately identifying patients with COVID-19; and 2) whether a definition for severe COVID-19 illness developed based on the Pfizer-BioNTech COVID-19 vaccine trial and a definition used by the World Health Organization [WHO]) can be used to accurately identify patients with severe COVID-19 illness in EMRs. The results showed that code U07.1 was not very accurate in identifying patients with COVID-19. On the other hand, the developed definition for severe COVID-19 illness was more accurate than the WHO definition and was able to identify most patients with severe COVID-19 illness in real-world data.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mei Sheng Duh", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Catherine Nguyen", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Heather Rubino", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Christopher Herrick", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Rose Chang", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Maral DerSarkissian", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Yichuan Grace Hsieh", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Azeem Banatwala", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Louise H. Yu", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Gregory Belsky", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Marykate E. Murphy", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Janet Boyle-Kelly", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Andrew Cagan", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Bruce E. Stangle", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Pierre Y. Cremieux", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Francesca Kolitsopoulos", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Shawn N. Murphy", - "author_inst": "Mass General Brigham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23295384", "rel_title": "Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections", @@ -14335,6 +15068,57 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.09.08.556901", + "rel_title": "The role of ion dissolution in metal and metal oxide surface inactivation of SARS-CoV-2", + "rel_date": "2023-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.08.556901", + "rel_abs": "Antiviral surface coatings are under development to prevent viral fomite transmission from high-traffic touch surfaces in public spaces. Coppers antiviral properties have been widely documented; but the antiviral mechanism of copper surfaces is not fully understood. We screened a series of metal and metal oxide surfaces for antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19). Copper and copper oxide surfaces exhibited superior anti-SARS-CoV-2 activity; however, level of antiviral activity was dependent upon the composition of the carrier solution used to deliver virus inoculum. We demonstrate that copper ions released into solution from test surfaces can mediate virus inactivation, indicating a copper ion dissolution-dependent antiviral mechanism. Level of antiviral activity is, however, not dependent on the amount of copper ions released into solution per se. Instead, our findings suggest that degree of virus inactivation is dependent upon copper ion complexation with other biomolecules (e.g., proteins/metabolites) in the virus carrier solution that compete with viral components. Although using tissue culture-derived virus inoculum is experimentally convenient to evaluate the antiviral activity of copper-derived test surfaces, we propose that the high organic content of tissue culture medium reduces the availability of \"uncomplexed\" copper ions to interact with the virus, negatively affecting virus inactivation and hence surface antiviral performance. We propose that laboratory antiviral surface testing should include virus delivered in a physiologically relevant carrier solution (saliva or nasal secretions when testing respiratory viruses) to accurately predict real-life surface antiviral performance when deployed in public spaces.\n\nImportanceThe purpose of evaluating antiviral activity of test surfaces in the laboratory is to identify surfaces that will perform efficiently in preventing fomite transmission when deployed on high-traffic touch surfaces in public spaces. The conventional method in laboratory testing is to use tissue culture-derived virus inoculum, however this study demonstrates that antiviral performance of test copper-containing surfaces is dependent on the composition of the carrier solution in which the virus inoculum is delivered to test surfaces. Therefore, we recommend that laboratory surface testing should include virus delivered in a physiologically relevant carrier solution, to accurately predict real-life test surface performance in public spaces. Understanding the mechanism of virus inactivation is key to future rational design of improved antiviral surfaces. Here, we demonstrate that copper ions released from copper surfaces into small liquid droplets containing SARS-CoV-2, is a mechanism by which the virus that causes COVID-19 can be inactivated.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jane Hilton", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Yoshiko Nanao", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Machiel Flokstra", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Meisam Askari", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Terry K Smith", + "author_inst": "St. Andrews University" + }, + { + "author_name": "Andrea Di Falco", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Phil DC King", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Peter Wahl", + "author_inst": "University of St Andrews" + }, + { + "author_name": "Catherine Sarah Adamson", + "author_inst": "University of St Andrews" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.09.08.556912", "rel_title": "Bayesian phylogenetics on globally emerging SARS-CoV-2 variant BA.2.86 suggest global distribution and rapid evolution", @@ -15517,105 +16301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.09.06.23294696", - "rel_title": "Predictors of SARS-CoV-2 anti-Spike IgG antibody levels following two COVID-19 vaccine doses among children and adults in the Canadian CHILD Cohort", - "rel_date": "2023-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.06.23294696", - "rel_abs": "BackgroundVaccination helps prevent SARS-CoV-2 infection and severe COVID-19. However, vaccine-induced humoral immune responses vary among individuals and wane over time. We aimed to describe the SARS-CoV-2 anti-spike IgG antibody response to vaccination and identify health and demographic factors associated with this response among children and adults.\n\nMethodsWe studied a subset of double-vaccinated children (n= 151; mean age: 12 {+/-}1.5 years, 46% female) and adults (n= 995; 44 {+/-}6.0 years, 60% female) from the Canadian CHILD Cohort. Dried blood spots were collected over two time periods (March 2021 to September 2021; October 2021 to January 2022). Antibody levels were quantified using automated chemiluminescent ELISAs. Demographic, vaccination, and health data were collected via online questionnaires. Associations were determined using multivariable regression.\n\nResultsOur cohort had SARS-CoV-2 anti-spike seropositivity rate of 97% following two COVID-19 vaccine doses. In both children and adults, the highest antibody levels were observed around three months post-vaccination and did not differ by biological sex. Higher antibody levels were associated with: prior SARS-CoV-2 infection ({beta}=0.15 scaled luminescence units, 95%CI, 0.06-0.24), age <18 years ({beta}=0.15, 95%CI 0.05-0.26) and receiving the Moderna mRNA ({beta}=0.23, 95%CI 0.11-0.34) or Pfizer-BioNTech mRNA vaccines ({beta}= 0.10, 95%CI, 0.02-0.18) vs. a combination of mRNA and Oxford-AstraZeneca viral vector vaccines. There were no differences in antibody levels when comparing a 3-8 vs. 9-16-week interval between vaccine doses.\n\nInterpretationWe identified key factors associated with post-vaccination antibody responses in children and adults, which could help improve future vaccine development and deployment among different population subgroups.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Rilwan Azeez", - "author_inst": "Department of Immunology, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Larisa Lotoski", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Geoffery L. Winsor", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Corey R. Arnold", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Yannick Galipeau", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Martin Pelchat", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Stephanie Goguen", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Elinor Simons", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Theo J. Moraes", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Piush J. Mandhane", - "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, AB, Canada" - }, - { - "author_name": "Stuart E. Turvey", - "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Shelly Bolotin", - "author_inst": "Centre for Vaccine Preventable Diseases, University of Toronto: Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "David M. Patrick", - "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Jared Bullard", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Lisa M. Lix", - "author_inst": "Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Natasha Doucas", - "author_inst": "CHILD Cohort Study National Parent Engagement Committee" - }, - { - "author_name": "Natalie Rodriguez", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Fiona S.L. Brinkman", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Padmaja Subbarao", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Marc-Andr\u00e9 Langlois", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Meghan Azad", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.08.23295177", "rel_title": "Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera", @@ -16385,6 +17070,53 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.09.05.23295085", + "rel_title": "The potential clinical impact and cost-effectiveness of the updated COVID-19 mRNA Fall 2023 vaccines in the United States", + "rel_date": "2023-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.05.23295085", + "rel_abs": "ObjectivesTo assess the potential clinical impact and cost-effectiveness of COVID-19 mRNA vaccines updated for Fall 2023 in adults [≥]18 years over a 1-year analytic time horizon (September 2023-August 2024).\n\nMethodsA compartmental Susceptible-Exposed-Infected-Recovered model was updated to reflect COVID-19 in summer 2023. Numbers of symptomatic infections, COVID-19 related hospitalizations and deaths, and costs and quality-adjusted life-years (QALYs) gained were calculated using a decision tree model. The incremental cost-effectiveness ratio (ICER) of a Moderna updated mRNA Fall 2023 vaccine (Moderna Fall Campaign) was compared to no additional vaccination. Potential differences between the Moderna and the Pfizer-BioNTech Fall 2023 vaccines were examined.\n\nResultsBase case results suggest the Moderna Fall Campaign would decrease the expected 64.2 million symptomatic infections by 7.2 million (11%) to 57.0 million. COVID-19-related hospitalizations and deaths are expected to decline by 343,000 (-29%) and 50,500 (-33%), respectively. The Moderna Fall Campaign would increase QALYs by 740,880 and healthcare costs by $5.7 billion relative to No Vaccine, yielding an ICER of $7,700 per QALY gained. Using a societal cost perspective, the ICER is $2,100. Sensitivity analyses suggest that vaccine effectiveness, COVID-19 incidence, hospitalization rates and costs drive cost-effectiveness. With a relative vaccine effectiveness (rVE) of Moderna versus Pfizer-BioNTech of 5.1% for infection and 9.8% for hospitalization, use of the Moderna vaccine is expected to prevent 24,000 more hospitalizations and 3,300 more deaths than the Pfizer-BioNTech vaccine.\n\nLimitations and ConclusionsAs COVID-19 becomes endemic, future incidence, including patterns of infection, are highly uncertain. Vaccine effectiveness of Fall 2023 vaccines is unknown, and it is unclear when a new variant that evades natural or vaccine immunity will emerge. Despite these limitations, the Moderna Fall 2023 vaccine can be considered cost-effective relative to no vaccine.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Michele Kohli", + "author_inst": "Quadrant Health Economics Inc." + }, + { + "author_name": "Michael Maschio", + "author_inst": "Quadrant Health Economics, Inc." + }, + { + "author_name": "Keya Joshi", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Amy Lee", + "author_inst": "Quadrant Health Economics, Inc." + }, + { + "author_name": "Kelly Fust", + "author_inst": "Quadrant Health Economics, Inc." + }, + { + "author_name": "Ekkehard Beck", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Nicolas Van de Velde", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Milton C. Weinstein", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2023.09.04.23294973", "rel_title": "IMPACT OF THE COVID-19 PANDEMIC ON ROUTINE HIV CARE AND ANTIRETROVIRAL TREATMENT OUTCOMES IN KENYA: A NATIONALLY REPRESENTATIVE ANALYSIS", @@ -17295,105 +18027,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2023.09.01.555815", - "rel_title": "Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86", - "rel_date": "2023-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.01.555815", - "rel_abs": "The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sijie Yang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yuanling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fanchong Jian", - "author_inst": "Peking University" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Peking University" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Peking University" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Nankai University" - }, - { - "author_name": "Yanli Xu", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Peng Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Lingling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Jing Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Xiao Niu", - "author_inst": "Peking University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Tianhe Xiao", - "author_inst": "Peking University" - }, - { - "author_name": "Ran An", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Yao Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Nankai University" - }, - { - "author_name": "Youchun Wang", - "author_inst": "Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.09.02.556038", "rel_title": "Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines", @@ -17983,6 +18616,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.08.31.555625", + "rel_title": "Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53", + "rel_date": "2023-09-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.31.555625", + "rel_abs": "COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jonathan D Lee", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Bridget L Menasche", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Maria Mavrikaki", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "Madison M Uyemura", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Su Min Hong", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Nina Kozlova", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Jin Wei", + "author_inst": "Yale University" + }, + { + "author_name": "Mia Madel Alfajaro", + "author_inst": "Yale University" + }, + { + "author_name": "Renata Filler", + "author_inst": "Yale University" + }, + { + "author_name": "Arne Muller", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Tanvi Saxena", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Ryan R Posey", + "author_inst": "Wyss Institute / Harvard Medical School" + }, + { + "author_name": "Priscilla Cheung", + "author_inst": "Boston Children's Hospital / Harvard Medical School" + }, + { + "author_name": "Taru Muranen", + "author_inst": "Harvard University / BIDMC" + }, + { + "author_name": "Jan Heng", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Joao A Paulo", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Frank J Slack", + "author_inst": "Harvard University / BIDMC" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.31.555805", "rel_title": "Immunogenicity and efficacy of a subcutaneously administered, adjuvanted vaccine containing modified S1 spike protein of SARS-CoV-2 variant C.1.2", @@ -18669,13 +19389,17 @@ "rel_date": "2023-08-31", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.30.555211", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. Specifically, L455F and F456L evades Class 1 NAbs, which could reduce the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.\n\nHighlightsO_LIL455F and F456L enhance the resistance to Class 1 NAbs\nC_LIO_LIL455F and F456L lower neutralization of XBB BTI convalescent plasma\nC_LIO_LIL455F+F456L flipping significantly increases ACE2 binding affinity\nC_LI", - "rel_num_authors": 20, + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade Class 1 NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.", + "rel_num_authors": 25, "rel_authors": [ { "author_name": "Fanchong Jian", "author_inst": "Peking University" }, + { + "author_name": "Leilei Feng", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, { "author_name": "Sijie Yang", "author_inst": "Tsinghua University" @@ -18684,6 +19408,10 @@ "author_name": "Yuanling Yu", "author_inst": "Changping Laboratory" }, + { + "author_name": "Lei Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, { "author_name": "Weiliang Song", "author_inst": "Peking University" @@ -18728,6 +19456,14 @@ "author_name": "Tianhe Xiao", "author_inst": "Peking University" }, + { + "author_name": "Ran An", + "author_inst": "Changping Laboratory" + }, + { + "author_name": "Yao Wang", + "author_inst": "Changping Laboratory" + }, { "author_name": "Qingqing Gu", "author_inst": "Changping Laboratory" @@ -18748,6 +19484,10 @@ "author_name": "Youchun Wang", "author_inst": "Chinese Academy of Medical Science & Peking Union Medical College" }, + { + "author_name": "Xiangxi Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, { "author_name": "Yunlong Richard Cao", "author_inst": "Peking University" @@ -18997,53 +19737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.30.23294839", - "rel_title": "Vaccination status and re-infection among COVID patients admitted in COVID High Dependency Unit (HDU) of a tertiary hospital in Eastern Nepal: A cross-sectional study", - "rel_date": "2023-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.30.23294839", - "rel_abs": "IntroductionThe relationship between COVID-19 vaccination and Coronavirus disease severity and outcomes remain topics of significant interest. This cross-sectional study done among COVID-19 patients admitted to the High-dependency unit of a tertiary hospital in Eastern Nepal aimed to assess the association between vaccination status, prior infection, and disease outcomes, and the modification of these associations by the presence or absence of comorbidities.\n\nMethodologyDemographic and clinical data were collected from 102 COVID-19 patients admitted to the High-Dependency Unit of Mechi Zonal Hospital, including information on vaccination status, comorbidities, disease severity, and outcomes. Statistical analysis, including chi-square tests and Fishers exact tests, was performed to examine the associations.\n\nResultsAmong the study participants, 49% had received at least one dose of COVID-19 vaccine. Vaccinated individuals had a significantly lower rate of severe disease compared to non-vaccinated individuals ({chi}{superscript 2}=10.05, p=0.002). Recovery and mortality rates did not differ significantly between the two groups ({chi}{superscript 2}=1.008, p=0.315). However, when stratified by comorbidities, vaccinated individuals with comorbidities had higher recovery rates compared to non-vaccinated individuals (85.29% vaccinated vs. 25.00% non-vaccinated, Fishers exact test p=0.024). Vaccinated individuals, both with and without comorbidities, had lower rates of severe disease compared to non-vaccinated individuals. However, the association was found to be significant only in individuals with comorbidities (12.50% vaccinated without comorbidities vs. 47.92% non-vaccinated, p=0.017; 23.53% vaccinated with comorbidities vs. 75.00% non-vaccinated, p=0.065).\n\nConclusionOur findings suggest that COVID-19 vaccination is associated with a reduced risk of severe disease among individuals with or without comorbidities and decreased risk of mortality among those with comorbidities. However, larger studies are needed to validate these findings and further explore the impact of vaccination on disease outcomes. These findings support the ongoing efforts to promote COVID-19 vaccination as a crucial public health intervention.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sujan Kafle", - "author_inst": "Provincial Hospital Bhadrapur" - }, - { - "author_name": "Varsha Chhetri", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Joshan Lal Bajracharya", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Lenish Pokharel", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Suyash Dawadi", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Ujwal Basnet", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Shreya Dhungana", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Durga Neupane", - "author_inst": "BP Koirala Institute of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.29.23293790", "rel_title": "Outpatient treatment with concomitant vaccine-boosted convalescent plasma for patients with immunosuppression and COVID-19", @@ -19841,6 +20534,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.08.29.555304", + "rel_title": "A short sequence in the tail of SARS-CoV-2 envelope protein controls accessibility of its PDZ Binding Motif to the cytoplasm.", + "rel_date": "2023-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.29.555304", + "rel_abs": "The carboxy terminal tail of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope protein (E) contains a PDZ-binding motif (PBM) which is crucial for coronavirus pathogenicity. During SARS-CoV-2 infection, the viral E protein is expressed within the Golgi apparatus membrane of host cells with its PBM facing the cytoplasm. In this work we study the molecular mechanisms controlling the presentation of the PBM to host PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins. We show that at the level of the Golgi apparatus, the PDZ-binding motif of the E protein is not detected by E C-terminal specific antibodies neither by PDZ domain-containing protein binding partner. Four alanine substitutions upstream of the PBM in the central region of the E protein tail is sufficient to generate immunodetection by anti-E antibodies and trigger robust recruitment of the PDZ domain-containing protein into the Golgi organelle. Overall, this work suggests that the presentation of the PBM to the cytoplasm is under conformational regulation mediated by the central region of the E protein tail and that PBM presentation probably does not occur at the surface of Golgi cisternae but likely at post-Golgi stages of the viral cycle.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Benoit Neitthoffer", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flavio Alvarez", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Larrous", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Celia Caillet-Saguy", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sandrine Etienne-Manneville", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Batiste Boeda", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.08.29.23294751", "rel_title": "Changes in respiratory infection trends during the COVID-19 pandemic in the haematologic malignancy patients", @@ -21047,61 +21779,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2023.08.21.553968", - "rel_title": "Antibody Neutralization of Emerging SARS-CoV-2: EG.5.1 and XBC.1.6", - "rel_date": "2023-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.21.553968", - "rel_abs": "SARS-CoV-2 variants EG.5.1 and XBC.1.6 have recently emerged, attracting increased attention due to their rapid expansion globally and in Australia, respectively. EG.5.1 evolved from Omicron subvariant XBB.1.9, harboring additional Q52H and F456L spike substitutions. The F456L mutation is located within the epitopes of many class-1 monoclonal antibodies (mAbs) directed to the receptor-binding domain (RBD), raising concerns about further antibody evasion. XBC.1.6, a descendant of a Delta-BA.2 recombinant, carries 15 additional spike mutations. The extent to which antibody evasion contributes to the growth advantage of XBC.1.6 in Australia remains to be determined. To assess the antibody evasion properties of the emergent variants, we conducted pseudovirus neutralization assays using sera from individuals who received three doses of COVID-19 mRNA monovalent vaccines plus one dose of a BA.5 bivalent vaccine, as well as from patients with BQ or XBB breakthrough infection. The assays were also performed using a panel of 14 mAbs that retained neutralizing activity against prior XBB subvariants. Our data suggested that EG.5.1 was slightly but significantly more resistant (< 2-fold) to neutralization by BQ and XBB breakthrough sera than XBB.1.16, which is known to be antigenically similar to XBB.1.5. Moreover, the F456L mutation in EG.5.1 conferred heightened resistance to certain RBD class-1 mAbs. In contrast, XBC.1.6 was more sensitive to neutralization by sera and mAbs than the XBB subvariants. Notably, XBB breakthrough sera retained only weak neutralization activity against XBB subvariants. In summary, EG.5.1 and XBC.1.6 exhibited distinct antibody evasion properties. The recent global expansion of EG.5.1 might be attributable, in part, to its enhanced neutralization resistance. That XBB breakthrough infections did not elicit a robust antibody neutralization response against XBB subvariants is indicative of immunological imprinting. The high prevalence of XBC.1.6 in Australia is not due to enhanced antibody evasion.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Qian Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Richard Ma Zhang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jerren Ho", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Hiroshi Mohri", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Riccardo Valdez", - "author_inst": "University of Michigan" - }, - { - "author_name": "David M Manthei", - "author_inst": "University of Michigan" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "University of Michigan School of Public Health" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.24.554732", "rel_title": "Mucosal antibody responses to SARS-CoV-2 booster vaccination and breakthrough infection", @@ -21635,6 +22312,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.24.23294559", + "rel_title": "Serological surveillance reveals a high exposure to SARS-CoV-2 and altered immune response among COVID-19 unvaccinated Cameroonian individuals", + "rel_date": "2023-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.24.23294559", + "rel_abs": "BackgroundSurveillance of COVID-19/SARS-CoV-2 dynamics is crucial to understanding natural history and providing insights into the populations exposure risk and specific susceptibilities. This study investigated the seroprevalence of SARS-CoV-2 antibodies, its predictors, and immunological status among unvaccinated patients in Cameroon.\n\nMaterials and MethodsA multicentre cross-sectional study was conducted between January and September 2022 in the town of Douala. Patients were consecutively recruited, and data of interest were collected using a questionnaire. Blood samples were collected to determine Immunoglobin titres (IgM and IgG) by ALFA, CD4+ cells by flow cytometry, and interferon gamma (IFN-{gamma}) and interleukin-6 (IL-6) by ELISA.\n\nResultsA total of 342 patients aged 41.5 {+/-} 13.9 years were included. Most participants (75.8%) were asymptomatic. The overall prevalence of IgM and IgG was 49.1% and 88.9%, respectively. Ageusia and anosmia have displayed the highest positive predictive values (90.9% and 82.4%) and specificity (98.9% and 98.3%). The predictors of IgM seropositivity were being aged 60 - 70 years (aOR = 0.54, p = 0.02) and ageusia (aOR = 9.31, p = 0.01), whereas those of IgG seropositivity included health facility (aOR = 0.23, p = 0.02) and ageusia (aOR = 0.21, p = 0.04). CD4+, IFN-{gamma}, and IL-6 were impaired in seropositive individuals, with a confounding role of socio-demographic factors or comorbidities.\n\nConclusionAlthough the WHO declared the end of COVID-19 as a public health emergency, the findings of this study indicate the need for continuous surveillance to adequately control the disease in Cameroon.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Arlette Flore Moguem Soubgui", + "author_inst": "University of Douala: Universite de Douala" + }, + { + "author_name": "Wilfred Steve Ndeme Mboussi", + "author_inst": "University of Douala: Universite de Douala" + }, + { + "author_name": "Loick Pradel Kojom Foko", + "author_inst": "University of Douala: Universite de Douala" + }, + { + "author_name": "Elis\u00e9e Libert Embolo Enyegue", + "author_inst": "ministry of scientific research and innovation" + }, + { + "author_name": "Martin Luther Koanga Mogtomo", + "author_inst": "University of Douala: Universite de Douala" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.24.23294551", "rel_title": "Participatory Approaches in Community Health in light of the COVID-19 Pandemic: A Scoping Review Protocol", @@ -22633,65 +23345,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.23.554434", - "rel_title": "SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling", - "rel_date": "2023-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.23.554434", - "rel_abs": "Interferons and regulated cell death pathways counteract virus spread and mount immune responses, but their deregulation often results in inflammatory pathologies. The RIP-homotypic interaction motif (RHIM) is a conserved protein domain critical for assembling higher-order amyloid-like signaling complexes inducing cell death. A few DNA viruses employ viral RHIMs mimicking host RHIMs to alleviate cell death-mediated antiviral defenses. Whether RNA viruses operate such viral RHIMs remains unknown. Host RHIM-protein signaling promotes lung damage and cytokine storm in respiratory RNA virus infections, arguing the presence of viral RHIMs in RNA viruses. Here, we report the identification of novel viral RHIMs in Nsp13 and Nsp14 of SARS-CoV-2 and other bat RNA viruses and provide a basis for bats as the hosts for the evolution of RHIMs in RNA viruses. Nsp13 expression promoted CoV-RHIM-1-dependent cell death after SARS-CoV-2 infection, and its RNA-binding channel conformation was critical for cell death function. Nsp13 interacted and promoted the formation of large insoluble complexes of ZBP1 and RIPK3. Unlike DNA virus RHIMs, SARS-CoV-2 Nsp13 did not restrict host RHIM-dependent cell death. Instead, it promoted ZBP1-RIPK3 signaling-mediated cell death dependent on intracellular RNA ligands. Intriguingly, SARS-CoV-2 genome fragments showed high Z-RNA forming propensity which bound to Z-RNA sensing Z domains and promoted Nsp13-dependent cell death. Our findings reveal the functional viral RHIMs in RNA viruses and the role of SARS-CoV-2 Nsp13 in cell death associated with Z-RNAs and ZBP1-RIPK3 signaling, allowing the understanding of mechanisms of cellular damage and cytokine storm in respiratory virus infections and COVID-19.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/554434v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (66K):\norg.highwire.dtl.DTLVardef@12bf222org.highwire.dtl.DTLVardef@25cc1forg.highwire.dtl.DTLVardef@17c2a2dorg.highwire.dtl.DTLVardef@b4f745_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sanchita Mishra", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Disha Jain", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Ayushi Amin Dey", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sahana Nagaraja", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Mansi Srivastava", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Oyahida Khatun", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Keerthana Balamurugan", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Micky Anand", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Shashank Tripathi", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Mahipal Ganji", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sannula Kesavardhana", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.24.554561", "rel_title": "Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain", @@ -23293,6 +23946,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2023.08.21.23293488", + "rel_title": "Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha", + "rel_date": "2023-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.21.23293488", + "rel_abs": "SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a threat, delaying interventions. Understanding the drivers of such silent spread and its epidemic impact is critical to inform future response planning. Here, we integrated spatio-temporal records of international mobility, local epidemic growth and genomic surveillance into a Bayesian framework to reconstruct the early dissemination of Alpha out of the UK in the first three months after emergence. We found that silent circulation lasted from days to months and was logarithmically associated with sequencing coverage. Social restrictions in certain countries likely slowed down the seeding of local transmission by weeks, mitigating the negative consequences of late detection. Revisiting the initial spread of Alpha supports local mitigation at the destination in case of emerging events.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Benjamin Faucher", + "author_inst": "Sorbonne Universite, INSERM, Institut Pierre Louis d'Epidemiologie et de sante publique (IPLESP), F75012, France" + }, + { + "author_name": "Chiara E. Sabbatini", + "author_inst": "Sorbonne Universite, Institut Pierre Louis d'Epidemiologie (IPLESP), F75012, France" + }, + { + "author_name": "Peter Czuppon", + "author_inst": "University of Munster" + }, + { + "author_name": "Moritz U. G. Kraemer", + "author_inst": "University of Oxford University College Oxford" + }, + { + "author_name": "Philippe Lemey", + "author_inst": "KU Leuven" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + }, + { + "author_name": "Francois Blanquart", + "author_inst": "College de France" + }, + { + "author_name": "Pierre-Yves Boelle", + "author_inst": "Sorbonne Universite, INSERM, Institut Pierre Louis d'Epidemiologie et de Sante Publique (IPLESP), F75012, France" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "Department of molecular medicine, University of Padova, 35121 Padova, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.18.23294107", "rel_title": "Post-COVID rebound of gonorrhoea in England", @@ -24411,29 +25115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.16.23294160", - "rel_title": "Unraveling COVID-19: Descriptive Analytics in a Middle-Income Country, Paving the Path Forward", - "rel_date": "2023-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.16.23294160", - "rel_abs": "The outbreak of COVID-19 unleashed an unprecedented global pandemic, leaving a profound impact on lives and economies worldwide. Recognizing its severity, the World Health Organization swiftly declared it a public health emergency of international concern. Tragically, the Philippines reported the first death case outside China, leading to a surge in cases following the first instance of local transmission. In response to this crisis, collaborative efforts have been underway to control the disease and minimize its health and socio-economic impacts. The COVID-19 epidemic curve holds vital insights into the history of exposure, transmission, testing, tracing, social distancing measures, community lockdowns, quarantine, isolation, and treatment, offering a comprehensive perspective on the nations response. One approach to gaining crucial insights is through meticulous analysis of available datasets, empowering us to inform future strategies and responses effectively. This paper aims to provide descriptive data analytics of the COVID-19 pandemic in the Philippines, summarizing the countrys fight by visualizing epidemiological and mobility datasets, revisiting scientific papers and news articles, and creating a timeline of the key issues faced during the pandemic. By leveraging these multifaceted analyses, policymakers and health authorities can make informed decisions to enhance preparedness, expand inter-agency cooperation, and combat future public health crises effectively. This study seeks to serve as a valuable resource, guiding nations worldwide in comprehending and responding to the challenges posed by COVID-19 and beyond.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Norvin Patadon Bansilan", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jomar Fajardo Rabajante", - "author_inst": "University of the Philippines Los Banos" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.17.553661", "rel_title": "Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD", @@ -24995,6 +25676,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.11.23294002", + "rel_title": "Evolution of Myocarditis Incidence at a Large Healthcare System Before and During COVID-19 Pandemic", + "rel_date": "2023-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.11.23294002", + "rel_abs": "BackgroundMyocarditis is a recognized complication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Emerging studies further suggest an associated risk of myocarditis following administration of messenger RNA (mRNA) COVID-19 vaccinations. coronavirus disease 2019 (COVID-19) vaccinations. We investigated the incidence of myocarditis throughout the COVID-19 pandemic across a large healthcare system in the Washington, DC, metropolitan area.\n\nMethodsThis retrospective analysis of patients admitted from 2017-2022. Myocarditis cases were temporally divided into two cohorts based on year of admission (pre-pandemic 2017-2019; pandemic 2020-2022), which were compared for overall myocarditis incidence. The primary endpoint was in-hospital mortality.\n\nResultsThe cohort included 573 myocarditis patients (pre-pandemic=208, pandemic=365). From 2017-2019, the total number and rate of myocarditis cases was consistent. Overall cases of myocarditis increased during the pandemic (97, 126, 142 patients in 2020, 2021, 2022, respectively). Interestingly, the rate of myocarditis cases not related to COVID-19 or the vaccines stayed consistent (0.0674%, 0.0676%, 0.0807%), but the rate of myocarditis related to COVID-19 or the vaccines myocarditis increased each year (0.0210%, 0.0416%, 0.0480%). In-hospital mortality was similar between the two pre-pandemic and pandemic cohorts (5.35% versus 7.7%, 0.276).\n\nConclusionAmong hospitalized patients, during the COVID-19 pandemic, the incidence of myocarditis increased as compared to the pre-pandemic era. It appears this increase is associated with either the SARS-CoV-2 infection or COVID-19 vaccination. In-hospital outcomes did not differ during the pandemic, but ongoing research is needed to evaluate the long-term impact of myocarditis during the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Brian C. Case", + "author_inst": "Medstar Washington Hospital Center" + }, + { + "author_name": "Ori Waksman", + "author_inst": "MedStar Washington Hospital Center" + }, + { + "author_name": "Hank Rappaport", + "author_inst": "MedStar Washington Hospital Center" + }, + { + "author_name": "Cheng Zhang", + "author_inst": "MedStar Washington Hospital Center" + }, + { + "author_name": "Ron Waksman", + "author_inst": "MedStar Washington Hospital Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2023.08.11.23293400", "rel_title": "Predicting subnational incidence of COVID-19 cases and deaths in EU countries", @@ -25917,49 +26633,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.08.13.553144", - "rel_title": "Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants", - "rel_date": "2023-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.13.553144", - "rel_abs": "A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth.\n\nHIGHLIGHTSO_LIModeled SARS-CoV-2 cross-neutralization using mutations at key sites\nC_LIO_LIIdentified resistance mutations and quantified relative impact\nC_LIO_LIAccurately predicted holdout variant and convalescent/vaccine sera neutralization\nC_LIO_LIShowed that the third dose of mRNA-1273 vaccination overcomes resistance mutations\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kshitij Wagh", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Xiaoying Shen", - "author_inst": "Duke University" - }, - { - "author_name": "James Theiler", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Bethany Girard", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Jean-Claude Marshall", - "author_inst": "Moderna, Inc., Cambridge, MA 02319, USA" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Bette Korber", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.14.553219", "rel_title": "Transmission bottleneck size estimation from de novo viral genetic variation", @@ -26437,6 +27110,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2023.08.10.552726", + "rel_title": "Additive Manufacturing Leveraged Microfluidic Setup for Sample to Answer Colorimetric Detection of Pathogens", + "rel_date": "2023-08-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.10.552726", + "rel_abs": "Colorimetric readout for the detection of infectious diseases is gaining traction at the point of care/need owing to its ease of analysis and interpretation, and integration potential with highly specific Loop-mediated amplification (LAMP) assays. However, coupling colorimetric readout with LAMP is rife with challenges including, rapidity, inter-user variability, colorimetric signal quantification, and user involvement in sequential steps of the LAMP assay, hindering its application. To address these challenges, for the first time, we propose a remotely smartphone-operated automated setup consisting of (i) an additively manufactured microfluidic cartridge, (ii) a portable reflected-light imaging setup with controlled epi-illumination (PRICE) module, and (iii) a control and data analysis module. The microfluidic cartridge facilitates sample collection, lysis, mixing of amplification reagents stored on-chip, and subsequent isothermal heating for initiation of amplification in a novel way by employing tunable elastomeric chambers and auxiliary components (heaters and linear actuators). PRICE offers a new imaging setup that captures the colorimetric change of the amplification media over a plasmonic nanostructured substrate in a controlled and noise-free environment for rapid minute-scale nucleic acid detection. The control and data analysis module employs microprocessors to automate cartridge operation in tandem with the imaging module. The different device components were characterized individually and finally, as a proof of concept, SARS-CoV-2 wild-type RNA was detected with a turnaround time of 13 minutes, showing the devices clinical feasibility. The suggested automated device can be adopted in future iterations for other detection and molecular assays that require sequential fluid handling steps.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sripadh Guptha Yedire", + "author_inst": "McGill University" + }, + { + "author_name": "Imman I. Hosseini", + "author_inst": "McGill University" + }, + { + "author_name": "Hamed Shieh", + "author_inst": "McGill University" + }, + { + "author_name": "Arash Khorrami Jahromi", + "author_inst": "McGill University" + }, + { + "author_name": "Tamer Abdel Fatah", + "author_inst": "McGill University" + }, + { + "author_name": "Mahsa Jalali", + "author_inst": "McGill University" + }, + { + "author_name": "Sara Mahshid", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.08.10.552845", "rel_title": "Pretrainable Geometric Graph Neural Network for Antibody Affinity Maturation", @@ -27295,69 +28011,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.07.23293304", - "rel_title": "High-throughput detection of neutralizing antibodies to SARS-CoV-2 variants using flow cytometry", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293304", - "rel_abs": "Detecting neutralizing antibodies (NAbs) to SARS-CoV-2 variants is crucial for controlling the spread of COVID-19. In this work, we developed a high-throughput assay for the broad systematic examination of NAbs to eleven SARS-CoV variants of concern (VOCs), which include D614G, Alpha, Beta, Gamma, Delta, Kappa, and Omicron sub-lineages BA.1, BA.2, BA.3, BA.4, and BA.5. The assay is cost-effective, reliable, 35-fold more sensitive than Luminex technology, and can include the new variants during SARS-CoV-2 evolution. Importantly, our results highly correlated with a commercial IgG serological assay (R = 0.89) and cPass, a U.S. FDA-approved surrogate virus neutralization test (sVNT) assay (R = 0.93). With our high-throughput NAb platform, we constructed a comprehensive overview of the interactions between SARS-CoV-2 VOCs Spike trimer proteins and ACE2 receptors, leading to the identification of a monoclonal Ab with broad neutralizing activity. Furthermore, when compared to the D614G variant, we found that the serum NAbs elicited by the third dose vaccine (administered after 28 days) demonstrated decreased inhibition to multiple SARS-CoV-2 variants, including Gamma (0.94x), Alpha (0.91x), Delta (0.91x), Beta (0.81x), Kappa (0.81x), BA.2 (0.44x), BA.1 (0.43x), BA.3 (0.41x), BA.5 (0.35x) and BA.4 (0.33x), in cohort of 56 vaccinated individuals. Altogether, our proteomics platform proves to be an effective tool to detect broad NAbs in the population and aid in the development of future COVID-19 vaccines and vaccination strategies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiaohan Zhang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Natio" - }, - { - "author_name": "Yajie Wang", - "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Mansheng Li", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Haolong Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Xiaomei Zhang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Xingming Xu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Di Hu", - "author_inst": "ProteomicsEra Medical Co., Ltd." - }, - { - "author_name": "Te Liang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yunping Zhu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yongzhe Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Bingwei Wang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xiaobo Yu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.08.552415", "rel_title": "Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5", @@ -27843,6 +28496,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2023.08.07.552249", + "rel_title": "phuEGO: A network-based method to reconstruct active signalling pathways from phosphoproteomics datasets", + "rel_date": "2023-08-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.07.552249", + "rel_abs": "Signalling networks are critical for virtually all cell functions. Our current knowledge of cell signalling has been summarised in signalling pathway databases, which, while useful, are highly biassed towards well-studied processes, and dont capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signalling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. Methods to extract active signalling signatures from such data struggle to produce unbiased and interpretable networks that can be used for hypothesis generation and designing downstream experiments.\n\nHere we present phuEGO, which combines three-layer network propagation with ego network decomposition to provide small networks comprising active functional signalling modules. PhuEGO boosts the signal-to-noise ratio from global phosphoproteomics datasets, enriches the resulting networks for functional phosphosites and allows the improved comparison and integration across datasets. We applied phuEGO to five phosphoproteomics data sets from cell lines collected upon infection with SARS CoV2. PhuEGO was better able to identify common active functions across datasets and to point to a subnetwork enriched for known COVID-19 targets. Overall, phuEGO provides a tool to the community for the improved functional interpretation of global phosphoproteomics datasets.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Girolamo Giudice", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Haoqi Chen", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Evangelia Petsalaki", + "author_inst": "European Bioinformatics Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.08.04.551867", "rel_title": "Mucosal and systemic immune dynamics associated with COVID-19 outcomes: a longitudinal prospective clinical study", @@ -28833,77 +29513,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.28.23293335", - "rel_title": "Healthcare resource utilization and costs associated with COVID-19 among pediatrics managed in the community or hospital setting in England: a population-based cohort study", - "rel_date": "2023-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.28.23293335", - "rel_abs": "BackgroundAlthough COVID-19 morbidity is significantly lower in pediatrics than in adults, the risk of severe COVID-19 may still pose substantial healthcare resource burden. This study aimed to describe healthcare resource utilization (HCRU) and costs associated with COVID-19 in pediatrics aged 1-17 years in England.\n\nMethodsA population-based retrospective cohort study of pediatrics with COVID-19 using Clinical Practice Research Datalink (CPRD Aurum) primary care data and, where available, linked Hospital Episode Statistics Admitted Patient Care (HES APC) secondary care data. HCRU and associated costs to the National Health Service (NHS) were stratified by age, risk of severe COVID-19, and immunocompromized status, separately for those with and without hospitalization records (hospitalized cohort: COVID-19 diagnosis August 2020-March 2021; primary care cohort: COVID-19 diagnosis August 2020-January 2022).\n\nResultsThis study included 564,644 patients in the primary care cohort and 60 in the hospitalized cohort. Primary care consultations were more common in those aged 1-4 years (face-to-face: 4.3%; telephone: 6.0%) compared to those aged 5-11 (2.0%; 2.1%) and 12-17 years (2.2%; 2.5%). In the hospitalized cohort, mean [SD] length of stay was longer (5.0 [5.8] days) among those aged 12-17 years (n=24) than those aged 1-4 (n=15; 1.8 [0.9] days) and 5-11 years (n=21; 2.8 [2.1] days).\n\nConclusionsMost pediatrics diagnosed with COVID-19 were managed in the community. However, hospitalizations were an important driver of HCRU and costs, particularly for those aged 12-17 years. Our results may help optimize the management and resource allocation of COVID-19 in this population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jingyan Yang", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Kathleen M Andersen", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Kiran K Rai", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Theo Tritton", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Tendai Mugwagwa", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Carmen Tsang", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Maya Reimbaeva", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Leah McGrath", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Poppy Payne", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Bethany Emma Backhouse", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Diana Mendes", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Rebecca Butfield", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Robert Wood", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Jennifer L Nguyen", - "author_inst": "Pfizer Inc" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.28.23293338", "rel_title": "Systematic Review and Meta-Analysis Protocol of the Efficacy and Safety of COVID-19 Drug Candidates Targeting Host Enzymes Involved in Immune Response", @@ -29409,6 +30018,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.02.23293563", + "rel_title": "Post-acute health care costs following SARS-CoV-2 infection: A retrospective cohort study of among 531,182 matched adults", + "rel_date": "2023-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.02.23293563", + "rel_abs": "Post-acute health care costs following SARS-CoV-2 infection are not known. Beginning 56 days following SARS-CoV-2 polymerase chain reaction (PCR) testing, we compared person-specific total and component health care costs across their distribution for the following year (test-positive versus test-negative, matched people; January 1, 2020-March 31, 2021). For 531,182 individuals, mean person-specific total health care costs were $513.83 (95% CI $387.37-$638.40) higher for test-positive females and $459.10 (95% CI $304.60-$615.32) higher for test-positive males, or >10% increase in mean per-capita costs, driven by hospitalization, long-term care, and complex continuing care costs. At the 99th percentile of each subgroup, person-specific health care costs were $12,533.00 (95% CI $9,008.50-$16,473.00) higher for test-positive females and $14,604.00 (95% CI $9,565.50-$19,506.50) for test-positive males, driven by hospitalization, specialist (males), and homecare costs (females). Cancer costs were lower. Six-month and 1-year costs differences were similar. These findings can inform planning for post-acute SARS-CoV-2 health care costs.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Candace D. McNaughton", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, Ontario, Canada; Sunnybrook Health" + }, + { + "author_name": "Peter C. Austin", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada" + }, + { + "author_name": "Zhiyin Li", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada" + }, + { + "author_name": "Atul Sivaswamy", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada" + }, + { + "author_name": "Timing Fang", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada" + }, + { + "author_name": "Husam Abdel-Qadir", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences); Department of Medicine & Institute of Health Policy , Management and Evaluation, University of " + }, + { + "author_name": "Jacob A. Udell", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences); Department of Medicine & Institute of Health Policy , Management and Evaluation, University of " + }, + { + "author_name": "Walter Wodchis", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences)" + }, + { + "author_name": "Douglas S. Lee", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences); Department of Medicine & Institute of Health Policy , Management and Evaluation, University of " + }, + { + "author_name": "Ivona Mostarac", + "author_inst": "Sunnybrook Research Institute, Toronto, Ontario Canada" + }, + { + "author_name": "Clare L. Atzema", + "author_inst": "ICES (formerly, the Institute for Clinical Evaluative Sciences), Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, Ontario, Canada; Sunnybrook Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.28.550997", "rel_title": "Tetherin restricts SARS-CoV-2 replication despite antagonistic effects of Spike and ORF7a", @@ -30527,129 +31195,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.07.28.550957", - "rel_title": "Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients", - "rel_date": "2023-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.28.550957", - "rel_abs": "The full spectrum of tissues affected by SARS-CoV-2 infection is crucial for deciphering the heterogenous clinical course of COVID-19. Here, we analyzed DNA methylation and histone modification patterns in circulating chromatin to assess cell type-specific turnover in severe and asymptomatic COVID-19 patients, in relation to clinical outcome. Patients with severe COVID-19 had a massive elevation of circulating cell-free DNA (cfDNA) levels, which originated in lung epithelial cells, cardiomyocytes, vascular endothelial cells and erythroblasts, suggesting increased cell death or turnover in these tissues. The immune response to infection was reflected by elevated B cell and monocyte/macrophage cfDNA levels, and by evidence of an interferon response in cells prior to cfDNA release. Strikingly, monocyte/macrophage cfDNA levels (but not monocyte counts), as well as lung epithelium cfDNA and vascular endothelial cfDNA, predicted clinical deterioration and duration of hospitalization. Asymptomatic patients had elevated levels of immune-derived cfDNA but did not show evidence of pulmonary or cardiac damage. Surprisingly, these patients showed elevated levels of vascular endothelial cell and erythroblast cfDNA, suggesting that sub-clinical vascular and erythrocyte turnover are universal features of COVID-19, independent of disease severity. Epigenetic liquid biopsies provide non-invasive means of monitoring COVID-19 patients, and reveal sub-clinical vascular damage and red blood cell turnover.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Roni Ben Ami", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Netanel Loyfer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Eden Cohn", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Gavriel Fialkoff", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Israa Sharkia", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Naama Bogot", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Danit Kochan", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "George Kalak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Amir Jarjoui", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Chen Chen-Shuali", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hava Azulai", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hezi Barhoum", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Nissim Arish", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Moshe M Greenberger", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "David Velleman", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ramzi Kurd", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Eli Ben Chetrit", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Davina Bohm", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Talya Wolak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ahmad Quteineh", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Gordon Cann", - "author_inst": "GRAIL LLC" - }, - { - "author_name": "Benjamin Glaser", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Nir Friedman", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Tommy Kaplan", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ruth Shemer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ariel Rokach", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Yuval Dor", - "author_inst": "Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.01.551417", "rel_title": "Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning", @@ -31451,6 +31996,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.07.30.551145", + "rel_title": "Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19", + "rel_date": "2023-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.30.551145", + "rel_abs": "As many as 10-30% of the over 760 million survivors of COVID-19 develop persistent symptoms, of which respiratory symptoms are among the most common. To understand the cellular and molecular basis for respiratory PASC, we combined a machine learning based analysis of lung computed tomography (CT) with flow cytometry, single-cell RNA-sequencing analysis of bronchoalveolar lavage fluid and nasal curettage samples, and alveolar cytokine profiling in a cohort of thirty-five patients with respiratory symptoms and radiographic abnormalities more than 90 days after infection with COVID-19. CT images from patients with PASC revealed abnormalities involving 73% of the lung, which improved on subsequent imaging. Interstitial abnormalities suggestive of fibrosis on CT were associated with the increased numbers of neutrophils and presence of profibrotic monocyte-derived alveolar macrophages in BAL fluid, reflecting unresolved epithelial injury. Persistent infection with SARS-CoV-2 was identified in six patients and secondary bacterial or viral infections in two others. These findings suggest that despite its heterogenous clinical presentations, respiratory PASC with radiographic abnormalities results from a common pathobiology characterized by the ongoing recruitment of neutrophils and profibrotic monocyte-derived alveolar macrophages driving lung fibrosis with implications for diagnosis and therapy.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Joseph I. Bailey", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Connor H. Puritz", + "author_inst": "Engineering Sciences and Applied Mathematics, McCormick School of Engineering, Northwestern University; Department of Molecular Biosciences, Weinberg College of" + }, + { + "author_name": "Karolina J. Senkow", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Nikolay S. Markov", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Estefani Diaz", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Emmy Jonasson", + "author_inst": "Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Zhan Yu", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Suchitra Swaminathan", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of M" + }, + { + "author_name": "Ziyan Lu", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Samuel Fenske", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Rogan A. Grant", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Hiam Abdala-Valencia", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Ruben J. Mylvaganam", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Janet Miller", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Robert I. Cumming", + "author_inst": "Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Duke University" + }, + { + "author_name": "Robert M. Tighe", + "author_inst": "Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Duke University" + }, + { + "author_name": "Kymberly M. Gowdy", + "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, College of Medicine, The Ohio State University" + }, + { + "author_name": "Ravi Kalhan", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Manu Jain", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Ankit Bharat", + "author_inst": "Division of Thoracic Surgery, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwestern Unive" + }, + { + "author_name": "Chitaru Kurihara", + "author_inst": "Division of Thoracic Surgery, Feinberg School of Medicine, Northwestern University" + }, + { + "author_name": "Ruben San Jose Estepar", + "author_inst": "Department of Radiology, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Raul San Jose Estepar", + "author_inst": "Department of Radiology, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "George R. Washko", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Ali Shilatifard", + "author_inst": "Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University; Simpson Querrey Institute for Epigenetics, Feinberg Sch" + }, + { + "author_name": "Jacob I. Sznajder", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwe" + }, + { + "author_name": "Karen M. Ridge", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwe" + }, + { + "author_name": "GR. Scott Budinger", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwe" + }, + { + "author_name": "Rosemary Braun", + "author_inst": "Engineering Sciences and Applied Mathematics, McCormick School of Engineering, Northwestern University; Department of Molecular Biosciences, Weinberg College of" + }, + { + "author_name": "Alexander V. Misharin", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwe" + }, + { + "author_name": "Marc A. Sala", + "author_inst": "Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University; Simpson Querrey Lung Institute for Translational Science, Northwe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.07.27.550709", "rel_title": "Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells", @@ -32250,7 +32934,7 @@ "rel_date": "2023-07-27", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.25.23293154", - "rel_abs": "Objectives: To establish a SARS-CoV-2 PCR testing programme in an academic institution to analyze saliva samples collected from asymptomatic staff and students. Design: PCR to detect SARS-CoV-2 RNA in saliva self-collected by asymptomatic students and staff members from King's College London, and their household contacts. Standards for diagnostics testing set by the DHSC (UK) were followed to develop an automated saliva PCR service for SARS-CoV-2 detection. Prospective study that run from December 2020 until July 2022. Setting: Testing took place in an academic institution including 18 different locations in London (UK). Participants: There were no selection criteria; asymptomatic participants were encouraged to test regularly (twice weekly when on campus). Main outcome measures: Number of tests, number of participants and positive rate. Results: 158,277 PCR tests were carried out on saliva, of which 2,989 were positive (1.89%), collected by 20,186 participants. Between 10-30% of campus footfall were tested. The positive rate was equivalent to that reported by the Office for National Statistics (UK), except for the period encompassing the delta variant; this wave was nearly absent in our cohort. We employed non-commercial reagents and an open source-inspired automated pipeline for sample processing. This rapidly developed service was awarded UKAS accreditation under the ISO15189 standard. Conclusions: Including academic institutions in pandemic preparedness is a critical consideration, considering the experience in developing, validating, and implementing economic and scalable testing solutions. Given the joint ventures in hospital pathology departments across the UK and the move to centralised, automated, commercial tests, focusing on academic centres that can carry out research and development to test for novel and re-emerging pathogens should be a top priority.", + "rel_abs": "Testing was paramount in the management of the COVID-19 pandemic. Our university established KCL TEST: a SARS-CoV-2 asymptomatic testing programme that enabled sensitive and accessible PCR testing of SARS-CoV-2 RNA in saliva. We performed 158,277 PCRs for our staff, students, and their household contacts, free of charge. Our average turnaround time was 16h and 37 mins from user registration to result delivery. KCL TEST combined open-source automation and in house non-commercial reagents, which allows for rapid deployment. Here we provide our blueprint, recently recommended for ISO15189 accreditation, and results to enable the rapid launch of diagnostic laboratories where and when needed, particularly in low-resource settings. Our data span over 18 months and parallels that of the UK Office for National Statistics, with a lower positive rate and virtually no delta wave. Our observations strongly support regular asymptomatic community testing to decrease outbreaks and provide safe working spaces. Universities can therefore provide agile, resilient, and accurate testing that reflects the infection rate and trend of the general population. We call for the integration of academic institutions in pandemic preparedness, with capabilities to rapidly deploy highly skilled staff, as well as develop, test and accommodate efficient low-cost pipelines.", "rel_num_authors": 36, "rel_authors": [ { @@ -32485,41 +33169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.25.550568", - "rel_title": "Experimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2", - "rel_date": "2023-07-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.25.550568", - "rel_abs": "Elk (Cervus canadensis) and mule deer (Odocoileus hemionus) were experimentally evaluated for susceptibility to SARS-CoV-2. Elk did not shed infectious virus but produced low-level serological responses. Mule deer shed and transmitted virus in addition to mounting pronounced serological responses; they could therefore play a role in the epidemiology of SARS-CoV-2.\n\nArticle Summary LineExperimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2 revealed that while elk are minimally susceptible to infection, mule deer become infected, shed infectious virus, and can infect naive contacts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Stephanie M Porter", - "author_inst": "United States Department of Agriculture" - }, - { - "author_name": "Airn E Hartwig", - "author_inst": "Colorado State University" - }, - { - "author_name": "Helle Bielefeldt-Ohmann", - "author_inst": "University of Queensland" - }, - { - "author_name": "Jeff Root", - "author_inst": "USDA" - }, - { - "author_name": "Angela Bosco-Lauth", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.07.25.550460", "rel_title": "Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions", @@ -33165,6 +33814,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.07.23.23293046", + "rel_title": "Reactivation of herpesvirus type-6 and IgA/IgM-mediated responses to activin-A underpin Long COVID, including affective symptoms and chronic fatigue syndrome.", + "rel_date": "2023-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.23.23293046", + "rel_abs": "AbstractO_ST_ABSBackgroundC_ST_ABSPersistent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reactivation of dormant viruses, and immune-oxidative responses are involved in Long COVID.\n\nObjectivesTo investigate whether Long COVID and depressive, anxiety and chronic fatigue syndrome (CFS) symptoms, are associated with IgA/IgM/IgG to SARS-CoV-2, human Herpesvirus type 6 (HHV-6), Epstein-Barr Virus (EBV), and immune-oxidative biomarkers.\n\nMethodsWe examined 90 Long COVID patients and 90 healthy controls. We measured serum IgA/IgM/IgG against HHV-6 and EBV and their deoxyuridine 5'-triphosphate nucleotidohydrolase (duTPase), SARS-CoV-2, and activin-A, C-reactive protein (CRP), advanced oxidation protein products (AOPP), and insulin resistance (HOMA2-IR).\n\nResultsLong COVID patients showed significant elevations in IgG/IgM-SARS-CoV-2, IgG/IgM-HHV-6 and HHV-6-duTPase, IgA/IgM-activin-A, CRP, AOPP, and HOMA2-IR. Neural network analysis yielded a highly significant predictive accuracy of 80.6% for the Long COVID diagnosis (sensitivity: 78.9%, specificity: 81.8%, area under the ROC curve=0.876); the topmost predictors were: IGA-activin-A, IgG-HHV-6, IgM-HHV-6-duTPase, IgG-SARS-CoV-2, and IgM-HHV-6 (all positively) and a factor extracted from all IgA levels to all viral antigens (inversely). The top-5 predictors of affective symptoms due to Long COVID were: IgM-HHV-6-duTPase, IgG-HHV-6, CRP, education, IgA-activin-A (predictive accuracy of r=0.636). The top-5 predictors of CFS due to Long COVID were in descending order: CRP, IgG-HHV-6-duTPase, IgM-activin-A, IgM-SARS-CoV-2, and IgA-activin-A (predictive accuracy: r=0.709).\n\nConclusionReactivation of HHV-6, SARS-CoV-2 persistence, and autoimmune reactions to activin-A combined with activated immune-oxidative pathways play a major role in the pathophysiology of Long COVID as well as the severity of affective symptoms and CFS due to Long COVID.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aristo Vojdani", + "author_inst": "Immunosciences Lab, Inc., Los Angeles, CA 90035, USA" + }, + { + "author_name": "Abbas F. Almulla", + "author_inst": "Faculty of Medicine, Chulalongkorn university" + }, + { + "author_name": "Bo Zhou", + "author_inst": "School of Medicine, University of Electronic Science and Technology of China" + }, + { + "author_name": "Hussein F. Al-Hakeim", + "author_inst": "Universit of Kufa" + }, + { + "author_name": "Michael Maes", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.07.21.23292948", "rel_title": "Mental health status and related factors influencing healthcare workers during the COVID-19 pandemic: a systematic review and meta-analysis", @@ -34083,33 +34767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2023.07.19.23292810", - "rel_title": "Several Mathematical Aspects on Daily Number of COVID-19 Infection Cases in Eight Southeast Asian Places", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292810", - "rel_abs": "The number of daily confirmed infected cases is a key parameter to determine emergency management actions to take. The mathematical characteristics of the daily infection number should be explored for working out appropriate control scheme. Several mathematical aspects on the daily number of infected cases will be discussed in 8 Southeastern Asian places using the confirmed daily infection numbers available in public websites. Phase space diagrams of plotting the daily infection rate estimated numerically against daily infection number on those tests are presented first. Modeling parameters including the Farrs Law are also discussed. A parameter is proposed to describe the extent of infection by estimating the transient daily infection number divided by the time.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "C.L. Chow", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "C.H. Cheng", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "W.K. Chow", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2023.07.21.23293001", "rel_title": "Unraveling COVID-19 Relationship with Anxiety Disorders and Symptoms", @@ -34241,7 +34898,7 @@ "rel_date": "2023-07-23", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292841", - "rel_abs": "Objective: To examine how hospital admissions for mental health and eating disorders changed at the beginning of the COVID-19 pandemic and with the return to fully in-person school with increased vaccine availability. Methods: Data from a tertiary care childrens hospital were examined for admissions to the hospital from March 2018 through March 2022, including children 6-20 years old admitted with ICD-10 codes for mental health and eating disorders. Interrupted time series (ITS) analyses were used to examine for changes at specific time points. Results: In the time between March 2018 through March 2022, 851 admissions met inclusion criteria for eating disorders and 1,505 admissions for other mental health diagnoses. In the first year of the pandemic, the ITS analysis showed a significant increase in admissions per month for eating disorders with a slope of 1.2 (95% CI: 0.2, 2.2) and for other mental health diagnoses, a slope of 1.9 (95% CI: 1.1, 2.7). In a longer-term ITS analysis, return to fully in-person school was associated with a subsequent decrease in admissions over time at -1.0 per month (95% CI: -2.1, 0.1). For other mental health diagnoses, return to school was associated with an initial drop and then an increase in admissions over time, slope of 2.2 (95% CI: -0.5, 3.8). Conclusion: The COVID-19 pandemic had an initial impact on admissions for eating disorders and other mental health that attenuated over time. We note differences in the association of return to school on eating disorders compared with other mental health diagnoses.", + "rel_abs": "ObjectiveTo examine how hospital admissions for mental health and eating disorders changed at the beginning of the COVID-19 pandemic and with the return to fully in-person school with increased vaccine availability.\n\nMethodsData from a tertiary care childrens hospital were examined for admissions to the hospital from March 2018 through March 2022, including children 6-20 years old admitted with ICD-10 codes for mental health and eating disorders. Interrupted time series (ITS) analyses were used to examine for changes at specific time points.\n\nResultsIn the time between March 2018 through March 2022, 851 admissions met inclusion criteria for eating disorders and 1,505 admissions for other mental health diagnoses. In the first year of the pandemic, the ITS analysis showed a significant increase in admissions per month for eating disorders with a slope of 1.2 (95% CI: 0.2, 2.2) and for other mental health diagnoses, a slope of 1.9 (95% CI: 1.1, 2.7). In a longer-term ITS analysis, return to fully in-person school was associated with a subsequent decrease in admissions over time at -1.0 per month (95% CI: - 2.1, 0.1). For other mental health diagnoses, return to school was associated with an initial drop and then an increase in admissions over time, slope of 2.2 (95% CI: -0.5, 3.8).\n\nConclusionThe COVID-19 pandemic had an initial impact on admissions for eating disorders and other mental health that attenuated over time. We note differences in the association of return to school on eating disorders compared with other mental health diagnoses.", "rel_num_authors": 6, "rel_authors": [ { @@ -34719,6 +35376,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.07.20.549884", + "rel_title": "Induction of antiviral gene expression by cyclosporine A, but not inhibition of cyclophilin A or B, contributes to its restriction of human coronavirus 229E infection in a lung epithelial cell line", + "rel_date": "2023-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.20.549884", + "rel_abs": "The development of antivirals with an extended spectrum of activity is an attractive possibility to protect against future emerging coronaviruses (CoVs). Cyclosporine A (CsA), a clinically approved immunosuppressive drug, has established antiviral activity against diverse unrelated viruses, including several CoVs. However, its antiviral mechanisms of action against CoV infection have remained elusive, precluding the rational design of non-immunosuppressive derivatives with improved antiviral activities. In this study, we evaluated the mechanisms of CsA against HCoV-229E infection in a human lung epithelial cell line. We demonstrate that the antiviral activity of CsA against HCoV-229E is independent of classical CsA target proteins, cyclophilin A or B, which are not required host factors for HCoV-229E in A549 cells. Instead, CsA treatment induces expression of antiviral genes in a manner dependent on interferon regulatory factor 1, but independent of classical interferon responses, which contributes to its inhibitory effect against HCoV-229E infection. Our results also point to a role for the HCoV-229E nucleoprotein in antagonizing activation of type I interferon, but we show that CsA treatment does not affect evasion of innate immune signaling pathways by HCoV-229E. Overall, our findings further the understanding of the antiviral mechanisms of CsA against CoV infection and highlight a novel immunomodulatory strategy to inhibit CoV infection that may inform future drug development efforts.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "John E. Mamatis", + "author_inst": "Queen's University" + }, + { + "author_name": "Carla E. Gallardo-Flores", + "author_inst": "Queen's University" + }, + { + "author_name": "Taylor Walsh", + "author_inst": "Queen's University" + }, + { + "author_name": "Ujjwal Sangwan", + "author_inst": "Queen's University" + }, + { + "author_name": "Che C. Colpitts", + "author_inst": "Queen's University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.19.549772", "rel_title": "Structure, Dynamics and Free Energy Studies on the Effect of Spot Mutations on SARS-CoV-2 Spike Protein Binding with ACE2 Receptor", @@ -35665,25 +36357,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.17.23292426", - "rel_title": "Intranasal lavage with hypochlorous acid safely reduces the symptoms in the ambulatory patient with COVID-19.", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292426", - "rel_abs": "OBJECTIVEThis study was designed to investigate intranasal lavage with a hypochlorous acid solution in the reduction of symptoms in the ambulatory COVID-19 patient.\n\nSTUDY DESIGNStudy approval granted by the Institutional Review Board of Reading Hospital (IRB 036-20), with informed consent obtained from all adult participants(age>18 years).\n\nSETTINGAll enrollees, taken from the same ambulatory testing facility, received nasopharyngeal swabs for COVID-19 testing by reverse transcription polymerase chain (RT-PCR) or the COVID-19 antigen specific test (Binax NOW, Abbott Lab)\n\nMETHODSConvenience sampling methodology was utilized. Each enrollee was provided with the study devices which included a Nasaflo Neti Pot (NeilMed Pharmaceutical, Inc.), and the hypochlorous acid solution (Vashe Wound Solution, Urgo Medical North America, LLC). Participants were instructed to irrigate each nostril with 120 cc (four ounces) of the solution for ten consecutive days, and record the presence or absence of symptoms in a scripted diary log.\n\nRESULTSThe study included 88 patients of which 74 (84.1%) completed the ten days of nasal lavage. All data analysis was conducted using SPSS version 25.0.\n\nChi square test of association found no significant difference related to gender, age group race, ethnicity, residence, or living arrangements (all p-values > 0.05). There were no statistical differences in any of the co-morbid conditions. Mild adverse reactions included burning, epistaxis, and oral metallic taste. No enrollees required mechanical ventilation. There were no deaths.\n\nCONCLUSIONThis study suggests the feasibility and safety of using intranasal lavage with a hypochlorous acid solution in relieving symptoms in the ambulatory Covid-19 patient.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monique Lisa Abner", - "author_inst": "Tower Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.14.548971", "rel_title": "Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens", @@ -36305,6 +36978,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dermatology" }, + { + "rel_doi": "10.1101/2023.07.14.23292649", + "rel_title": "Early Biological Markers of Post-Acute Sequelae of SARS-CoV-2 Infection", + "rel_date": "2023-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.14.23292649", + "rel_abs": "To understand the roles of acute phase viral dynamics and host immune responses in PASC, we enrolled 136 participants within 5 days of their first positive SARS-CoV-2 real-time PCR. Participants self-collected nasal specimens up to 21 times within the first 28 days after symptom onset; Interviewer-administered clinical questionnaires and blood samples were collected at enrollment and days 9, 14, 21, 28, and month 4 and 8 post-symptom. Defining PASC as the presence of any symptom new or worse since infection reported at their 4-month visit, we compared viral markers (quantity and duration of viral RNA load, infectious viral load, and plasma N-antigen level) and host immune markers (IL-6, IL-10, TNF-, IFN-, IFN-{gamma}, MCP, IP-10, and Spike IgG) over the acute period. In comparison to those who fully recovered, those who developed PASC demonstrated significantly higher maximum levels of SARS-CoV-2 RNA, infectious virus, and N-antigen, longer duration of viral shedding, and lower Spike-specific IgG levels within the first 10 days of the acute phase of illness. No significant differences were identified among a panel of host immune markers, though there was a trend toward higher initial levels of certain markers (e.g., MCP-1, IFN-, and IFN-{gamma}) in those who went on to develop PASC. Early viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC. These findings highlight the importance of understanding the early biological markers from acute SARS-CoV-2 infection in the natural history of PASC.\n\nOnset Sentence SummaryEarly viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Scott Lu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael J Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David V Glidden", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michelle Davidson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kara Lugtu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jesus Pineda-Ramirez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michel Tassetto", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Miguel Garcia-Knight", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amethyst Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sarah A Goldberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jessica Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Maya Forbes", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sara Park", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ana Martinez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew So", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Aidan Donovan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Badri Viswanathan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin Donohue", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David McIlwain", + "author_inst": "Stanford University" + }, + { + "author_name": "Brice Gaudilliere", + "author_inst": "Stanford University" + }, + { + "author_name": "Khamal Anglin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Brandon Yee", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ahmed A Chenna", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "John Winslow", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "Christos Petropoulos", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "Melissa Briggs-Hagen", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Raul Andino", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Claire Midgley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jeffrey N Martin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sharon Saydeh", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "J Daniel Kelly", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.14.23292680", "rel_title": "Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US", @@ -37207,33 +38023,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.07.12.548725", - "rel_title": "Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium", - "rel_date": "2023-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.12.548725", - "rel_abs": "Both spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. The purpose of our study was to determine the SARS-CoV-2 entry mechanism using mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, while TMPRSS2 inhibitors had minimal impact, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ann Song", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Rattapol Phandthong", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Prue Talbot", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.07.12.23292570", "rel_title": "COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH", @@ -37815,6 +38604,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.07.11.548309", + "rel_title": "Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein", + "rel_date": "2023-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.11.548309", + "rel_abs": "The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG{downarrow}X motif found in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "H. T. Henry Chan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lennart Brewitz", + "author_inst": "University of Oxford" + }, + { + "author_name": "Claire Strain-Damerell", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Petra Lukacik", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Martin A. Walsh", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Christopher J. Schofield", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fernanda Duarte", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.07.10.548406", "rel_title": "Effects of aluminum-salt, CpG and emulsion adjuvants on the stability and immunogenicity of a virus-like particle displaying the SARS-CoV-2 receptor binding domain (RBD)", @@ -38168,7 +39000,7 @@ "rel_date": "2023-07-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.08.23292389", - "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1d828f6org.highwire.dtl.DTLVardef@696bf2org.highwire.dtl.DTLVardef@12de548org.highwire.dtl.DTLVardef@28181f_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1de5908org.highwire.dtl.DTLVardef@a72147org.highwire.dtl.DTLVardef@79eff1org.highwire.dtl.DTLVardef@177c3c4_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 5, "rel_authors": [ { @@ -38941,45 +39773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.06.23292296", - "rel_title": "Long-term symptom profiles after COVID-19 vs other acute respiratory infections: a population-based observational study (COVIDENCE UK)", - "rel_date": "2023-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292296", - "rel_abs": "BackgroundLong COVID is a well recognised, if heterogeneous, entity. Acute respiratory infections (ARIs) due to other pathogens may cause long-term symptoms, but few studies compare post-acute sequelae between SARS-CoV-2 and other ARIs. We aimed to compare symptom profiles between people with previous SARS-CoV-2 infection, people with previous non-COVID-19 ARIs, and contemporaneous controls, and to identify clusters of long-term symptoms.\n\nMethodsCOVIDENCE UK is a prospective, population-based UK study of ARIs in adults. We analysed data on 16 potential long COVID symptoms and health-related quality of life (HRQoL), reported in January, 2021, by participants unvaccinated against SARS-CoV-2. We classified participants as having previous SARS-CoV-2 infection or previous non-COVID-19 ARI ([≥]4 weeks prior) or no reported ARI. We compared symptoms by infection status using logistic and fractional regression, and identified symptom clusters using latent class analysis (LCA).\n\nFindingsWe included 10,203 participants (1343 [13.2%] with SARS-CoV-2 infection, 472 [4.6%] with non-COVID-19 ARI). Both types of infection were associated with increased prevalence/severity of most symptoms and decreased HRQoL compared with no infection. Participants with SARS-CoV-2 infection had increased odds of taste/smell problems and hair loss compared with participants with non-COVID-19 ARIs. Separate LCA models identified three symptom severity groups for each infection type. In the most severe groups (including 23% of participants with SARS-CoV-2, and 21% with non-COVID-19 ARI), SARS-CoV-2 infection presented with a higher probability of memory problems, difficulty concentrating, hair loss, and taste/smell problems than non-COVID-19 ARI.\n\nInterpretationBoth SARS-CoV-2 and non-COVID-19 ARIs are associated with a wide range of long-term symptoms. Research on post-acute sequelae of ARIs should extend from SARS-CoV-2 to include other pathogens.\n\nFundingBarts Charity.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Google Scholar for studies on post-acute sequelae of COVID-19 and other acute respiratory infections (ARIs), published up to May 24, 2023. We used search terms relating to COVID-19 and other ARIs (\"COVID-19\", \"SARS\", \"severe acute respiratory syndrome\", \"Middle East respiratory\", \"MERS\", \"respiratory infection\", \"influenza\", \"flu\") and post-acute symptoms (\"long COVID\", \"post-acute\", \"PACS\", \"sequelae\", \"long-term\"). Previous studies have shown a wide range of post-acute sequelae for COVID-19, affecting people with all severities of the acute disease. The few studies that have compared long-term symptoms between people with COVID-19 and non-COVID-19 ARIs have generally found a higher symptom burden among people with COVID-19; however, these studies have been restricted to hospitalised patients or electronic health record data, and thus do not capture the full picture in the community. Research into long COVID phenotypes has been inconclusive, with some analyses classifying people with long COVID according to the types of symptoms experienced, and others classifying them according to the overall severity of their symptoms.\n\nAdded value of this studyIn this population-based study of ARIs in the community, we observed high symptom burden among people with previous SARS-CoV-2 infection when compared with controls, highlighting the extensive reach of long COVID. Our finding of a similar symptom burden among people with non-COVID-19 ARIs suggests that post-acute sequelae of other ARIs may be going unrecognised, particularly given that the vast majority did not experience a severe acute infection. Latent class analyses of symptoms identified groupings based on overall symptom severity, rather than symptom types, for both SARS-CoV-2 infections and non-COVID-19 ARIs, suggesting that overall symptom burden may best characterise the experience of people with post-acute sequelae. Notably, among participants with the most severe symptoms, only half of those with previous SARS-CoV-2 infection attributed their symptoms to long COVID, suggesting they either did not believe the infection was the cause, or they did not consider their symptoms severe enough to qualify as long COVID.\n\nImplications of all the available evidenceThe long-term symptoms experienced by some people with previous ARIs, including SARS-CoV-2, highlights the need for improved understanding, diagnosis, and treatment of post-acute infection syndromes. As much-needed research into long COVID continues, we must take the opportunity to investigate and consider the post-acute burden of ARIs due to other pathogens.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Giulia Vivaldi", - "author_inst": "Blizard Institute and Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Paul E Pfeffer", - "author_inst": "Barts Health NHS Trust, London, UK; Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Mohammad Talaei", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Jayson Basera", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Seif O Shaheen", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Adrian R Martineau", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry; and Asthma UK Centre for Applied Research; Queen Mary University of London, London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.07.05.23292278", "rel_title": "Intracardiac Thrombus in COVID-19 Inpatients: A Nationwide Study of Incidence, Predictors and Outcomes", @@ -39601,6 +40394,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.07.02.547368", + "rel_title": "Alternative cell entry mechanisms for SARS-CoV-2 and multiple animal viruses", + "rel_date": "2023-07-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.02.547368", + "rel_abs": "The cell entry mechanism of SARS-CoV-2, the causative agent of the COVID-19 pandemic, is not fully understood. Most animal viruses hijack cellular endocytic pathways as an entry route into the cell. Here, we show that in cells that do not express serine proteases such as TMPRSS2, genetic depletion of all dynamin isoforms blocked the uptake and strongly reduced infection with SARS-CoV-2 and its variant Delta. However, increasing the viral loads partially and dose-dependently restored infection via a thus far uncharacterized entry mechanism. Ultrastructural analysis by electron microscopy showed that this dynamin-independent endocytic processes appeared as 150-200 nm non-coated invaginations and was efficiently used by numerous mammalian viruses, including alphaviruses, influenza, vesicular stomatitis, bunya, adeno, vaccinia, and rhinovirus. Both the dynamin-dependent and dynamin-independent infection of SARS-CoV-2 required a functional actin cytoskeleton. In contrast, the alphavirus Semliki Forest virus, which is smaller in diameter, required actin only for the dynamin-independent entry. The presence of TMPRSS2 protease rescued SARS-CoV-2 infection in the absence of dynamins. Collectively, these results indicate that some viruses such as canine parvovirus and SARS-CoV-2 mainly rely on dynamin for endocytosis-dependent infection, while other viruses can efficiently bypass this requirement harnessing an alternative infection entry route dependent on actin.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Ravi Ojha", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Anmin Jiang", + "author_inst": "University of Queensland" + }, + { + "author_name": "Elina Mantyla", + "author_inst": "Tampere University" + }, + { + "author_name": "Naphak Modhiran", + "author_inst": "University of Queensland" + }, + { + "author_name": "Robert Witte", + "author_inst": "University of Zurich" + }, + { + "author_name": "Arnaud Gaudin", + "author_inst": "University of Queensland" + }, + { + "author_name": "Lisa De Zanetti", + "author_inst": "Ghent University" + }, + { + "author_name": "Rachel Gormal", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Maija Vihinen-Ranta", + "author_inst": "University of Jyvaskyla" + }, + { + "author_name": "Jason Mercer", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Maarit Suomalainen", + "author_inst": "University of Zurich" + }, + { + "author_name": "Urs F Greber", + "author_inst": "University of Zurich" + }, + { + "author_name": "Yohei Yamauchi", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Pierre Yves-Lozach", + "author_inst": "University Lyon" + }, + { + "author_name": "Ari Helenius", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Olli Vapalahti", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Paul Young", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Daniel Watterson", + "author_inst": "University of Queensland" + }, + { + "author_name": "Frederic A Meunier", + "author_inst": "University of Queensland" + }, + { + "author_name": "Merja Joensuu", + "author_inst": "The Univeristy of Queensland" + }, + { + "author_name": "Giuseppe Balistreri", + "author_inst": "University of Helsinki" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.06.30.547193", "rel_title": "Absence of Coronavirus in terns in the Western Indian Ocean?", @@ -41031,193 +41923,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2023.06.29.546792", - "rel_title": "Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures", - "rel_date": "2023-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.29.546792", - "rel_abs": "Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Wenliang Wang", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Manoj Hariharan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Anna Bartlett", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Cesar Barragan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Rosa Castanon", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Vince Rothenberg", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Haili Song", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Joseph Nery", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Andrew Aldridge", - "author_inst": "Duke University School of Medicine, Bryan Research Building, 311 Research Drive, Durham, NC 27710, USA" - }, - { - "author_name": "Jordan Altshul", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Mia Kenworthy", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wubin Ding", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Hanqing Liu", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wei Tian", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Jingtian Zhou", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Huaming Chen", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Bei Wei", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Irem B Gunduz", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "Todd Norell", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Timothy J Broderick", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Micah McClain", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Lisa Satterwhite", - "author_inst": "Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA" - }, - { - "author_name": "Thomas Burke", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Xiling Shen", - "author_inst": "Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA" - }, - { - "author_name": "Chris Woods", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Vance G Fowler", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Duke Clinical " - }, - { - "author_name": "Felicia Ruffin", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Parinya Panuwet", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Dana B Barr", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Jennifer L Beare", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Anthony K Smith", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Rachel R Spurbeck", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Sindhu Vangeti", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Irene Ramos", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "German Nudelman", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Stuart C Sealfon", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Flora Castellino", - "author_inst": "U.S. Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, Wa" - }, - { - "author_name": "Anna Maria Walley", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Tom Evans", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Fabian Muller", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "William J Greenleaf", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Joseph R Ecker", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA., Howard Hughes Medical Institute, The " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2023.06.29.546885", "rel_title": "Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication", @@ -41955,6 +42660,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.23.23291828", + "rel_title": "Growing inequities by immigration group among older adults: Population-based analysis of access to primary care and return to in-person visits during the COVID-19 pandemic in British Columbia, Canada.", + "rel_date": "2023-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.23.23291828", + "rel_abs": "BackgroundThe onset of the COVID-19 pandemic drove a rapid and widespread shift to virtual care, followed by a gradual return to in-person visits. Virtual visits may offer more convenient access to care for some, but others may experience challenges accessing care virtually, and some medical needs must be met in-person. Experiences of the shift to virtual care and benefits of in-person care may vary by immigration experience (immigration status and duration), official language level, and age. We examined use of virtual care and return to in-person visits in the Canadian province of British Columbia (BC), comparing patterns by age and across immigration groups, including length of time in Canada and language level (English) at time of arrival.\n\nMethodsWe used linked administrative health and immigration data to examine total primary care visits (virtual or in-person) and return to in-person visits during the COVID-19 pandemic (2019/20-2021/2) in BC. We examined the proportion of people with any primary care visits and with any in-person visit within each year as measures of access to primary care. We estimated the odds of any primary care visit and any in-person visit by immigration group and official language level assessed prior to arrival: non-immigrants, long-term immigrants, recent immigrants (<5 years) with high assessed English level and recent immigrants (<5 years) with low assessed English level, stratified by age.\n\nResultsIn general, changes in access to primary care (odds of any visit and odds of any in-person visit) were similar across immigration groups over the study period. However, we observed substantial disparities in access to primary care by immigration group among people aged 60+, particularly in recent immigrants with low official language level (0.42, 0.40-0.45). These disparities grew wider over the course of the pandemic.\n\nConclusionThough among younger adults changes in access to primary care between 2019-2021 were similar across immigration groups, we observed significant and growing inequities among older adults, with particularly limited access among adults who immigrated recently and with low assessed English level. Targeted interventions to ensure acceptable, accessible care for older immigrants are needed.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cecilia Sierra-Heredia", + "author_inst": "Faculty of Health Sciences, Simon Fraser University" + }, + { + "author_name": "Elmira Tayyar", + "author_inst": "Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Yasmin Bozorgi", + "author_inst": "Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Padmini Thakore", + "author_inst": "Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Selamawit Hagos", + "author_inst": "Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Ruth Carrillo", + "author_inst": "Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Stefanie Machado", + "author_inst": "Faculty of Health Sciences, Simon Fraser University. Centre for Gender & Sexual Health Equity" + }, + { + "author_name": "Sandra Peterson", + "author_inst": "Centre for Health Services and Policy Research, University of British Columbia" + }, + { + "author_name": "Shira Goldenberg", + "author_inst": "Centre for Gender & Sexual Health Equity. School of Public Health, San Diego State University" + }, + { + "author_name": "Mei-ling Wiedmeyer", + "author_inst": "Centre for Gender & Sexual Health Equity. Department of Family Practice, University of British Columbia" + }, + { + "author_name": "Ruth Lavergne", + "author_inst": "Centre for Gender & Sexual Health Equity. Department of Family Medicine, Faculty of Medicine, Dalhousie University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2023.06.23.23291776", "rel_title": "Patient characteristics associated with clinically coded long COVID: an OpenSAFELY study using electronic health records", @@ -43129,85 +43893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.06.28.23291986", - "rel_title": "The Role of VSL#3 in the Treatment of Fatigue and Other Symptoms in Long Covid-19 Syndrome: a Randomized, Double-blind, Placebo-controlled Pilot Study (DELong#3)", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291986", - "rel_abs": "Long COVID, also known as Post-acute COVID-19 Syndrome (PACS), is a chronic condition affecting individuals who have recovered from acute COVID-19. It is currently estimated that around 65 million people worldwide suffer from Long COVID. It is characterized by a range of symptoms, including fatigue, exertion intolerance, neurocognitive and sensory impairment, sleep disturbance, myalgia/arthralgia, and dysautonomia. Among them fatigue has emerged as a burdensome and pervasive issue, significantly impacting the quality of life and daily functioning of Long COVID patients. Alterations in the composition of the intestinal microbiota has been reported in COVID-19 patients. Dysbiosis persists even after several months of recovery from acute SARS-CoV-2 infection.\n\nBased on this evidence, we carried out a phase 3, randomized, double-blind, placebo-controlled trial aimed at evaluating the efficacy of VSL#3(R), a consortium of probiotic bacterial strains, in reducing fatigue and improving various aspects of patients well-being in patients with Long COVID syndrome.\n\nHighlightsO_LIPatients suffering from Long-COVID manifest a variety of persistent symptoms impacting daily functioning;\nC_LIO_LIFatigue emerged as a burdensome and pervasive issue, significantly impacting the quality of life;\nC_LIO_LIVSL#3(R) treatment significantly reduced the Chalder Fatigue Scale scores as compared to placebo\nC_LIO_LIChalder Fatigue Scale scores remained significantly reduced in the treatment group 4 weeks post intervention.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Flavio Caprioli", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gra" - }, - { - "author_name": "Beatrice Marinoni", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandro Rimondi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Federico Bottaro", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Clorinda Ciafardini", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Chiara Amoroso", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Martina Muia", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Bruna Caridi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Daniele Noviello", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Marco Mantero", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Francesco Blasi", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Roberta Ferrucci", - "author_inst": "ASST Santi Paolo e Carlo, San Paolo University Hospital, 20142 Milan, Italy;6Aldo Ravelli Center for Neurotechnology and Experimental Brain Therapeutics, Depart" - }, - { - "author_name": "Federica Facciotti", - "author_inst": "Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Maurizio Vecchi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.06.27.23291947", "rel_title": "Examining the inter-relationships between social isolation and loneliness and their correlates among older British adults before and during the COVID-19 lockdown: evidence from four British longitudinal studies", @@ -43753,6 +44438,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.06.26.546514", + "rel_title": "A pseudovirus-based method to dynamically mimic SARS-CoV-2-associated cell-to-cell fusion and transmission", + "rel_date": "2023-06-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.26.546514", + "rel_abs": "SARS-CoV-2 has caused the global tremendous loss and continues to evolve to generate variants. Entry of SARS-CoV-2 into the host cells is primarily mediated by Spike (S), which binds to the host receptor hACE2 and initiates virus-cell membrane fusion. Cell fusion contributes to viral entry, cell-to-cell transmission and tissue damage in COVID-19 patients. Many reporter assays have been developed to study S-mediated cell fusion by equally coculturing S-expressing cells and hACE2-positive cells. However, these strategies cannot fully simulate cell-to-cell fusion and transmission of SARS-CoV-2 infection, in which virions from a single target cell transmit to the neighbor cells and induce syncytia formation. Here, we design a pseudovirus-based method to dynamically mimic cell-to-cell fusion and transmission of SARS-CoV-2. We coculture a small number of pseudovirus-producing 293FT cells and a large number of hACE2-expressing 293T cells, and demonstrate that a single cell producing S-pseudotyped virions can induce significant syncytia of hACE2-positive cells. This pseudovirus-based method is a powerful tool to screen and estimate potential inhibitors of S-driven syncytia. Moreover, this strategy can also be utilized to explore fusogenic ability of SARS-CoV-2 variants. Together, the pseudovirus-based method we report here will be beneficial to drug screening and scientific research against SARS-CoV-2 or future emerging coronavirus.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Xiangpeng Sheng", + "author_inst": "Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, China" + }, + { + "author_name": "Yi Yang", + "author_inst": "Department of Thoracic Surgery, Ruijin Hospital North Campus, Shanghai Jiaotong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Fang Zhu", + "author_inst": "School of Medicine, Guizhou University, Guiyang, China" + }, + { + "author_name": "Fan Yang", + "author_inst": "State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of C" + }, + { + "author_name": "Honghua Wang", + "author_inst": "Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China" + }, + { + "author_name": "Ronggui Hu", + "author_inst": "Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.06.24.546363", "rel_title": "Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS-COV-2 targeting virus-specific enzymes", @@ -44535,121 +45259,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.16.23291450", - "rel_title": "High rates of SARS-CoV-2 infection in pregnant Ugandan women and association with stunting in infancy", - "rel_date": "2023-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291450", - "rel_abs": "BackgroundSARS-CoV-2 has been well studied in resource-rich areas but many questions remain about effects of infection in African populations, particularly in vulnerable groups such as pregnant women.\n\nMethodsWe describe SARS-CoV-2 immunoglobulin (Ig) G and IgM antibody responses and clinical outcomes in mother-infant dyads enrolled in malaria chemoprevention trials in Uganda.\n\nResultsFrom December 2020 to February 2022, among 400 unvaccinated pregnant women, serologic assessments revealed that 128 (32%) were seronegative for anti-SARS-CoV-2 IgG and IgM at enrollment and delivery, 80 (20%) were infected either prior to or early in pregnancy, and 192 (48%) were infected or re-infected with SARS-CoV-2 during pregnancy. We observed preferential binding of plasma IgG to Wuhan-Hu-1-like antigens in individuals seroconverting up to early 2021, and to Delta variant antigens in a subset of individuals in mid-2021. Breadth of IgG binding to all variants improved over time. No participants experienced severe respiratory illness during the study. SARS-CoV-2 infection in early pregnancy was associated with lower median length-for-age Z-score at age 3 months compared with no infection or late pregnancy infection (- 1.54 versus -0.37 and -0.51, p=0.009).\n\nConclusionPregnant Ugandan women experienced high levels of SARS-CoV-2 infection without severe respiratory illness. Variant-specific serology testing demonstrated evidence of antibody affinity maturation at the population level. Early gestational SARS-CoV-2 infection was associated with shorter stature in early infancy.\n\nFundingThis work was supported by: Stanford MCHRI/Stephen Bechtel Endowed Fellowship in Pediatric Translational Medicine (KJ), Swiss National Science Foundation PRIMA grant PR00P3_208580 (KR), the Bill and Melinda Gates Foundation, and NIAID (T32-AI052073, U01- AI141308, U01-AI155325).", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Karen Blake Jacobson", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Katharina R\u00f6ltgen", - "author_inst": "Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland" - }, - { - "author_name": "Brandon Lam", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Patience Nayebare", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Abel Kakuru", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jimmy Kizza", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Miriam Aguti", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Felistas Nankya", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jessica Briggs", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Saki Takahashi", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Isabel Rodriguez-Barraquer", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Kattria van der Ploeg", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Jacob N. Wohlstadter", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "George B. Sigal", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "Michelle E. Roh", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Joaniter I. Nankabirwa", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Gloria Cuu", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Stephanie L. Gaw", - "author_inst": "Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Maternal-Fetal Medicine, UCSF, San Francisco, CA, USA" - }, - { - "author_name": "Philip J. Rosenthal", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Moses R. Kamya", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Isaac Ssewanyana", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Grant Dorsey", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Scott D. Boyd", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Prasanna Jagannathan", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.16.23291442", "rel_title": "Vaccines at Velocity: Evaluating Potential Lives Saved by Earlier Vaccination in the COVID-19 Pandemic", @@ -45431,6 +46040,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.06.14.23291380", + "rel_title": "A single blinded, phase IV, adaptive randomised control trial to evaluate the safety of coadministration of seasonal influenza and COVID-19 vaccines (The FluVID study)", + "rel_date": "2023-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.14.23291380", + "rel_abs": "ObjectivesWe evaluated the frequency of moderate and severe adverse events following coadministration of seasonal influenza vaccine (SIV) versus placebo with COVID-19 vaccines among adults to support practice guidelines.\n\nMethodsFluVID is a participant-blinded, phase IV, randomised control trial. On the same day as the participants scheduled COVID-19 vaccine, participants were randomised to receive SIV or saline placebo; those assigned placebo at visit one then received SIV a week later, and vice versa. Self-reported adverse events were collected for daily seven days following each visit.\n\nThe primary endpoint was any solicited adverse event of at least moderate severity occurring up to seven days following receipt of SIV or placebo. This was modelled using a Bayesian logistic regression model. Analyses were performed by COVID-19 vaccine type and dose number.\n\nResultsOverall, 248 participants were enrolled; of these, 195 had received BNT162b2 and 53 had received mRNA1273 COVID-19 vaccines according to national guidelines. After randomisation, 119 were assigned to receive SIV and 129 were assigned to receive placebo at visit one.\n\nAdverse events were most frequently reported as mild (grade 1) in nature. Among 142 BNT162b2 booster dose one and 43 BNT162b2 booster dose two recipients, the posterior median risk difference for moderate/severe adverse events following SIV versus placebo was 13% (95% credible interval [CrI] -0.03 to 0.27) and 13% (95%CrI -0.37 to 0.12), respectively. Among 18 mRNA1273 booster dose one and 35 mRNA1273 booster dose two recipients, the posterior median risk difference of moderate/severe adverse events following influenza vaccine versus placebo was 6% (95%CrI -0.29 to 0.41) and -4% (95%CrI -0.30 to 0.23), respectively.\n\nConclusionAdverse events following SIV and COVID-19 co-administration were generally mild and occurred with similar frequency to events following COVID-19 vaccine alone. We found no evidence to justify routine separation of SIV and COVID-19 vaccine doses.\n\nClinical trial registrationACTRN12621001063808\n\nHighlightsO_LIThe coadministration of mRNA COVID-19 and influenza vaccines typically resulted in mild events that were limited to 4 days.\nC_LIO_LIFrequency and nature of adverse events were similar to those in other randomised trials.\nC_LIO_LIThis trial demonstrates a suitable design for evaluating vaccine schedules and coadministration.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jessica A Ramsay", + "author_inst": "Telethon Kids Institute" + }, + { + "author_name": "Mark Jones", + "author_inst": "University of Sydney" + }, + { + "author_name": "Ann Marie Vande More", + "author_inst": "Royal Prince Alfred Hospital" + }, + { + "author_name": "Stephanie L Hunt", + "author_inst": "Royal Prince Alfred Hospital" + }, + { + "author_name": "Phoebe CM Williams", + "author_inst": "University of Sydney" + }, + { + "author_name": "Mitch Messer", + "author_inst": "Telethon Kids Institute" + }, + { + "author_name": "Nicholas Wood", + "author_inst": "National Centre for Immunisation Research and Surveillance" + }, + { + "author_name": "Kristine Macartney", + "author_inst": "National Centre for Immunisation Research and Surveillance" + }, + { + "author_name": "Frederick J Lee", + "author_inst": "Royal Prince Alfred Hospital" + }, + { + "author_name": "Warwick J Britton", + "author_inst": "Centenary Institute" + }, + { + "author_name": "Thomas L Snelling", + "author_inst": "University of Sydney" + }, + { + "author_name": "Ian D Caterson", + "author_inst": "Royal Prince Alfred Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.06.17.545443", "rel_title": "Detecting episodic evolution through Bayesian inference of molecular clock models", @@ -46473,57 +47145,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.14.544985", - "rel_title": "Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides increased sequence coverage", - "rel_date": "2023-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.14.544985", - "rel_abs": "Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a proteins conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of glycopeptides has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their isotopic mass shifts from deuteration. Inclusion of the deu-terated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.\n\nAbstract Figure\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC=\"FIGDIR/small/544985v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@1d8e1f6org.highwire.dtl.DTLVardef@1db0774org.highwire.dtl.DTLVardef@c68d1eorg.highwire.dtl.DTLVardef@15aed98_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christopher A Haynes", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Theodore R Keppel", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Betlehem Mekonnen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sarah H Osman", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Yu Zhou", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Adrian R Woolfitt", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jakub Baudys", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John R Barr", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Dongxia Wang", - "author_inst": "Centers for Disease Control and Prevention (CDC)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.06.14.544834", "rel_title": "Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV", @@ -47345,6 +47966,65 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.06.13.543274", + "rel_title": "Mycobiome analyses of critically ill COVID-19 patients suggests antifungal prophylaxis may be protective against A. fumigatus-associated mortality", + "rel_date": "2023-06-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.13.543274", + "rel_abs": "RationaleCovid-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment.\n\nObjectivesTo understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA, the impact of antifungal use and its role in patient outcome.\n\nMethodsWe performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing and Aspergillus fumigatus burden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa prevalence and taxa abundances.\n\nResultsRespiratory mycobiomes were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality. The use of antifungals at ICU admission was associated with an absence of A. fumigatus.\n\nConclusionsOur findings suggest that systemic antifungal treatment at ICU admission may be protective against A. fumigatus-associated mortality in CAPA.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Danielle Weaver", + "author_inst": "The University of Manchester, Manchester, UK" + }, + { + "author_name": "Sara Gago", + "author_inst": "The University of Manchester, Manchester, UK" + }, + { + "author_name": "Matteo Bassetti", + "author_inst": "Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy Infectious Diseases Unit, IRCCS San Martino Polyclinic Hospital, Genoa, Italy" + }, + { + "author_name": "Daniele Roberto Giacobbe", + "author_inst": "Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy Infectious Diseases Unit, IRCCS San Martino Polyclinic Hospital, Genoa, Italy" + }, + { + "author_name": "Juergen Prattes", + "author_inst": "Division of Infectious Diseases, Medical University of Graz, Graz, Austria" + }, + { + "author_name": "Martin Hoenigl", + "author_inst": "Division of Infectious Diseases, Medical University of Graz, Graz, Austria; Biotech Med, Graz; Translational Medical Mycology Research Unit, ECMM Excellence Cen" + }, + { + "author_name": "Florian Reizine", + "author_inst": "Centre Hospitalier Universitaire de Rennes Medical Intensive Care Unit, Rennes, France" + }, + { + "author_name": "H\u00e9l\u00e8ne Guegan", + "author_inst": "Universite de Rennes, CHU, INSERM, Irset: Institut de Recherche en Sante, Environnement et Travail, UMR_S 1085, Rennes, France; Centre Hospitalier Universitaire" + }, + { + "author_name": "Jean-Pierre Gangneux", + "author_inst": "Universite de Rennes, CHU, INSERM, Irset: Institut de Recherche en Sante, Environnement et Travail, UMR_S 1085, Rennes, France; Centre Hospitalier Universitaire" + }, + { + "author_name": "Mike J Bromley", + "author_inst": "The University of Manchester, Manchester, UK" + }, + { + "author_name": "Paul Bowyer", + "author_inst": "The University of Manchester, Manchester, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.06.09.23291222", "rel_title": "Comparison of incidence and prognosis of myocardial injury in patients with COVID-19-related respiratory failure and other pulmonary infections: a contemporary cohort study", @@ -48299,41 +48979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.06.09.23291202", - "rel_title": "Trends in medication use after the onset of the COVID-19 pandemic in the Republic of Ireland: an interrupted time series study", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.09.23291202", - "rel_abs": "The COVID-19 pandemic had a substantial impact on healthcare delivery, particularly in general practice. This study aimed to evaluate how dispensing of medications in primary care in Ireland changed following the COVID-19 pandemics onset compared to expected trends. This interrupted time series study used data on medications prescribed in general practice 2016-2022 to patient eligible for state health cover, approximately one third of the population. Dispensing volumes for all therapeutic subgroups (ATC2 codes) and commonly dispensed medications were summarised. Pre-pandemic data was used to forecast expected trends (with 99% prediction intervals) using the Holt-Winters method, and these were compared to observed dispensing from March 2020 onwards. Most (31/77) therapeutic subgroups had dispensing significantly different from forecast in March 2020. Drugs for obstructive airway disease had the largest difference, with dispensing 26.2% (99%CI 19.5%-33.6%) higher than forecasted. Only two subgroups were significantly lower than forecasted, other gynaecologicals (17.7% lower, 99%CI 6.3%-26.6%) and dressings (11.6%, 99%CI 9.4%-41.6%). Dispensing of amoxicillin products and oral prednisolone were lower than forecasted in the months following the pandemics onset, particularly during winter 2020/2021. There was a spike in dispensing for many long-term medications in March 2020, while pandemic restrictions likely contributed to reductions for other medications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Molly Mattsson", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "Jung Ah Hong", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "John Scott Frazer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Glenn Ross Frazer", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Frank Moriarty", - "author_inst": "RCSI University of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.06.07.23290927", "rel_title": "SARS-CoV-2 infections among 12 000 pregnant women, 2020, Finland - cross-testing of neutralization assays", @@ -49003,6 +49648,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.06.07.544062", + "rel_title": "Single-cell RNA sequencing reveals HIF1A as a severity-sensitive immunological scar in circulating monocytes of convalescent comorbidity-free COVID-19 patients", + "rel_date": "2023-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.07.544062", + "rel_abs": "COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is characterized by a wide range of clinical symptoms and a poorly predictable disease course. Although in-depth transcriptomic investigations of peripheral blood samples from COVID-19 patients have been performed, the detailed molecular mechanisms underlying an asymptomatic, mild or severe disease course, particularly in patients without relevant comorbidities, remain poorly understood. While previous studies have mainly focused on the cellular and molecular dissection of ongoing COVID-19, we set out to characterize transcriptomic immune cell dysregulation at the single-cell level at different time points in patients without comorbidities after disease resolution to identify signatures of different disease severities in convalescence. With single-cell RNA sequencing we reveal a role for hypoxia-inducible factor 1-alpha (HIF1A) as a severity-sensitive long-term immunological scar in circulating monocytes of convalescent COVID-19 patients. Additionally, circulating complexes formed by monocytes with either T cells or NK cells represent a characteristic cellular marker in convalescent COVID-19 patients irrespective of their preceding symptom severity. Together, these results provide cellular and molecular correlates of recovery from COVID-19 and could help in immune monitoring and in the design of new treatment strategies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Christina Zielinski", + "author_inst": "Leibniz Institute for Natural Products Research and Infection Biology" + }, + { + "author_name": "Lilly May", + "author_inst": "Leibniz Institute for Natural Product Research and Infection Biology" + }, + { + "author_name": "Chang-Feng Chu", + "author_inst": "Leibniz Institute for Natural Product Research and Infection Biolog" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.06.07.544141", "rel_title": "An evolutionarily conserved strategy for ribosome binding and inhibition by \u03b2-coronavirus non-structural protein 1", @@ -49977,41 +50649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.03.543542", - "rel_title": "Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown", - "rel_date": "2023-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.03.543542", - "rel_abs": "Covid-19 lockdowns provided ecologists with a rare opportunity to examine how animals behave when humans are absent. Indeed many studies reported various effects of lockdowns on animal activity, especially in urban areas and other human-dominated habitats. We explored how Covid-19 lockdowns in Israel have influenced bird activity in an urban environment by using continuous acoustic recordings to monitor three common bird species that differ in their level of adaptation to the urban ecosystem: (1) the hooded crow, an urban exploiter, which depends heavily on anthropogenic resources; (2) the rose-ringed parakeet, an invasive alien species that has adapted to exploit human resources; and (3) the graceful prinia, an urban adapter, which is relatively shy of humans and can be found urban habitats with shrubs and prairies. Acoustic recordings provided continuous monitoring of bird activity without an effect of the observer on the animal. We performed dense sampling of a 1.3 square km area in northern Tel-Aviv by placing 17 recorders for more than a month in different micro-habitats within this region including roads, residential areas and urban parks. We monitored both lockdown and no-lockdown periods. We portray a complex dynamic system where the activity of specific bird species depended on many environmental parameters and decreases or increases in a habitat- dependent manner during lockdown. Specifically, urban exploiter species decreased their activity in most urban habitats during lockdown, while human adapter species increased their activity during lockdown especially in parks where humans were absent. Our results also demonstrate the value of different habitats within urban environments for animal activity, specifically highlighting the importance of urban parks. These species- and habitat-specific changes in activity might explain the contradicting results reported by others who have not performed a habitat specific analysis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Congnan Sun", - "author_inst": "Hebei Normal university" - }, - { - "author_name": "Yoel Hassin", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Arjan Boonman", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Assaf Shwartz", - "author_inst": "Israel Institute of Technology" - }, - { - "author_name": "Yossi Yovel", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2023.06.03.543589", "rel_title": "A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism", @@ -50573,6 +51210,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.06.02.23290867", + "rel_title": "Comparative Analysis of Decision Trees on Two COVID-19 Symptom Datasets", + "rel_date": "2023-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.02.23290867", + "rel_abs": "ObjectiveThis study compares decision trees on two COVID-19 symptom datasets to assess their performance and feature importance in predicting and understanding infection patterns.\n\nMethodsWe created decision trees on Israeli and Swedish COVID-19 infection datasets. Performance metrics were used to assess their predictive capabilities, and feature importance analysis identified significant variables in the decision-making process.\n\nResultsThe study observed different performance levels of decision trees on the COVID-19 datasets. The Swedish dataset achieved high accuracy and F1-score without hyperparameter tuning, while the Israeli dataset improved significantly with Extreme Gradient Boosting. Dataset characteristics impact the selection of an optimal decision tree algorithm. The key variable in both datasets was sore throat.\n\nConclusionThis study compares decision trees on COVID-19 infection datasets, emphasizing the importance of dataset characteristics in selecting an optimal algorithm. Identifying significant features enhances understanding of infection patterns, benefiting decision-making and prediction accuracy in infectious disease analysis.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Somchai Saengamnatdej", + "author_inst": "Naresuan University Faculty of Medical Science" + }, + { + "author_name": "Phuangphet Waree Molee", + "author_inst": "Naresuan University Faculty of Medical Science" + }, + { + "author_name": "Prateep Warnnissorn", + "author_inst": "Naresuan University Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.02.23290871", "rel_title": "Comparative B cell and antibody responses induced by adenoviral vectored and mRNA vaccines against COVID-19", @@ -52255,73 +52919,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2023.05.31.543022", - "rel_title": "Universal features of Nsp1-mediated translational shutdown by coronaviruses", - "rel_date": "2023-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.31.543022", - "rel_abs": "Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Katharina Schubert", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Evangelos D. Karousis", - "author_inst": "University of Bern" - }, - { - "author_name": "Ivo Ban", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Christopher Lapointe", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marc Leibundgut", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Emilie Baeumlin", - "author_inst": "University of Bern" - }, - { - "author_name": "Eric Kummerant", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Alain Scaiola", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Tanja Schoenhut", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Jana Ziegelmueller", - "author_inst": "University of Bern" - }, - { - "author_name": "Joseph Puglisi", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Oliver Muehlemann", - "author_inst": "University of Bern" - }, - { - "author_name": "Nenad Ban", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.31.543129", "rel_title": "CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development", @@ -52979,6 +53576,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.29.542735", + "rel_title": "Antibodies against SARS-CoV-2 control complement-induced inflammatory responses to SARS-CoV-2", + "rel_date": "2023-05-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.29.542735", + "rel_abs": "Dysregulated immune responses contribute to pathogenesis of COVID-19 leading to uncontrolled and exaggerated inflammation observed during severe COVID-19. However, it remains unclear how immunity to SARS-CoV-2 is induced and subsequently controlled. Notably, here we have uncovered an important role for complement in the induction of innate and adaptive immunity to SARS-CoV-2. Complement rapidly opsonized SARS-CoV-2 via the lectin pathway. Complement-opsonized SARS-CoV-2 efficiently interacted with dendritic cells (DCs), inducing type I IFN and pro-inflammatory cytokine responses, which were inhibited by antibodies against the complement receptors (CR)3 and CR4. These data suggest that complement is important in inducing immunity via DCs in the acute phase against SARS-CoV-2. Strikingly, serum from COVID-19 patients as well as monoclonal antibodies against SARS-CoV-2 attenuated innate and adaptive immunity induced by complement-opsonized SARS-CoV-2. Blocking the FcyRII, CD32, restored complement-induced immunity. These data strongly suggest that complement opsonization of SARS-CoV-2 is important for inducing innate and adaptive immunity to SARS-CoV-2. Subsequent induction of antibody responses is important to limit the immune responses and restore immune homeostasis. These data suggest that dysregulation in complement and FcyRII signalling might underlie mechanisms causing severe COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Marta Bermejo-Jambrina", + "author_inst": "Department of Experimental Immunology, Amsterdam UMC location AMC, Amsterdam, The Netherlands. Amsterdam institute for Infection and Immunity, Infectious Disea" + }, + { + "author_name": "Lieve E.H. van der Donk", + "author_inst": "Department of Experimental Immunology, Amsterdam UMC location AMC, Amsterdam, The Netherlands. Amsterdam institute for Infection and Immunity, Infectious Disea" + }, + { + "author_name": "John L. van Hamme", + "author_inst": "Department of Experimental Immunology, Amsterdam UMC location AMC, Amsterdam, The Netherlands. Amsterdam institute for Infection and Immunity, Infectious Disea" + }, + { + "author_name": "Doris Wilflingseder", + "author_inst": "Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Godelieve de Bree", + "author_inst": "Department of Internal Medicine, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands. Amsterdam institute for Infection and Immunity" + }, + { + "author_name": "Maria Prins", + "author_inst": "Department of Internal Medicine, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands. Department of Infectious Diseases, Public Heal" + }, + { + "author_name": "Menno de Jong", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Pythia Nieuwkerk", + "author_inst": "Department of Medical Psychology (J3-2019-1), Amsterdam UMC location AMC University of Amsterdam, Amsterdam, The Netherlands. Department of Infectious Diseases," + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC University of Amsterdam, Amsterdam, The Netherlands" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "Department of Experimental Immunology, Amsterdam UMC location AMC, Amsterdam, The Netherlands. Amsterdam institute for Infection and Immunity, Infectious Disea" + }, + { + "author_name": "Teunis Geijtenbeek", + "author_inst": "Amsterdam Medical Centers, University of Amsterdam" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.05.25.23290471", "rel_title": "Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study", @@ -54721,93 +55377,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.05.23.542024", - "rel_title": "A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects Against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection", - "rel_date": "2023-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.23.542024", - "rel_abs": "The pandemic of the coronavirus disease 2019 (COVID-19) has created the largest global health crisis in almost a century. Following exposure to SARS-CoV-2, the virus particles replicate in the lungs, induce a \"cytokine storm\" and potentially cause life-threatening inflammatory disease. Low frequencies of function SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs of COVID-19 patients were associated with severe cases of COVID-19. The apparent low level of T cell-attracting CXCL9, CXCL10, and CXCL11 chemokines in infected lungs may not be sufficient enough to assure the sequestration and/or homing of CD4+ and CD8+ T cells from the circulation into infected lungs. We hypothesize that a Coronavirus vaccine strategy that boosts the frequencies of functional SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs would lead to better protection against SARS-CoV-2 infection, COVID19-like symptoms, and death. In the present study, we designed and pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope//CXCL11 prime/pull mucosal Coronavirus vaccine. This prime/pull vaccine strategy consists of intranasal delivery of a lung-tropic adeno-associated virus type 9 (AAV-9) vector that incorporates highly conserved human B, CD4+ CD8+ cell epitopes of SARS-CoV-2 (prime) and pulling the primed B and T cells into the lungs using the T cell attracting chemokine, CXCL-11 (pull). We demonstrated that immunization of HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice with this multi-epitope//CXCL11 prime/pull Coronavirus mucosal vaccine: (i) Increased the frequencies of CD4+ and CD8+ TEM, TCM, and TRM cells in the lungs; and (ii) reduced COVID19-like symptoms, lowered virus replication, and prevented deaths following challenge with SARS-CoV-2. These findings discuss the importance of bolstering the number and function of lung-resident memory CD4+ and CD8+ T cells for better protection against SARS-CoV-2 infection, COVID-19-like symptoms, and death.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Latifa Zayou", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Swayam Prakash", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Nisha R Dhanushkodi", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Afshana Quadiri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Izabela Coimbra Ibraim", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Mahmoud Singer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amirah Salem", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amin Mohammed Shaik", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Berfin Suzer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amruth Chilukuri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jennifer Tran", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Pauline Chau Nguyen", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Miyo Sun", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Kathy K Hormi-Carver", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Ahmed Belmouden", - "author_inst": "Laboratory of Cell Biology and Molecular Genetics, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco" - }, - { - "author_name": "Hawa Vahed", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "Jeffrey B Ulmer", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "LBACHIR BENMOHAMED", - "author_inst": "GHEI/UCI School of Medecine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.05.25.542297", "rel_title": "Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors", @@ -55565,6 +56134,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.05.24.542061", + "rel_title": "Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC)", + "rel_date": "2023-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.24.542061", + "rel_abs": "The COVID-19 (Corona Virus Disease 19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is causing enormous difficulties in the worlds economies and there is uncertainty as to whether the current prophylactic measures will offer adequate protection globally after the appearance of virus variants that like that indicated as Omicron emerged in the presence of global vaccine-based immunization. While several studies are available describing the main differences in the spike protein of Omicron compared to the other variants previously emerged, there was no structural insights into the 3CL-protease (3CLpro) associated to the new variant. Herein, we performed a computational study based on genomic data and amino acid sequences available in the most updated COVID-19-related databases that allowed us to build up in silico the 3D structure of Omicron 3CLpro. Moreover, by molecular dynamics simulation we demonstrated that currently available drugs acting as inhibitors of the SARS-CoV-2 main protease could be less effective in the case of Omicron variant due to the different chemical interactions in the binding site occurred after the recent amino acid mutations. Ultimately, our study highlights the need of exploiting in silico and in vitro methods to discover novel 3CLpro inhibitors starting from the computationally based structure we presented herein, and more in general to direct the major efforts to targeting the most conserved 3CLpro regions that appeared unchanged in the context of the Omicron variant.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Samee Ullah", + "author_inst": "National Center for Bioinformatics (NCB), Islamabad 45320, Pakistan" + }, + { + "author_name": "Afreenish Amir", + "author_inst": "National Institute of Health (NIH), Islamabad 4400, Pakistan" + }, + { + "author_name": "Aamer Ikram", + "author_inst": "National Institute of Health (NIH), Islamabad 4400, Pakistan" + }, + { + "author_name": "Giovanni Nicola Roviello", + "author_inst": "Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples, Italy" + }, + { + "author_name": "Caterina Vicidomini", + "author_inst": "Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples, Italy" + }, + { + "author_name": "Rosanna Palumbo", + "author_inst": "Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.05.17.23290107", "rel_title": "Psychiatric hospital admissions and linkages to ambulatory services in the Western Cape Province of South Africa (2015-2022): trends, risk factors, the impact of the COVID-19 pandemic and possible opportunities for intervention", @@ -56711,45 +57319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.16.23290033", - "rel_title": "Viral rebound among patients receiving COVID-19 convalescent plasma for treatment of Covid-19 in Uganda.", - "rel_date": "2023-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.16.23290033", - "rel_abs": "BackgroundViral rebound has been reported in people infected with COVID-19 treated with nirmatrelvir/ritonavir, and some cases been reported in patients who did not receive any antiviral treatment. Since the course of COVID-19 has not yet been well defined, we evaluated the incidence of viral rebound among COVID-19 patients treated with COVID-19 Convalescent Plasma (CCP) in Uganda.\n\nMethodsIn the CCP trail, 136 patients were enrolled between 21st September 2020 and 2nd December 2020 who presented to the Mulago National Referral COVID-19 treatment unit. Patients with a positive SARS-CoV-2 reverse transcriptase (RT)-PCR test irrespective of disease severity were hospitalised and randomised to receive either COVID-19 CCP plus standard of care (SOC) or SOC alone. SARS-CoV-2 RT-PCR was done at baseline and on days 3, 5, 7, 14 and 28 post randomisation or until two consecutive negative RT-PCR results were obtained, whichever occurred first. We analysed for occurrence of viral rebound. Viral rebound was defined as a positive SARS-CoV-2 RT-PCR test following a prior negative test.\n\nFindings20% of the participants had viral rebound. Viral rebounders were predominantly male. The median age was 45-64 years and they had at least one co-morbidity. There was no difference in the rebound rates in the study arms, and participants with hypertension had more rebound rates compared to those with other co-morbidities.\n\nInterpretationViral RNA rebound was common among patients receiving CCP. Viral rebound may be a result of the biphasic nature of COVID-19 infection, and not a consequence of the therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Patricia Alupo", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winters Muttamba", - "author_inst": "Makerere University Lung Institute ; 2.\tDivision of Infection and Global Health, School of Medicine, University of St Andrews; St. Andrews, United Kingdom" - }, - { - "author_name": "Levicatus Mugenyi", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Ivan Kimuli", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winceslaus Katagira", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Bruce Kirenga", - "author_inst": "Makerere University College of Health Sciences, Department of Medicine. 2. Makerere University Lung Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.19.23290234", "rel_title": "Defining the Subtypes of Long COVID and Risk Factors for Prolonged Disease", @@ -57359,6 +57928,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.17.541173", + "rel_title": "Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2", + "rel_date": "2023-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.17.541173", + "rel_abs": "Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes which link substrate release and opening of the cytoplasmic gate, and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Huanyu Z. Li", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Ashley C.W. Pike", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Gamma Chi", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Jesper S. Hansen", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Sarah G. Lee", + "author_inst": "University of Birmingham, School of Biosciences" + }, + { + "author_name": "Karin E.J. Rodstrom", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Simon R. Bushell", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "David Speedman", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Adam Evans", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Dong Wang", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Didi He", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Leela Shrestha", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Chady Nasrallah", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Nicola A. Burgess-Brown", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "Timonthy R. Dafforn", + "author_inst": "University of Birmingham, School of Biosciences" + }, + { + "author_name": "Elisabeth P. Carpenter", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + }, + { + "author_name": "David B. Sauer", + "author_inst": "University of Oxford, Centre for Medicines Discovery" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.05.16.23289144", "rel_title": "Reduction in Spontaneous and Iatrogenic Preterm Births in Twin Pregnancies During COVID-19 Lockdown in Melbourne, Australia: A Multicenter Cohort Study", @@ -58497,37 +59149,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.05.14.540726", - "rel_title": "Metformin an anti-diabetic drug, possess ACE-2 receptor-SARS- Cov-2 RBD binding antagonist activity, anti-inflammatory and cytokine inhibitory properties suitable for treatment of COVID-19", - "rel_date": "2023-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.14.540726", - "rel_abs": "Metformin is a widely used and is a safe anti-diabetic drug. It has also been shown to have anti-inflammatory and anti-viral activities in humans and animal models. Specifically we explored its activity in SARS-CoV-2 initiated COVID19 disease. Here we show that metformin 1. blocks the binding of SARS-CoV-2 spike protein receptor binding domain RBD to human ACE2 receptor 2. We also show that it has anti-inflammatory effects and reduces cytokine secretion as well as blocks the recruitment of monocytes to endothelial cells 3. Finally we show its activity in a hamster in vivo model of SARS-CoV-2 infection as a nasal formulation. Based on the safety and the therapeutic properties relevant to COVID-19 it is feasible to propose a nasal spray of metformin that can be used in treatment of this disease. A nasal spray would deliver the drug to the target organ lung and spare other organs which get exposed upon oral dosing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Uday Saxena", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Kranti Meher", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Saranya K", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Subrahmanyam Vangala", - "author_inst": "Reagene Innovations Pvt Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2023.05.10.23289325", "rel_title": "Composite interventions on outcomes of severely and critically ill patients with COVID-19 in Shanghai, China", @@ -58969,6 +59590,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.10.540228", + "rel_title": "D614G and Omicron SARS-CoV-2 variant spike proteins differ in the effects of N-glycan modifications on spike expression, virus infectivity, and neutralization by some therapeutic antibodies", + "rel_date": "2023-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.10.540228", + "rel_abs": "The SARS-CoV-2 spike glycoprotein has 22 potential N-linked glycosylation sites per monomer that are highly conserved among diverse variants, but how individual glycans affect virus entry and neutralization of Omicron variants has not been extensively characterized. Here we compared the effects of specific glycan deletions or modifications in the Omicron BA.1 and D614G spikes on spike expression, processing, and incorporation into pseudoviruses, as well as on virus infectivity and neutralization by therapeutic antibodies. We found that loss of potential glycans at spike residues N717 and N801 each conferred a loss of pseudovirus infectivity for Omicron but not for D614G or Delta variants. This decrease in infectivity correlated with decreased spike processing and incorporation into Omicron pseudoviruses. Oligomannose-enriched Omicron pseudoviruses generated in GnTI- cells or in the presence of kifunensine were non-infectious, whereas D614G or Delta pseudoviruses generated under similar conditions remained infectious. Similarly, authentic SARS-CoV-2 grown in the presence of kifunensine decreased titers more for the BA.1.1 variant than Delta or D614G variants relative to their respective, untreated controls. Finally, we found that loss of some N-glycans, including N343 and N234, increased the maximum percent neutralization by the class 3 S309 monoclonal antibody against D614G but not BA.1 variants, while these glycan deletions altered the neutralization potency of the class 1 COV2-2196 and Etesevimab monoclonal antibodies without affecting maximum percent neutralization. The maximum neutralization by some antibodies also varied with the glycan composition, with oligomannose-enriched pseudoviruses conferring the highest percent neutralization. These results highlight differences in the interactions between spike glycans and residues among SARS-CoV-2 variants that can affect spike expression, virus infectivity, and susceptibility of variants to antibody neutralization.\n\nAuthor summary (non-technical)The SARS-CoV-2 spike surface protein is covered in glycans that may affect its function and ability to evade antibodies. Omicron variants have over 30 mutations compared to the D614G variant, yet all 22 potential N-glycosylation sites are highly conserved. Here we compared the impact of glycan changes in the spikes of the Omicron and D614G variants on virus infectivity and neutralization. We found that loss of specific glycans in the transmembrane subunit of spike greatly reduced Omicron, but not D614G, spike expression and incorporation into pseudoviruses. Changes in the overall glycan composition also reduced the infectivity of Omicron pseudovirus and authentic virus more than D614G pseudoviruses and authentic viruses. We further show that changes in specific glycans directly or indirectly affected susceptibility of pseudoviruses to therapeutic antibodies, but the effects differed among the variants. These findings highlight differences in the interplay between spike glycans and amino acid residues among SARS-CoV-2 variants that can contribute to spike plasticity and modify spike expression, function, and immune evasion properties.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sabrina Lusvarghi", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Charles B. Stauft", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Russell Vassell", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Brittany Williams", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Haseebullah Baha", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Wei Wang", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Sabari Nath Neerukonda", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Tony Wang", + "author_inst": "U.S. Food and Drug Administration" + }, + { + "author_name": "Carol D. Weiss", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.05.10.23289809", "rel_title": "Factors associated with the near miss of pregnant and postpartum women hospitalized by Covid-19", @@ -60111,57 +60783,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.08.539897", - "rel_title": "Evolving spike-protein N-glycosylation in SARS-CoV-2 variants", - "rel_date": "2023-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.08.539897", - "rel_abs": "It has been three years since SARS-CoV-2 emerged and the world plunged into a \"once in a century\" pandemic. Since then, multiple waves of infection have swept through the human population, led by variants that were able to evade any acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune response, both of which are impacted by host-installed N-glycans. We compared the N-glycan landscape of recombinantly expressed, stabilized, soluble spike-protein trimers representing seven of the most prominent SARS-CoV-2 variants and found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose-to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sabyasachi Baboo", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jolene K Diedrich", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jeffrey Copps", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Bhavya Singh", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Patrick T Garrett", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "James C Paulson", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "John R Yates III", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.08.539929", "rel_title": "Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection", @@ -60735,6 +61356,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2023.05.05.23289209", + "rel_title": "Vaccine effectiveness of BNT162b2 mRNA Covid-19 Vaccine in Children below 5 Years in German Primary Care", + "rel_date": "2023-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.05.23289209", + "rel_abs": "BackgroundDespite the approval of BNT162b2 mRNA vaccine for children aged 6 months to 4 years by the European Medicines Agency (EMA) and the Federal Drug Administration (FDA) in 2022, no data on vaccine effectiveness (VE) of BNT162b2 are available in this age group. We here report on the VE of BNT162b2 during an Omicron BA.1-2 dominant period.\n\nMethodsAn authentication-based retrospective survey was performed between April 14th 2022 and May 9th 2022 in individuals that had registered children for off-label SARS-CoV-2 vaccination in Germany. We used Cox regression to estimate relative VE of two BNT162b2 doses, with the period between first and second vaccine dose as reference period (24.8+-0.6 days) and >=7 days after Dose 2 to before Dose 3 as post-vaccination period (59.5+-23.6 days).\n\nResultsThe present analysis included 4615 children aged 2.8+-1.2 years (mean+-standard deviation) who had received their first dose of BNT162b2 on January 1st 2022 or thereafter. VE was substantial for protection from any SARS-CoV-2 infection (VE: 53.1% [95% confidence interval (CI): 36.3-69.6%], p<0.001), symptomatic SARS-CoV-2 infections (VE: 57.5% [95% CI: 40.8-74.2%], p<0.001), and SARS-CoV-2 infections leading to medication use (VE: 66.2% [95% CI: 43.7-88.7%], p<0.001). Differences in dosage of BNT162b2 yielded no change in VE.\n\nConclusionThis study offers a first industry-independent insight in the potential VE of two doses of the BNT162b2 vaccine in children aged below 5 years, as currently only immunogenicity data by the manufacturer Pfizer/BioNTech are available. Limitations include the retrospective study design, and that the reported VE does not necessarily correspond to currently circulating SARS-CoV-2 variants.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Christoph Strumann", + "author_inst": "Institute of Family Medicine, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany" + }, + { + "author_name": "Otavio Ranzani", + "author_inst": "Barcelona Institute for Global Health, ISGlobal, Universitat Pompeu Fabra (UPF), Barcelona, Spain" + }, + { + "author_name": "Jeanne Moor", + "author_inst": "Department of General Internal Medicine, Inselspital University Hospital Bern and Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerlan" + }, + { + "author_name": "Reinhard Berner", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Nicole Toepfner", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Cho-Ming Chao", + "author_inst": "University Childrens Hospital, University Medical Center Rostock, University of Rostock, Rostock and Department of Pediatrics, Helios University Medical Center," + }, + { + "author_name": "Matthias B. Moor", + "author_inst": "CLINTEC Division of Renal Medicine and LABMED Division of Pathology, Karolinska Institutet, Stockholm, Sweden and Department of Nephrology and Hypertension, Uni" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.08.23289637", "rel_title": "SARS-CoV-2 Infection Biomarkers Reveal an Extended RSAD2 Dependant Metabolic Pathway", @@ -61653,89 +62317,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2023.05.03.23289435", - "rel_title": "Improved access to diabetic retinopathy screening through primary care-based teleophthalmology during the COVID-19 pandemic", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289435", - "rel_abs": "BackgroundPrimary care practices play a critical role in ensuring that patients with diabetes undergo an annual eye examination, the importance of which is underscored by the Healthcare Effectiveness Data and Information Set (HEDIS) quality measures. Store-and-forward teleophthalmology, where ocular images are read remotely by an ophthalmologist, has the potential to facilitate this role.\n\nMethodsIn this report, we aim to measure if using a primary care-based teleophthalmology program improves access to eye examinations for diabetic patients as reflected in HEDIS measures. Over a 20-month period, non-mydriatic fundus photographs were obtained at five primary care sites in the San Francisco Bay Area from patients with a new or existing diagnosis of diabetes mellitus type 1 or 2 who needed an annual eye examination. Collected photographs were evaluated remotely by vitreoretinal specialists for diabetic retinopathy. Our primary measures were the proportion and number of annual eye exams of diabetic patients in primary care clinics that participated in the teleophthalmology program compared to clinics that did not participate. Additional measures included the number of patients with DR who were identified through the program, gradeability of fundus photographs, and characteristics of the study population.\n\nResultsThe program screened 760 unique patients, 84 of whom were found to have DR (11.1%). The rate of ungradable photos was 9.7%, which was greater for patients who self-reported as racially non-White. For the duration of the study, including during the COVID-19 pandemic, both the proportion and number of diabetic patients receiving annual eye examination increased (17.1% increase in proportion, 14.8% increase in number). In comparison, primary care sites that did not offer the teleophthalmology service declined in these measures (2.3% decrease in proportion, 17.0% decrease in number).\n\nConclusionsPrimary care-based teleophthalmology improves access to eye exam for diabetic patients and identifies patients with diabetic retinopathy across diverse communities.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Karen Chen", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Eliot Dow", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marina Basina", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Jimmy Dang", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Nergis Khan", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Michael Kim", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marcie Lynn Levine", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kapil Mishra", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Chandrashan Perera", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Anuradha Phadke", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marilyn Tan", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kirsti Weng", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Diana Do", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Vinit B Mahajan", - "author_inst": "Stanford University" - }, - { - "author_name": "Prithvi Mruthyunjaya", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ted Leng", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "David Myung", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2023.05.02.23289345", "rel_title": "Persistent immune abnormalities discriminate post-COVID syndrome from convalescence", @@ -62653,6 +63234,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2023.05.03.23289084", + "rel_title": "Effect of Nirmatrelvir/Ritonavir (Paxlovid) on Hospitalization among Adults with COVID-19: an EHR-based Target Trial Emulation from N3C", + "rel_date": "2023-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289084", + "rel_abs": "This study leverages electronic health record data in the National COVID Cohort Collaboratives (N3C) repository to investigate disparities in Paxlovid treatment and to emulate a target trial assessing its effectiveness in reducing COVID-19 hospitalization rates. From an eligible population of 632,822 COVID-19 patients seen at 33 clinical sites across the United States between December 23, 2021 and December 31, 2022, patients were matched across observed treatment groups, yielding an analytical sample of 410,642 patients. We estimate a 65% reduced odds of hospitalization among Paxlovid-treated patients within a 28-day follow-up period, and this effect did not vary by patient vaccination status. Notably, we observe disparities in Paxlovid treatment, with lower rates among Black and Hispanic or Latino patients, and within socially vulnerable communities. Ours is the largest study of Paxlovids real-world effectiveness to date, and our primary findings are consistent with previous randomized control trials and real-world studies.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Abhishek Bhatia", + "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC, USA." + }, + { + "author_name": "Alexander J Preiss", + "author_inst": "RTI International, Durham, NC, USA." + }, + { + "author_name": "Xuya Xiao", + "author_inst": "School of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA." + }, + { + "author_name": "M. Daniel Brannock", + "author_inst": "RTI International, Durham, NC, USA." + }, + { + "author_name": "G. Caleb Alexander", + "author_inst": "School of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA." + }, + { + "author_name": "Robert F Chew", + "author_inst": "RTI International, Durham, NC, USA." + }, + { + "author_name": "Megan Fitzgerald", + "author_inst": "Patient-Led Research Collaborative, NY, USA." + }, + { + "author_name": "Elaine Hill", + "author_inst": "University of Rochester, Department of Public Health Sciences and Department of Economics, Rochester, NY, USA" + }, + { + "author_name": "Elizabeth P Kelly", + "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC, USA." + }, + { + "author_name": "Hemalkumar B Mehta", + "author_inst": "School of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA." + }, + { + "author_name": "Charisse Madlock-Brown", + "author_inst": "University of Tennessee Health Science Center, Memphis, TN, USA." + }, + { + "author_name": "Kenneth J Wilkins", + "author_inst": "National Institute of Diabetes & Digestive & Kidney Diseases, Office of the Director, National Institutes of Health, Bethesda, MD, USA" + }, + { + "author_name": "Christopher G Chute", + "author_inst": "School of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA." + }, + { + "author_name": "Melissa Haendel", + "author_inst": "University of Colorado Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Richard Moffitt", + "author_inst": "Stony Brook University, Stony Brook, NY, US" + }, + { + "author_name": "Emily R Pfaff", + "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC, USA." + }, + { + "author_name": "- The N3C Consortium", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.03.23289458", "rel_title": "What happened to health labour markets during COVID-19? Insights from a survey of medical doctors in Brazil", @@ -64239,29 +64903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2023.04.27.23289205", - "rel_title": "Characterization and Resistance to Mutation of a Single-Channel Multiplex PCR Assay for SARS-CoV-2", - "rel_date": "2023-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289205", - "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used worldwide to provide valuable public health data. RT-qPCR is frequently used as a quantitative methodology for wastewater surveillance but is susceptible to mutations in target regions. These mutations may lead to misinterpretation of surveillance data; a drop in signal could be concluded to be a result of lower viral load, when in fact it is caused by reduced detection efficiency. We describe a novel approach to mitigating the impacts of such mutations: monitoring the cumulative signal from two targets (N1 and N2) via independent amplification reactions using identically labeled probes; a \"single-channel multiplex\" approach. Using the IDEXX Water SARS-CoV-2 RT-qPCR test, we demonstrate equivalent intra-assay repeatability and quantitative results from the combined N1N2 test when compared to individual N1 and N2 assays. Furthermore, we show that while mutations in B.1.1.529, BA.5.2, and BA.5.2.1 significantly impact the performance of the N1 assay, the impact on the N1N2 assay was negligible, and nearly within acceptable margin of error for technical replicates. These findings demonstrate that a single-channel multiplex approach can be used to improve the robustness of wastewater surveillance and minimize the risk of future mutations leading to unreliable public health data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Amy L. Pednault", - "author_inst": "IDEXX Laboratories, Inc." - }, - { - "author_name": "Brian M Swalla", - "author_inst": "IDEXX Laboratories, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.28.23289257", "rel_title": "The COV50 classifier predicts frailty and future death, independent from SARS-CoV-2 infection", @@ -65051,6 +65692,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.04.27.23289229", + "rel_title": "State and County-Level Factors Associated with the Effectiveness of Stay-At-Home Orders Issued in the United States in Response to COVID-19", + "rel_date": "2023-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289229", + "rel_abs": "TitleState and County-Level Factors Associated with the Effectiveness of Stay-At-Home Orders Issued in the United States in Response to COVID-19\n\nBackgroundTo slow the spread of COVID-19 and protect medical facilities from overflowing, Stay-At-Home Orders (SAHOs) were issued in the United States during the spring of 2020. These orders had variable levels of effectiveness and profound consequences that continue to manifest long after their termination. This study aimed to assess if state and county-level population characteristics could explain variability in SAHO effectiveness as measured by the effective reproductive number (Rt).\n\nMethodsWe calculated the Rt for the 40 states which enacted SAHOs, and also for a sample of 289 counties that issued SAHOs in 2020, using EpiEstim R Package based on the states and counties daily case data. We determined SAHOs to be effective if, three weeks after their implementation, Rt was equal to or less than one. Wilcoxon rank sum tests and logistic regression were used to determine if population characteristics (age, income, level of education, political orientation, percent of non-English speaking people, racial and ethnic compositions), and percentage of frontline workers, percent of eligible people vaccinated by July 2021, level of viral transmission, and other Non-Pharmaceutical-Interventions (NPI) enacted before the SAHO, were associated with effectiveness of SAHOs.\n\nResultsSAHOs were effective in 20 (50%) states. No significant differences were found in the characteristics studied between states with effective and ineffective SAHOs. SAHOs were effective in 54% of counties. Counties with effective SAHOs had fewer days of NPIs before the SAHOs in comparison to counties with ineffective SAHOs (Median 24 vs. 34, p-value 0.005). All other characteristics considered showed non-significant differences. In multivariate analysis, days of NPIs before the SAHOs remained the only significant factor for effective SAHOs in studied counties.\n\nConclusionOur analysis suggests that SAHO effectiveness may be influenced by the implementation of prior public health interventions but is not likely to be related to the other characteristics studied. These findings should be considered when assessing when and how to implement SAHOs in future epidemics to limit the spread of an infectious respiratory disease.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Forrest DL Barker", + "author_inst": "UCSF: University of California San Francisco" + }, + { + "author_name": "Ali Mirzadadeh", + "author_inst": "UCSF: University of California San Francisco" + }, + { + "author_name": "Neelam Sekhri Feachem", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.25.23289115", "rel_title": "Quantifying the Risk of General Health and Early COVID-19 Spread in Residential Buildings with Deep Learning and Expert-augmented Machine Learning", @@ -66257,57 +66925,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.04.20.23288904", - "rel_title": "Aerosol Jet Printing Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection", - "rel_date": "2023-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.20.23288904", - "rel_abs": "An aerosol jet printing enabled dual-function biosensor for the sensitive detection of pathogens using SARS-CoV-2 RNA as an example has been developed. A CRISPR-Cas13: guide-RNA complex is activated in the presence of a target RNA, leading to the collateral trans-cleavage of ssRNA probes that contain a horseradish peroxidase (HRP) tag. This, in turn, catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by HRP, resulting in a color change and electrochemical signal change. The colorimetric and electrochemical sensing protocol does not require complicated target amplification and probe immobilization and exhibits a detection sensitivity in the femtomolar range. Additionally, our biosensor demonstrates a wide dynamic range of 5 orders of magnitude. This low-cost aerosol inkjet printing technique allows for an amplification-free and integrated dual-function biosensor platform, which operates at physiological temperature and is designed for simple, rapid, and accurate point-of-care (POC) diagnostics in either low-resource settings or hospitals.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Li Liu", - "author_inst": "University of California,Riverside" - }, - { - "author_name": "Zhiheng Xu", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Adrian Moises Molina Vargas", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Steve Dollery", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Michael Schrlau", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Denis Cormier", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Mitchell O'Connell", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Gregory Tobin", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Ke Du", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.24.23288921", "rel_title": "Immune signature of patients with cardiovascular disease - in-depth immunophenotyping predicts increased risk for a severe course of COVID-19", @@ -66997,6 +67614,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.22.537917", + "rel_title": "SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response", + "rel_date": "2023-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.22.537917", + "rel_abs": "Coronaviruses (CoV), including SARS-CoV-2, modulate host proteostasis through activation of stress-responsive signaling pathways such as the Unfolded Protein Response (UPR), which remedies misfolded protein accumulation by attenuating translation and increasing protein folding capacity. While CoV nonstructural proteins (nsps) are essential for infection, little is known about the role of nsps in modulating the UPR. We characterized the impact of SARS-CoV-2 nsp4, a key driver of replication, on the UPR using quantitative proteomics to sensitively detect pathway-wide upregulation of effector proteins. We find nsp4 preferentially activates the ATF6 and PERK branches of the UPR. Previously, we found an N-terminal truncation of nsp3 (nsp3.1) can suppress pharmacological ATF6 activation. To determine how nsp3.1 and nsp4 tune the UPR, their co-expression demonstrated that nsp3.1 suppresses nsp4-mediated PERK, but not ATF6 activation. Re-analysis of SARS-CoV-2 infection proteomics data revealed time-dependent activation of PERK targets early in infection, which subsequently fades. This temporal regulation suggests a role for nsp3 and nsp4 in tuning the PERK pathway to attenuate host translation beneficial for viral replication while avoiding later apoptotic signaling caused by chronic activation. This work furthers our understanding of CoV-host proteostasis interactions and highlights the power of proteomic methods for systems-level analysis of the UPR.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jonathan P Davies", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Athira Sivadas", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Katherine R Keller", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Richard JH Wojcikiewicz", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Lars Plate", + "author_inst": "Vanderbilt University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.04.24.538100", "rel_title": "The enigma of the SARS-CoV-2 microcirculation dysfunction: evidence for modified endothelial junctions.", @@ -68371,61 +69023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.04.17.23288710", - "rel_title": "COVID-19 testing avoidance among patients with cardiovascular disease", - "rel_date": "2023-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288710", - "rel_abs": "BackgroundRapid coronavirus 2019 (COVID-19) testing in symptomatic cases is extremely important for preventing the spread of COVID-19 infection and early therapeutic intervention. In contrast, whether symptomatic patients are tested depends largely on their health literacy, interpretation, and knowledge of COVID-19. We aimed to investigate the rate of COVID-19 testing avoidance despite having common cold symptoms in patients with cardiovascular disease and examine factors related to testing avoidance.\n\nMethodsA large-scale epidemiological questionnaire survey, the Japan COVID-19 and Society Internet Survey 2022 (JACSIS), was conducted online from April to May 2022. The rate of COVID-19 testing avoidance was investigated in patients aged 20 to 80 years with cardiovascular risk factors (hypertension, dyslipidemia, or diabetes) or a history of cardiovascular disease (angina, myocardial infarction, or stroke), only those exhibiting common cold symptoms during the 2 months in the survey.\n\nResultsOf the 1,565 eligible patients, 58% (909 patients) did not undergo COVID-19 testing. Multivariate analysis revealed that older age, obesity, non-walking regularly, long sedentary time, eating alone, frequent snacking, and having received 4 COVID-19 vaccinations were independently associated with testing avoidance.\n\nConclusionsIn the chronic phase of the COVID-19 pandemic, prompt COVID-19 testing at the time of symptomatic disease is important, and strategies to reduce testing hesitancy should be considered.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Koichiro Matsumura", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Osaka International Cancer Institute" - }, - { - "author_name": "Eijiro Yagi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takeshi Ijichi", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Misaki Hasegawa", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Nobuhiro Yamada", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Yohei Funauchi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Kazuyoshi Kakehi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takayuki Kawamura", - "author_inst": "Kinki University Faculty of Medicine" - }, - { - "author_name": "Gaku Nakazawa", - "author_inst": "Kindai University Faculty of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.18.23288715", "rel_title": "Preliminary clinical characteristics of Pediatric Covid-19 cases during the ongoing Omicron XBB.1.16 driven surge in a north Indian city", @@ -69275,6 +69872,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.04.17.23288637", + "rel_title": "Post-COVID-19 syndrome and insulin resistance 20 months after a mild COVID-19", + "rel_date": "2023-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288637", + "rel_abs": "ObjectiveSARS-CoV-2 infection is associated with impaired glucose metabolism. Although the mechanisms are not fully understood, insulin resistance (IR) appears to be a central factor. Patients who had a severe acute phase, but even asymptomatic or with mild COVID-19, have an increased risk of T2DM. After the acute phase, post-COVID-19 syndrome (PCS) also seems to be related to this metabolic disturbance, but there is a paucity of studies. This study aims to evaluate a possible relationship between PCS and IR after mild COVID-19 and, if confirmed, whether there are differences by sex.\n\nSubjects and methodsRetrospective observational cohort study including subjects who had mild COVID-19 between April and September 2020 in a community setting. None had been vaccinated against SARS-CoV-2 at inclusion, and previous T2DM and liver disease were exclusion criteria. Patients who met NICE criteria were classified as PCS+. Epidemiological and laboratory data were analysed. Three assessments were performed: 1E (pre-COVID-19, considered baseline and reference for comparisons), 2E (approximately 3 months after the acute phase), and 3E (approximately 20 months after the acute phase).\n\nA triglyceride-to-glucose (TyG) index [≥]8.74 was considered IR. Albumin-to-globulin ratio (AGR) and lactate dehydrogenase (LDH) were assessed as inflammatory markers. Bivariate analyses were performed, using nonparametric and repeated measures tests.\n\nA subsample without metabolic disorder or CVD (age126 mg/dL.\n\nThe subgroups with IR highest prevalence at 3E were those of BMI [≥]25 kg/m2 and PCS+. The subgroup without CVD presented a significant increase in the TyG index (TyG1=7.80 [0.1] vs. TyG3= 8.28 [0.1]; p=0.017). LDH1 was significantly correlated with TyG3 in both sexes (rho=0.214 in women, rho=0.298 in men); in contrast, LDH2 and LDH3 did not present such an association.\n\nIn multivariable analysis, PCS has shown to be an independent and predictive variable of TyG index in women with BMI<25 kg/m2, after adjustment for age, hypertension, BMI, Charlson comorbidity index, AGR1, AGR2, LDH1, number of symptoms of acute COVID-19, and number of days of the acute episode ({beta}=0.350; p=0.039).\n\nConclusionsPCS has played a secondary role in predicting IR, showing a modest effect compared to BMI or prior hypertension. A significant increase in IR has been noted 20 months after mild COVID-19, both in cases of previous baseline IR and in those without previous IR. Basal serum LDH has shown to be predictive of current TyG, regardless of elevated LDH after SARS-CoV-2 infection. There were profound differences between women and men, confirming the need for a sex-stratified analysis when addressing the relation between PCS and glycemic alterations.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "PATRICIA FIERRO", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "DAVID MARTIN", + "author_inst": "Camargo Costa Primary Care Center. Camargo. Cantabria. Spain." + }, + { + "author_name": "EMILIO PARIENTE-RODRIGO", + "author_inst": "Servicio Cantabro de Salud. IDIVAL." + }, + { + "author_name": "ANA GARCIA-GARRIDO", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "HECTOR BASTERRECHEA", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "BENEDETTA PETITTA", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "CAMILA BIANCONI", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "SARA HERRAN", + "author_inst": "Universidad de Cantabria. Santander. Cantabria. Spain." + }, + { + "author_name": "ANDREA BERRUETA", + "author_inst": "Universidad de Cantabria. Santander. Cantabria. Spain." + }, + { + "author_name": "ASCENSION JORRIN", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "ALICIA GOMEZ-PEREZ", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "RAQUEL CASADO", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "ALFREDO CUADRADO", + "author_inst": "Camargo Interior Primary Care Center. Muriedas. Cantabria. Spain." + }, + { + "author_name": "CARMEN RAMOS-BARRON", + "author_inst": "Camargo Costa Primary Care Center. IDIVAL. Camargo. Cantabria. Spain." + }, + { + "author_name": "JOSE L HERNANDEZ-HERNANDEZ", + "author_inst": "Internal Medicine Department. Hospital Universitario Marques de Valdecilla. IDIVAL. Santander. Cantabria. Spain." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.13.23288469", "rel_title": "Empagliflozin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", @@ -70361,37 +71033,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.11.23288130", - "rel_title": "Clinical Performance of BD Veritor\u2122 Assay Across SARS-CoV-2 Variants", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288130", - "rel_abs": "BackgroundDifferent rates of morbidity, mortality, transmission, and immune escape are associated with various strains of the SARS-CoV-2 virus. With the emergence of new strains during seasonal outbreaks, ensuring that antigen-based immunoassays can detect SARS-CoV-2 infections across identified circulating viral variants is a crucial component of infection control efforts.\n\nObjectiveTo validate the performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 Assay (BD Veritor assay) to detect SARS-CoV-2 across variants of concern (VOC) and variants of interest (VOI).\n\nMethodsUsing the Illumina NextSeq 2000 Sequencer, viral sequencing was performed on prospectively collected, then frozen, SARS-CoV-2 RT-PCR positive nasal swabs stored in universal transport media (UTM). Specimens from symptomatic and asymptomatic individuals were included in the study. Using the information obtained from the sequencing analysis, the performance of the BD Veritor System assay was evaluated against the highly sensitive molecular RT-PCR Quidel Lyra SARS-CoV-2 assay for each variant.\n\nResultsThe resulting PPA was 97.4% (95% CI: 86.8, 99.5) for detection of SARS-CoV-2 across all variants identified by Next Generation Sequencing (i.e., WHO-labeled variants Alpha, Delta, Gamma, Iota, Lambda, as well as two other non-labeled variants), with a 100% PPA for five of the six variant labels identified.\n\nConclusionThe results demonstrate the robust performance of the BD Veritor assay in detecting SARS-CoV-2 in clinical nasal specimens in selected variants. As new variants emerge, additional studies will be beneficial to ensure the sustained performance of SARS-CoV-2 assays.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Karen Eckert", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Sebastian Gutierrez", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Brittany Knight", - "author_inst": "MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd., Kansas City, MI" - }, - { - "author_name": "Lauren Cooper", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.12.23288362", "rel_title": "Bivalent COVID-19 booster vaccines induce cross-reactive but not BA.5-specific antibodies in polyclonal serum", @@ -70965,6 +71606,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.04.12.536590", + "rel_title": "Evaluation of mRNA-LNP and adjuvanted protein SARS-CoV-2 vaccines in a maternal antibody mouse model", + "rel_date": "2023-04-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.12.536590", + "rel_abs": "Maternal antibodies (matAbs) protect against a myriad of pathogens early in life; however, these antibodies can also inhibit de novo immune responses against some vaccine platforms. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) matAbs are efficiently transferred during pregnancy and protect infants against subsequent SARS-CoV-2 infections. It is unknown if matAbs inhibit immune responses elicited by different types of SARS-CoV-2 vaccines. Here, we established a mouse model to determine if SARS-CoV-2 spike-specific matAbs inhibit immune responses elicited by recombinant protein and nucleoside-modified mRNA-lipid nanoparticle (mRNA-LNP) vaccines. We found that SARS-CoV-2 mRNA-LNP vaccines elicited robust de novo antibody responses in mouse pups in the presence of matAbs. Recombinant protein vaccines were also able to circumvent the inhibitory effects of matAbs when adjuvants were co-administered. While additional studies need to be completed in humans, our studies raise the possibility that mRNA-LNP-based and adjuvanted protein-based SARS-CoV-2 vaccines have the potential to be effective when delivered very early in life.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ross N. England", + "author_inst": "Penn" + }, + { + "author_name": "Elizabeth M. Drapeau", + "author_inst": "Penn" + }, + { + "author_name": "Reihaneh Hosseinzadeh", + "author_inst": "Acuitas" + }, + { + "author_name": "Drew Weissman", + "author_inst": "Penn" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "Penn" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.04.12.536671", "rel_title": "SARS-CoV-2 selectively induces the expression of unproductive splicing isoforms of interferon, class I MHC and splicing machinery genes", @@ -72354,29 +73030,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.07.23288262", - "rel_title": "COVID-19 Vaccine Uptake And Its Associated Factors among general population In Basmaia City in Baghdad 2022", - "rel_date": "2023-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.07.23288262", - "rel_abs": "ObjectiveVaccination is a vital cornerstone of public health, which has saved countless lives throughout history. Therefore, achieving high vaccination uptake rates is essential for successful vaccination programs. Unfortunately, vaccine uptake has been hindered by deferent factors and challenges. The objective of this study is to assess COVID-19 vaccine uptake and associated factors among the general population.\n\nMethodsThis study is a descriptive cross-sectional study conducted in Basmaia city, Baghdad from June to October 2022. Data were collected through a semi-structured questionnaire using multi-stage random sampling. Statistical analysis was performed using descriptive statistics, chi-square analysis, Mann-Whitney test, and binary and multivariable logistic regression.\n\nResultsThe prevalence of COVID-19 vaccine uptake was 70.4%. The most common reason for getting vaccinated was protection from the disease, while fear of side effects and not needing the vaccine were the main reasons for refusal.\n\nThe study found that gender, age, education level, job title, risk perception, knowledge, and attitude towards the vaccine were significantly associated with COVID-19 vaccine uptake. Males were 2.273 times more likely to get vaccinated than females, and older age groups had higher odds of vaccination than younger age groups. Those with higher education levels were also more likely to receive the vaccine. Participants with higher risk perception, knowledge, and positive attitude towards the vaccine were more likely to get vaccinated.\n\nAnd found that mandatory vaccination policies may negatively impact uptake of subsequent vaccine doses.\n\nConclusionThe study found a high prevalence of COVID-19 vaccine uptake, with gender, age, education level, and job title being significant factors associated with vaccine uptake. Additionally, mandatory vaccination policies may have a negative impact on the uptake of subsequent vaccine doses. Public health efforts should prioritize addressing these factors to increase vaccine uptake.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hussein Abdalrahim Alhlew", - "author_inst": "ministry of health" - }, - { - "author_name": "Mohammad Asaad Albayaty", - "author_inst": "al-Kindy college of medicine, Baghdad university" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.04.07.23288300", "rel_title": "Association between PM2.5 air pollution, temperature, and sunlight during different infectious stages with the case fatality of COVID-19 in the United Kingdom: a modeling study", @@ -73014,6 +73667,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.05.23288196", + "rel_title": "Incidence of Symptoms Associated with Post-Acute Sequelae of SARS-CoV-2 infectionin Non-Hospitalized Vaccinated Patients Receiving Nirmatrelvir-Ritonavir", + "rel_date": "2023-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.05.23288196", + "rel_abs": "BackgroundThe role of Nirmatrelvir plus ritonavir (NMV-r) in preventing post-acute sequelae of SARS-CoV-2 infection (PASC) is unknown. The objective of this study is to assess the effect of NMV-r in non-hospitalized, vaccinated patients on the occurrence of PASC.\n\nMethodsWe performed a comparative retrospective cohort study utilizing data from the TriNetX research network, including vaccinated patients [≥]18 years old who subsequently developed Covid-19 between December 2021-April 2022. Cohorts were based on NMV-r administration within five days of diagnosis. Based on previously validated broad and narrow definitions, the main outcome was the presence of symptoms associated with PASC. Outcomes were assessed between 30-180 days and 90-180 days after the index Covid-19 infection.\n\nResults1,004 patients remained in each cohort after propensity-score matching. PASC (broad definition) occurred in 425 patients (42%) in the NMV-r cohort, vs. 480 patients (48%) in the control cohort (OR 0.8 CI 0.67-0.96; p=0.01) from 30-180 days and in 273 patients (27%) in the NMV-r cohort, as compared to 347 patients (35%) in the control cohort (OR 0.707, CI 0.59-0.86; p<0.001) from 90-180 days. Narrowly defined PASC was reported in 337 (34%) patients in the NMV-r and 404 (40%) in the control cohort between 30-180 days (OR=0.75, CI 0.62-0.9, p=0.002) and in 221 (22%) in the NMV-r cohort as compared to in 278 (28%) patients in the control cohort (OR=0.7, CI 0.63-0.9, p=0.003) between 90 -180 days.\n\nConclusionsNMV-r treatment in non-hospitalized vaccinated patients with Covid-19 was associated with a reduction in the development of symptoms commonly observed with PASC and healthcare utilization.\n\nKey PointsAssessment of Nirmatrelvir plus ritonavir (NMV-r) in preventing post-acute sequelae of SARS-CoV-2 infection (PASC), based on broad and narrow definitions in non-hospitalized, vaccinated patients between 30-180 days and 90-180 days.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "RUSHIN PATEL", + "author_inst": "Lahey Hospital and Medical Center" + }, + { + "author_name": "Sourbha S Dani", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Sumanth Khadke", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Javaria Ahmad", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Jui Shah", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Neev Mehta", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Kenneth Wener", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Daniel P McQuillen", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "George Abraham", + "author_inst": "Saint Vincent Hospital" + }, + { + "author_name": "Jeremy Faust", + "author_inst": "Brigham And Women's Hospital" + }, + { + "author_name": "Jason Maley", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Smita Patel", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Janet Mullington", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Robert Wachter", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Anne Mosenthal", + "author_inst": "Lahey Hospital And Medical Center" + }, + { + "author_name": "Paul Sax", + "author_inst": "Brigham And Women's Hospital" + }, + { + "author_name": "Sarju Ganatra", + "author_inst": "Lahey Hospital and Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.05.23288113", "rel_title": "Direct and indirect impact of the COVID-19 pandemic on the survival of kidney transplant recipients: a national observational study in France.", @@ -74248,93 +74984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.04.01.23287538", - "rel_title": "Trends in weight gain recorded in English primary care before and during the Coronavirus-19 pandemic: an observational cohort study using the OpenSAFELY platform", - "rel_date": "2023-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.01.23287538", - "rel_abs": "BackgroundWe investigated which clinical and sociodemographic characteristics were associated with unhealthy patterns of weight gain amongst adults living in England during the pandemic.\n\nMethodsWith the approval of NHS England we conducted an observational cohort study of Body Mass Index (BMI) changes between March 2015 and March 2022 using the OpenSAFELY-TPP platform. We estimated individual rates of weight gain before and during the pandemic, and identified individuals with rapid weight gain (>0{middle dot}5kg/m2/year) in each period. We also estimated the change in rate of weight gain between the prepandemic and pandemic period and defined extreme-accelerators as the ten percent of individuals with the greatest increase (>1{middle dot}84kg/m2/year). We estimated associations with these outcomes using multivariate logistic regression.\n\nFindingsWe extracted data on 17,742,365 adults (50{middle dot}1% female, 76{middle dot}1% White British). Median BMI increased from 27{middle dot}8kg/m2 [IQR:24{middle dot}3-32{middle dot}1] in 2019 (March 2019 to February 2020) to 28{middle dot}0kg/m2 [24{middle dot}4-32{middle dot}6] in 2021. Rapid pandemic weight gain (n=3,214,155) was associated with female sex (male vs female: aOR 0{middle dot}76 [95%CI:0{middle dot}76-0{middle dot}76]); younger age (50-59-years vs 18-29-years: aOR 0{middle dot}60 [0{middle dot}60-0{middle dot}61]); White British ethnicity (Black Caribbean vs White British: aOR 0{middle dot}91 [0{middle dot}89-0{middle dot}94]); deprivation (least-deprived-IMD-quintile vs most-deprived: aOR 0{middle dot}77 [0{middle dot}77-0{middle dot}78]); and long-term conditions, of which mental health conditions had the greatest effect (e.g. depression (aOR 1{middle dot}18[1{middle dot}17-1{middle dot}18])). Similar characteristics increased risk of extreme acceleration (n=2,768,695).\n\nInterpretationWe found female sex, younger age, deprivation and mental health conditions increased risk of unhealthy patterns of pandemic weight gain. This highlights the need to incorporate sociodemographic, physical, and mental health characteristics when formulating post-pandemic research, policies, and interventions targeting BMI.\n\nFundingNIHR", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Miriam Samuel", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Robin Y Park", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sophie V Eastwood", - "author_inst": "University College London, London, United Kingdom" - }, - { - "author_name": "Fabiola Eto", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Daniel Stow", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Sebastian Bacon", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "William J Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Diabetes Research Centre, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Jonathan Valabhji", - "author_inst": "Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sarah Finer", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.03.30.23287969", "rel_title": "A Graph Embedding Approach for Deciphering the Longitudinal Associations of Global Mobility and COVID-19 Cases", @@ -74932,6 +75581,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.03.31.535072", + "rel_title": "Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2", + "rel_date": "2023-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.31.535072", + "rel_abs": "Measurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against SARS-CoV-2. These antibodies are temporarily dynamic; due to waning, antibody levels will drop below detection thresholds over time. As a result, epidemiological studies could underestimate population protection, given that antibodies are a marker for protective immunity.\n\nDuring the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to plan public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects.\n\nThis paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. This approach can be integrated in general frameworks, allowing complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sebastian Alexander Mueller", + "author_inst": "Technische Universitaet Berlin" + }, + { + "author_name": "Sydney Paltra", + "author_inst": "Technische Universitaet Berlin" + }, + { + "author_name": "Jakob Rehmann", + "author_inst": "Technische Universitaet Berlin" + }, + { + "author_name": "Kai Nagel", + "author_inst": "Technische Universitaet Berlin" + }, + { + "author_name": "Tim O.F. Conrad", + "author_inst": "Zuse Institut Berlin" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.03.30.535005", "rel_title": "S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness", @@ -76041,25 +76725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2023.03.28.23287762", - "rel_title": "Early real world evidence on the relative SARS-COV-2 vaccine effectiveness of bivalent COVID-19 booster doses: a rapid review.", - "rel_date": "2023-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287762", - "rel_abs": "The objective of this review is to give an overall view of COVID-19 bivalent vaccines knowledge and to explore their early available real world effectiveness evidence in the Omicron era.\n\nPresently, bivalent vaccines are generally offered to all groups eligible for their next booster, as defined by the national vaccination campaign, with varying policies between countries.\n\nThe use of bivalent vaccines is supported by immunogenity studies, which, nevetheless, have led to contradictory conclusions, and are not generally designed to measure clinical impact.\n\nIn order to critically appraise the available research on real world effectiveness, a systematic literature search was performed: out of 876 references examined, 14 studies were finally included and extracted. The findings of this review demonstrate modest to moderate additional protection of vaccination with bivalent BA.4-5 or BA.1 mRNA-booster vaccines against COVID-19 associated illness and hospitalization, -if compared with having received a monovalent dose as booster-, during a period when BA.5 and other Omicron sublineage viruses predominated globally,\n\nConsidering the complexity of the current immunity situation at global level, and the high level of heterogeneity both at study and at review level, these findings must be taken with caution. Further research on SARS-CoV-2 vaccine effectiveness against emerging SARS-CoV-2 variants is encouraged.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monica Sane Schepisi", - "author_inst": "UniCamillus, International Medical University, Rome, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.24.23287658", "rel_title": "Safety and Immunogenicity of the NVX-CoV2373 Vaccine as a Booster in Adults Previously Vaccinated with the BBIBP-CorV Vaccine: An Interim Analysis", @@ -76549,6 +77214,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.29.23287591", + "rel_title": "Coronavirus pathogenesis in mice explains the SARS-CoV-2 multi-organ spread by red blood cell hitch-hiking", + "rel_date": "2023-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.29.23287591", + "rel_abs": "SARS-CoV-2 infection causes a multisystemic disease that affects numerous organs beyond the respiratory system. Thus, it is well known that COVID-19 is associated with a wide range of hematological disorders; however, it remains unclear how the SARS-CoV-2 virus is able to navigate from tissue to tissue. In this work, we performed a comprehensive analysis of the pleiotropic effects of a prototypical coronavirus in its natural host, the validated preclinical model of murine hepatitis virus (MHV). Throughout this study we compared our results with the real-world data from COVID-19 patients (including autopsies). Thus, the presence of viral RNA was only detected in less than 25% of the human serum samples, whereas all had multiple positive nasal swabs for SARS-CoV-2. Notably, we found viral RNA not only in lungs, but also in heart and kidney of deceased COVID-19 patients. Subsequently, we investigated the association between viral organotropism and clinical manifestations employing the MHV murine model. Results from RT-qPCR and viral infectivity showcased the presence of viral RNA and infectious particles in multiple organs including liver, lung, brain, heart, kidney, spleen and pancreas, and even the blood of infected mice. Surprisingly, when comparing plasma and red blood cells (RBCs)-enriched fraction, higher viral load levels were detected in RBCs, with decreased RBC count, and hematocrit and hemoglobin levels in infected mice. Next, we treated infected mice with hemin triggering more aggressive symptoms. Strikingly, when combining hemin treatment with chloroquine (a compound that known to interact with the heme group and induces a conformational change in its structure) the infection and its clinical manifestations were distinctly attenuated. Computational docking suggested that heme is able to bind to MHV Spike protein in a similar way to the one, experimentally observed for SARS-CoV-2. Overall, our results lead to a global perspective of COVID-19 beyond the canonical focus on the respiratory system, and strongly support the multi-organ extent of coronavirus infection through specific interactions with RBC hemoproteins.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Ayelen Toro", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Ana Paula Arevalo", + "author_inst": "Unidad de Biotecnologia en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Marianoel Pereira-Gomez", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Agustina Sabater", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Eric Adriano Zizzi", + "author_inst": "Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada" + }, + { + "author_name": "Gaston Pascual", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Sofia Lage-Vickers", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Jorge Luis Porfido", + "author_inst": "Unidad de Biotecnologia en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Ines Achinelli", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Rocio Seniuk", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Juan Bizzotto", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Pilar Moreno", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Alicia Costabile", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Alvaro Fajardo", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Fernando Rodriguez", + "author_inst": "Unidad de Cuidados Intensivos, Hospital Espanol ?Juan Jose Crottoggini?, Administracion de Servicios de Salud del Estado, Montevideo 11800, Uruguay" + }, + { + "author_name": "Nicolas Nin", + "author_inst": "Unidad de Cuidados Intensivos, Hospital Espanol ?Juan Jose Crottoggini?, Administracion de Servicios de Salud del Estado, Montevideo 11800, Uruguay" + }, + { + "author_name": "Pablo Sanchis", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Nicolas Anselmino", + "author_inst": "Department of Genitourinary Medical Oncology and The David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Can" + }, + { + "author_name": "Labanca Estefania", + "author_inst": "Department of Genitourinary Medical Oncology and The David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Can" + }, + { + "author_name": "Javier Cotignola", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Nora Navone", + "author_inst": "Department of Genitourinary Medical Oncology and The David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Can" + }, + { + "author_name": "Daniel Alonso", + "author_inst": "Centro de Oncologia Molecular y Traslacional y Plataforma de Servicios Biotecnologicos, Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, B" + }, + { + "author_name": "Elba Vazquez", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + }, + { + "author_name": "Francesco Gentile", + "author_inst": "Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada" + }, + { + "author_name": "Artem Cherkasov", + "author_inst": "Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, BC V6H 3Z6, Canada" + }, + { + "author_name": "Gonzalo Moratorio", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Martina Crispo", + "author_inst": "Unidad de Biotecnologia en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay" + }, + { + "author_name": "Geraldine Gueron", + "author_inst": "Laboratorio de Inflamacion y Cancer, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C142" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.27.23287812", "rel_title": "Looking under the lamp-post: quantifying the performance of contact tracing in the United States during the SARS-CoV-2 pandemic", @@ -77459,65 +78251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.24.23287700", - "rel_title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "rel_date": "2023-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "rel_abs": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jack D Wilkinson", - "author_inst": "University of Manchester" - }, - { - "author_name": "Evangelia Demou", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Mark Cherrie", - "author_inst": "Institute of Occupational Medicine" - }, - { - "author_name": "Rhiannon Edge", - "author_inst": "University of Lancaster" - }, - { - "author_name": "Matthew Gittins", - "author_inst": "University of Manchester" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Theocharis Kromydas", - "author_inst": "University of Glasgow" - }, - { - "author_name": "WIll Mueller", - "author_inst": "Institute for Occupational Medicine" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martie van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Sarah Rhodes", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2023.03.24.534062", "rel_title": "Intra-Host Mutation Rate of Acute SARS-CoV-2 Infection During the Initial Pandemic Wave", @@ -78267,6 +79000,41 @@ "type": "new results", "category": "zoology" }, + { + "rel_doi": "10.1101/2023.03.16.23287365", + "rel_title": "Estimating the Impact of Pre-Exposure Prophylaxis (PrEP) on Mortality in COVID-19 Patients: A Causal Inference Approach", + "rel_date": "2023-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.16.23287365", + "rel_abs": "Traditional machine learning (ML) approaches learn to recognize patterns in the data but fail to go beyond observing associations. Such data-driven methods can lack generalizability when the data is outside the independent and identically distributed (i.i.d) setting. Using causal inference can aid data-driven techniques to go beyond learning spurious associations and frame the data-generating process in a causal lens. We can combine domain expertise and traditional ML techniques to answer causal questions on the data. Hypothetical questions on alternate realities can also be answered with such a framework. In this paper, we estimate the causal effect of Pre-Exposure Prophylaxis (PrEP) on mortality in COVID-19 patients from an observational dataset of over 120,000 patients. With the help of medical experts, we hypothesize a causal graph that identifies the causal and non-causal associations, including the list of potential confounding variables. We use estimation techniques such as linear regression, matching, and machine learning (meta-learners) to estimate the causal effect. On average, our estimates show that taking PrEP can result in a 2.1% decrease in the death rate or a total of around 2,540 patients lives saved in the studied population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ajan Subramanian", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Yong Huang", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Melissa D. Pinto", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Charles A Downs", + "author_inst": "University Of Miami" + }, + { + "author_name": "Amir Rahmani", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.03.23.533961", "rel_title": "Adverse outcomes in SARS-CoV-2 infected pregnant mice are gestational age-dependent and resolve with antiviral treatment", @@ -79117,57 +79885,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.20.23287264", - "rel_title": "Nasopharyngeal Angiotensin Converting Enzyme 2 (ACE2) Expression as a Risk-Factor for SARS-CoV-2 Transmission in Concurrent Hospital Associated Outbreaks", - "rel_date": "2023-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.20.23287264", - "rel_abs": "BackgroundWidespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patients nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.\n\nMethodsEpidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases.\n\nResultsThe infection tracing transmission network provided n = 76 potential transmission events across n = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers (P = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2. Multivariable analysis found that the association between ACE2 transcription and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one unit change in ACE2 transcription decreases the number of secondary cases (B = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one unit change in ACE2 transcription increases the number of secondary cases (B = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients.\n\nConclusionOur study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Aidan M Nikiforuk", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Kevin S Kuchinski", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Katy Short", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Susan Roman", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Agatha N Jassem", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "David M Patrick", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.20.23287490", "rel_title": "The Change of Screen Time and Screen Addiction, and their Association with Psychological Well-being During the COVID-19 Pandemic: An Analysis of US Country-Wide School-Age Children and Adolescents Between 2018 and 2020", @@ -79813,6 +80530,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.19.23287460", + "rel_title": "Data-driven control of airborne infection risk and energy use in buildings", + "rel_date": "2023-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.19.23287460", + "rel_abs": "The global devastation of the COVID-19 pandemic has led to calls for a revolution in heating, ventilation, and air conditioning (HVAC) systems to improve indoor air quality (IAQ), due to the dominant role of airborne transmission in disease spread. While simple guidelines have recently been suggested to improve IAQ mainly by increasing ventilation and filtration, this goal must be achieved in an energy-efficient and economical manner and include all air cleaning mechanisms. Here, we develop a simple protocol to directly, quantitatively, and optimally control transmission risk while minimizing energy cost. We collect a large dataset of HVAC and IAQ measurements in buildings and show how models of infectious aerosol dynamics and HVAC operation can be combined with sensor data to predict transmission risk and energy consumption. Using this data, we also verify that a simple safety guideline is able to limit transmission risk in full data-driven simulations and thus may be used to guide public health policy. Our results provide a comprehensive framework for quantitative control of transmission risk using all available air cleaning mechanisms in an indoor space while minimizing energy costs to aid in the design and automated operation of healthy, energy-efficient buildings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Michael James Risbeck", + "author_inst": "Johnson Controls International" + }, + { + "author_name": "Alexander Ethan Cohen", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Jonathan D Douglas", + "author_inst": "Johnson Controls International" + }, + { + "author_name": "Zhanhong Jiang", + "author_inst": "Johnson Controls International" + }, + { + "author_name": "Carlo M Fanone", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Karen Bowes", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Jim Doughty", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Martin Turnbull", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Louis DiBerardinis", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Young M Lee", + "author_inst": "Johnson Controls International" + }, + { + "author_name": "Martin Z. Bazant", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.19.23287462", "rel_title": "Safety and Effectiveness of SA58 Nasal Spray against SARS-CoV-2 family transmission: an exploratory single-arm trial", @@ -81110,73 +81886,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.16.23287322", - "rel_title": "Serial SARS-CoV-2 antibody titers in vaccinated dialysis patients: prevalence of unrecognized infection and duration of seroresponse", - "rel_date": "2023-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.16.23287322", - "rel_abs": "Rationale & ObjectiveSARS-CoV-2 infections are likely underdiagnosed, but the degree of underdiagnosis among maintenance dialysis patients is unknown. Durability of the immune response after third vaccine doses in this population also remains uncertain. This study tracked antibody levels to 1) assess the rate of undiagnosed infections and 2) characterize seroresponse durability after third doses.\n\nStudy DesignRetrospective observational study\n\nSetting & ParticipantsSARS-CoV-2 vaccinated patients receiving maintenance dialysis through a national dialysis provider. Immunoglobulin G spike antibodies (anti-spike IgG) titers were assessed monthly following vaccination.\n\nExposure(s)Two and three doses of SARS-CoV-2 vaccine\n\nOutcome(s)Undiagnosed and diagnosed SARS-CoV-2 infections; anti-spike IgG titers over time\n\nAnalytical Approach\"Undiagnosed\" SARS-CoV-2 infections were identified as an increase in anti-spike IgG titer of [≥] 100 BAU/mL, not associated with receipt of vaccine or \"diagnosed\" SARS-CoV-2 infection (by PCR or antigen test). In descriptive analyses, anti-spike IgG titers were followed over time.\n\nResultsAmong 2660 patients without prior COVID-19 who received an initial two-dose vaccine series, 371 (76%) SARS-CoV-2 infections were diagnosed and 115 (24%) were undiagnosed. Among 1717 patients without prior COVID-19 who received a third vaccine dose, 155 (80%) SARS-CoV-2 infections were diagnosed and 39 (20%) were undiagnosed. In both cohorts, anti-spike IgG levels declined over time. Of the initial two-dose cohort, 66% had a titer [≥] 500 BAU/mL in the first month, with 23% maintaining a titer [≥] 500 BAU/mL at six months. Of the third dose cohort, 95% had a titer [≥] 500 BAU/mL in the first month after the third dose, with 76% maintaining a titer [≥] 500 BAU/mL at six months.\n\nLimitationsAssays used had upper limits.\n\nConclusionsAmong maintenance dialysis patients, 20-24% of SARS-CoV-2 infections were undiagnosed. Given this populations vulnerability to COVID-19, ongoing infection control measures are needed. A three-dose primary mRNA vaccine series optimizes seroresponse rate and durability.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Vladimir Ladik", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Jill Frament", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Christos Argyropoulos", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Kenneth Abreo", - "author_inst": "Louisiana State University, Health Sciences Center" - }, - { - "author_name": "Andrew Chin", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Reginald Gladish", - "author_inst": "Nephrology of North Alabama" - }, - { - "author_name": "Loay Salman", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Eduardo K Lacson Jr.", - "author_inst": "Dialysis Clinic Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2023.03.16.23287360", "rel_title": "Relative vaccine effectiveness (rVE) of mRNA COVID-19 boosters in the UK vaccination programme, during the Spring-Summer (monovalent vaccine) and Autumn-Winter 2022 (bivalent vaccine) booster campaigns: a prospective test negative case-control study", @@ -82022,6 +82731,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.15.529513", + "rel_title": "Modelling the viral dynamics of the SARS-CoV-2 Delta and Omicron variants in different cell types", + "rel_date": "2023-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.15.529513", + "rel_abs": "We use viral kinetic models fitted to viral load data from in vitro studies to explain why the SARS-CoV-2 Omicron variant replicates faster than the Delta variant in nasal cells, but slower than Delta in lung cells, which could explain Omicrons higher transmission potential and lower severity. We find that in both nasal and lung cells, viral infectivity is higher for Omicron but the virus production rate is higher for Delta. However, the differences are unequal between cell types, and ultimately leads to the basic reproduction number and growth rate being higher for Omicron in nasal cells, and higher for Delta in lung cells. In nasal cells, Omicron alone can enter via a TMPRSS2-independent pathway, but it is primarily increased efficiency of TMPRSS2-dependent entry which accounts for Omicrons increased activity. This work paves the way for using within-host mathematical models to understand the transmission potential and severity of future variants.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Clare P McCormack", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ada W C Yan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan C Brown", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ksenia Sukhova", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas P Peacock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ilaria Dorigatti", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.03.13.23286935", "rel_title": "Comparison of Capillary Blood Self-Collection using the Tasso-SST Device with Venous Phlebotomy for anti-SARS-CoV-2 Antibody Measurement", @@ -83076,73 +83828,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.03.12.23287049", - "rel_title": "The cost of primary care consultations associated with long COVID in non-hospitalised patients: a retrospective cohort study using UK primary care data", - "rel_date": "2023-03-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.12.23287049", - "rel_abs": "ObjectivesTo assess incremental costs of primary care consultations associated with post-Covid-19 condition or long COVID, to estimate associated national costs for the United Kingdom population, and to assess risk factors associated with increased costs.\n\nDesignA retrospective cohort study using a propensity score matching approach with an incremental cost method to estimate primary care consultation costs associated with long COVID.\n\nSettingUK based primary care general practitioner (GP), nurse and physiotherapist consultation data from the Clinical Practice Research Datalink Aurum primary care database from 31st January 2020 to 15th April 2021.\n\nParticipants472,173 non-hospitalised adults with confirmed SARS-CoV-2 infection were 1:1 propensity score matched to a pool of eligible patients with the same index date, the same number of prior consultations, and similar background characteristics, but without a record of COVID-19. Patients diagnosed with Long COVID (3,871) and those with World Health Organisation (WHO) defined symptoms of long COVID (30,174) formed two subgroups within the cohort with confirmed SARS-CoV-2 infection.\n\nMain outcome measuresCosts were calculated using a bottom-up costing approach with consultation cost per working hour in pound sterling ({pound}) obtained from the Personal Social Services Research Units Unit Costs of Health and Social Care 2021. The average incremental cost in comparison to patients with no record of COVID-19 was produced for each patient group, considering only consultation costs at least 12 weeks from the SARS-CoV-2 infection date or matched date for the comparator group (from 15th April 2020 to 15th April 2021). A sensitivity analysis was undertaken which restricted the study population to only those who had at least 24 weeks of follow-up. National costs were estimated by extrapolating incremental costs to the cumulative incidence of COVID-19 in the UK Office for National Statistics COVID-19 Infection Survey. The impacts of risk factors on the cost of consultations beyond 12 weeks from SARS-CoV-2 infection were assessed using an econometric ordinary least squares (OLS) regression model, where coefficients were interpreted as the percentage change in cost due to a unit increase in the specific factor.\n\nResultsThe incremental cost of primary care consultations potentially associated with long COVID was {pound}2.44 per patient with COVID-19 per year. This increased to {pound}5.72 in the sensitivity analysis. Extrapolating this to the UK population produced a cost estimate of {pound}23,382,452 (90% credible interval: {pound}21,378,567 to {pound}25,526,052) or {pound}54,814,601 (90% credible interval: {pound}50,116,967 to {pound}59,839,762) in the sensitivity analysis. Among patients with COVID-19 infection, a long COVID diagnosis and longer-term reporting of symptoms were associated with a 43% and 44% increase in primary care consultation costs respectively, compared to patients without long COVID symptoms. Older age (49% relative increase in costs in those aged 80 years or older compared to those aged 18 to 29 years), female sex (4% relative increase in costs compared to males), obesity (4% relative increase in costs compared to those of normal weight), comorbidities and the number of prior consultations were all associated with an increase in the cost of primary care consultations. By contrast, those from black ethnic groups had a 6% reduced relative cost compared to those from white ethnic groups.\n\nConclusionsThe costs of primary care consultations associated with long COVID in non-hospitalised adults are substantial. Costs are significantly higher among those diagnosed with long COVID, those with long COVID symptoms, older adults, females, and those with obesity and comorbidities.\n\nWhat is already known on this topic?O_LILong COVID is a global public health challenge, with millions of people affected worldwide.\nC_LIO_LIPeople with a history of long COVID use health services, including primary care, at a higher rate than uninfected individuals even beyond the period of acute infection.\nC_LIO_LIThe cost of this increased healthcare use is unknown, impeding planning and forecasting of resource requirements needed to adequately support people with long COVID.\nC_LI\n\nWhat this study adds?O_LIBeyond 12 weeks from acute infection, non-hospitalised adults with a history of SARS-CoV-2 infection cost primary care services an additional {pound}2.44 per patient per year greater on average than patients with no prior evidence of infection.\nC_LIO_LIDue to the high incidence of COVID-19, this represents a substantial cost to primary care services, in the UK exceeding {pound}20 million for consultations associated with long COVID.\nC_LIO_LIThese incremental costs are greater in those with a formal diagnosis of long COVID, those reporting related symptoms, older adults, females, and those with obesity.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jake Tufts", - "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust, Lancashire, UK" - }, - { - "author_name": "Dawit T Zemedikun", - "author_inst": "School of Population and Global Health (M431), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Naijie Guan", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Krishna Gokhale", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Puja Myles", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tim Williams", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tom Marshall", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Melanie Calvert", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK; Birmingham Health Partners Centre for Regulatory Science and Innovati" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Long Covid SOS, Charity registered in England & Wales, 11A Westland Road, Faringdon, Oxfordshire, UK" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Louise Jackson", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Shamil Haroon", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.03.11.23287138", "rel_title": "How long is the long COVID? a retrospective analysis of football players in two major European Championships.", @@ -83684,6 +84369,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.11.532212", + "rel_title": "In vitro comparison of SARS-CoV-2 variants", + "rel_date": "2023-03-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.11.532212", + "rel_abs": "The Coronaviridae family hosts various coronaviruses responsible for many diseases, from the common cold, severe lung infections to pneumonia. SARS-CoV-2 was discovered to be the etiologic agent of the Coronavirus pandemic, and numerous basic and applied laboratory techniques were utilized in virus culture and examination of the disease. Understanding the replication kinetics and characterizing the virus effect on different cell lines is crucial for developing in vitro studies. With the emergence of multiple variants of SARS-CoV-2, a comparison between their infectivity and replication in common cell lines will give us a clear understanding of the characteristic differences in pathogenicity. In this study, we compared the cytopathic effect (CPE) and replication of Wild Type (WT), Omicron (B.1.1.529), and Delta (B.1.617.2) variants on 5 different cell lines; VeroE6, VeroE6 expressing high endogenous ACE2, VeroE6 highly expressing human ACE2 (VeroE6/ACE2) and TMPRSS2 (VeroE6/hACE2/ TMPRSS2), Calu3 cells highly expressing human ACE2 and A549 cells. All 3 VeroE6 cell lines were susceptible to WT strain, where CPE and replication were observed. Along with being susceptible to Wild type, VeroE6/hACE2/TMPRSS2 cells were susceptible to both omicron and delta strains, whereas VeroE6/ACE2 cells were only susceptible to omicron in a dose-dependent manner. No CPE was observed in both human lung cell lines, A549 and Calu3/hACE2, but Wild type and omicron replication was observed. As SAR-CoV-2 continues to evolve, this data will benefit researchers in experimental planning, viral pathogenicity analysis, and providing a baseline for testing future variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kruttika S. Phadke", + "author_inst": "Iowa State University" + }, + { + "author_name": "Nathaniel B. A. Higdon", + "author_inst": "Iowa State University" + }, + { + "author_name": "Bryan H. Bellaire", + "author_inst": "Iowa State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.03.11.532204", "rel_title": "Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals", @@ -84650,33 +85362,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.09.23287043", - "rel_title": "Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287043", - "rel_abs": "IntroductionInfection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses in the respiratory epithelium and peripheral immune cells is not yet fully understood.\n\nMethodsIn this study, we integrated multiple public scRNA-seq datasets of nasopharyngeal swab and peripheral blood results to investigate the gene regulatory networks (GRNs) of healthy individuals and COVID-19 patients with mild/moderate and severe disease, respectively. Similar and dissimilar regulons were identified within or between epithelial and immune cells during COVID-19 severity progression. The relative transcription factors (TFs) and their targets were used to construct GRNs among different infection sites and conditions.\n\nResultsBetween respiratory epithelial and peripheral immune cells, different TFs tended to be used to regulate the activity of a cell between healthy individuals and COVID-19 patients, although they had some TFs in common. For example, XBP1, FOS, STAT1, and STAT2 were activated in both the epithelial and immune cells of virus-infected individuals. In contrast, severe COVID-19 cases exhibited activation of CEBPD in peripheral immune cells, while CEBPB was exclusively activated in respiratory epithelial cells. Moreover, in patients with severe COVID-19, CEBPD upregulated S100A8 and S100A9 in CD14 and CD16 monocytes, while S100A9 genes were co-upregulated by different regulators (SPEDEF and ELF3) in goblet and squamous cells. The cell-cell communication analysis suggested that epidermal growth factor receptor signaling among epithelial cells contributes to mild/moderate disease, and chemokine signaling among immune cells contributes to severe disease.\n\nConclusionsThis study identified cell type- and condition-specific regulons in a wide range of cell types from the initial infection site to the peripheral blood, and clarified the diverse mechanisms of maladaptive responses to SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lin Zhang", - "author_inst": "Tohoku University" - }, - { - "author_name": "Hafumi Nishi", - "author_inst": "Tohoku University; Ochanomizu University" - }, - { - "author_name": "Kengo Kinoshita", - "author_inst": "Tohoku University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.09.23287034", "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review", @@ -85658,6 +86343,29 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2023.03.07.23286904", + "rel_title": "The impact of signal variability on epidemic growth rate estimation from wastewater surveillance data", + "rel_date": "2023-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286904", + "rel_abs": "BackgroundTesting samples of waste water for markers of infectious disease became a widespread method of surveillance during the COVID-19 pandemic. While these data generally correlate well with other indicators of national prevalence, samples that cover localised regions tend to be highly variable over short time scales.\n\nMethodsWe introduce a procedure for estimating the realtime growth rate of pathogen prevalence using time series data from wastewater sampling. The number of copies of a target gene found in a sample is modelled as time-dependent random variable whose distribution is estimated using maximum likelihood. The output depends on a hyperparameter that controls the sensitivity to variability in the underlying data. We apply this procedure to data reporting the number of copies of the N1 gene of SARS-CoV-2 collected at water treatment works across Scotland between February 2021 and February 2023.\n\nResultsThe real-time growth rate of the SARS-CoV-2 prevalence is estimated at 121 wastewater sampling sites covering a diverse range of locations and population sizes. We find that the sensitivity of the fitting procedure to natural variability determines its reliability in detecting the early stages of an epidemic wave. Applying the procedure to hospital admissions data, we find that changes in the growth rate are detected an average of 2 days earlier in wastewater than in hospital admissions data.\n\nConclusionWe provide a robust method to generate reliable estimates of epidemic growth from highly variable data. Applying this method to samples collected at wastewater treatment works provides highly responsive situational awareness to inform public health.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ewan Colman", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Rowland Raymond Kao", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.07.23286893", "rel_title": "Dosing of convalescent plasma and hyperimmune anti-SARS-CoV-2 1 immunoglobulins: a phase I/II dose finding study", @@ -86348,165 +87056,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.06.23286834", - "rel_title": "SARS-CoV-2 viral replication persists in the human lung for several weeks after onset of symptomatic severe COVID-19 and is associated with attenuated pulmonary immunity and variant-specific clinical sequalae", - "rel_date": "2023-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286834", - "rel_abs": "RationaleIn the upper respiratory tract replicating (culturable) SARS-CoV-2 is recoverable for [~] 4 to 8 days after symptom onset, however, there is paucity of data about the frequency or duration of replicating virus in the lower respiratory tract (i.e. the human lung).\n\nObjectivesWe undertook lung tissue sampling (needle biopsy), shortly after death, in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patents served as a control group.\n\nMethodsLung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling and immunohistochemistry.\n\nResults38% (16/42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 weeks) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (p<0.05). Nasopharyngeal culture was negative in 23.1% (6/26) of decedents despite lung culture positivity. This, hitherto, undescribed bio-phenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary pro-inflammatory response but with concurrent viral culture positivity.\n\nConclusionsConcurrent, rather than sequential active viral replication continues to drive a heightened pro-inflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe COVID-19 disease.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSInvestigations to understand SARS-CoV-2 viral shedding (determined by PCR or antigen testing) have extensively focused on samples from the upper respiratory tract. The widely accepted view is that acute severe SARS-CoV-2 infection is characterised by a viral replicative phase in the first week of symptomatic illness followed by a pro-inflammatory immunopathologic phase peaking in the second and third weeks of illness. However, it remains unclear whether detection of SARS-CoV-2 beyond 2 weeks after symptom onset in published studies represent active replication competent virus because it may represent residual genomic or antigenic material in the tissue.\n\nWhat This Study Adds to the FieldWe have identified a, hitherto, undescribed bio-phenotype of acute severe COVID-19 characterised by persisting viral replication in the lung for up to 4 weeks after symptom onset. [~]40% of acute severe COVID-19 intensive care unit (ICU) decedents (n=42) had nasopharyngeal swab culture positivity at [~]2 weeks post-symptom onset versus only [~]5% in a group of ambulatory control patients (n=18). There was compartment-specific (nasopharynx versus lung) discordance. The phenotype of lung-specific persisting viral replication was associated with variant-specific accelerated death, an exaggerated inflammatory response, and attenuated T-cell immunity in the lung (based on histopathological and transcriptomic studies). This challenges the traditional view that viral replication occurs during the first 5 to 10 days of illness, which is followed by an effector or hyperinflammatory phase. This is the first study, to our knowledge, to systematically culture virus from the human lung and map out its related clinical determinants, and which describes the human lung transcriptomic profile of culture-positive versus culture-negative patients with severe COVID-19 disease.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Michele Tomasicchio", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Shameem Jaumdally", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Anil Pooran", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aliasgar Esmail", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lindsay Wilson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Andrea Kotze", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lynn Semple", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Stuart Meier", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Komala Pillay", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Riyaadh Roberts", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Raymond Kriel", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Richard Meldau", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Suzette Oelofse", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Carley Mandviwala", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jessica Burns", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rolanda Londt", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malika Davids", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Charnay van der Merwe", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aqeedah Roomaney", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Louie Kuhn", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Tahlia Perumal", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Scott", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Martin Hale", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Vicky Baillie", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Sana Mahtab", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rageema Joseph", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Ivan Joubert", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jenna Piercy", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Thomson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Fredericks", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malcolm Miller", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marta Nunes", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Shabir Madhi", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Keertan Dheda", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.06.531252", "rel_title": "Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics", @@ -87260,6 +87809,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.04.531078", + "rel_title": "Tau protein aggregation associated with SARS-CoV-2 main protease", + "rel_date": "2023-03-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.04.531078", + "rel_abs": "The primary function of virus proteases is the proteolytic processing of the viral polyprotein. These enzymes can also cleave host cell proteins, which is important for viral pathogenicity, modulation of cellular processes, viral replication, the defeat of antiviral responses and modulation of the immune response. It is known that COVID-19 can influence multiple tissues or organs and that infection can damage the functionality of the brain in multiple ways. After COVID-19 infections, amyloid-{beta}, neurogranin, tau and phosphorylated tau were detected extracellularly, implicating possible neurodegenerative processes.\n\nThe present study describes the possible induction of protein aggregation by the SARS-CoV-2 3CL protease (3CLpro) possibly relevant in neuropathology, such as aggregation of tau, alpha-synuclein and TPD-43. Further investigations demonstrated that tau was proteolytically cleaved by the viral protease 3CL and, consequently, generated aggregates. However, more evidence is needed to confirm that COVID-19 is able to trigger neurodegenerative diseases.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Raphael J Eberle", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Monika A Coronado", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Ian Gering", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Karolina Korostov", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Anja Stefanski", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Kai Stuehler", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Victoria Kraemer-Schulien", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Lara Bloemeke", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Oliver Bannach", + "author_inst": "Forschungszentrum Juelich" + }, + { + "author_name": "Dieter Willbold", + "author_inst": "Forschungszentrum Juelich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.03.05.531227", "rel_title": "Predicting the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein", @@ -88270,41 +88874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.02.23286561", - "rel_title": "Bivalent booster effectiveness against severe COVID-19 outcomes in Finland, September 2022 - January 2023", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286561", - "rel_abs": "Bivalent COVID-19 vaccines were introduced in 2022 but knowledge of their effectiveness against severe COVID-19 outcomes is currently limited. In Finnish register-based cohort analyses, we compared the risk of severe COVID-19 outcomes among those who received bivalent vaccination (exposed) between September 2022 and March 2023 to those who did not (unexposed). Among elderly aged 65-110 years, bivalent vaccination reduced the risk of hospitalisation and death due to COVID-19 in September-December 2022; the hazard ratios comparing exposed and unexposed ranged from 0.37 to 0.45 during the first 31-60 days since bivalent vaccination. However, in January-March 2023 the effect disappeared possibly indicating immune evasion of new SARS-CoV-2 variants, waning of vaccine effectiveness and increased presence of hybrid immunity. Among the chronically ill aged 18-64 years bivalent vaccination did not reduce the risk of severe COVID-19 outcomes. These results are important for developing COVID-19 vaccines and programmes worldwide.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eero Poukka", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Hanna Nohynek", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Sirkka Goebeler", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Tuija Leino", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Ulrike Baum", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.02.23286686", "rel_title": "Impact of COVID-19 pandemic on the etiology and characteristics of community-acquired pneumonia among children requiring bronchoalveolar lavage in northern China", @@ -88886,6 +89455,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.02.23286698", + "rel_title": "A novel approach for estimating vaccine efficacy for infections with multiple disease outcomes: application to a COVID-19 vaccine trial", + "rel_date": "2023-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286698", + "rel_abs": "Vaccines can provide protection against infection or reduce disease progression and severity. Vaccine efficacy (VE) is typically evaluated independently for different outcomes, but this can cause biased estimates of VE. We propose a new analytical framework based on a model of disease progression for VE estimation for infections with multiple possible outcomes of infection: Joint analysis of multiple outcomes in vaccine efficacy trials (JAMOVET). JAMOVET is a Bayesian hierarchical regression model that controls for biases and can evaluate covariates for VE, the risk of infection, and the probability of progression. We applied JAMOVET to simulated data, and data from COV002 (NCT04400838), a phase 2/3 trial of ChAdOx1 nCoV-19 (AZD1222) vaccine. Simulations showed that biases are corrected by explicitly modelling disease progression and imperfect test characteristics. JAMOVET estimated ChAdOx1 nCoV-19 VE against infection (VEin) at 47% (95% CI 36-56) and progression to symptoms (VEpr) at 48% (95% CI 32-61). This implies a VE against symptomatic infection of 72% (95% CI 63-80), consistent with published trial estimates. VEin decreased with age while VEpr increased with age. JAMOVET is a powerful tool for evaluating diseases with multiple dependent outcomes and can be used to adjust for biases and identify predictors of key outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Lucy R Williams", + "author_inst": "Imperial College London" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew J Pollard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicholas C Grassly", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.02.23286693", "rel_title": "The impact of early anti-SARS-CoV-2 antibody production on the length of hospitalization stay among COVID-19 patients", @@ -90048,33 +90648,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2023.02.28.530489", - "rel_title": "Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants", - "rel_date": "2023-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.28.530489", - "rel_abs": "The evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity, conformational plasticity, protein stability and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined conformational dynamics of the spike trimers that agrees with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2 and BA.2.75 trimers we showed that the key network positions driving long-range signaling are associated with the major stability hotspots that are inter-connected along potential communication pathways, while sites of Omicron mutations may often correspond to weak spots of stability and allostery but are coupled to the major stability hotspots through interaction networks. The presented analysis of the BA.1, BA.2 and BA.2.75 trimers suggested that thermodynamic stability of BA.1 and BA.2.75 variants may be intimately linked with the residue interaction network organization that allows for a broad ensemble of allosteric communications in which signaling between structural stability hotspots may be modulated by the Omicron mutational sites. The findings provided plausible rationale for mechanisms in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Mohammed Alshahrani", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman Unversity" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.02.26.23286261", "rel_title": "SARS-CoV-2 post-vaccine surveillance studies in Australian children and adults with cancer: SerOzNET Statistical Analysis Plan", @@ -90708,6 +91281,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.02.24.23286187", + "rel_title": "Coping with drug resistant tuberculosis alongside COVID-19 and other stressors in Zimbabwe: a qualitative study.", + "rel_date": "2023-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.24.23286187", + "rel_abs": "BackgroundHouseholds in low-resource settings are more vulnerable to events which adversely affect their livelihoods, including shocks such as the death of a family member, inflation, droughts and more recently COVID-19. Drug Resistant Tuberculosis (DR-TB) is also another shock that inflicts physical, psychological and socioeconomic burden on individuals and households. We describe experiences and coping strategies among people affected by DR-TB and their households in Zimbabwe during the COVID-19 pandemic, 2020 to 2021.\n\nMethodsWe conducted 16 in-depth interviews with adults who had just completed or were completing treatment. Interview themes included health seeking behaviour, impact of DR-TB on livelihoods and coping strategies adopted during treatment. We analysed data using thematic analyses.\n\nResultsHealth seeking from providers outside the public sector, extra-pulmonary TB and health system factors resulted in delayed DR-TB diagnosis and treatment and increased financial drain on households. DR-TB reduced productive capacity and narrowed job opportunities leading to income loss that continued even after completion of treatment. Household livelihood was further adversely affected by lockdowns due to COVID-19, outbreaks of bird flu and cattle disease. Stockouts of DR-TB medicines, common during COVID-19, exacerbated loss of productive time and transport costs as medication had to be accessed from other clinics that were further away. Reversible coping strategies included: reducing number of meals; relocating in search of caregivers and/or family support; spending savings; negotiating with school authorities to keep children in school. Some households had to adopt irreversible coping strategies such as selling productive assets and withdrawing children from school.\n\nConclusionDR-TB combined with COVID-19 and other stressors pushed households into deeper poverty, and vulnerability. Multi-sectoral approaches that combine health systems, psychosocial and economic interventions are crucial to mitigate diagnostic delays and suffering, and meaningfully support people with DR-TB and their households to compensate the loss of livelihoods during and post DR-TB treatment.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Collins Timire", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Katharina Kranzer", + "author_inst": "London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases" + }, + { + "author_name": "Debora Pedrazzoli", + "author_inst": "London School of Hygiene and Tropical Medicine Faculty of Epidemiology and Population Health" + }, + { + "author_name": "Fungai Kavenga", + "author_inst": "Ministry of Health and Child Care" + }, + { + "author_name": "Samuel Kasozi", + "author_inst": "Ministry of Health and Child Care" + }, + { + "author_name": "Fredrick Mbiba", + "author_inst": "Biomedical Research and Training Institute" + }, + { + "author_name": "Virginia Bond", + "author_inst": "London School of Hygiene and Tropical Medicine Department of Global Health and Development" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.22.23286287", "rel_title": "Disability evaluation in patients with Guillain-Barre syndrome and SARS-CoV-2 infection from a neurological reference center in Peru", @@ -91834,25 +92450,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.15.23285880", - "rel_title": "Has the COVID-19 pandemic ended or not? opinions from the public in the U.S.", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285880", - "rel_abs": "Recently President Joe Biden announced the end to the COVID-19 pandemic in the US but some scientists expressed different opinions. This study aimed to examine the view of the end of the COVID-19 pandemic among the public. Data were collected in September 2022 from an online crowdsourcing platform, and respondents answered if they believed that the pandemic has ended in the United States or not. Logistic regressions were used to estimate the likelihood of agreeing on the end of the pandemic, adjusted by demographics and several related variables. Among 2983 respondents, 78.1% believed that the COVID-19 pandemic had ended, and the percentage decreased to 66.5% after adding weights. Males, younger adults, Hispanics, those with higher levels of educational attainment, those with middle levels of household income, those living in suburban or rural areas, and those living in states that voted for the Republican party in the 2020 Presidential Election were more likely to believe that the pandemic had ended, compared with their counterparts. With about one-third of Americans did not agree that the pandemic had ended and marked demographical and geographical differences, the timing and the way of the pandemic end announcement should be deliberately cautious.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yong Yang", - "author_inst": "University of Memphis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.16.23286009", "rel_title": "Vaccine-induced correlate of protection against fatal COVID-19 in the old and frail during waves of neutralization resistant variants of concern.", @@ -92690,6 +93287,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2023.02.17.23286079", + "rel_title": "Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286079", + "rel_abs": "AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures.\n\nMethods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded.\n\nConclusionsFew workplace surface samples were positive for SARS-CoV-2 RNA and positive samples typically contained low levels of nucleic acid. Although these data may infer a low probability of fomite transmission or other forms of transmission within the workplace, Ct values may have been lower at the time of contamination. Workplace environmental sampling identified lapses in COVID-control measures within individual sites and showed trends through the pandemic.\n\nSignificance and Impact of the StudyPrior to this study, few published reports investigated SARS-CoV-2 RNA contamination within workplaces experiencing cases of COVID-19. This report provides extensive data on environmental sampling identifying trends across workplaces and through the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ian George Nicholls", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Antony Spencer", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Yiqun Chen", + "author_inst": "Health and Safety Executive" + }, + { + "author_name": "Allan Bennett", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Barry Atkinson", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.17.23286084", "rel_title": "Tempo-spatial dynamics of COVID-19 in Germany: A phase model based on a pandemic severity indicator", @@ -93672,65 +94304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.21.23286181", - "rel_title": "Associations between SARS-CoV-2 infection and incidence of new chronic condition diagnoses: a systematic review", - "rel_date": "2023-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286181", - "rel_abs": "Because of the large number of infected individuals, an estimate of the future burdens of the long-term consequences of SARS-CoV-2 infection is needed. This systematic review examined associations between SARS-CoV-2 infection and incidence of categories of and selected chronic conditions, by age and severity of infection (inpatient vs. outpatient/mixed care). MEDLINE and EMBASE were searched (Jan 1, 2020 to Oct 4, 2022) and reference lists scanned. We included observational studies from high-income OECD countries with a control group adjusting for sex and comorbidities. Identified records underwent a two-stage screening process. Two reviewers screened 50% of titles/abstracts, after which DistillerAI acted as second reviewer. Two reviewers then screened the full texts of stage one selections. One reviewer extracted data and assessed risk of bias; results were verified by another. Random-effects meta-analysis estimated pooled hazard ratios (HR). GRADE assessed certainty of the evidence. Twenty-five studies were included. Among the outpatient/mixed SARS-CoV-2 care group, there is high certainty of a small-to-moderate increase (i.e., HR 1.26 to 1.99) among adults [≥]65 years of any cardiovascular condition, and of little-to-no difference (i.e., HR 0.75 to 1.25) in anxiety disorders for individuals <18, 18-64, and [≥]65 years old. Among 18-64 and [≥]65 year-olds receiving outpatient/mixed care there are probably (moderate certainty) large increases (i.e., HR [≥]2.0) in encephalopathy, interstitial lung disease, and respiratory failure. After SARS-CoV-2 infection, there is probably an increased risk of diagnoses for some chronic conditions; whether the magnitude of risk will remain stable into the future is uncertain.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lindsay A. Gaudet", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jennifer Pillay", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sabrina Saba", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dianne Zakaria", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Nicholas Cheta", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "H\u00e9l\u00e8ne Gardiner", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Larry Shaver", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Jacqueline Middleton", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Maria Tan", - "author_inst": "University of Alberta" - }, - { - "author_name": "Ben Vandermeer", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lisa Hartling", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.14.23285860", "rel_title": "REAL-WORLD EFFECTIVENESS OF NIRMATRELVIR/RITONAVIR ON COVID-19-ASSOCIATED HOSPITALIZATION PREVENTION: A POPULATION-BASED COHORT STUDY IN THE PROVINCE OF QUEBEC, CANADA", @@ -94212,6 +94785,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.02.20.23286191", + "rel_title": "Longitudinal dynamics of Streptococcus pneumoniae carriage and SARS-CoV-2 infection in households with children.", + "rel_date": "2023-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.20.23286191", + "rel_abs": "BackgroundTo characterize interferences between Streptococcus pneumoniae and SARS-CoV-2 we investigated the longitudinal patterns of viral infection and pneumococcal carriage in households infected with SARS-CoV-2.\n\nMethodsSARS-CoV-2 and pneumococcus were detected with quantitative molecular methods in saliva from members of eighty participating households. Samples were collected between October 2020 and January 2021 from n=197 adults and n=118 children of which n=176 adults and n=98 children had a complete set of ten samples collected within 42 days since enrolment. Time-dependent Cox models were used to evaluate the associations between SARS-CoV-2 and pneumococcal carriage.\n\nResultsIn the entire cohort, cumulative pneumococcal carriage and SARS-CoV-2 infection rates were 58% and 65%, respectively. Pneumococcal abundances were associated with an increased risk of SARS-CoV-2 infection (HR 1.14, 95% CI, 1.01 - 1.29, P=0.04) and delayed clearance of SARS-CoV-2 infection (HR 0.90, 95% CI, 0.82 - 0.99, P=0.03). Elevated viral loads were observed among pneumococcal carriers and individuals with high overall bacterial 16S abundances, however, there were no longitudinal differences in viral loads in linear mixed-effects models. Individuals with high 16S abundances displayed delayed viral clearance (HR 0.65, 95% CI 0.55 - 0.78, P<0.0001).\n\nConclusionsAlthough we found insufficient evidence for a strong impact of SARS-CoV-2 infection on pneumococcal carriage. Results from the current study suggest that pneumococcal carriers may have an increased risk of SARS-CoV-2 infection and high pneumococcal abundances and 16S abundances may be associated with elevated viral loads and delayed clearance of SARS-CoV-2 infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Willem R. Miellet", + "author_inst": "Wilhelmina Children's Hospital, Utrecht University Medical Centre" + }, + { + "author_name": "Rob Mariman", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Dirk Eggink", + "author_inst": "National Institute for Public Health and The Environment (RIVM)" + }, + { + "author_name": "Mioara A Nicolaie", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Janieke van Veldhuizen", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Gerlinde Pluister", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Lisa M Kolodziej", + "author_inst": "Amsterdam University Medical Centres" + }, + { + "author_name": "Steven van Lelyveld", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Sjoerd M Euser", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Elisabeth A.M. Sanders", + "author_inst": "Wilhelmina Children's Hospital, Utrecht University Medical Centre" + }, + { + "author_name": "Marianne A van Houten", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Krzysztof Trzcinski", + "author_inst": "Wilhelmina Children's Hospital, Utrecht University Medical Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.13.23285847", "rel_title": "The Equilibrium and Pandemic Waves of COVID-19 in the US", @@ -95222,69 +95858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.17.23286083", - "rel_title": "Prevalence of anti-SARS-CoV-2 antibodies in people attending the two main Goma markets in the eastern Democratic Republic of Congo", - "rel_date": "2023-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286083", - "rel_abs": "According to official data, the Democratic Republic of the Congo (DRC) has a low prevalence of the coronavirus disease 19 (COVID-19) pandemic. The goal of this cross-sectional study was to determine the COVID-19 seroprevalence in people attending Gomas two largest markets, Kituku and Virunga. This study was conducted between September and November 2021, overlapping by one month with another similar study carried out in a slum of Bukavu, and using the same methodology.\n\nCOVID-19 unvaccinated participants (n = 796 including 454 vendors and 342 customers, 60% of whom were women) were surveyed. The median age of vendors and customers was 34.2 and 30.1 years, respectively.\n\nThe crude and adjusted anti-SARS-CoV-2 antibody seroprevalence rates were 70.2% (95 % CI 66.9-73.4%) and 98.8% (95% CI 94.1-100%), respectively, with no difference between vendors and customers. COVID-19 symptoms were mild or absent in 58.9% and 41.1% of participants with anti-SARS-CoV-2 antibodies respectively. COVID-19 did not require hospitalisation for any of the seropositive participants.\n\nThese findings are consistent with those reported in Bukavu. They confirm that SARS-CoV-2 spread without causing severe symptoms in densely populated settlements and markets, and suggest that many COVID-19 cases went unreported. Based on these results, relevance of an untargeted hypothetical vaccination programme in these communities should be questioned.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Prudence Ndeba Mitangala", - "author_inst": "Universite Catholique de Bukavu, Bukavu, Sud Kivu, Democratic Republic of Congo and Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic" - }, - { - "author_name": "Leonid Mwana Wa Bene Irenge", - "author_inst": "Center for Applied Molecular Technologies (CTMA) Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54-B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium " - }, - { - "author_name": "Edgar Tsongo Musubao", - "author_inst": "Institut de Techniques Medicales, Goma, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jean Bosco Mbeva Kahindo", - "author_inst": "Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Patrick Ndeba Ayonga", - "author_inst": "Departement des maladies infectieuses et tropicales, Universite de Bordeaux, France" - }, - { - "author_name": "Israel Kyembwa Safari", - "author_inst": "Inspection provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Janvier Bonane Kubuya", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Edmon Namegabe Ntabe", - "author_inst": "Universite libre des pays des grands lacs, Goma Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Raphael Kakongo Senga Kabangwa", - "author_inst": "Laboratoire Provincial Ami Labo Nord Kivu , Democratic Republic of Congo" - }, - { - "author_name": "Guy Ndongala Mutombo", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jerome Ambroise", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - }, - { - "author_name": "JEAN-LUC GALA", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.16.23286061", "rel_title": "How well do we do social distancing?", @@ -95790,6 +96363,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.15.23285941", + "rel_title": "Underreporting of SARS-CoV-2 infections during the first wave of the 2020 COVID-19 epidemic in Finland - Bayesian inference based on a series of serological surveys", + "rel_date": "2023-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285941", + "rel_abs": "In Finland, the first wave of the COVID-19 epidemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took place from March to June 2020, with the majority of COVID-19 cases diagnosed in the extended capital region. The magnitude and trend in the incidence of COVID-19 is one way to monitor the course of the epidemic. The diagnosed COVID-19 cases are a subset of the infections and therefore the COVID-19 incidence underestimates the SARS-CoV-2 incidence. The likelihood that an individual with SARS-CoV-2 infection is diagnosed with COVID-19 depends on the clinical manifestation as well as the infection testing policy and capacity. These factors may fluctuate over time and the underreporting of infections changes accordingly. Quantifying the extent of underreporting allows the assessment of the true incidence of infection. To obtain information on the incidence of SARS-CoV-2 infection in Finland, a series of serological surveys was initiated in April 2020. We develop a Bayesian inference approach and apply it to data from the serological surveys, registered COVID-19 cases, and external data, to estimate the time-dependent underreporting of SARS-Cov-2 infections during the first wave of the COVID-19 epidemic in Finland. There were 1 to 5 (95% probability) SARS-CoV-2 infections for every COVID-19 case during the first wave of the COVID-19 epidemic in Finland. The underreporting was highest before April when there were 4 to 17 (95% probability) infections for every COVID-19 case. It is likely that between 0.5%-1.0% (50% probability) and no more than 1.5% (95% probability) of the population in the extended capital region were infected with SARS-CoV-2 by the beginning of July 2020.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tuomo A Nieminen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Kari Auranen", + "author_inst": "University of Turku" + }, + { + "author_name": "Sangita Kulathinal", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Tommi Harkanen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Merit Melin", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Arto A Palmu", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Jukka Jokinen", + "author_inst": "Finnish Institute for Health and Welfare" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.15.23285942", "rel_title": "Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England", @@ -97276,65 +97892,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.13.528349", - "rel_title": "Propylene glycol inactivates respiratory viruses and prevents airborne transmission", - "rel_date": "2023-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.13.528349", - "rel_abs": "Viruses are vulnerable as they transmit between hosts and we aimed to exploit this critical window. We found that the ubiquitous, safe, inexpensive and biodegradable small molecule propylene glycol (PG) has robust virucidal activity. Propylene glycol rapidly inactivates influenza, SARS-CoV-2 and a broad range of other enveloped viruses, and reduces disease burden in mice when administered intranasally at concentrations commonly found in nasal sprays. Most critically, aerosolized PG efficiently abolishes influenza and SARS-CoV-2 infectivity within airborne droplets, potently preventing infection at levels significantly below those well-tolerated by mammals. We present PG vapor as a first-in-class non-toxic airborne virucide, to prevent transmission of existing and emergent viral pathogens, with clear and immediate implications for public health.\n\nOne-sentence summaryPropylene glycol is a potent and safe virucidal compound that could be used to limit and control infections.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christine T Styles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katie E Flight", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan C Brown", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michael Vanden Oever", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas P Peacock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ziyin Wang", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rosie Millns", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "John S Tregoning", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rachel S Edgar", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.13.528235", "rel_title": "P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium", @@ -97972,6 +98529,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.10.527914", + "rel_title": "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA", + "rel_date": "2023-02-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.10.527914", + "rel_abs": "The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step in understanding how condensation is realized. Here, we focus on the role of the RNA Binding Domain (RBD) and its flanking disordered N-Terminal Domain (NTD) tail, using single-molecule Forster Resonance Energy Transfer and coarse-grained simulations. We quantified contact site size and binding affinity for nucleic acids and concomitant conformational changes occurring in the disordered region. We found that the disordered NTD increases the affinity of the RBD for RNA by about 50-fold. Binding of both nonspecific and specific RNA results in a modulation of the tail configurations, which respond in an RNA length-dependent manner. Not only does the disordered NTD increase affinity for RNA, but mutations that occur in the Omicron variant modulate the interactions, indicating a functional role of the disordered tail. Finally, we found that the NTD-RBD preferentially interacts with single-stranded RNA and that the resulting protein:RNA complexes are flexible and dynamic. We speculate that this mechanism of interaction enables the Nucleocapsid protein to search the viral genome for and bind to high-affinity motifs.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jasmine Cubuk", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Jhullian J Alston", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "J Jerem\u00edas Incicco", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Alex S Holehouse", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Kathleen B Hall", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Melissa D Stuchell-Brereton", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Andrea Soranno", + "author_inst": "Washington University in St Louis" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.02.13.528205", "rel_title": "Regulatory T Cell-like Response to SARS-CoV-2 in Jamaican Fruit Bats Transduced with Human ACE2", @@ -98842,61 +99442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.02.08.23285645", - "rel_title": "Mental health, gender, and care-seeking behavior during the COVID-19 pandemic in Sweden: An exploratory study", - "rel_date": "2023-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285645", - "rel_abs": "ObjectiveTo explore the prevalence of care-seeking avoidance behavior in relation to gender and to describe the effect of (and potential interaction between) gender and care-seeking on mental health during the COVID-19 pandemic in Sweden.\n\nMethodsWe performed a cross-sectional study among 27,562 participants of the Omtanke2020 Study, using data collected at three time points concerning sociodemographic factors, mental health symptoms, and care-seeking behavior. Network analysis and prevalence ratios calculated from modified Poisson regressions were used to explore the relationship between gender, care-seeking behavior, and mental health symptoms (depression, anxiety, and COVID-19-related distress).\n\nResultsIn our study, women reported a higher prevalence of mental health symptoms and avoidance of care-seeking due to COVID-19, compared to men. At baseline and six months thereafter, female gender was positively associated with COVID-19-related distress and previous mental health diagnosis. At 12 months after baseline, female gender was positively associated with anxiety and avoidance of care-seeking for mental health. However, previous mental health diagnosis and care avoidance were more strongly associated with a higher prevalence of mental health symptoms among men, compared to women.\n\nConclusionThis study highlights gender differences in mental health outcomes and care-seeking behavior during the COVID-19 pandemic in Sweden.\n\nFundingThis work was supported with grants from Nordforsk (COVIDMENT, 105668 and 138929).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Katalin Vincze", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Gillian Murphy", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Mary Barker", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anna K K\u00e4hler", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Emma M Frans", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Patrick F Sullivan", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden; Department of Psychiatry, University of North Carolina, Chapel Hill," - }, - { - "author_name": "Unnur A Valdimarsd\u00f3ttir", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center of Public Health Sciences, University of" - }, - { - "author_name": "Fang Fang", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anik\u00f3 Lovik", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Unit of Methodology and Statistics, Department " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.08.23285589", "rel_title": "Clinical severity prediction of COVID-19 admitted patients in Spain: SEMI and REDISSEC cohorts", @@ -99590,6 +100135,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.10.528032", + "rel_title": "SARS-CoV-2 NSP5 Antagonizes the MHC II Antigen Presentation Pathway by Hijacking Histone Deacetylase 2", + "rel_date": "2023-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.10.528032", + "rel_abs": "SARS-CoV-2 interferes with antigen presentation by downregulating MHC II on antigen presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. This downregulation of CIITA is independent of NSP5s proteolytic activity, and rather, NSP5 delivers HDAC2 to the CIITA promoter via an IRF3-dependent mechanism. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 can limit MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nima Taefehshokr", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Alex Lac", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Angela M Vrieze", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Brandon H Dickson", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Peter N Guo", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Catherine Jung", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Eoin N Blythe", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Corby Fink", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Jimmy D Dikeakos", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Gregory A Dekaban", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Bryan Heit", + "author_inst": "University of Western Ontario" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.02.09.527892", "rel_title": "Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2", @@ -100596,33 +101200,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.02.08.23285651", - "rel_title": "Individual costs and societal benefits of interventions during the COVID-19 pandemic", - "rel_date": "2023-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285651", - "rel_abs": "Individual and societal reactions to an ongoing pandemic can lead to social dilemmas: In some cases, each individual is tempted to not follow an intervention, but for the whole society it would be best if they did. Now that in most countries the extent of regulations to reduce SARS-CoV-2 transmission is very small, interventions are driven by individual decision-making. Assuming that individuals act in their best own interest, we propose a framework in which this situation can be quantified, depending on the protection the intervention provides to a user and to others, the risk of getting infected, and the costs of the intervention. We discuss when a tension between individual and societal benefits arises and which parameter comparisons are important to distinguish between different regimes of intervention use.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Arne Traulsen", - "author_inst": "MPI Evolutionary Biology" - }, - { - "author_name": "Simon A Levin", - "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University" - }, - { - "author_name": "Chadi M Saad-Roy", - "author_inst": "University of California Berkeley, Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.02.23285352", "rel_title": "Safety, Virology, Pharmacokinetics, and Clinical Experience of High-dose Intravenous Sotrovimab for the Treatment of Mild to Moderate COVID-19: An Open-label Clinical Trial", @@ -101348,6 +101925,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2023.02.04.23285479", + "rel_title": "Understanding the Impact of Social Engagement Activities, Health Protocol Maintenance, and Social Interaction on Depression During Covid-19 Pandemic Among Older Americans", + "rel_date": "2023-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.04.23285479", + "rel_abs": "ObjectivesDepression is a critical public health concern among older Americans. However, little is known about how older adults social engagement activities, health protocol maintenance, and social interaction (both physically and virtually) potentially contribute to their feelings of depression.\n\nMethodsData were collected from the Covid-19 supplement to the National Health and Aging Trend Study (NHATS) and core longitudinal follow-up study. A total of 3,181 Medicare-eligible older adults between June and December 2020 were examined how self-reported depression is related to social engagement activities, health protocols, social interaction with friends and family (F&F), and doctors using multiple logistic regression.\n\nResultsThis study reveals that the lack of social engagement activities, such as birthday parties and long-term care visits significantly contributes to older adults depression (OR: 1.34, 90% CI: 1.07-1.68, p=0.012, and OR: 1.28, 90% CI: 1.01-1.65, p=0.053 respectively). Subsequently, health protocols compliance with washing hands and wearing masks in public places were more likely 2.36 times and 3.44 times higher symptoms of depression for the older adults than those who were not maintaining those protocols (OR: 2.36, 90% CI: 1.24-4.57, p=0.009, OR: 3.44, 90% CI: 1.97-6.17, p<0.001 respectively). Furthermore, the lack of virtual social interaction via phone and text message with F&F is significantly related to depression whereas email or video call are not significantly related to depression for older adults. During Covid-19 pandemic, in-person visits with doctors significantly reduced patients depression on the other hand email communication significantly increased. However other virtual interactions with doctors did not significantly associate with patients depression.\n\nConclusionThe lack of social engagement, maintaining health protocols, and lacking virtual interactions over the phone significantly increase depression symptoms for older adults during the Covid-19 pandemic. Therefore, it would be beneficial to take initiative to engage older adults in a variety of social activities to make them feel more connected to their community. The older population should be contacted by phone during the Covid-19 pandemic with encouraging messages and informed of the importance of maintaining health protocols.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Roungu Ahmmad", + "author_inst": "University of Mississippi Medical Center, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.02.03.23285405", "rel_title": "Predicting COVID-19 case status from self-reported symptoms and behaviors using data from a massive online survey", @@ -102354,29 +102950,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.02.03.526970", - "rel_title": "Epidemic patterns of emerging variants with dynamical social distancing", - "rel_date": "2023-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.03.526970", - "rel_abs": "Motivated by the emergence of new variants during the COVID-19 pandemic, we consider an epidemiological model of disease transmission dynamics, where novel strains appear by mutations of the virus. In the considered scenarios, disease prevalence in the population is modulated by social distancing. We study the various patterns that are generated under different assumptions of cross-immunity. If recovery from a given strain provides immunity against all previous strains, but not against more novel strains, then we observe a very regular sequential pattern of strain replacement where newer strains predominate over older strains. However, if protection upon recovery holds only against that particular strain and none of the others, we find much more complicated dynamics with potential recurrence of earlier strains, and co-circulation of various strains. We compare the observed patterns with genomic analysis we have seen during the COVID-19 pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Golsa Sayyar", - "author_inst": "University of Szeged" - }, - { - "author_name": "Gergely Rost", - "author_inst": "University of Szeged" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2023.02.02.526749", "rel_title": "Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic", @@ -103262,6 +103835,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.01.23284949", + "rel_title": "Determinants of COVID-19 vaccine uptake in the Netherlands: an ecological analysis", + "rel_date": "2023-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.01.23284949", + "rel_abs": "BackgroundWhile overall COVID-19 vaccine uptake is high in the Netherlands, it lags behind in certain subpopulations.\n\nAimWe aimed to identify determinants associated with COVID-19 vaccine uptake at neighbourhood level to inform the strategy to improve uptake and guide research into barriers for vaccination. We focused on those aged 50 years and older, since they are at highest risk of severe disease.\n\nMethodsWe performed an ecological study using national vaccination register and socio-demographic data at neighbourhood level. Using univariate and multivariable generalized additive models we examined the (potentially non-linear) effect of each determinant on uptake.\n\nResultsIn those over 50 years of age, a higher proportion of individuals with a non-Western migration background and higher voting proportions for right-wing Christian and conservative political parties were at neighbourhood level univariately associated with lower COVID-19 vaccine uptake. In contrast, higher socioeconomic status and higher voting proportions for right-wing liberal, progressive liberal and Christian middle political parties were associated with higher uptake. Multivariable results differed from univariate results in that a higher voting proportion for progressive left-wing political parties was also associated with higher uptake. In addition, with regard to migration background only a Turkish background remained significant.\n\nConclusionWe identified determinants associated with COVID-19 vaccine uptake at neighbourhood level and observed heterogeneity between different subpopulations. Since the goal of the vaccination campaign is not only to reduce suffering and death by improving the average uptake, but also to reduce health inequity, it is important to focus on these hard-to-reach populations.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lisanne J.E. Labuschagne", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Naomi Smorenburg", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Jan van de Kassteele", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Ben Bom", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Anne de Weerdt", + "author_inst": "Public Health and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Susan Hahne", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.01.23285322", "rel_title": "Household Hardships during the COVID-19 Pandemic: Examining Household Vulnerability and Responses to Pandemic Related Shocks in Eastern Ethiopia", @@ -104372,61 +104988,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.29.23285159", - "rel_title": "Probable transmission of SARS-CoV-2 from an African lion to zoo employees", - "rel_date": "2023-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285159", - "rel_abs": "Animal to human transmission of SARS-CoV-2 has not previously been reported in a zoo setting. A vaccinated African lion with physical limitations requiring hand feeding tested positive for SARS-CoV-2 after development of respiratory signs. Zoo employees were screened, monitored prospectively for development of symptoms, then re-screened as indicated, with confirmation by RT-PCR and whole-genome virus sequencing when possible. Trace-back investigation narrowed the source of infection to one of five people. Three exposed employees subsequently developed symptoms, two with viral genomes identical to the lions. Forward contact tracing investigation confirmed probable lion-to-human transmission.\n\nClose contact with large cats is a risk factor for bidirectional zoonotic SARS-CoV-2 transmission that should be considered when occupational health and biosecurity practices at zoos are designed and implemented. SARS-CoV-2 rapid testing and detection methods in big cats and other susceptible animals should be developed and validated to facilitate timely implementation of One Health investigations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Audrey A Siegrist", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Kira L Richardson", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Ria R Ghai", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Brian Pope", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jamie Yeadon", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Betsy Culp", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Casey Barton Behravesh", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Lixia Liu", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jennifer A Brown", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Leslie Boyer", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.30.526314", "rel_title": "Fitness effects of mutations to SARS-CoV-2 proteins", @@ -105064,6 +105625,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.27.23285032", + "rel_title": "Geotemporal analysis of COVID-19 in the Dominican Republic 2020-2021", + "rel_date": "2023-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.27.23285032", + "rel_abs": "IntroductionCoronavirus disease (COVID-19) was first identified in China in December of 2019 and has spread globally since. The Dominican Republic confirmed its first case on March 1st, 2020.\n\nObjectiveTo analyze the spatial distribution of the incidence of COVID-19 and its correlation with the Human Development Index in the Dominican Republic from March of 2020 to March of 2021.\n\nMethodsThe cumulative incidence rates of COVID-19, number of deaths, lethality, mortality and Human Development Index of the provinces in the Dominican Republic were used from governmental sources and were analyzed in the Microsoft Excel 2016 program.\n\nResultsDuarte was the province with the highest mortality per 100.000 inhabitants (68.94), followed by the Distrito Nacional (71,613 cases), Santo Domingo (49,759 cases) and Santiago (27,632 cases) with the highest number of cases. The 7-day moving average peak for new cases was July 30 of 2020 and the peak for new deaths occurred on September 6 of 2020. The highest positivity rate (40%) was reported in August of 2020. Lastly, an increase of 1.0 on the Human Development Index corresponded to a 10.7% increase in the incidence rates per province.\n\nConclusionPrevention strategies should be strengthened by the Dominican government to reduce the contagion curve and thus reduce its spread and impact on the Human Development Index", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andreina Moreno", + "author_inst": "Hospital Pediatrico Dr. Hugo Mendoza" + }, + { + "author_name": "Carla Gonzalez", + "author_inst": "Hospital Pediatrico Dr. Hugo Mendoza" + }, + { + "author_name": "Lilian Pimentel", + "author_inst": "Hospital Pediatrico Dr. Hugo Mendoza" + }, + { + "author_name": "Manuel Emilio Colome-Hidalgo", + "author_inst": "Hospital Pediatrico Dr. Hugo Mendoza" + }, + { + "author_name": "Demian Arturo DAHM Herrera Morban", + "author_inst": "Hospital Pediatrico Dr. Hugo Mendoza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.27.23285063", "rel_title": "Ethical Issues in Residency Education Related to the COVID-19 Pandemic: A Narrative Inquiry Study", @@ -106198,81 +106794,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2023.01.25.23284428", - "rel_title": "Primary care coding activity related to the use of online consultation systems or remote consulting: an analysis of 53 million peoples' health records using OpenSAFELY", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.25.23284428", - "rel_abs": "BackgroundThe pandemic accelerated work by the NHS in England to enable and stimulate use of online consultation systems across all practices, for improved access to primary care.\n\nObjectiveWe aimed to explore general practice coding activity associated with the use of online consultation systems in terms of trends, COVID-19 effect, variation and quality.\n\nMethodsWith the approval of NHS England, OpenSAFELY-TPP and OpenSAFELY-EMIS were used to query and analyse in situ records of electronic health record systems of over 53 million patients in over 6,400 practices, mainly in 2019-2020. SNOMED CT codes relevant to online consultation systems and written online consultations were identified. Coded events were described by volumes, practice coverage, trends pre- and post-COVID-19 and inter-practice and sociodemographic variation.\n\nResults3,550,762 relevant coding events were found in TPP practices, with code eConsultation detected in 84% of practices. Coding activity related to digital forms of interaction increased rapidly from March 2020 at the onset of the COVID-19 pandemic, though we found large variation in coding instance rates among practices in England. Code instances were more commonly found among females, those aged 18-40, those least deprived or white. eConsultation coded activity was more commonly found recorded among patients with a history of asthma or depression.\n\nConclusionsWe successfully queried general practice coding activity relevant to the use of online consultation systems, showing increased adoption as well as key areas of variation during the COVID-19 pandemic. The work can be expanded to support monitoring of coding quality and underlying activity. In future, large-scale impact evaluation studies can be implemented within the platform, namely looking at resource utilisation and patient outcomes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Martina Fonseca", - "author_inst": "NHS England" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - }, - { - "author_name": "Caroline E Walters", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan Pearson", - "author_inst": "NHS England" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ofra Koffman", - "author_inst": "NHS England" - }, - { - "author_name": "Minal Bakhai", - "author_inst": "NHS England" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.01.24.23284885", "rel_title": "Impact of vaccination and risk factors on COVID-19 mortality amid delta surge in Libya: a single centre cohort study", @@ -106902,6 +107423,193 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.23.23284848", + "rel_title": "Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children", + "rel_date": "2023-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.23.23284848", + "rel_abs": "BackgroundCOVID-19 is a complex multisystem disease, frequently associated with kidney injury. Since the beginning of the COVID-19 pandemic, we observed a striking increase in the incidence of acute tubulointerstitial nephritis (aTIN) without or with uveitis (TINUs) among children. This prompted us to examine whether SARS-CoV-2 might be the underlying trigger.\n\nMethodsWe conducted a French nationwide retrospective cohort study. We included all consecutive children diagnosed with aTIN or TINUs of undetermined cause between April-2020 and March-2021. SARS-CoV-2 antibody responses were tested by a luciferase immunoprecipitation system and compared to age-matched controls. Immunohistochemistry, immunofluorescence and molecular microbiology analyses were performed on kidney biopsies.\n\nResultsForty-eight children were included with a median age at diagnosis of 14.7 years (9.4-17.6). aTIN and TINUs incidence rates increased 3-fold and 12-fold, respectively, compared to pre-pandemic years. All patients had impaired kidney function with a median eGFR of 31.9 ml/min/1.73m{superscript 2} at diagnosis. Kidney biopsies showed lesions of acute tubulointerstitial nephritis and 25% of patients had fibrosis. No patient had concomitant acute COVID-19. All 16 children tested had high anti-N IgG titers and one had anti-S IgGs. Next-generation sequencing failed to detect any infectious agents in kidney biopsies. However, SARS-CoV-2 RNA was detected by PCR in two kidney samples supporting a potential direct link between SARS-CoV-2 and aTIN/TINUs.\n\nConclusionsWe describe a novel form of post-acute COVID-19 syndrome in children, unique in its exclusive kidney and eye involvement, and its distinctive anti-SARS-CoV-2 N+/S-serological profile. Our results support a causal association linking SARS-CoV-2 infection to this newly-reported burst of renal/eye inflammation.", + "rel_num_authors": 43, + "rel_authors": [ + { + "author_name": "Marina Avramescu", + "author_inst": "Pediatric Nephrology, MARHEA Reference Center, INSERM U1163, Imagine Institute, Paris Cite University, Necker-Enfants Malades Hospital, APHP, Paris, France" + }, + { + "author_name": "Pierre Isnard", + "author_inst": "Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France" + }, + { + "author_name": "Sarah Temmam", + "author_inst": "Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France" + }, + { + "author_name": "Agnes Chevalier", + "author_inst": "Department of Pediatric Nephrology, Arnaud-de-Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France" + }, + { + "author_name": "Paul Bastard", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France; Paris Cite " + }, + { + "author_name": "Mikael Attia", + "author_inst": "Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France" + }, + { + "author_name": "Romain Berthaud", + "author_inst": "Pediatric Nephrology, MARHEA Reference Center, INSERM U1163, Imagine Institute, Paris Cite University, Necker-Enfants Malades Hospital, APHP, Paris, France" + }, + { + "author_name": "Marc Fila", + "author_inst": "Department of Pediatric Nephrology, Arnaud-de-Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France." + }, + { + "author_name": "Claire Dossier", + "author_inst": "Department of Pediatric Nephrology, Robert Debre Hospital, Paris Cite University, Paris, France" + }, + { + "author_name": "Julien Hogan", + "author_inst": "Department of Pediatric Nephrology, Robert Debre Hospital, Paris Cite University, Paris, France" + }, + { + "author_name": "Tim Ulinski", + "author_inst": "Department of Pediatric Nephrology, Armand Trousseau Hospital, Paris, France" + }, + { + "author_name": "Damia Leguevaques", + "author_inst": "Department of Pediatric Nephrology, CHRU de Lille, Lille, France" + }, + { + "author_name": "Ferielle Louillet", + "author_inst": "Department of Pediatrics, Rouen University Hospital, F 76000, Rouen, France" + }, + { + "author_name": "Edouard Martinez Casado", + "author_inst": "Department of Pediatrics, Rouen University Hospital, F 76000, Rouen, France" + }, + { + "author_name": "Jean-Michel Halimi", + "author_inst": "Department of Adult Nephrology, CHRU de Tours, Tours, France." + }, + { + "author_name": "Sylvie Cloarec", + "author_inst": "Department of Pediatric Nephrology, Clocheville Hospital, CHRU de Tours, Tours, France." + }, + { + "author_name": "Ariane Zaloszyc", + "author_inst": "Department of Pediatric Nephrology, CHU de Strasbourg, Strasbourg, France." + }, + { + "author_name": "Camille Faudeux", + "author_inst": "Department of Pediatrics, Pediatric Nephrology unit, L'Archet Hospital, University Hospital of Nice, Nice, France." + }, + { + "author_name": "Caroline Rousset-Rouviere", + "author_inst": "Department of Multidisciplinary Pediatrics, Pediatric Nephrology Unit, APHM, Marseille, France." + }, + { + "author_name": "Stephanie Clave", + "author_inst": "Department of Multidisciplinary Pediatrics, Pediatric Nephrology Unit, APHM, Marseille, France." + }, + { + "author_name": "Jerome Harambat", + "author_inst": "Department of Pediatrics, Pediatric Nephrology Unit, SoRare Reference Center, Bordeaux University Hospital, Bordeaux, France." + }, + { + "author_name": "Edouard Rollot", + "author_inst": "Department of Pediatrics, Pediatric Nephrology Unit, SoRare Reference Center, Bordeaux University Hospital, Bordeaux, France." + }, + { + "author_name": "Thomas Simon", + "author_inst": "Department of Pediatric Nephrology, SoRare Reference Center, Toulouse University Hospital, Toulouse, France." + }, + { + "author_name": "Megan Nallet-Amate", + "author_inst": "Pediatric Department, Dijon University Hospital, Dijon, France." + }, + { + "author_name": "Bruno Ranchin", + "author_inst": "Pediatric Nephrology Unit, Nephrogones reference center, Hopital Femme Mere Enfant, Hospices Civils de Lyon, European Rare Kidney Disease Reference Network cent" + }, + { + "author_name": "Justine Bacchetta", + "author_inst": "Pediatric Nephrology Unit, Nephrogones reference center, Hopital Femme Mere Enfant, Hospices Civils de Lyon, European Rare Kidney Disease Reference Network cent" + }, + { + "author_name": "Florence Porcheret", + "author_inst": "Pediatric Department, Nantes University Hospital, Nantes, France." + }, + { + "author_name": "Josselin Bernard", + "author_inst": "Pediatric Department, Nantes University Hospital, Nantes, France." + }, + { + "author_name": "Amelie Ryckewaert", + "author_inst": "Department of Pediatric Nephrology, CHU de Rennes, Rennes, France." + }, + { + "author_name": "Anne Jamet", + "author_inst": "Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Paris Cite University, Paris, France." + }, + { + "author_name": "Jacques Fourgeaud", + "author_inst": "Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Paris Cite University, Paris, France." + }, + { + "author_name": "Nicolas Da Rocha", + "author_inst": "Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France" + }, + { + "author_name": "Philippe Perot", + "author_inst": "Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France." + }, + { + "author_name": "Nicolas Kuperwasser", + "author_inst": "Paris Cite University, INSERM U1151, CNRS UMR 8253, Necker Enfants Malades Institute, Department Croissance et Signalisation , Paris, France" + }, + { + "author_name": "Naim Bouazza", + "author_inst": "EA 7323, Universite Paris, Pharmacologie et evaluations therapeutiques chez l'enfant et la femme enceinte. Unite de Recherche Clinique, Hopital Tarnier, Paris, " + }, + { + "author_name": "Marion Rabant", + "author_inst": "Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France" + }, + { + "author_name": "Jean-Paul Duong Van Huyen", + "author_inst": "Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France" + }, + { + "author_name": "Matthieu P Robert", + "author_inst": "Department of Ophthalmology, Necker-Enfants Malades Hospital, APHP, Paris Cite University, Paris, France." + }, + { + "author_name": "Julien Zuber", + "author_inst": "Department of Nephrology and Kidney Transplantation, Necker-Enfants Malades Hospital, APHP, Paris Cite University, Paris, France." + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker-Enfants Malades Hospital, Paris, France; Paris Cite " + }, + { + "author_name": "marc eloit", + "author_inst": "institut pasteur" + }, + { + "author_name": "Isabelle Sermet-Gaudelus", + "author_inst": "INSERM" + }, + { + "author_name": "Olivia Boyer", + "author_inst": "Pediatric Nephrology, MARHEA Reference Center, INSERM U1163, Imagine Institute, Paris Cite University, Necker-Enfants Malades Hospital, APHP, Paris, France." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2023.01.24.23284980", "rel_title": "Estimations of SARS-CoV-2 endemic characteristics", @@ -108016,33 +108724,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.23.525275", - "rel_title": "Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting", - "rel_date": "2023-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.23.525275", - "rel_abs": "Many positive-strand RNA viruses, including all known coronaviruses, employ programmed -1 ribosomal frameshifting (-1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate -1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced -1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced -1 PRF in vitro and in cells. Consistent with the crucial role of efficient -1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells. Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lian-Huan Wei", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Yu Sun", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Junjie U. Guo", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.01.24.525203", "rel_title": "Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.", @@ -108676,6 +109357,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.01.22.23284880", + "rel_title": "COVision: Convolutional Neural Network for the Differentiation of COVID-19 from Common Pulmonary Conditions using CT Scans", + "rel_date": "2023-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.22.23284880", + "rel_abs": "With the growing amount of COVID-19 cases, especially in developing countries with limited medical resources, it is essential to accurately and efficiently diagnose COVID-19. Due to characteristic ground-glass opacities (GGOs) and other types of lesions being present in both COVID-19 and other acute lung diseases, misdiagnosis occurs often: 26.6% of the time in manual interpretations of CT scans. Current deep-learning models can identify COVID-19 but cannot distinguish it from other common lung diseases like bacterial pneumonia. Concretely, COVision is a deep-learning model that can differentiate COVID-19 from other common lung diseases, with high specificity using CT scans and other clinical factors. COVision was designed to minimize overfitting and complexity by decreasing the number of hidden layers and trainable parameters while still achieving superior performance. Our model consists of two parts: the CNN which analyzes CT scans and the CFNN (clinical factors neural network) which analyzes clinical factors such as age, gender, etc. Using federated averaging, we ensembled our CNN with the CFNN to create a comprehensive diagnostic tool. After training, our CNN achieved an accuracy of 95.8% and our CFNN achieved an accuracy of 88.75% on a validation set. We found a statistical significance that COVision performs better than three independent radiologists with at least 10 years of experience, especially in differentiating COVID-19 from pneumonia. We analyzed our CNN activation maps through Grad-CAMs and found that lesions in COVID-19 presented peripherally, closer to the pleura, whereas pneumonia lesions presented centrally.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kush Parikh", + "author_inst": "Troy High School" + }, + { + "author_name": "Timothy Josh Mathew", + "author_inst": "Troy High School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2023.01.22.23284878", "rel_title": "Wastewater-based surveillance can be used to model COVID-19-associated workforce absenteeism", @@ -109778,77 +110482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2023.01.16.23284626", - "rel_title": "High proportion of Ugandans with pre-pandemic SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell responses", - "rel_date": "2023-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284626", - "rel_abs": "The estimated mortality rate of the SARS-CoV-2 pandemic varied greatly around the world with multiple countries in East, Central, and West Africa having significantly lower rates of COVID-19 related fatalities than many resource-rich nations with significantly earlier wide-spread access to life-saving vaccines. One possible reason for this lower mortality could be the presence of pre-existing cross-reactive immunological responses in these areas of the world. To explore this hypothesis, stored peripheral blood mononuclear cells (PBMC) from Ugandans collected from 2015-2017 prior to the COVID-19 pandemic (n=29) and from hospitalized Ugandan COVID-19 patients (n=3) were examined using flow-cytometry for the presence of pre-existing SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell populations using four T-cell epitope mega pools. Of pre-pandemic participants, 89.7% (26/29) had either CD4+ or CD8+, or both, SARS-CoV-2 specific T-cell responses. Specifically, CD4+ T-cell reactivity (72.4%) and CD8+ T-cell reactivity (65.5%) were relatively similar, and 13 participants (44.8%) had both types of cross-reactive types of T-cells present. There were no significant differences in response by sex in the population. The rates of cross-reactive T-cell populations in these Ugandans is higher than previous estimates from resource-rich countries like the United States (20-50% reactivity). It is unclear what role, if any, this cross-reactivity played in decreasing COVID-19 related mortality in Uganda and other African countries, but does suggest that a better understanding of global pre-existing immunological cross-reactivity could be an informative data of epidemiological intelligence moving forward.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Annemarie Namuniina", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Enoch S Muyanja", - "author_inst": "Emory University" - }, - { - "author_name": "Victoria M Biribawa", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Brenda A Okech", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Aloysious Ssemaganda", - "author_inst": "University of Manitoba Max Rady College of Medicine" - }, - { - "author_name": "Matt A Price", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Nancy Hills", - "author_inst": "UCSF: University of California San Francisco" - }, - { - "author_name": "Ann Nanteza", - "author_inst": "Makerere University" - }, - { - "author_name": "Bernard Ssentalo Bagaya", - "author_inst": "Makerere University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Catherine Riou", - "author_inst": "UCT Faculty of Health Sciences: University of Cape Town Faculty of Health Sciences" - }, - { - "author_name": "Steven J Reynolds", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Ronald M Galwango", - "author_inst": "RHSP: Rakai Health Sciences Program" - }, - { - "author_name": "Andrew Davidson Redd", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.20.23284812", "rel_title": "Immunogenicity, Safety and Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA Vaccination in Immunocompromised Adolescents and Young Adults: A systematic Review and Meta-Analyses", @@ -110490,6 +111123,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.18.524660", + "rel_title": "SARS-CoV-2 Omicron XBB.1.5 may be a cautionary variant by in silico study", + "rel_date": "2023-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.18.524660", + "rel_abs": "In this research, we aimed to predict the relative risk of the recent new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the basis of our previous research. We first performed molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) to determine the binding affinities to human cells of three new variants of SARS-CoV-2: Omicron BQ.1, XBB, and XBB.1.5 We then investigated the three variants to discover the evolutionary distance of the spike protein gene (S gene) from the Wuhan, Omicron BA.1, and Omicron BA.4/5 variants, to understand the changes in the S gene.\n\nThe results indicated that the XBB.1.5 variant had the highest binding affinity of the spike protein with ACE2 and the longest evolutionary distance of the S gene. This in silico evidence suggested that the XBB.1.5 variant may produce infections that spread more widely and faster than can infections of preexisting variants.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Aki Sugano", + "author_inst": "Toyama University Hospital" + }, + { + "author_name": "Haruyuki Kataguchi", + "author_inst": "Toyama University Hospital" + }, + { + "author_name": "Mika Ohta", + "author_inst": "Toyama University Hospital" + }, + { + "author_name": "Yoshiaki Someya", + "author_inst": "Toyama University Hospital" + }, + { + "author_name": "Shigemi Kimura", + "author_inst": "Kobe University Graduate School of Medicine" + }, + { + "author_name": "Yoshimasa Maniwa", + "author_inst": "Kobe University Graduate School of Medicine" + }, + { + "author_name": "Toshihide Tabata", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yutaka Takaoka", + "author_inst": "Toyama University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.01.19.23284768", "rel_title": "Trajectories of COVID-19: a longitudinal analysis of many nations and subnational regions", @@ -111620,61 +112300,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.01.18.524384", - "rel_title": "Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung", - "rel_date": "2023-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.18.524384", - "rel_abs": "Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated depletion of specific epithelial cell types and GFP-labeling of dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncovered new cell types, some of which likely represent epithelial precursors, propose goblet cells as progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also found that DTA-expressing cells can persist in the lung, express specific inflammatory factors, and resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to defined epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Leila R Martins", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lina Sieverling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Michelle Michelhans", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Chiara Schiller", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Cihan Erkut", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Sergio Triana", - "author_inst": "European Molecular Biology Laboratory (EMBL), Heidelberg, Germany" - }, - { - "author_name": "Stefan Froehling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lars Velten", - "author_inst": "Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain." - }, - { - "author_name": "Hanno Glimm", - "author_inst": "National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germ" - }, - { - "author_name": "Claudia Scholl", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.01.17.524469", "rel_title": "A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease", @@ -112364,6 +112989,165 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.16.524211", + "rel_title": "The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis", + "rel_date": "2023-01-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.16.524211", + "rel_abs": "Children infected with SARS-CoV-2 rarely progress to respiratory failure, but the risk of mortality in infected people over 85 years of age remains high, despite vaccination and improving treatment options. Here, we take a comprehensive, multidisciplinary approach to investigate differences in the cellular landscape and function of paediatric (<11y), adult (30- 50y) and elderly (>70y) nasal epithelial cells experimentally infected with SARS-CoV-2. Our data reveal that nasal epithelial cell subtypes show different tropism to SARS-CoV-2, correlating with age, ACE2 and TMPRSS2 expression. Ciliated cells are a viral replication centre across all age groups, but a distinct goblet inflammatory subtype emerges in infected paediatric cultures, identifiable by high expression of interferon stimulated genes and truncated viral genomes. In contrast, infected elderly cultures show a proportional increase in ITGB6hi progenitors, which facilitate viral spread and are associated with dysfunctional epithelial repair pathways.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC=\"FIGDIR/small/524211v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (61K):\norg.highwire.dtl.DTLVardef@dab12aorg.highwire.dtl.DTLVardef@1a57334org.highwire.dtl.DTLVardef@12e7983org.highwire.dtl.DTLVardef@2bbe6e_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Maximillian Woodall", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Ana-Maria Cujba", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Kaylee B Worlock", + "author_inst": "UCL Respiratory, UCL, London" + }, + { + "author_name": "Katie-Marie Case", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Tereza Masonou", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Masahiro Yoshida", + "author_inst": "UCL Respiratory, UCL, London" + }, + { + "author_name": "Krzysztof Polanski", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Ni Huang", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Rik GH Lindeboom", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Lira Mamanova", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Liam Bolt", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Laura Richardson", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Samuel Ellis", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Machaela Palor", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Thomas Burgoyne", + "author_inst": "UCL Institute of Ophthalmology, University College London, London" + }, + { + "author_name": "Andreia Pinto", + "author_inst": "Royal Brompton Hospital, London" + }, + { + "author_name": "Dale A Moulding", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Timothy D. McHugh", + "author_inst": "UCL Centre for Clinical Microbiology, Royal Free Campus, London" + }, + { + "author_name": "Aarash Saleh", + "author_inst": "Royal Free Hospital NHS Foundation Trust, London" + }, + { + "author_name": "Eliz Kilich", + "author_inst": "University College London Hospitals NHS Foundation Trust, London" + }, + { + "author_name": "Puja Mehta", + "author_inst": "UCL Respiratory, UCL, London" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Department of Infectious Disease, Imperial College London, London" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, London" + }, + { + "author_name": "Paolo De Coppi", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Colin R Butler", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Heloise Vinette", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Sundando Roy", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Judith Breuer", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Rachel C Chambers", + "author_inst": "UCL Respiratory, UCL, London" + }, + { + "author_name": "Wendy E Heywood", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Kevin Mills", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Robert E Hynds", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Kerstin B Meyer", + "author_inst": "Wellcome Sanger Institute, Cambridge" + }, + { + "author_name": "Marko Z Nikolic", + "author_inst": "UCL Respiratory, UCL, London" + }, + { + "author_name": "Claire M Smith", + "author_inst": "UCL Great Ormond Street Institute of Child Health, London" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.01.15.524078", "rel_title": "SARS-CoV-2 Envelope protein triggers depression and dysosmia via TLR2 mediated neuroinflammation", @@ -113414,65 +114198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.10.523518", - "rel_title": "Anthracyclines inhibit SARS-CoV-2 infection", - "rel_date": "2023-01-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.10.523518", - "rel_abs": "Vaccines and drugs are two effective medical interventions to mitigate SARS-CoV-2 infection. Three SARS-CoV-2 inhibitors, remdesivir, paxlovid, and molnupiravir, have been approved for treating COVID-19 patients, but more are needed, because each drug has its limitation of usage and SARS-CoV-2 constantly develops drug resistance mutations. In addition, SARS-CoV-2 drugs have the potential to be repurposed to inhibit new human coronaviruses, thus help to prepare for future coronavirus outbreaks. We have screened a library of microbial metabolites to discover new SARS-CoV-2 inhibitors. To facilitate this screening effort, we generated a recombinant SARS-CoV-2 Delta variant carrying the nano luciferase as a reporter for measuring viral infection. Six compounds were found to inhibit SARS-CoV-2 at the half maximal inhibitory concentration (IC50) below 1 M, including the anthracycline drug aclarubicin that markedly reduced viral RNA-dependent RNA polymerase (RdRp)-mediated gene expression, whereas other anthracyclines inhibited SARS-CoV-2 by activating the expression of interferon and antiviral genes. As the most commonly prescribed anti-cancer drugs, anthracyclines hold the promise of becoming new SARS-CoV-2 inhibitors.\n\nIMPORTANCEMicrobial metabolites are a rich source of bioactive molecules. The best examples are antibiotics and immunosuppressants that have transformed the practice of modern medicine and saved millions of lives. Recently, some microbial metabolites were reported to have antiviral activity, including the inhibition of Zika virus and Ebola virus. In this study, we discovered several microbial metabolites that effectively inhibit SARS-CoV-2 infection, including anthracyclines that have also been shown to inhibit other viruses including Ebola virus through enhancing interferon responses, which indicates potentially broad antiviral properties of these microbial metabolites and can lead to the discovery of pan-antiviral molecules.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zhen Wang", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Qinghua Pan", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Ling Ma", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jianyuan Zhao", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Fiona McIntosh", - "author_inst": "Research Institute of the McGill University Health Centre" - }, - { - "author_name": "Zhenlong Liu", - "author_inst": "McGill University" - }, - { - "author_name": "Shilei Ding", - "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Rongtuan Lin", - "author_inst": "Lady Davis Institute for Medical Research, McGill University" - }, - { - "author_name": "Cen Shan", - "author_inst": "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Chen Liang", - "author_inst": "Lady Davis Institute for Medical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.01.12.23284481", "rel_title": "Data-driven Targeting of COVID-19 Vaccination Programs: An Analysis of the Evidence on Impact, Implementation, Ethics and Equity", @@ -114162,6 +114887,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.01.11.523649", + "rel_title": "Vectored Immunoprophylaxis and Treatment of SARS-CoV-2 Infection", + "rel_date": "2023-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.11.523649", + "rel_abs": "Vectored immunoprophylaxis was first developed as a means to establish engineered immunity to HIV through the use of an adeno-associated viral vector expressing a broadly neutralizing antibody. We have applied this concept to establish long-term prophylaxis against SARS-CoV-2 by adeno-associated and lentiviral vectors expressing a high affinity ACE2 decoy receptor. Administration of decoy-expressing AAV vectors based on AAV2.retro and AAV6.2 by intranasal instillation or intramuscular injection protected mice against high-titered SARS-CoV-2 infection. AAV and lentiviral vectored immunoprophylaxis was durable and active against recent SARS-CoV-2 Omicron subvariants. The AAV vectors were also effective when administered up to 24 hours post-infection. Vectored immunoprophylaxis could be of value for immunocompromised individuals for whom vaccination is not practical and as a means to rapidly establish protection from infection. Unlike monoclonal antibody therapy, the approach is expected to remain active despite continued evolution viral variants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Takuya Tada", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Belinda M Dcosta", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Julia Minnee", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Nathaniel R Landau", + "author_inst": "NYU Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.01.12.523465", "rel_title": "The natural tannins oligomeric proanthocyanidins and punicalagin are potent inhibitors of infection by SARS-CoV-2 in vitro", @@ -115136,65 +115892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.09.23284380", - "rel_title": "Effectiveness of an eHealth Intervention for Reducing Psychological Distress and Increasing COVID-19 Knowledge and Protective Behaviors among Ethnoracially Diverse Sexual and Gender Minority Adults: A Quasi-experimental Study (#SafeHandsSafeHearts)", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284380", - "rel_abs": "PurposeLesbian, gay, bisexual, transgender, queer, and other persons outside of heteronormative and cisgender identities (LGBTQ+) and ethnic/racial minority populations are at heightened vulnerability amid the Covid-19 pandemic. Systemic marginalization and resulting adverse social determinants of health contribute to health disparities among these populations that result in more severe consequences due to Covid-19 and the public health measures to control it. We developed and tested a tailored online intervention (#SafeHandsSafeHearts) to support ethnoracially diverse LGBTQ+ individuals in Toronto, Canada amid the pandemic.\n\nMethodsWe used a quasi-experimental pre-test post-test design to evaluate the effectiveness of a 3-session, peer-delivered eHealth intervention in reducing psychological distress and increasing Covid-19 knowledge and protective behaviors. Individuals [≥]18-years-old, resident in Toronto, and self-identified as sexual or gender minority were recruited online. Depressive and anxiety symptoms, Covid-19 knowledge and protective behaviors were assessed at baseline, 2-weeks postintervention, and 2-months follow-up. We used generalized estimating equations and zero-truncated Poisson models to evaluate the effectiveness of the intervention on the four primary outcomes.\n\nResultsFrom March to November 2021, 202 participants (median age, 27 years [Interquartile rage: 23-32]) were enrolled in #SafeHandsSafeHearts. Over half (54%, n=110) identified as cisgender lesbian or bisexual women or women who have sex with women, 26.2% (n=53) cisgender gay or bisexual men or men who have sex with men, and 19.3% (n=39) transgender or nonbinary individuals. The majority (75.7%, n=143) were Black and other people of color. The intervention led to statistically significant reductions in the prevalence of clinically significant depressive and anxiety symptoms, and increases in Covid-19 protective behaviors from baseline to postintervention.\n\nConclusionWe demonstrated the effectiveness of a brief, peer-delivered eHealth intervention for ethnoracially diverse LGBTQ+ communities in reducing psychological distress and increasing protective behaviors amid the Covid-19 pandemic. Implementation through community-based health services with trained peer educators supports feasibility, acceptability, and the importance of engaging ethnoracially diverse LGBTQ+ communities in pandemic response preparedness. This trial is registered with ClinicalTrials.gov, number NCT04870723.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Peter A. Newman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Venkatesan Chakrapani", - "author_inst": "Centre for Sexuality and Health Research and Policy" - }, - { - "author_name": "Notisha Massaquoi", - "author_inst": "University of Toronto Scarborough" - }, - { - "author_name": "Charmaine C. Williams", - "author_inst": "University of Toronto" - }, - { - "author_name": "Wangari Tharao", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Suchon Tepjan", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Surachet Roungprakhon", - "author_inst": "Rajamangala University of Technology Phra Nakhon" - }, - { - "author_name": "Joelleann Forbes", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Sarah Sebastian", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Pakorn Akkakanjanasupar", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Muna Aden", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.11.23284427", "rel_title": "Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients", @@ -115684,6 +116381,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.06.23284202", + "rel_title": "Long Covid symptoms and diagnosis in primary care: a cohort study using structured and unstructured data in The Health Improvement Network primary care database", + "rel_date": "2023-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284202", + "rel_abs": "BACKGROUNDLong Covid is a widely recognised consequence of COVID-19 infection, but little is known about the burden of symptoms that patients present with in primary care, as these are typically recorded only in free text clinical notes. Our objectives were to compare symptoms in patients with and without a history of COVID-19, and investigate symptoms associated with a Long Covid diagnosis.\n\nMETHODSWe used primary care electronic health record data from The Health Improvement Network (THIN), a Cegedim database. We included adults registered with participating practices in England, Scotland or Wales. We extracted information about 89 symptoms and Long Covid diagnoses from free text using natural language processing. We calculated hazard ratios (adjusted for age, sex, baseline medical conditions and prior symptoms) for each symptom from 12 weeks after the COVID-19 diagnosis.\n\nFINDINGSWe compared 11,015 patients with confirmed COVID-19 and 18,098 unexposed controls. Only 20% of symptom records were coded, with 80% in free text. A wide range of symptoms were associated with COVID-19 at least 12 weeks post-infection, with strongest associations for fatigue (adjusted hazard ratio (aHR) 3.99, 95% confidence interval (CI) 3.59, 4.44), shortness of breath (aHR 3.14, 95% CI 2.88, 3.42), palpitations (aHR 2.75, 95% CI 2.28, 3.32), and phlegm (aHR 2.88, 95% CI 2.30, 3.61). However, a limited subset of symptoms were recorded within 7 days prior to a Long Covid diagnosis in more than 20% of cases: shortness of breath, chest pain, pain, fatigue, cough, and anxiety / depression.\n\nCONCLUSIONNumerous symptoms are reported to primary care at least 12 weeks after COVID-19 infection, but only a subset are commonly associated with a GP diagnosis of Long Covid.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anoop Dinesh Shah", + "author_inst": "University College London" + }, + { + "author_name": "Anuradhaa Dinesh Subramanian", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jadene Lewis", + "author_inst": "University College London" + }, + { + "author_name": "Samir Dhalla", + "author_inst": "The Health Improvement Network Ltd." + }, + { + "author_name": "Elizabeth Ford", + "author_inst": "Brighton and Sussex Medical School" + }, + { + "author_name": "Shamil Haroon", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Valerie Kuan", + "author_inst": "University College London" + }, + { + "author_name": "Krishnarajah Nirantharakumar", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.09.23284297", "rel_title": "The importance of increasing primary vaccinationsagainst COVID-19 in Europe", @@ -116814,153 +117558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.05.23284214", - "rel_title": "The impact of the COVID-19 pandemic on Antipsychotic Prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: A federated analysis of 59 million patients primary care records in situ using OpenSAFELY", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.05.23284214", - "rel_abs": "BackgroundThe COVID-19 pandemic significantly affected health and social care services. We aimed to explore whether this impacted the prescribing rates of antipsychotics within at-risk populations.\n\nMethodsWith the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We then calculated the monthly prevalence of antipsychotic prescribing in the population, as well as the incidence of new prescriptions in each month over the study period (Jan 2019-Dec 2021).\n\nResultsThe average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30-83.19) in Q1 2019 to 90.1 (95% CI 89.68-90.60) in Q4 2021 and from 154.61 (95% CI 153.79-155.43) in Q1 2019 to 166.95 (95% CI 166.23-167.67) in Q4 2021 in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the average monthly rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29-123.66) in Q1 2019 to 119.29 (95% CI 118.68-119.91) in Q4 2021, and from 54.91 (95% CI 54.52-55.29) in Q1 2019 to 51.04 (95% CI 50.74-51.35) in Q4 2021 respectively.\n\nConclusionsDuring each of the lockdowns in 2020, we observed a significant spike in antipsychotic prescribing in the dementia and care home groups. We have shown that these peaks are likely due to prescribing of antipsychotics for palliative care purposes and may have been linked to pre-emptive prescribing, when on-site medical visits would have been restricted. Over the study period, we observed gradual increases in antipsychotic use in patients with dementia and in care homes and a decrease in their use in patients with learning disability or autism.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Orla Macdonald", - "author_inst": "Oxford Health NHS FT" - }, - { - "author_name": "Amelia Green", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Andrew Brown", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Ben Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Colm Andrews", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Shaun O'Hanlon", - "author_inst": "EMIS" - }, - { - "author_name": "Alex Eavis", - "author_inst": "EMIS" - }, - { - "author_name": "Richard Jarvis", - "author_inst": "EMIS" - }, - { - "author_name": "Dima Avramov", - "author_inst": "EMIS" - }, - { - "author_name": "Ian Wood", - "author_inst": "EMIS" - }, - { - "author_name": "Nasreen Parkes", - "author_inst": "EMIS" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.01.05.23284247", "rel_title": "Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals", @@ -117502,6 +118099,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.06.522977", + "rel_title": "Omicron Spike Protein Is Vulnerable to Reduction", + "rel_date": "2023-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.06.522977", + "rel_abs": "SARS-CoV-2 virus spike (S) protein is an envelope protein responsible for binding to the ACE2 receptor, driving subsequent entry into host cells. The existence of multiple disulfide bonds in the S protein makes it potentially susceptible to reductive cleavage. Using a tri-part split luciferase-based binding assay, we evaluated the impacts of chemical reduction on S proteins from different virus variants and found that those from the Omicron family are highly vulnerable to reduction. Through manipulation of different Omicron mutations, we found that alterations in the receptor binding module (RBM) are the major determinants of this vulnerability. Specifically we discovered that Omicron mutations facilitate the cleavage of C480-C488 and C379-C432 disulfides, which consequently impairs binding activity and protein stability. The vulnerability of Omicron S proteins suggests a mechanism that can be harnessed to treat specific SARS-CoV-2 strains.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Igor Stagljar", + "author_inst": "University of Toronto" + }, + { + "author_name": "Zhong Yao", + "author_inst": "University of Toronto" + }, + { + "author_name": "Betty Geng", + "author_inst": "University of Toronto" + }, + { + "author_name": "Edyta Marcon", + "author_inst": "University of Toronto" + }, + { + "author_name": "Shuye Pu", + "author_inst": "University of Toronto" + }, + { + "author_name": "Hua Tang", + "author_inst": "University of Toronto" + }, + { + "author_name": "John Merluza", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Alexander Bello", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Jamie Snider", + "author_inst": "University of Toronto" + }, + { + "author_name": "Ping Lu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Heidi Wood", + "author_inst": "Public Health Agency of Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.01.05.23284180", "rel_title": "Oral Azvudine (FNC) Tablets in Patients infected with SARS-CoV-2 Omicron Variant: A Retrospective Cohort Study", @@ -119156,45 +119812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.02.23284119", - "rel_title": "Participant Demographics and Testing Trends: A Community Pandemic Response Program", - "rel_date": "2023-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.02.23284119", - "rel_abs": "ObjectiveThis study aimed to identify demographic characteristics of test participants and changes in testing participation over time in a community pandemic-response program launched in a college town in California, USA.\n\nMethodsWe described overall testing participation, identified demographic characteristics of frequent testers, and evaluated changes in testing participation over four different periods of the COVID-19 pandemic.\n\nResultsA total of 770,165 tests were performed between November 18, 2020, and June 30, 2022, among 89,924 residents of Yolo County (41.1% of population), with significant participation from racially/ethnically diverse participants and across age groups. Most positive cases (49.9%) were captured during Omicron, which also corresponds to the period with the highest daily participation (895 per 100K population). The proportion of participants which we considered \"frequent testers\" (28.9% vs. 39.7%, p < 0.0001) and individuals that tested once (39.5% vs. 47.9%, p < 0.0001) increased significantly from Delta to Omicron. Women (58.8%), participants of age 19-34 years (38.8%), and White (53.2%) tested more frequently throughout the program. The proportion of tests conducted among Latinos remained steady around 18% over time, with the exception of the post-Omicron period (13%).\n\nConclusionThe unique features of a pandemic response program that supported communitywide access to free asymptomatic testing provides a unique opportunity to evaluate adherence to testing recommendations, and testing trends over time. Identification of individual and group-level factors associated with testing behaviors is essential to improve access and protect communities at-large.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yury E Garcia", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Leslie Solis", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Maria L Daza-Torres", - "author_inst": "University of California, Davis" - }, - { - "author_name": "J Cricelio Montesinos-Lopez", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Brad H Pollock", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Miriam Nuno", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.02.23284120", "rel_title": "The time between vaccination and infection impacts immunity against SARS-CoV-2 variants", @@ -119812,6 +120429,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.01.22284075", + "rel_title": "The illusion of personal health decisions for infectious disease management: disease spread in social contact networks", + "rel_date": "2023-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.01.22284075", + "rel_abs": "Close contacts between individuals provide opportunities for the transmission of diseases, including COVID-19. Individuals take part in many different types of interactions, including those with classmates, co-workers, and household members; the conglomeration of all of these interactions produces a complex social contact network interconnecting individuals across the population. Thus, while an individual might decide their own risk tolerance in response to a threat of infection, the consequences of such decisions are rarely so confined, propagating far beyond any one person. We asses the effect of different population-level risk-tolerance regimes, population structure in the form of age and household-size distributions, and different types of interactions on epidemic spread in plausible human contact networks to gain insight into how contact network structure affects pathogen spread through a population. In particular, we find that changes in behaviour of vulnerable individuals in isolation is insufficient to reduce those individuals infection risk, that population structure can have varied and counter-acting effects on epidemic outcomes, and that, in general, interactions among co-workers have a greater contribution to disease spread than do interactions among children at school. Taken together, these results promote a nuanced understanding of disease spread on contact networks, with implications for public health strategies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Matthew Michalska-Smith", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Eva Enns", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Lauren A White", + "author_inst": "National Socio-Environmental Synthesis Center, University of Maryland" + }, + { + "author_name": "Marie LJ Gilbertson", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Meggan E Craft", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.31.22284088", "rel_title": "Impaired humoral immunity to BQ.1.1 in convalescent and vaccinated patients", @@ -121054,53 +121706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.24.22283920", - "rel_title": "COVID-19 in Cambodia: Epidemiology, Response, and Lessons Learned, 27 January 2020 to 30 June 2022", - "rel_date": "2022-12-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.24.22283920", - "rel_abs": "As a member state of the International Health Regulation 2005, Cambodia has been continuously strengthening its capacity to respond to health emergencies and prevent the international spread of diseases. Despite this, Cambodias capacity to prevent, detect, and rapidly respond to public health threats remained limited at the onset of the pandemic. This paper describes epidemiological phases, response phases, strategy, and lessons learned in Cambodia between 27 January 2020 and 30 June 2022. We classified epidemiological phases in Cambodia into three phases, in which Cambodia responded using eight measures: (1) detect, isolate/quarantine; (2) face coverings, hand hygiene, and physical distancing measures; (3) risk communication and community engagement; (4) school closures; (5) border closures; (6) public event and gathering cancellation; (7) vaccination; and (8) lockdown. The measures corresponded to six strategies: (1) setting up and managing a new response system, (2) containing the spread with early response, (3) strengthening the identification of cases and contacts, (4) strengthening care for COVID-19 patients, (5) boosting vaccination coverage, and (6) supporting disadvantaged groups. Finally, ten lessons were learned for future health emergency responses. Findings suggest that Cambodia successfully contained the spread of SARS-CoV-2 in the first year and quickly attained high vaccine coverage by the second year of the response. The core of this success was the strong political will and high level of cooperation from the public. However, Cambodia needs to further improve its infrastructure for quarantining and isolating cases and close contacts and laboratory capacity for future health emergencies.\n\nSUMMARY BOXO_LICOVID-19 spread globally, but how the pandemic played out in each country depended on various factors, including government responses and the general publics adherence to COVID-19 measures.\nC_LIO_LIEarly response--Early detection, Early isolation, Early tracing, Early treatment, and Early education--is the core of successful SARS-CoV-2 containment.\nC_LIO_LIAchieving high vaccination coverage quickly leads to a decline in the number of deaths and to eventual full re-opening of the country.\nC_LIO_LIResponding to the pandemic requires decisive leadership and good governance, that refers to decisions being made quickly, in a timely manner, and without delay.\nC_LIO_LIHigh level of cooperation from the public is a fundamental factor for success in containing the spread in the early phase, and the massively successful vaccination campaign in the later stage.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Srean Chhim", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Grace Marie Ku", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Sothiro Mao", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Willem van de Put", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Wim Van Damme", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Por Ir", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Chhorvann Chhea", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Vandine Or", - "author_inst": "Ministry of Health, Phnom Penh, Cambodia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.27.22283698", "rel_title": "Safety and Effectiveness of SA58 Nasal Spray against COVID-19 Infection in Medical Personnel\uff1aAn Open-label, Blank-controlled Study", @@ -121798,6 +122403,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2022.12.30.22284063", + "rel_title": "Effectiveness of Sotrovimab in Preventing COVID-19-related Hospitalizations or Deaths Among U.S. Veterans", + "rel_date": "2022-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.30.22284063", + "rel_abs": "BackgroundData on effectiveness of sotrovimab preventing COVID-19-related hospitalization or mortality, particularly after the emergence of the Omicron variant, are limited.\n\nMethodDetermine the real-world clinical effectiveness of sotrovimab for prevention of 30-day COVID-19 related hospitalization or mortality using a retrospective cohort within the U.S. Department of Veterans Affairs (VA) healthcare system.\n\nVeterans aged [≥]18 years, diagnosed with COVID-19 between December 1, 2021, and April 4, 2022, were included. Sotrovimab recipients (n=2,816) were exactly matched to untreated controls (n=11,250) on date of diagnosis, vaccination status, and region.\n\nThe primary outcome was COVID-19-related hospitalization or all-cause mortality within 30 days from diagnosis. Cox proportional hazards modeling estimated the hazard ratios (HR) and 95% Confidence Interval (CI) for the association between receipt of sotrovimab and outcomes.\n\nResultsDuring BA.1 dominance, compared to matched controls, sotrovimab-treated patients had a 70% lower risk hospitalization within 30 days or mortality (HR 0.30; 95%CI, 0.23-0.40), a 66% lower risk of 30-day hospitalization (HR 0.34; 95%CI, 0.25-0.46), and a 77% lower risk of 30-day all-cause mortality (HR 0.23; 95%CI, 0.14-0.38). During BA.2 dominance sotrovimab-treated patients had a 71% (HR .29; 95%CI, 0.08-0.98) lower risk of 30-day COVID-19-related-hospitalization, emergency, or urgent care. Limitations include confounding by indication.\n\nConclusionsUsing national real-world data from high risk and predominantly vaccinated Veterans, administration of sotrovimab, compared with no treatment, was associated with reduced risk of 30-day COVID-19-related hospitalization or all-cause mortality during the Omicron BA.1 period and reduced risk of progression to severe COVID-19 during the BA.2 dominant period.\n\nSummaryExamination of national real-world evidence demonstrates sotrovimab is effective in preventing at risk positive COVID-19 cases from progressing to severe SARS-CoV-2 infections compared to matched untreated cases during Delta and early Omicron variant waves in the U.S. Veteran population.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yinong Young-Xu", + "author_inst": "VA Medical Center White River Junction Vermont" + }, + { + "author_name": "Caroline Korves", + "author_inst": "White River Junction Veterans Affairs Medical Center" + }, + { + "author_name": "Gabrielle Zwain", + "author_inst": "White River Junction Veterans Affairs Medical Center" + }, + { + "author_name": "Sacha Satram", + "author_inst": "Vir Biotechnology, San Francisco, California, USA" + }, + { + "author_name": "Myriam Drysdale", + "author_inst": "GSK, Brentford, Middlesex, UK" + }, + { + "author_name": "Carolina Reyes", + "author_inst": "Vir Biotechnology, San Francisco, California, USA" + }, + { + "author_name": "Mindy M Cheng", + "author_inst": "Vir Biotechnology, San Francisco, California, USA" + }, + { + "author_name": "Lauren Epstein", + "author_inst": "Atlanta Veterans Affairs Medical Center, Decatur, GA" + }, + { + "author_name": "Vincent C Marconi", + "author_inst": "Atlanta Veterans Affairs Medical Center, Decatur, GA" + }, + { + "author_name": "Adit Ginde", + "author_inst": "Department of Emergency Medicine, University of Colorado School of Medicine, Aurora. CO" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.28.22284001", "rel_title": "A Statistical Analysis on COVID-19 Pandemic in the City of Toronto", @@ -122780,57 +123440,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.12.25.22283942", - "rel_title": "Study COVID-19 Severity of Patients Admitted to Emergency Room (ER) with Chest X-ray Images", - "rel_date": "2022-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.25.22283942", - "rel_abs": "We have conducted a study of the COVID-19 severity with the chest x-ray images, a private dataset collected from our collaborator St Bernards Medical Center. The dataset is comprised of chest x-ray images from 1,550 patients who were admitted to emergency room (ER) and were all tested positive for COVID-19. Our study is focused on the following two questions: (1) To predict patients hospital staying duration, based on the chest x-ray image which was taken when the patient was admitted to the ER. The length of stay ranged from zero hours to 95 days in the hospital and followed a power law distribution. Based on our testing results, it is hard for the prediction models to detect strong signal from the chest x-ray images. No model was able to perform better than a trivial most-frequent classifier. However, each model was able to outperform the most-frequent classifier when the data was split evenly into four categories. This would suggest that there is signal in the images, and the performance may be further improved by the addition of clinical features as well as increasing the training set. (2) To predict if a patient is COVID-19 positive or not with the chest x-ray image. We also tested the generalizability of training a prediction model on chest x-ray images from one hospital and then testing the model on images captures from other sites. With our private dataset and the COVIDx dataset, the prediction model can achieve a high accuracy of 95.9%. However, for our hold-one-out study of the generalizability of the models trained on chest x-rays, we found that the model performance suffers due to a significant reduction in training samples of any class.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jonathan Stubblefield", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Christopher Saldivar", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Anna De Feria", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "James Riddle", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Abhijit Shivkumar", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Jason Causey", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jake Qualls", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jennifer Fowler", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Xiuzhen Huang", - "author_inst": "Arkansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.12.24.22283835", "rel_title": "Literature analysis of the efficacy of COVID-19 vaccinations", @@ -123576,6 +124185,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.23.22283899", + "rel_title": "US Public Opinion as to Whether \"The Pandemic is Over,\" September to October 2022", + "rel_date": "2022-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.23.22283899", + "rel_abs": "ImportanceUS public health guidance has increasingly shifted responsibility for actions to minimize ongoing impacts of COVID-19 onto individuals. During September to October 2022, the World Health Organization continued to characterize COVID-19 as a pandemic. Yet, public perceptions of the pandemic status of COVID-19 and its associations with COVID-19-related behaviors were unknown.\n\nObjectiveTo assess US public opinion on the characterization of COVID-19 as a pandemic.\n\nDesign, Setting, and ParticipantsThe COVID-19 Outbreak Public Evaluation (COPE) Initiative internet-based surveys, administered to 4985 US adults during September to October 2022. Demographic quota sampling and survey weighting were employed to improve sample representativeness of the US population by age, sex, and combined race and ethnicity.\n\nExposuresThe COVID-19 pandemic.\n\nMain Outcomes and MeasuresResponse to the statement, \"The pandemic is over.\" Response options included Strongly agree, Somewhat agree, Neutral, Somewhat disagree, and Strongly disagree.\n\nResultsOverall, 5015 US adults completed The COPE Initiative surveys (response rate, 56.2%), and 4985 (99.4%) provided complete information for all analyzed variables and were included in this analysis. Only 1657 (33.2%) respondents agreed with the statement \"the pandemic is over,\" while 2141 (43.0%) disagreed and the remaining 1187 (23.8%) were neutral about the statement. Agreement that the pandemic was over was most strongly associated with having received fewer COVID-19 vaccines, lesser concern about SARS-CoV-2 variant viruses, and less frequent engagement in COVID- 19 preventive behaviors, such as mask usage in public spaces, as well as increasingly conservative political ideology, roles as unpaid caregivers of both children and adults, younger age, male sex, and significant disabilities.\n\nConclusions and RelevanceAs of September to October 2022, US public opinion was mixed on the characterization of COVID-19 as a pandemic. Belief the pandemic was over was associated with less frequent engagement in COVID-19 preventive\\behaviors, highlighting the important role of public health communication. Demographic groups to prioritize tailored public health messaging about the pandemic status were identified. Continued assessment of public perceptions about the state of the pandemic is warranted entering Year 4 of the COVID-19 pandemic.\n\nKey Points\n\nQuestionAs of September to October 2022, what was US public opinion as to whether COVID-19 remained a pandemic?\n\nFindingsIn this demographically representative survey study of 4985 US adults, only 1 in 3 respondents agreed with the statement \"the pandemic is over;\" 43% of adults disagreed. Agreement that the pandemic was over was associated with less engagement in COVID-19 preventive behaviors and more political conservatism.\n\nMeaningAs of September to October 2022, US public opinion was divided regarding the status of COVID-19 as a pandemic and is associated with COVID-19-related behaviors, underscoring important public health and policy implications of this designation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mark \u00c9 Czeisler", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Matthew D Weaver", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Rashon I Lane", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Shantha MW Rajaratnam", + "author_inst": "Monash University" + }, + { + "author_name": "Mark E Howard", + "author_inst": "Austin Health" + }, + { + "author_name": "Charles A Czeisler", + "author_inst": "Brigham and Women's Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.23.22283868", "rel_title": "Pediatric Nirmatrelvir/Ritonavir Prescribing Patterns During the COVID-19 Pandemic", @@ -124966,65 +125614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.12.22.521201", - "rel_title": "Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages", - "rel_date": "2022-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.22.521201", - "rel_abs": "The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Franck Touret", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - }, - { - "author_name": "Emilie Giraud", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jerome Bourret", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Jaouen Tran-Rajau", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jeanne Chiaravalli", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Frederic Lemoine", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Fabrice Agou", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Sylvie Van Der Werf", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.22.22283830", "rel_title": "To test or not to test? A new behavioral epidemiology framework for COVID-19", @@ -125470,6 +126059,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2022.12.22.22283763", + "rel_title": "\"Side effects of Vero cell vaccination against Covid-19 among medical students of Nepalgunj Medical College\"-A Post Vaccination survey", + "rel_date": "2022-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283763", + "rel_abs": "Background and aimsSevere Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) is a highly transmissible virus causing Coronavirus disease (COVID-19). Its symptoms include fever, dry cough, and shortness of breath. Vaccine plays a significant role in controlling infectious disease and lesser health resources are used, and there is increased allocation of those resources for disease management. Vero Cell is an inactivated vaccine against COVID-19 manufactured by Sinopharm Company of China and recommended for people above 18 years by the World Health Organization. It is administered in two doses of 0.5 ml, 14-28 days apart. The goal of our study was to determine post-vaccination side effects of both the first(1st) and the second(2nd) dose among participants of Nepalgunj Medical College Teaching Hospital (NGMCTH), Kohalpur, Banke, Nepal.\n\nMethodsA prospective cross-sectional study was conducted among undergraduate medical students and intern doctors of Nepalgunj Medical College. A comprehensive structured questionnaire was designed and distributed following each dose of vaccination. Data were collected from 6th January 2022 to 6th April 2022 and entered in Microsoft Excel and analyzed using the statistical package for social sciences (SPSS) version 22. Analyzed data were presented using simple descriptive statistics with appropriate tables.\n\nResultsOut of 156 participants, the majority were males (66.7%), within the age group of 21-24. The most frequently encountered symptom was pain at the injection site, predominantly seen in males. Among all the tested variables, the second dose of vaccination showed a significant association with sex. All the predominant symptoms exhibited a significant association following vaccination, except for pain at the injection site (p-value <0.05).\n\nConclusionsVaccine has proven to be a lifesaving breakthrough during the peak of the COVID-19 outbreak and has been precisely efficacious in a developing country like Nepal.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rupak K.C.", + "author_inst": "Nepalgunj Medical College, Nepal" + }, + { + "author_name": "Sibika Malla", + "author_inst": "Nepalgunj Medical College, Nepal" + }, + { + "author_name": "Aashish Jung Pandey", + "author_inst": "Nepalgunj Medical College, Nepal" + }, + { + "author_name": "Merina Shrestha", + "author_inst": "Nepalgunj Medical College, Nepal" + }, + { + "author_name": "Saharoj Siddiqui", + "author_inst": "Nepalgunj Medical College, Nepal" + }, + { + "author_name": "Suraj Adhikari", + "author_inst": "Matrishishu Miteri Government Hospital, Gandaki, Nepal" + }, + { + "author_name": "Niranjan KC", + "author_inst": "Patan Academy of Health Science, Nepal" + }, + { + "author_name": "Rumi KC", + "author_inst": "Sahid Gangalal National Heart Center, Kathmandu, Nepal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.21.22283781", "rel_title": "An at-home and electro-free COVID-19 rapid test based on colorimetric RT-LAMP", @@ -126436,25 +127072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.19.22283681", - "rel_title": "Tracking the COVID-19 vaccine equity, distribution, and cases in the global south", - "rel_date": "2022-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283681", - "rel_abs": "The rapid development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to make an important contribution in reducing both viral transmission and disease burden. In this study, we tracked the COVID-19 vaccine equity, distribution, and cases in global south countries using country-level data from Our World in Data using an event study analysis. We used data from 149 global south and 59 non-global south countries from January 2020 to May 2022. All non-global south and 90.32% of global south countries had universal availability of vaccines. The median time since the introduction of the first COVID-19 vaccine in the global south was almost eight weeks later than in non-global south countries. The median number of people fully vaccinated per hundred (68.8 vs 50.31), and the total number of boosters administered per hundred (45.7 vs. 13.02) were higher in non-global south countries compared to global south countries. Using the event study analysis, we found a significant reduction of COVID-19 new cases and deaths after the first COVID-19 vaccination rollout compared to the baseline in global south countries, average coefficient p-value <0.001. Programs aiming at improving vaccine access and distribution to global south countries are essential to effectively control COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tigist Mekonnen Melesse", - "author_inst": "World Bank Group" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.12.20.22282909", "rel_title": "The onset of late severe lung impairment in COVID-19 is associated with high inflammation markers at admission and metabolic syndrome markers", @@ -127112,6 +127729,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.12.19.521064", + "rel_title": "Different B cell activation patterns in asymptomatic and symptomatic COVID-19 patients", + "rel_date": "2022-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.19.521064", + "rel_abs": "Early and persistent defects in B cell subsets such as memory B cells were shown to be correlated with poor outcomes in COVID-19 patients. This research aimed to develop a molecular pathway model to understand the B cell development in COVID-19. A B cell transcriptomics dataset, obtained from COVID-19 patients, was analyzed on the resulting pathway model to study B cell activation. The pathway showed two distinct gene expression profiles between asymptomatic and symptomatic patients. In asymptomatic patients, there is an increase in transcript levels of antiviral interferon-stimulated genes such as ISG15, IFITM1, and NEAT1 and a driving gene for the extrafollicular pathway CXCR4 indicating a formation of plasmablast. In symptomatic patients, the results suggest an inhibition occurring at the germinal center hinting at a reduction in memory B cell production. Transcripts of driver gene CXCR5 involved in germinal center development is one of the most downregulated genes. This could contribute to the shortage in the formation of memory B cells in COVID-19. Concluding, in SARS-CoV-2 infection, B cells follow different activation routes in asymptomatic and symptomatic patients. In this study, we constructed a pathway that allowed us to analyze and interpret activation patterns of B cells in COVID-19 patients and their link to disease severity. Importantly, the pathway and approach can be reused for further research in COVID-19 or other diseases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nhung Pham", + "author_inst": "Maastricht University" + }, + { + "author_name": "Nuray Talih", + "author_inst": "Maastricht University" + }, + { + "author_name": "Friederike Ehrhart", + "author_inst": "Maastricht University" + }, + { + "author_name": "Chris Evelo", + "author_inst": "Maastricht University" + }, + { + "author_name": "Martina Kutmon", + "author_inst": "Maastricht University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.19.22283700", "rel_title": "Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021", @@ -128586,97 +129238,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.18.22283646", - "rel_title": "Association between SARS-CoV-2 Infection and Select Symptoms and Conditions 31 to 150 Days After Testing among Children and Adults", - "rel_date": "2022-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.18.22283646", - "rel_abs": "BackgroundAn increasing number of studies have described new and persistent symptoms and conditions as potential post-acute sequelae of SARS-CoV-2 infection (PASC). However, it remains unclear whether certain symptoms or conditions occur more frequently among persons with SARS-CoV-2 infection compared with those never infected with SARS-CoV-2. We compared the occurrence of specific COVID-associated symptoms and conditions as potential PASC 31 to 150 days following a SARS-CoV-2 test among adults ([≥]20 years) and children (<20 years) with positive and negative test results documented in the electronic health records (EHRs) of institutions participating in PCORnet, the National Patient-Centered Clinical Research Network.\n\nMethods and FindingsThis study included 3,091,580 adults (316,249 SARS-CoV-2 positive; 2,775,331 negative) and 675,643 children (62,131 positive; 613,512 negative) who had a SARS-CoV-2 laboratory test (nucleic acid amplification or rapid antigen) during March 1, 2020-May 31, 2021 documented in their EHR. We identified hospitalization status in the day prior through the 16 days following the SARS-CoV-2 test as a proxy for the severity of COVID-19. We used logistic regression to calculate the odds of receiving a diagnostic code for each symptom outcome and Cox proportional hazard models to calculate the risk of being newly diagnosed with each condition outcome, comparing those with a SARS-CoV-2 positive test to those with a negative test. After adjustment for baseline covariates, hospitalized adults and children with a positive test had increased odds of being diagnosed with [≥]1 symptom (adults: adjusted odds ratio[aOR], 1.17[95% CI, 1.11-1.23]; children: aOR, 1.18[95% CI, 1.08-1.28]) and shortness of breath (adults: aOR, 1.50[95% CI, 1.38-1.63]; children: aOR, 1.40[95% CI, 1.15-1.70]) 31-150 days following a SARS-CoV-2 test compared with hospitalized individuals with a negative test. Hospitalized adults with a positive test also had increased odds of being diagnosed with [≥]3 symptoms (aOR, 1.16[95% CI, 1.08 - 1.26]) and fatigue (aOR, 1.12[95% CI, 1.05 - 1.18]) compared with those testing negative. The risks of being newly diagnosed with type 1 or type 2 diabetes (aHR, 1.25[95% CI, 1.17-1.33]), hematologic disorders (aHR, 1.19[95% CI, 1.11-1.28]), and respiratory disease (aHR, 1.44[95% CI, 1.30-1.60]) were higher among hospitalized adults with a positive test compared with those with a negative test. Non-hospitalized adults with a positive SARS-CoV-2 test had higher odds of being diagnosed with fatigue (aOR, 1.11[95% CI, 1.05-1.16]) and shortness of breath (aOR, 1.22[95% CI, 1.15-1.29]), and had an increased risk (aHR, 1.12[95% CI, 1.02-1.23]) of being newly diagnosed with hematologic disorders (i.e., venous thromboembolism and pulmonary embolism) 31-150 days following SARS-CoV-2 test compared with those testing negative. The risk of being newly diagnosed with certain conditions, such as mental health conditions and neurological disorders, was lower among patients with a positive viral test relative to those with a negative viral test.\n\nConclusionsPatients with SARS-CoV-2 infection were at higher risk of being diagnosed with certain symptoms and conditions, particularly fatigue, respiratory symptoms, and hematological abnormalities, after acute infection. The risk was highest among adults hospitalized after SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yongkang Zhang", - "author_inst": "Cornell University Joan and Sanford I Weill Medical College" - }, - { - "author_name": "Alfonso Romieu-Hernandez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tegan K Boehmer", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Eduardo Azziz-Baumgartner", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Thomas Carton", - "author_inst": "Louisiana Public Health Institute" - }, - { - "author_name": "Adi V. Gundlapalli", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Julia Fearrington", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Kshema Nagavedu", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Katherine Dea", - "author_inst": "Statlog" - }, - { - "author_name": "Erick Moyneur", - "author_inst": "Statlog" - }, - { - "author_name": "Lindsey G. Cowell", - "author_inst": "UT Southwestern: The University of Texas Southwestern Medical Center" - }, - { - "author_name": "Rainu Kaushal", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Kenneth H Mayer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jon Puro", - "author_inst": "OCHIN: Oregon Community Health Information Network" - }, - { - "author_name": "Sonja A Rasmussen", - "author_inst": "University of Florida" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Clinic" - }, - { - "author_name": "Mark G Weiner", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Sharon Saydeh", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jason P Block", - "author_inst": "Harvard Pilgrim Health Care Inc" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.19.22283668", "rel_title": "A retrospective analysis of COVID-19 non-pharmaceutical interventions for Mexico and Peru: a modeling study", @@ -128801,7 +129362,7 @@ "rel_date": "2022-12-19", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283660", - "rel_abs": "Background The COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England. Objectives A. To determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations. B. To estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination. C. To assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations. Methods This population-based study uses the QResearch database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible. We will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of severe COVID-19 outcomes after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals. Ethics and dissemination QResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", + "rel_abs": "BackgroundThe COVID-19 pandemic has affected millions of people globally with major health, social and economic consequences, prompting development of vaccines for use in the general population. However, vaccination uptake is lower in some groups, including in pregnant women, because of concerns regarding vaccine safety. There is evidence of increased risk of adverse pregnancy and neonatal outcomes associated with SARS-CoV-2 infection, but fear of vaccine-associated adverse events on the baby both in short and longer term is one of the main drivers of low uptake for this group. Other vaccines commonly used in pregnancy include influenza and pertussis. These both have reportedly higher uptake compared with COVID-19 vaccination, which may be because they are perceived to be safer. In this study, we will undertake an independent evaluation of the uptake, effectiveness and safety of COVID-19 vaccinations in pregnant women using the QResearch primary care database in England.\n\nObjectivesO_LITo determine COVID-19 vaccine uptake in pregnant women compared to uptake of influenza and pertussis vaccinations.\nC_LIO_LITo estimate COVID-19 vaccine effectiveness in pregnant women by evaluating the risk of severe COVID-19 outcomes following vaccination.\nC_LIO_LITo assess the safety of COVID-19 vaccination in pregnancy by evaluating the risks of adverse pregnancy and perinatal outcomes and adverse events of special interest for vaccine safety after COVID-19 vaccination compared with influenza and pertussis vaccinations.\nC_LI\n\nMethodsThis population-based study uses the QResearch(R) database of primary health care records, linked to individual-level data on hospital admissions, mortality, COVID-19 vaccination, SARS-CoV-2 testing data and congenital anomalies. We will include women aged 16 to 49 years with at least one pregnancy during the study period of 30th December 2020 to the latest date available. Babies born during the study period will be identified and linked to the mothers record, where possible.\n\nWe will describe vaccine uptake in pregnant women by trimester and population subgroups defined by demographics and other characteristics. Cox proportional hazards multivariable regression will be used to identify factors associated with vaccine uptake. The effectiveness of COVID-19 vaccines in pregnant women will be assessed using a nested matched case-control design to assess hospitalisation, intensive care admission and death with COVID-19. Cases who had the outcome will be matched with up to 10 controls who did not have the outcome on that date by age, calendar date and trimester of pregnancy using incidence density sampling for the occurrence of each outcome after each vaccine dose compared with unvaccinated individuals. For the safety analysis, we will we use logistic regression analyses to determine unadjusted and adjusted odds ratios for the occurrence of maternal (e.g. miscarriage, ectopic pregnancy and gestational diabetes) and perinatal outcomes (e.g. stillbirth, small for gestational age and congenital anomalies) by vaccination status compared to unvaccinated individuals. For the adverse events of special interest for vaccine safety (e.g. venous thromboembolism, myocarditis and Guillain Barre syndrome), we will use time varying Royston-Palmar regression analyses to determine unadjusted and adjusted hazard ratios for the occurrence of each outcome by vaccination status to unvaccinated individuals.\n\nEthics and disseminationQResearch is a Research Ethics Approved Research Database with ongoing approval from the East Midlands Multi-Centre Research Ethics Committee (Ref: 18/EM/0400). This study was approved by the QResearch Scientific Committee on 9th June 2022. This research protocol has been developed with support from a patient and public involvement panel, who will continue to provide input throughout the duration of the study. Research findings will be submitted to pre-print servers such as MedRxIv, academic publication and disseminated more broadly through media releases and community groups and conference presentations.", "rel_num_authors": 17, "rel_authors": [ { @@ -129362,6 +129923,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.16.22283251", + "rel_title": "Sustained reductions in life-threatening invasive bacterial diseases during the first two years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries participating in the IRIS Consortium", + "rel_date": "2022-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283251", + "rel_abs": "BackgroundThe Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis and Streptococcus agalactiae. Here we analyse the incidence and distribution of disease during the first two years of the pandemic.\n\nMethodsLaboratories in 30 countries/territories representing five continents submitted case data from 2018-2021 to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype/group were examined. Interrupted time series analyses quantified the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models estimated effect sizes and forecasted counterfactual trends by hemisphere.\n\nFindingsOverall, 116,841 cases were analysed: 76,481 (2018-2019, pre-pandemic) plus 40,360 (2020-2021, pandemic). During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio: 0.47; 95% confidence interval: 0.40-0.55), H influenzae (0.51; 0.40-0.66) and N meningitidis (0.26; 0.21-0.31), whereas no significant changes were observed for the non-respiratory-transmitted pathogen S agalactiae (1.02; 0.75-1.40). No major changes in the distribution of cases were observed when stratified by patient age or serotype/group. An estimated 36,289 (17,145-55,434) cases of invasive bacterial disease were averted during the first two years of the pandemic among IRIS participating countries/territories.\n\nInterpretationCOVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae and N meningitidis during the first two years of the pandemic, but cases began to increase in some countries as pandemic restrictions were lifted.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSEarly in the COVID-19 pandemic the IRIS Consortium reported a significant reduction in invasive disease due to respiratory-transmitted bacterial pathogens, which was associated with the implementation of COVID-19 stringency measures and changes in human social behaviour. All 26 countries/territories participating in IRIS at the time experienced a significant reduction in infections between January and May 2020, compared with the previous two years. In particular, S pneumoniae infections decreased by 68% at four weeks after COVID-19 containment measures were imposed, and by 82% at eight weeks.\n\nAdded value of this studyThese new data from the expanded IRIS Consortium across 30 countries/territories demonstrated a sustained reduction in invasive disease throughout the first two years of the COVID-19 pandemic. Using time series modelling, we estimated that over 36,000 cases of invasive bacterial disease were averted in 2020-2021 among the countries participating in IRIS; however, minor increases in disease in the latter half of 2021 require close monitoring to understand the nature of re-emerging cases.\n\nImplications of all the available evidenceFuture epidemics and pandemics will occur, and we need to understand not only the pathogen that is directly responsible for the pandemic, but also that population-level responses to an epidemic or pandemic more broadly affect overall human health and other microbes. IRIS provides evidence for the effects of such public health responses on severe invasive bacterial infections across many countries. Moreover, these IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to healthcare service planning and provision of policies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Shaw", + "author_inst": "University of Oxford" + }, + { + "author_name": "Angela B Brueggemann", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.14.22282041", "rel_title": "The Impact of Freeze-Thaw Cycles on the Integrity of SARS-COV-2 Viral Culture Fluids and Clinical Remnant Samples in Antigen or Nucleic Acid Testing", @@ -130308,45 +130892,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.16.520599", - "rel_title": "Cholesterol and ceramide facilitate SARS-CoV-2 Spike protein-mediated membrane fusion", - "rel_date": "2022-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520599", - "rel_abs": "SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together, and its fusion peptide (FP) that interacts with and perturb the membrane structure to trigger fusion. Recent studies suggest that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. We found that cholesterol and ceramide both facilitated fusion, suggesting that targeting lipids could be effective against SARS-CoV-2. As proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. We found that CPZ inhibited S-mediated membrane fusion and thus potentially SARS-CoV-2 entry.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kristina Niort", - "author_inst": "Inserm" - }, - { - "author_name": "Julia Dancourt", - "author_inst": "Inserm" - }, - { - "author_name": "Erwan Boedec", - "author_inst": "Inserm" - }, - { - "author_name": "Zahra Al Amir Dache", - "author_inst": "Inserm" - }, - { - "author_name": "Gregory Lavieu", - "author_inst": "Inserm" - }, - { - "author_name": "David Tareste", - "author_inst": "Inserm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.12.14.520265", "rel_title": "COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses", @@ -131032,6 +131577,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.12.12.22283200", + "rel_title": "COVID-19 Vaccination in Pregnancy: The Impact of Multimorbidity and Smoking Status on Vaccine Hesitancy, a Cohort Study of 25,111 Women in Wales, UK", + "rel_date": "2022-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283200", + "rel_abs": "BackgroundMultimorbidity and pregnancy are two risk factors for more severe outcomes after a SARS-CoV-2 infection, thus vaccination uptake is important for pregnant women living with multimorbidity. This study aimed to examine the impact of multimorbidity, smoking status, and demographics (age, ethnic group, area of deprivation) on vaccine hesitancy among pregnant women in Wales using electronic health records (EHR) linkage.\n\nMethodsThis cohort study utilised routinely collected, individual-level, anonymised population-scale linked data within the Secure Anonymised Information Linkage (SAIL) Databank. Pregnant women were identified from 13th April 2021 to 31st December 2021. Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy by multimorbidity and smoking status, as well as depression, diabetes, asthma, and cardiovascular conditions independently. Variation in uptake by; multimorbidity, smoking status, and demographics was examined jointly and separately for the independent conditions using hazard ratios (HR) from the Cox regression model. A bootstrapping internal validation was conducted to assess the performance of the models.\n\nResultsWithin the population cohort, 8,203 (32.7%) received at least one dose of the COVID-19 vaccine during pregnancy, with 8,572 (34.1%) remaining unvaccinated throughout the follow-up period, and 8,336 (33.2%) receiving the vaccine postpartum. Women aged 30 years or older were more likely to have the vaccine in pregnancy. Those who had depression were slightly but significantly more likely to have the vaccine compared to those without depression (HR = 1.08, 95% CI 1.03 to 1.14, p = 0.02). Women living with multimorbidity (> 1 health condition) were 1.12 times more likely to have the vaccine compared to those living without multimorbidity (HR = 1.12, 95% CI 1.04 to 1.19, p = 0.001). Vaccine uptakes were significantly lower among both current smokers and former smokers compared to never smokers (HR = 0.87, 95% CI 0.81 to 0.94, p < 0.001 and HR = 0.92, 95% CI 0.85 to 0.98, p = 0.015 respectively). Uptake was also lower among those living in the most deprived areas compared to those living in the most affluent areas (HR = 0.89, 95% CI 0.83 to 0.96, p = 0.002). The validated model had similar performance and revealed that multimorbidity, smoking status, age, and deprivation level together have a significant impact on vaccine hesitancy (p < 0.05 for all).\n\nConclusionYounger women, living without multimorbidity (zero or only one health condition), current and former smokers, and those living in the more deprived areas are less likely to have the vaccine, thus, a targeted approach to vaccinations may be required for these groups. Women living with multimorbidity are slightly but significantly less likely to be hesitant about COVID-19 vaccination when pregnant.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mohamed Mhereeg", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Hope Jones", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Jonathan Kennedy", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Mike Seaborne", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Michael Parker", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Natasha Kennedy", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + }, + { + "author_name": "Ashley Akbari", + "author_inst": "Population Data Science, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, UK" + }, + { + "author_name": "Luisa Zuccolo", + "author_inst": "Health Data Science Centre, Fondazione Human Technopole, Milan, Italy" + }, + { + "author_name": "Amaya Azcoaga-Lorenzo", + "author_inst": "School of Medicine, University of St Andrews, Scotland, UK and Hospital Rey Juan Carlos. Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz. Madrid. Sp" + }, + { + "author_name": "Alisha Davies", + "author_inst": "Research and Evaluation Division, Public Health Wales, UK." + }, + { + "author_name": "Krishnarajah Nirantharakumar", + "author_inst": "Institute of Applied Health Research, Birmingham University, Birmingham, UK." + }, + { + "author_name": "Sinead Brophy", + "author_inst": "National Centre for Population Health and Wellbeing Research, Swansea University Medical School, Faculty of Medicine, Health and Life Science, Swansea, Wales, U" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.14.22283460", "rel_title": "Modelling the adjustment of COVID-19 response and exit from dynamic zero-COVID in China", @@ -132301,73 +132909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.10.22283287", - "rel_title": "Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.10.22283287", - "rel_abs": "Convalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but its efficacy in intensive care unit (ICU) patients in a low and middle income country setting such as Suriname is unknown. Bedside plasma separation using the HemoClear device made convalescent plasma therapy accessible as treatment option in Suriname. Two hundred patients with severe SARS-CoV-2 infection requiring intensive care were recruited. Fifty eight patients (29%) received COVID-19 convalescent plasma (CCP) treatment in addition to standard of care (SOC). The CCP treatment and SOC groups were matched by age, sex, and disease severity scores. Mortality in the CCP treatment group was significantly lower than in the SOC group (21% versus 39%; Fishers exact P = 0.0133). Multivariate analysis using ICU days showed that CCP treatment reduced mortality (hazard ratio [HR], 0.35; 95% CI, 0.18-0.66; P = 0.001), while complication of acute renal failure (creatinine levels >110 mol/L; HR, 4.45; 95%CI, 2.54-7.80; P < 0.0001) was independently associated with death. Decrease in chest X-ray score in the CCP treatment group (median -3 points, IQR -4 to -1) was significantly greater than in the SOC group (median -1 point, IQR -3 to 1, Mann Whitney P = 0.0004). Improvement in PaO2/FiOs ratio was also significantly greater in the CCP treatment group (median 83, IQR 8 to 140) than in the SOC group (median 35, IQR -3 to 92, Mann Whitney P = 0.0234). Further research is needed for HemoClear-produced CCP as therapy in SARS-CoV-2 infections together with adequately powered, randomized controlled trials.\n\nImportanceThis study compares mortality and other endpoints between intensive care unit (ICU) COVID-19 patients treated with convalescent plasma plus standard of care (CCP), and a control group of patients hospitalized in the same medical ICU facility treated with standard of care alone (SOC) in a low and middle income country (LMIC) setting using bedside donor whole blood separation by gravity (HemoClear) to produce the CCP. It demonstrates a significant 65% survival improvement in HemoClear-produced CCP recipients (HR 0.35; 95% CI, 0.19-0.66; P = 0.001). Although this is an exploratory study, it clearly shows the benefit of using the HemoClear-produced CCP in ICU patients in the Suriname LMIC setting. Additional studies can further substantiate our findings and their applicability to both LMICs and high income countries and the use of CCP as a prepared readiness method to combat new viral pandemics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rosita Bihariesingh-Sanchit", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rakesh Bansie", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Navin Ramdhani", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rishi Mangroo", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Debra Bustamente", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Ernesto Diaz", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Cesar Fung A Foek", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Iswardath Thakoer", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Stephen C. Vreden", - "author_inst": "Foundation for Scientific Research Suriname (SWOS)" - }, - { - "author_name": "Zaheeb Choudry", - "author_inst": "Horacio Oduber Hospital" - }, - { - "author_name": "Angelique Bastienne van 't Wout", - "author_inst": "Van 't Wout Pharma Consulting" - }, - { - "author_name": "Dimitri A. Diavatopoulos", - "author_inst": "Radboud University Medical Center, Radboud Institute for Molecular Life Sciences" - }, - { - "author_name": "Arno P. Nierich", - "author_inst": "HemoClear BV" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.10.22283298", "rel_title": "The Use and Safety Risk of Repurposed Drugs for COVID-19 patients: Lessons Learned Utilizing the Food and Drug Administrations Adverse Event Reporting System", @@ -133133,6 +133674,29 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.12.12.520110", + "rel_title": "Long COVID: G Protein-Coupled Receptors (GPCRs) responsible for persistent post-COVID symptoms", + "rel_date": "2022-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.12.520110", + "rel_abs": "As of early December 2022, COVID-19 had a significant impact on the lives of people all around the world, with over 630 million documented cases and over 6 million deaths. A recent clinical analysis revealed that under certain conditions, a patients disease symptoms are more likely to persist. Long COVID is characterised by many symptoms that continue long after the SARS-CoV-2 infection has resolved. This work utilised computational methods to analyse the persistence of COVID symptoms after recovery and to identify the relevant genes. Based on functional similarity, differentially expressed genes (DEGs) of SARS-CoV-2 infection and 255 symptoms of long covid were examined, and potential genes were identified based on the rank of functional similarity. Then, hub genes were identified by analysing the interactions between proteins. Using the identified key genes and the drug-gene interaction score, FDA drugs with potential for possible alternatives were identified. Also discovered were the gene ontology and pathways for 255 distinct symptoms. A website (https://longcovid.omicstutorials.com/) with a list of significant genes identified as biomarkers and potential treatments for each symptom was created. All of the hub genes associated with the symptoms, GNGT1, GNG12, GNB3, GNB4, GNG13, GNG8, GNG3, GNG7, GNG10, and GNAI1, were discovered to be associated with G-protein coupled receptors. This demonstrates that persistent COVID infection affects various organ systems and promotes chronic inflammation following infection. CTLA4, PTPN22, KIT, KRAS, NF1, RET, and CTNNB1 were identified as the common genes that regulate T-cell immunity via GPCR and cause a variety of symptoms, including autoimmunity, cardiovascular, dermatological, general symptoms, gastrointestinal, pulmonary, reproductive, genitourinary, and endocrine symptoms (RGEM). Among other functions, they were found to be involved in the positive regulation of protein localization to the cell cortex, the regulation of triglyceride metabolism, the binding of G protein-coupled receptors, the binding of G protein-coupled serotonin receptors, the heterotrimeric G-protein complex, and the cell cortex region. These biomarker data, together with the gene ontology and pathway information that accompanies them, are intended to aid in determining the cause and improving the efficacy of treatment.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sanisha Das", + "author_inst": "Management and Science University" + }, + { + "author_name": "Suresh Kumar", + "author_inst": "Management & Science University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.12.13.22283400", "rel_title": "Long term anti-SARS-CoV-2 antibody kinetics and correlate of protection against Omicron BA.1/BA.2 infection", @@ -134051,33 +134615,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.12.08.22283265", - "rel_title": "Mental health self-care during the COVID-19 pandemic: a prospective cohort study in Australia", - "rel_date": "2022-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.08.22283265", - "rel_abs": "Pandemic public health measures have affected mental health for many people, resulting in varied approaches to mental health self-care. During 27 April - 26 July 2020, we surveyed a cohort of 1646 Australians, who were in paid employment prior to the pandemic, on changes in work, health, and managing their mental health concerns. Lifestyle changes were most the most frequently reported action to manage mental health concerns (78%), and were more common for women (OR=2.33, 95%CI=[1.82, 3.03]), and people experiencing recent work loss (OR=1.54, 95%CI=[1.04, 2.28]). Mental health self-care was more common for people experiencing psychological distress, or with pre-exisiting mental health conditions. Talking to friends about mental health, exercise and dietary changes, were more common for women and younger adults. Findings highlight potential benefits of reducing barriers to formal mental health services and supports during crises, particularly for people who less commonly seek help, and those experiencing psychological distress.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daniel Griffiths", - "author_inst": "Monash University" - }, - { - "author_name": "Vinsensia Maharani Kanya Dhira Pradipta", - "author_inst": "Monash University" - }, - { - "author_name": "Alex Collie", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.08.22283272", "rel_title": "Duration of viral shedding of the Omicron variant in asymptomatic and mild COVID-19 cases from Shanghai, China", @@ -134747,6 +135284,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.08.519588", + "rel_title": "Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2", + "rel_date": "2022-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.08.519588", + "rel_abs": "The recent emergence of multi-sample multi-condition single-cell multi-cohort studies allow researchers to investigate different cell states. The effective integration of multiple large-cohort studies promises biological insights into cells under different conditions that individual studies cannot provide. Here, we present scMerge2, a scalable algorithm that allows data integration of atlas-scale multi-sample multi-condition single-cell studies. We have generalised scMerge2 to enable the merging of millions of cells from single-cell studies generated by various single-cell technologies. Using a large COVID-19 data collection with over five million cells from 1000+ individuals, we demonstrate that scMerge2 enables multi-sample multi-condition scRNA-seq data integration from multiple cohorts and reveals signatures derived from cell-type expression that are more accurate in discriminating disease progression. Further, we demonstrate that scMerge2 can remove dataset variability in CyTOF, imaging mass cytometry and CITE-seq experiments, demonstrating its applicability to a broad spectrum of single-cell profiling technologies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yingxin Lin", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Yue Cao", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Elijah Willie", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Ellis Patrick", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Jean Yee Hwa Yang", + "author_inst": "University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.12.03.519007", "rel_title": "Increased migratory/activated CD8+ T cell and low avidity SARS-CoV-2 reactive cellular response in post-acute COVID-19 syndrome", @@ -135865,53 +136437,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.02.22281853", - "rel_title": "Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies", - "rel_date": "2022-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22281853", - "rel_abs": "The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. \"Superspreading,\" or \"over-dispersion,\" is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thayer L Anderson", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Anjalika Nande", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Carter Merenstein", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Brinkley Raynor", - "author_inst": "Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Anisha Oommen", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Michael Z Levy", - "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104" - }, - { - "author_name": "Alison L Hill", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.04.22282996", "rel_title": "COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting", @@ -136621,6 +137146,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.01.22283006", + "rel_title": "SARS-CoV-2 infection- induced seroprevalence among children and associated risk factors during pre- and omicron-dominant wave, from January 2021 through November 2022, Thailand: Longitudinal study", + "rel_date": "2022-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.01.22283006", + "rel_abs": "BackgroundSevere acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic in young children. Therefore, the true rate of infection is likely underestimated. Few data are available on the rate of infections in young children, and studies on the SARS-CoV-2 seroprevalence among children during omicron wave are limited. Our study aims to assess the SARS-CoV-2 infection-induced seroprevalence among children and estimated the associated risk factors for seropositivity.\n\nMethodsA longitudinal serological survey was conducted from January 2021 through November 2022. Samples were tested for anti-nucleocapsid (N) IgG, anti-receptor binding domain (RBD) IgG using a chemiluminescent microparticle immunoassay (CMIA) and detected anti-RBD Immunoglobulin (Ig) using an electrochemiluminescence immunoassay (ECLIA). The vaccination and SARS-CoV-2 infection history were collected.\n\nResultsA total of 452 serum samples were obtained from 249 children aged 5-7 years old who were annually followed-up in the longitudinal serological survey. Of these, 191 participants provided samples at two serial time points, including during the pre-and omicron dominant wave. Overall, seroprevalence induced by SARS-CoV-2 infection was increased from 9.1% (95%CI: 0.6-12.6%) during the pre-omicron wave to 49.7% (95%CI: 35.9-66.8%) during the omicron wave. Amongst seropositive individuals, the infection-induced seroprevalence was lower in vaccinated participants than those with no vaccination (40.4% vs. 57.4%; risk ratio, 0.71; 95%CI: 0.52-0.95). Nevertheless, the ratio of seropositive cases per recalled infection was 1.56 during the omicron dominant wave. In addition, overall seroprevalence induced by infection, vaccination and hybrid immunity was 76.6% (151/197; 95%CI: 54.6-97.9%) between January and November 2022.\n\nConclusionsour study reports an increase in infection-induced seroprevalence among children during the omicron wave. These findings highlight that estimating seroprevalence is crucial to monitor SARS-CoV-2 exposure, particularly in asymptomatic infection, and help to optimize public health policies and determine the effect of immunization in the pediatric population.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Jiratchaya Puenpa", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Jira Chansaenroj", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Siriporn Songtaisarana", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Chulalongkorn University Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.01.22282927", "rel_title": "Epidemiology and outcomes of SARS-CoV-2 infection associated with anti-nucleocapsid seropositivity in Cape Town, South Africa", @@ -137715,77 +138307,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.12.02.22283026", - "rel_title": "Healthcare in England was affected by the COVID-19 pandemic across the pancreatic cancer pathway: a cohort study using OpenSAFELY-TPP", - "rel_date": "2022-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283026", - "rel_abs": "BackgroundHealthcare across all sectors, in the UK and globally, was negatively affected by the COVID-19 pandemic. We analysed healthcare services delivered to people with pancreatic cancer from January 2015 to March 2023 to investigate the effect of the COVID-19 pandemic.\n\nMethodsWith the approval of NHS England, and drawing from a nationally representative OpenSAFELY-TPP dataset of 24 million patients (over 40% of the English population), we undertook a cohort study of people diagnosed with pancreatic cancer. We queried electronic healthcare records for information on the provision of healthcare services across the pancreatic cancer pathway. To estimate the effect of the COVID-19 pandemic, we predicted the rates of healthcare services if the pandemic had not happened. We used generalised linear models (GLM) and the pre-pandemic data from January 2015 to February 2020 to predict rates in March 2020 to March 2023. The 95% confidence intervals of the predicted values were used to estimate the significance of the difference between the predicted and observed rates.\n\nResultsThe rate of pancreatic cancer and diabetes diagnoses in the cohort was not affected by the pandemic. There were 26,840 people diagnosed with pancreatic cancer from January 2015 to March 2023. The mean age at diagnosis was 72 ({+/-}11 SD), 48% of people were female, 95% were of White ethnicity and 40% were diagnosed with diabetes. We found a reduction in surgical resections by 25% to 28% during the pandemic. In addition, 20%, 10% and 4% fewer people received BMI, HbA1c and liver function tests respectively before they were diagnosed with pancreatic cancer. There was no impact of the pandemic on the number of people making contact with primary care, but the number of contacts increased on average by 1 to 2 per person amongst those who made contact. Reporting of jaundice decreased by 28%, but recovered within twelve months into the pandemic. Emergency department visits, hospital admissions and deaths were not affected.\n\nConclusionsThe pandemic affected healthcare in England across the pancreatic cancer pathway. Positive lessons could be learnt from the services that were resilient and those that recovered quickly. The reductions in healthcare experienced by people with cancer have the potential to lead to worse outcomes. Current efforts should focus on addressing the unmet needs of people with cancer.\n\nFundingThis work was jointly funded by the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2-0073), and Health Data Research UK (HDRUK2021.000, 2021.0157). This work was funded by Medical Research Council (MRC) grant reference MR/W021390/1 as part of the postdoctoral fellowship awarded to AL and undertaken at the Bennett Institute, University of Oxford. The views expressed are those of the authors and not necessarily those of the NIHR, NHS England, UK Health Security Agency (UKHSA) or the Department of Health and Social Care. Funders had no role in the study design, collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Agnieszka Lemanska", - "author_inst": "University of Surrey" - }, - { - "author_name": "Colm D Andrews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adam Frampton", - "author_inst": "Oncology Section, Surrey Cancer Research Institute, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK and HPB Surgical Unit," - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Keith J Roberts", - "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "University College London" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.30.22282946", "rel_title": "Discovering Social Determinants of Health from Case Reports using Natural Language Processing: Algorithmic Development and Validation", @@ -138375,6 +138896,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.02.22282981", + "rel_title": "Protection of hybrid immunity against SARS-CoV-2 reinfection and severe COVID-19 during periods of Omicron variant predominance in Mexico", + "rel_date": "2022-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22282981", + "rel_abs": "BACKGROUNDWith widespread transmission of the Omicron SARS-CoV-2 variant, reinfections have become increasingly common. Here, we explored the role hybrid immunity, primary infection severity, and variant predominance on the risk of reinfection and severe COVID-19 during periods of Omicron predominance in Mexico.\n\nMETHODSWe analyzed reinfections in Mexico in individuals with [≥]90 days from a previous primary infection using a national surveillance registry of SARS-CoV-2 cases from March 3rd, 2020, until August 13th, 2022. Immunity-generating events included primary infection, partial or full vaccination and vaccine boosting. Reinfections were matched by age and sex with controls with primary SARS-CoV-2 infection and negative RT-PCR or antigen test [≥]90 days after infection to explore risk factors for reinfection and reinfection-associated severe COVID-19. We also explored the protective role of heterologous vs. homologous vaccine boosters against reinfection or severe COVID-19 in fully vaccinated individuals.\n\nRESULTSWe detected 231,202 SARS-CoV-2 reinfections in Mexico, with most occurring in unvaccinated individuals (41.55%). Over 207,623 reinfections occurred during periods of Omicron (89.8%), BA.1 (36.74%) and BA.5 (33.67%) subvariant predominance and a case-fatality rate of 0.22%. Vaccination protected against reinfection, without significant influence of the order of immunity-generating events and provided >90% protection against severe reinfections. Heterologous booster schedules were associated with [~]11% and [~]54% lower risk for reinfection and reinfection-associated severe COVID-19 respectively, modified by time-elapsed since the last immunity-generating event.\n\nCONCLUSIONSSARS-CoV-2 reinfections have increased during periods of Omicron predominance. Hybrid immunity provides protection against reinfection and reinfection-associated severe COVID-19, with potential benefit from heterologous booster schemes.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for the terms \"SARS-CoV-2\" AND \"reinfection\" AND \"hybrid immunity\" until November 20th, 2022, and identified a few population studies previously conducted in Israel, Sweden, Qatar, United States and Canada which explored risk of reinfection and the protective role of hybrid immunity in individuals with one, two or three doses of COVID-19 vaccines, predominantly during periods of predominance of Omicron BA.1 and BA.2 subvariants. Notably, no studies were conducted in any Latin American country or reported on the benefit of heterologous booster schemes or the order of immunity-generating events.\n\nAdded value of this studyWe report the results of nation-wide study in Mexico of over 230,000 SARS-CoV-2 reinfections, with [~]90% occurring during periods of Omicron predominance. We identified that vaccination provided additional benefit on reducing the risk of SARS-CoV-2 reinfection, with the highest benefit observed in individuals with complete vaccination and booster protocols prior to primary infection or with primary infection during periods of BA.1 and BA.2 subvariant predominance. Hybrid immunity also provides a substantial reduction in the risk of reinfection-associated severe COVID-19, with >90% reduction in risk compared to unvaccinated individuals with previous SARS-CoV-2 infection, regardless of the order of immunity-generating events. Finally, heterologous COVID-19 booster schedules were associated with [~]11% and [~]54% lower risk for reinfection and reinfection-associated severe COVID-19 respectively, modified by time-elapsed since the last immunity-generating event.\n\nImplications of all the available evidenceOur results support that COVID-19 vaccination and boosters provide additional benefit to protect against SARS-CoV-2 reinfection and reinfection-associated severe COVID-19. The use of heterologous boosters appears to provide additional protection in previously infected individuals and such schemes may prove beneficial to increase vaccination coverage as newer, more transmissible variants emerge.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jos\u00e9 Antonio Gonz\u00e1lez-Montes", + "author_inst": "Mexican Ministry of Health" + }, + { + "author_name": "Christian Arturo Zaragoza-Jim\u00e9nez", + "author_inst": "Mexican Ministry of Health" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Cardiologia \"Ignacio Chavez\"" + }, + { + "author_name": "Carlos Alberto Ferm\u00edn-Mart\u00ednez", + "author_inst": "National Autonomous University of Mexico" + }, + { + "author_name": "Daniel Ram\u00edrez-Garc\u00eda", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Rosaura Idania Guti\u00e9rrez-Vargas", + "author_inst": "Mexican Ministry of Health" + }, + { + "author_name": "Gabriel Garc\u00eda-Rodr\u00edguez", + "author_inst": "Mexican Ministry of Health" + }, + { + "author_name": "Hugo L\u00f3pez-Gatell", + "author_inst": "Mexican Ministry of Health" + }, + { + "author_name": "Sergio Iv\u00e1n Vald\u00e9s-Ferrer", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.02.22282944", "rel_title": "Associations between area-level health-related social factor indices and risk of acute COVID-19: An EHR-based cohort study from the RECOVER program", @@ -139653,61 +140233,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.11.29.22282857", - "rel_title": "Vaccine hesitancy, reactogenicity and immunogenicity of BNT162b2 and CoronaVac in pediatric patients with neuromuscular diseases", - "rel_date": "2022-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282857", - "rel_abs": "IntroductionCOVID-19 causes global health and psychosocial devastation, particularly to high-risk patients such as those with neuromuscular diseases (NMDs). The mRNA-based BNT162b2 and inactivated whole-virus CoronaVac are two novel COVID-19 vaccines widely used across the world that confer immune protection to healthy individuals. However, hesitancy towards COVID-19 vaccination was common for patients with NMDs early in the pandemic due to the paucity of data on the safety and efficacy in this specific patient population. Therefore, we examined the underlying factors associated with vaccine hesitancy across time for these patients and included the assessment of the reactogenicity and immunogenicity of these two vaccines.\n\nMethodsPediatric patients were screened from our NMD registry. For the vaccine hesitancy arm, those aged 8-18 years with no cognitive delay were invited to complete surveys in January and April 2022. For the reactogenicity and immunogenicity arm, patients aged 2-21 years were enrolled for COVID-19 vaccination between June 2021 to April 2022. Participants recorded adverse reactions (ARs) for 7 days after vaccination. Peripheral blood was obtained before BNT162b2 or CoronaVac and within 49 days after vaccination to measure their serological antibody responses as compared to healthy children and adolescents.\n\nResultsForty-one patients completed vaccine hesitancy surveys for both timepoints, and 22 joined our reactogenicity and immunogenicity arm of the study. Two or more family members vaccinated against COVID-19 was positively associated with intention of vaccination (odds ratio 11.7, 95% CI 1.81-75.1, p=0.010). Pain at the injection site, fatigue and myalgia were the commonest ARs. Most ARs were mild (75.5%, n=71/94). All 19 patients seroconverted against the wildtype SARS-CoV-2 after two doses of BNT162b2 or CoronaVac, although there was lower neutralization against the Omicron BA.1 variant.\n\nDiscussionThis study demonstrated vaccine hesitancy amongst patients with NMDs was influenced by family members and changed across time. BNT162b2 and CoronaVac were safe and immunogenic even for patients on low-dose corticosteroids. Future research is required to assess the durability of the COVID-19 vaccines, the effectiveness of booster doses and other routes of administration against emerging SARS-CoV-2 variants for these patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael Kwan Leung Yu", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Hoi Shan Sophelia Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Samuel Cheng", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Daniel Leung", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Sau Man Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Amy Ka Yan Suen", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Wilfred Hing Sang Wong", - "author_inst": "1Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Malik Peiris", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Yu Lung Lau", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Jaime S Rosa Duque", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.30.22282922", "rel_title": "Epidemiological impact of a large number of incorrect negative SARS-CoV-2 test results in South West England during September and October 2021", @@ -140273,6 +140798,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.11.27.518117", + "rel_title": "Fc-gamma receptor-dependent antibody effector functions are required for vaccine protection against infection by antigenic variants of SARS-CoV-2", + "rel_date": "2022-11-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.27.518117", + "rel_abs": "Emerging SARS-CoV-2 variants with antigenic changes in the spike protein are neutralized less efficiently by serum antibodies elicited by legacy vaccines against the ancestral Wuhan-1 virus. Nonetheless, these vaccines, including mRNA-1273 and BNT162b2, retained their ability to protect against severe disease and death, suggesting that other aspects of immunity control infection in the lung. Although vaccine-elicited antibodies can bind Fc gamma receptors (Fc{gamma}Rs) and mediate effector functions against SARS-CoV-2 variants, and this property correlates with improved clinical COVID-19 outcome, a causal relationship between Fc effector functions and vaccine-mediated protection against infection has not been established. Here, using passive and active immunization approaches in wild-type and Fc-gamma receptor (Fc{gamma}R) KO mice, we determined the requirement for Fc effector functions to protect against SARS-CoV-2 infection. The antiviral activity of passively transferred immune serum was lost against multiple SARS-CoV-2 strains in mice lacking expression of activating Fc{gamma}Rs, especially murine Fc{gamma}R III (CD16), or depleted of alveolar macrophages. After immunization with the preclinical mRNA-1273 vaccine, protection against Omicron BA.5 infection in the respiratory tract also was lost in mice lacking Fc{gamma}R III. Our passive and active immunization studies in mice suggest that Fc-Fc{gamma}R engagement and alveolar macrophages are required for vaccine-induced antibody-mediated protection against infection by antigenically changed SARS-CoV-2 variants, including Omicron strains.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Samantha R. Mackin", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Pritesh Desai", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Bradley M. Whitener", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Courtney E. Karl", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Meizi Liu", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Darin K. Edwards", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Taras M. Chicz", + "author_inst": "Ragon Insititute" + }, + { + "author_name": "Ryan P. McNamara", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Galit Alter", + "author_inst": "Moderna" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.11.24.22282651", "rel_title": "Comparative effectiveness of heterologous booster schedules with AZD1222, BNT162b2, or mRNA-1273 vaccines against COVID-19 during omicron predominance in the Nordic countries", @@ -141247,45 +141831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.29.22282887", - "rel_title": "Disruption in seasonality, patient characteristics and disparities of respiratory syncytial virus infection among young children in the US during and before the COVID-19 pandemic: 2010-2022", - "rel_date": "2022-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282887", - "rel_abs": "Respiratory syncytial virus (RSV) infections and hospitalization have surged sharply among young children. Here we test how the seasonal patterns of RSV infections in 2022 compared with those from other COVID-19 pandemic and pre-pandemic years. For this purpose, we analyzed a nation-wide and real-time database of electronic health records of 56 million patients across 50 states in the US. The monthly incidence rate of first-time RSV infection in young children (<5 years of age) and very young children (<1 year of age) followed a seasonal pattern from 2010 to 2019 with increases during the autumn, peaking in winter, subsiding in spring and summer. This seasonal pattern was significantly disrupted during the COVID-19 pandemic. In 2020, the incidence rate of RSV infections was remarkably low throughout the year. In 2021, the RSV season expanded to 9 months starting in the early summer and peaking in October. In 2022, RSV infections started to rise in May and were significantly higher than in previous years reaching a historically highest incidence rate in November 2022. There were significant racial and ethnic disparities in the peak RSV infection rate during 2010-2021 and the disparities further exacerbated in 2022 with peak incidence rate in black and Hispanic children 2-3 times that in white children. Among RSV-infected children in 2022, 19.2% had prior documented COVID-19 infection, significantly higher than the 9.7% among uninfected children, suggesting that prior COVID-19 could be a risk factor for RSV infection or that there are common risk factors for both viral infections. Our study calls for continuous monitoring of RSV infection in young children alongside its clinical outcomes and for future work to assess potential COVID-19 related risk factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lindsey Wang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "pamela B Davis", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Nathan A Berger", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "David C Kaelber", - "author_inst": "Metrohealth" - }, - { - "author_name": "Nora Volkow", - "author_inst": "National Institute on Drug Abuse" - }, - { - "author_name": "Rong Xu", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.29.518406", "rel_title": "Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins", @@ -142099,6 +142644,53 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.11.24.517882", + "rel_title": "SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects", + "rel_date": "2022-11-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.24.517882", + "rel_abs": "Experimental findings for SARS-CoV-2 related to the glycan biochemistry of coronaviruses indicate that attachments from spike protein to glycoconjugates on the surfaces of red blood cells (RBCs), other blood cells and endothelial cells are key to the infectivity and morbidity of COVID-19. To provide further insight into these glycan attachments and their potential clinical relevance, the classic hemagglutination (HA) assay was applied using spike protein from the Wuhan, Alpha, Delta and Omicron B.1.1.529 lineages of SARS-CoV-2 mixed with human RBCs. The electrostatic potential of the central region of spike protein from these four lineages was studied through molecular modeling simulations. Inhibition of spike protein-induced HA was tested using the macrocyclic lactone ivermectin (IVM), which is indicated to bind strongly to SARS-CoV-2 spike protein glycan sites. The results of these experiments were, first, that spike protein from these four lineages of SARS-CoV-2 induced HA. Omicron induced HA at a significantly lower threshold concentration of spike protein than for the three prior lineages and was much more electropositive on its central spike protein region. IVM blocked HA when added to RBCs prior to spike protein and reversed HA when added afterwards. These results validate and extend prior findings on the role of glycan bindings of viral spike protein in COVID-19. They furthermore suggest therapeutic options using competitive glycan-binding agents such as IVM and may help elucidate rare serious adverse effects (AEs) associated with COVID-19 mRNA vaccines which use spike protein as the generated antigen.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Celine Boschi", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + }, + { + "author_name": "David E Scheim", + "author_inst": "US Public Health Service (Inactive Reserve)" + }, + { + "author_name": "Audrey Bancod", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + }, + { + "author_name": "Muriel Millitello", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + }, + { + "author_name": "Marion Le Bideau", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + }, + { + "author_name": "Philippe Colson", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + }, + { + "author_name": "Jacques Fantini", + "author_inst": "INSERM UMR S 1072, Aix-Marseille Universite, 13015 Marseille, France" + }, + { + "author_name": "Bernard La Scola", + "author_inst": "MEPHI, Aix-Marseille Universite, Institut de Recherche pour le Developpement (IRD), Assistance Publique - Hopitaux de Marseille (AP-HM), IHU Mediterranee Infect" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.11.24.517008", "rel_title": "Extracellular disintegration of viral proteins as an innovative strategy for developing broad-spectrum antivirals against coronavirus", @@ -143313,49 +143905,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.23.22282686", - "rel_title": "Assessment of Attitude and Hesitancy Towards Covid-19 Vaccine among Hepatitis B and C Patients in Pakistan", - "rel_date": "2022-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282686", - "rel_abs": "OBJECTIVEThe research aimed to evaluate the attitude and perceptions towards the covid-19 vaccine among Hepatitis B and C patients in Peshawar, Khyber Pakhtunkhwa, Muzaffarabad, Azad Kashmir, Pakistan.\n\nMETHODSA survey-based study was adopted to evaluate the attitude of Hepatitis B and C patients towards immunization against covid-19 in Peshawar (KPK) and Muzaffarabad (AJK) cities of Pakistan. The study continued from January 2020 to February 2021. Participants were also assessed for their perception towards covid-19 vaccination.\n\nRESULTSA total of 839 (33.6%) individuals participated in the study. About 52 % of Hepatitis B patients were immunized against Covid-19, whereas the number of Hepatitis C patients was recorded at around 48%. About 53.7 % of participants refused to get the vaccine without any reason. About 63.2% of patients showed concern about the insufficient data available on the vaccine safety and efficacy published by the Public Health Department. Individuals with higher education were observed to be more open towards vaccination then those without a formal education. More than half of the participants (61.5 %) were concerned about the interference of the vaccine with their hepatitis treatment whereas 54.7 % patients refused vaccine because of a poor liver condition.\n\nCONCLUSIONSThe data indicated that limited data availability regarding the vaccine efficacy in viral hepatitis patients and negative attitudes of people toward covid-19 vaccination is the main cause of Covid-19 vaccination refusal among hepatitis B and C patients.\n\nDESCRIPTORSHepatitis B, Hepatitis C, covid-19, immunization, vaccine refusal, Pakistan.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Farheen Shafique", - "author_inst": "University of Azad Jammu and Kashmir Muzaffarabad, Pakistan" - }, - { - "author_name": "Mahreen Ul Hassan", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Butt", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Siddique", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Nazia Akbar", - "author_inst": "Hazara University" - }, - { - "author_name": "Azra Abrar", - "author_inst": "Abasyn University Peshawar, Pakistan" - }, - { - "author_name": "Irshad Rehman", - "author_inst": "University of Peshawar, Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.23.22282648", "rel_title": "An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia", @@ -144109,6 +144658,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.11.21.22282601", + "rel_title": "Cost of In-patient Management of Covid-19 Patients in a Tertiary Hospital in Kuwait", + "rel_date": "2022-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.21.22282601", + "rel_abs": "BackgroundAmong the GCC countries affected by COVID-19 infections, Kuwait was impacted with 658,520 cases and 2,563 deaths as reported by WHO on September 30, 2022. However, the impact of the COVID-19 epidemic on the economy of Kuwait especially in health sector is unknown.\n\nObjectiveThe aim of this study is to determine the total cost of COVID-19 in-patient management in Kuwait.\n\nMethodRetrospective design was employed in this study. A total 485 Covid-19 patients admitted to a tertiary hospital assigned to manage Covid-19 cases was randomly selected for this study from 1st May to 31st September 2021. Data on sociodemographic, length of stay (LOS), discharge status and comorbidity were obtained from the patients medical records. Among others, data on cost in this study cover administration, utility, pharmacy, radiology, laboratory, nursing, and ICU costs. The unit cost per admission was imputed using a step-down costing method with three levels of cost centers. The unit cost was multiplied by the individual patients length of stay to obtain the cost of care per patient per admission.\n\nFindingsThe mean cost of Covid-19 inpatient per episode of care was KD 2,216 (SD=2,018) equals to US$ 7,344 (SD=6,688) with the average length of stay of 9.4 (SD=8.5) days per admission. The total treatment costs of Covid-19 inpatient (n=485) were estimated to be KD 1,074,644 (US$ 3,561,585), in which the physician and nursing care cost were the largest share of costs (42.1%) with KD 452,154 (US$ 1,498,529). The second- and third-largest costs were intensive care (20.6%) of KD 221,439 (US$ 733,893) and laboratory costs (10.2%) of KD 109,264 (US$ 362,123). The average cost for severe Covid-19 patient was KD 4,626 (US$ 15,332), which is almost three times higher than the non-severe patients of KD 1,544 (US$ 5,117).\n\nConclusionThe cost of managing Covid-19 cases is substantial. The cost information can assist hospital managers and policymakers in designing more efficient interventions, especially for the management of high-risk groups.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Amrizal Muhammad Nur", + "author_inst": "Kuwait University Health Sciences Centre" + }, + { + "author_name": "Syed Mohamed Aljunid", + "author_inst": "Kuwait University Health Sciences Centre" + }, + { + "author_name": "Mohammad Almari", + "author_inst": "Kuwait University Health Sciences Centre" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2022.11.21.22282594", "rel_title": "Inability to work following COVID-19 vaccination among healthcare workers - an important aspect for future booster vaccinations", @@ -145139,49 +145715,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.20.517193", - "rel_title": "Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines", - "rel_date": "2022-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.20.517193", - "rel_abs": "Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ronaldo da Silva Francisco Junior", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Cristina dos Santos Ferreira", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Yasmmin Martins", - "author_inst": "Instituto de Calculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina" - }, - { - "author_name": "Thiago Moreno L Souza", - "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro" - }, - { - "author_name": "Enrique Medina-Acosta", - "author_inst": "Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Flu" - }, - { - "author_name": "Ana Tereza Ribeiro de Vasconcelos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.11.21.517338", "rel_title": "Ultrasound treatment inhibits SARS-CoV-2 in vitro infectivity", @@ -145975,6 +146508,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.11.16.22282346", + "rel_title": "The CANDID Study: impact of COVID-19 on critical care nurses and organisational outcomes: implications for the delivery of critical care services. A questionnaire study before and during the pandemic.", + "rel_date": "2022-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.16.22282346", + "rel_abs": "ObjectiveTo use a model of occupational stress to quantify and explain the impact of working in critical care during the Covid-19 pandemic on critical care nurses and organisational outcomes.\n\nParticipantsCritical care nurses (CCNs) who worked in the UK NHS between January to November 2021 (n=461).\n\nMethodsA self-reported survey measured the components of the Job-Demand Reward model of occupational stress. Job-demands, job-resources, health impairment (mental health (GHQ-12), burnout (MBI), PTSD symptoms (PCL-5)), work engagement and six organisational outcomes (commitment, job satisfaction, changing jobs, certainty about the future, quality of care, patient safety) were measured. Data were compared to baseline data (n=557) collected between April to October 2018. Regression analyses identified predictors of health impairment, work engagement and organisational outcomes.\n\nFindingsCompared to 2018, CCNs were at elevated risk of probable psychological distress (GHQ-12, OR 6.03 [95% C.I. 4.75 to 7.95]; burnout emotional exhaustion, OR 4.02 [3.07 to 5.26]; burnout depersonalisation, OR 3.18 [1.99 to 5.07]; burnout accomplishment, OR 1.53 [1.18 to 1.97]). A third of CCNs reported probable PTSD. Job demands predicted psychological distress and job demands increased during the pandemic. Resources reduced the negative impact of job demands on psychological distress, but this moderating effect of resources was not observed at higher levels of demand. CCNs were less engaged in their work. Job and personal resources predicted work engagement and were reduced during the pandemic. All six organisational outcomes were impaired. Lack of resources, especially reduced learning opportunities, lack of focus on staff wellbeing, and reduced focus on quality predicted worse organisational outcomes.\n\nConclusionsThe NHS needs to prioritise the welfare of CCNs, implement workplace change/planning, and support them to recover from the pandemic. The NHS is struggling to retain CCNs and, unless staff welfare is improved, quality of care and patient safety will likely decline.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Louise McCallum", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Janice Rattray", + "author_inst": "University of Dundee" + }, + { + "author_name": "Beth Pollard", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Jordan Millar", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Alastair Hull", + "author_inst": "University of Dundee" + }, + { + "author_name": "Pam Ramsay", + "author_inst": "University of Dundee" + }, + { + "author_name": "Lisa Salisbury", + "author_inst": "Queen Margaret University" + }, + { + "author_name": "Teresa Scott", + "author_inst": "NHS Grampian" + }, + { + "author_name": "Stephen Cole", + "author_inst": "NHS Tayside" + }, + { + "author_name": "Diane Dixon", + "author_inst": "University of Aberdeen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.11.16.22282408", "rel_title": "STRENGTH OF ASSOCIATION BETWEEN GENERALIZED/NONSPECIFIC COVID-19 SIGNS & SYMPTOMS WITH SARS-COV 2 SPECIFIC ORF, N, E GENES IDENTIFIED THROUGH REAL TIME PCR.", @@ -146929,45 +147517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.11.18.22282510", - "rel_title": "Mindfulness supports emotional resilience in children during the COVID-19 Pandemic", - "rel_date": "2022-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.18.22282510", - "rel_abs": "An important aspect of mental health in children is emotional resilience, the capacity to adapt to, and recover from, stressors and emotional challenges. Variation in trait mindfulness, ones disposition to attend to experiences with an open and nonjudgmental attitude, may be an important individual difference in children that supports emotional resilience. In this study, we investigated whether trait mindfulness was related to emotional resilience in response to stressful changes in education and home-life during the COVID-19 pandemic in the United States. We conducted a correlational study examining self-report data from July 2020 to February 2021, from 163 eight-to-ten-year-old children living in the US. Higher trait mindfulness scores correlated with less stress, anxiety, depression, and negative affect in children, and lower ratings of COVID-19 impact on their lives. Mindfulness moderated the relationship between COVID-19 child impact and negative affect. Children scoring high on mindfulness showed no correlation between rated COVID-19 impact and negative affect, whereas those who scored low on mindfulness showed a positive correlation between child COVID-19 impact and negative affect. Higher levels of trait mindfulness may have helped children to better cope with a wide range of COVID-19 stressors. Future studies should investigate the mechanisms by which trait mindfulness supports emotional resilience in children.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Isaac N Treves", - "author_inst": "MIT: Massachusetts Institute of Technology" - }, - { - "author_name": "Cindy Li", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kimberly Wang", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ola Ozernov-Palchik", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Halie Olson", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "John Gabrieli", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.16.22282406", "rel_title": "Special Olympics global report on COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities", @@ -147617,6 +148166,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.11.11.516239", + "rel_title": "Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis", + "rel_date": "2022-11-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516239", + "rel_abs": "The COVID-19 pandemic has greatly impacted the global economy and health care systems, illustrating the urgent need for timely and inexpensive responses to a pandemic threat in the form of vaccines and antigen tests. The causative agent of COVID-19 is SARS-CoV-2. The spike protein on the virus surface interacts with the human angiotensin-converting enzyme (ACE2) via the so-called receptor binding domain (RBD), facilitating virus entry. The RBD thus represents a prime target for vaccines, therapeutic antibodies, and antigen test systems. Currently, antigen testing is mostly conducted by qualitative flow chromatography or via quantitative ELISA-type assays. The latter mostly utilize materials like protein-adhesive polymers and gold or latex particles. Here we present an alternative ELISA approach using inexpensive materials and permitting quick detection based on components produced in the microbial model Ustilago maydis. In this fungus, heterologous proteins like biopharmaceuticals can be exported by fusion to unconventionally secreted chitinase Cts1. As a unique feature, the carrier chitinase binds to chitin allowing its additional use as a purification or immobilization tag. In this study, we produced different mono- and bivalent SARS-CoV-2 nanobodies directed against the viral RBD as Cts1 fusions and screened their RBD binding affinity in vitro and in vivo. Functional nanobody-Cts1 fusions were immobilized on chitin forming an RBD tethering surface. This provides a solid base for future development of an inexpensive antigen test utilizing unconventionally secreted nanobodies as RBD trap and a matching ubiquitous and biogenic surface for immobilization.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Magnus Philipp", + "author_inst": "Heinrich Heine University D\u00fcsseldorf" + }, + { + "author_name": "Lisa M\u00fcller", + "author_inst": "Institute for Virology, Medical Faculty, University of D\u00fcsseldorf" + }, + { + "author_name": "Marcel Andr\u00e9e", + "author_inst": "Institute for Virology, Medical Faculty, University of D\u00fcsseldorf" + }, + { + "author_name": "Kai P. Hussnaetter", + "author_inst": "Heinrich Heine University D\u00fcsseldorf" + }, + { + "author_name": "Heiner Schaal", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf" + }, + { + "author_name": "Michael Feldbr\u00fcgge", + "author_inst": "Heinrich Heine University D\u00fcsseldorf" + }, + { + "author_name": "Kerstin Schipper", + "author_inst": "Heinrich Heine University D\u00fcsseldorf" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.11.15.22282363", "rel_title": "Ethical reporting of research on violence against women and children during COVID-19: Analysis of 75 studies and recommendations for future guidelines", @@ -148679,109 +149271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.12.22282116", - "rel_title": "Conceptualising the Episodic Nature of Disability among Adults Living with Long COVID: A Qualitative Study", - "rel_date": "2022-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.12.22282116", - "rel_abs": "ObjectivesTo describe episodic nature of disability among adults living with Long COVID.\n\nMethodsWe conducted a community-engaged qualitative descriptive study involving online semi-structured interviews and participant visual illustrations. We recruited participants via collaborator community organizations in Canada, Ireland, United Kingdom, and United States.\n\nParticipantsAdults who self-identified as living with Long COVID. We purposively recruited for diversity in age, gender, race/ethnicity, sexual orientation, and duration since initial COVID-19 infection.\n\nMain Outcome Measure(s)We used a semi-structured interview guide to explore experiences of disability living with Long COVID, specifically health-related challenges and how they were experienced over time. We asked participants to draw their health trajectory and conducted a group-based content analysis.\n\nResultsAmong the 40 participants, the median age was 39 years (interquartile range: 32, 49); majority were women (63%), white (73%), heterosexual (75%), and living with Long COVID for [≥]1 year (83%). Participants described their disability experiences as episodic in nature, characterized by fluctuations in presence and severity of health-related challenges (disability) that may occur both within a day and over the long-term living with Long COVID. They described living with ups and downs, flare-ups, and peaks followed by crashes, troughs, and valleys, likened to a yo-yo rolling hills, and rollercoaster ride with relapsing/remitting, waxing/waning, fluctuations in health. Drawn illustrations demonstrated variety of trajectories across health dimensions, some more episodic than others. Uncertainty intersected with the episodic nature of disability, characterized as unpredictability of episodes, their length, severity and triggers, and process of long-term trajectory, which had implications on broader health.\n\nConclusionsAmong this sample of adults living with Long COVID, experiences of disability were described as episodic, characterized by fluctuating health challenges, which may be unpredictable in nature. Results help to better understand experiences of disability among adults living with Long COVID to inform healthcare and rehabilitation.\n\nKEY MESSAGESO_LIWhat is already known on this topic: Globally, a growing number of individuals are living with persistent and prolonged signs and symptoms following infection consistent with COVID-19, referred to as Long COVID, Post COVID-19 Condition (PCC) or Post-acute sequelae of SARS-CoV2 (PASC). Individuals living with Long COVID are experiencing a range of symptoms and impairments that impact their ability to carry out day to day activities or engage in social and community life roles.\nC_LIO_LIWhat this study adds: Disability living with Long COVID was described as episodic, characterized by fluctuations in presence and severity of health related challenges, which may be unpredictable in nature, occurring both within the day, and over the long-term of months and years living with Long COVID.\nC_LIO_LIHow this study might affect research, practice or policy: Results will help researchers, healthcare providers, policymakers, employers, and community members to better understand experiences of disability among adults living with Long COVID, to inform future disability measurement, health and rehabilitation care and service delivery, programs and policies for insurance, return to work, and workplace accommodations.\nC_LI", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Kelly O'Brien", - "author_inst": "Univesrity of Toronto" - }, - { - "author_name": "Darren A Brown", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust" - }, - { - "author_name": "Kiera McDuff", - "author_inst": "University of Toronto" - }, - { - "author_name": "Natalie St. Clair-Sullivan", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Patricia Solomon", - "author_inst": "McMaster University" - }, - { - "author_name": "Soo Chan Carusone", - "author_inst": "McMaster University" - }, - { - "author_name": "Lisa McCorkell", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Hannah Wei", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Susie Goulding", - "author_inst": "COVID Long-Haulers Support Group Canada, Canada" - }, - { - "author_name": "Margaret O'Hara", - "author_inst": "Long Covid Support, United Kingdom" - }, - { - "author_name": "Catherine Thomson", - "author_inst": "Long COVID Physio, United Kingdom" - }, - { - "author_name": "Niamh Roche", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Ruth Stokes", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Jaime H. Vera", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Kristine Erlandson", - "author_inst": "University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, United States" - }, - { - "author_name": "Colm Bergin", - "author_inst": "St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Larry Robinson", - "author_inst": "Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada" - }, - { - "author_name": "Angela M. Cheung", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Brittany Torres", - "author_inst": "University of Toronto, Ontario, Canada" - }, - { - "author_name": "Lisa Avery", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Ciaran Bannan", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Richard Harding", - "author_inst": "King's College London, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.11.11.22282032", "rel_title": "COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)", @@ -149367,6 +149856,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.08.22282042", + "rel_title": "Arrayed Imaging Reflectometry monitoring of anti-viral antibody production throughout vaccination and breakthrough Covid-19", + "rel_date": "2022-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.08.22282042", + "rel_abs": "Immune responses to COVID-19 infection and vaccination are individual and varied. There is a need to understand the timeline of vaccination efficacy against current and yet to be discovered viral mutations. Assessing immunity to SARS-CoV-2 in the context of immunity to other respiratory viruses is also valuable. Here we demonstrate the capability of a fully automated prototype Arrayed Imaging Reflectometry (AIR) system to perform reliable longitudinal serology against a 34-plex respiratory array. The array contains antigens for respiratory syncytial virus, seasonal influenza, common human coronaviruses, MERS, SARS-CoV-1, and SARS-CoV-2. AIR measures a change in reflectivity due to the binding of serum antibodies to the antigens on the array. Samples were collected from convalescent COVID-19 donors and individuals vaccinated with a two-dose mRNA vaccine regimen. Vaccinated samples were collected prior to the first dose, one week after the first dose, one week after the second dose, and monthly thereafter. Information following booster dose and/or breakthrough infection is included for a subset of subjects. Longitudinal samples of vaccinated individuals demonstrate a rise and fall of SARS-CoV-2 spike antibodies in agreement with general knowledge of the adaptive immune response and other studies. Linear Regression analysis was performed to understand the relationship between antibodies binding to different antigens on the array. Our analysis identified strong correlations between closely related influenza virus strains as well as correlations between SARS-CoV-2, SARS-CoV-1, and human coronavirus 229E. A small test of using diluted whole blood from a fingerstick provided clean arrays with antibody binding comparable to serum. Potential applications include assessing immunity in the context of exposure to multiple respiratory viruses, clinical serology, population monitoring to facilitate public health recommendations, and vaccine development against new viruses and virus mutations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alanna M Klose", + "author_inst": "University of Rochester School of Medicine and Dentistry" + }, + { + "author_name": "Gabrielle Kosoy", + "author_inst": "University of Rochester School of Medicine and Dentistry" + }, + { + "author_name": "Benjamin L Miller", + "author_inst": "University of Rochester School of Medicine and Dentistry" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.11.05.22281904", "rel_title": "Learning from the past: a short term forecast method for the COVID-19 incidence curve", @@ -150629,89 +151145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.11.07.22282028", - "rel_title": "Comparison of the reactogenicity and immunogenicity between two-dose mRNA COVID-19 vaccine and inactivated followed by an mRNA vaccine in children aged 5 - 11 years", - "rel_date": "2022-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282028", - "rel_abs": "ObjectiveTo compare the reactogenicity and immunogenicity between the two-dose mRNA COVID-19 vaccine regimen and one or two doses of inactivated vaccine followed by an mRNA vaccine regimen in healthy children between 5-11 years of age.\n\nMethodsA prospective cohort study was performed at King Chulalongkorn Memorial Hospital in Thailand between March to June 2022. Healthy children between 5-11 years of age were enrolled and received the two-dose mRNA COVID-19 vaccine (BNT162b2) regimen or the inactivated (CoronaVac) vaccine followed by the BNT162b2 vaccine regimen. In addition, healthy children who received two doses of BBIBP-CorV between 1-3 months prior were enrolled to receive a heterologous BNT162b2 as a third dose (booster).\n\nReactogenicity was assessed by a self-reported online questionnaire. Immunogenicity analysis was performed to determine binding and surrogate neutralizing antibodies to SARS-CoV-2 wild-type and Omicron variants.\n\nResultsOverall, 166 eligible children were enrolled. Local and systemic AE which occurred within 7 days after vaccination were mild to moderate and well-tolerated. At one-month, post-two or post-three doses, children vaccinated with two-dose BNT162b2, CoronaVac/BNT162b2, and two-dose BBIBP-CorV followed by BNT162b2 elicited similar levels of anti-receptor-binding domain (RBD) IgG. However, the two-dose BNT162b2 and two-dose BBIBP-CorV followed by BNT162b2 groups elicited higher neutralizing activities against Omicron BA.2 variant than the CoronaVac/BNT162b2 group.\n\nConclusionThe heterologous, CoronaVac vaccine followed by the BNT162b2 vaccine, regimen elicited lower neutralizing activities against the emerging Omicron BA.2 variant than the two-dose mRNA regimen. A third dose (booster) mRNA vaccine should be prioritized for this group.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Harit Phowatthanasathian", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sirapa Klinfueng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ratchadawan Aeemjinda", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nongkanok Khanarat", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.07.22282030", "rel_title": "Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses.", @@ -151361,6 +151794,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.09.22282142", + "rel_title": "Assessing the Effect of Selective Serotonin Reuptake Inhibitors in the Prevention of Post-Acute Sequelae of COVID-19", + "rel_date": "2022-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.09.22282142", + "rel_abs": "ImportancePost-acute sequelae of COVID-19 (PASC) produce significant morbidity, prompting evaluation of interventions that might lower risk. Selective serotonin reuptake inhibitors (SSRIs) potentially could modulate risk of PASC via their central, hypothesized immunomodulatory, and/or antiplatelet properties and therefore may be postulated to be of benefit in patients with PASC, although clinical trial data are lacking.\n\nObjectivesThe main objective was to evaluate whether SSRIs with agonist activity at the sigma-1 receptor lower the risk of PASC, since agonism at this receptor may serve as a mechanism by which SSRIs attenuate an inflammatory response. A secondary objective was to determine whether potential benefit could be traced to sigma-1 agonism by evaluating the risk of PASC among recipients of SSRIs that are not S1R agonists.\n\nDesignRetrospective study leveraging real-world clinical data within the National COVID Cohort Collaborative (N3C), a large centralized multi-institutional de-identified EHR database. Presumed PASC was defined based on a computable PASC phenotype trained on the U09.9 ICD-10 diagnosis code to more comprehensively identify patients likely to have the condition, since the ICD code has come into wide-spread use only recently.\n\nSettingPopulation-based study at US medical centers.\n\nParticipantsAdults ([≥] 18 years of age) with a confirmed COVID-19 diagnosis date between October 1, 2021 and April 7, 2022 and at least one follow up visit 45 days post-diagnosis. Of the 17 933 patients identified, 2021 were exposed at baseline to a S1R agonist SSRI, 1328 to a non-S1R agonist SSRI, and 14 584 to neither.\n\nExposuresExposure at baseline (at or prior to COVID-19 diagnosis) to an SSRI with documented or presumed agonist activity at the S1R (fluvoxamine, fluoxetine, escitalopram, or citalopram), an SSRI without agonist activity at S1R (sertraline, an antagonist, or paroxetine, which does not appreciably bind to the S1R), or none of these agents.\n\nMain Outcome and MeasurementDevelopment of PASC based on a previously validated XGBoost-trained algorithm. Using inverse probability weighting and Poisson regression, relative risk (RR) of PASC was assessed.\n\nResultsA 26% reduction in the RR of PASC (0.74 [95% CI, 0.63-0.88]; P = 5 x 10-4) was seen among patients who received an S1R agonist SSRI compared to SSRI unexposed patients and a 25% reduction in the RR of PASC was seen among those receiving an SSRI without S1R agonist activity (0.75 [95% CI, 0.62 - 0.90]; P = 0.003) compared to SSRI unexposed patients.\n\nConclusions and RelevanceSSRIs with and without reported agonist activity at the S1R were associated with a significant decrease in the risk of PASC. Future prospective studies are warranted.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSDo Selective Serotonin Reuptake Inhibitors with and without agonist activity at the sigma-1 receptor (S1R) prevent Post-Acute Sequelae of COVID-19?\n\nFindingsIn this retrospective study leveraging real-world clinical data that included 17 933 patients, a 28% reduction in risk of PASC was observed for S1R agonist SSRIs and a 25% reduction in risk of PASC was observed for non-S1R agonist SSRIs, both versus controls, using a computable phenotype to define PASC.\n\nMeaningSSRIs may play a role in managing the long term disease burden of COVID-19. Future prospective studies are warranted to confirm these findings and evaluate potential mechanisms of action.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hythem Sidky", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "David K Sahner", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Andrew T Girvin", + "author_inst": "Palantir Technologies, Denver, CO" + }, + { + "author_name": "Nathan Hotaling", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Sam G Michael", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Ken Gersing", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "- The N3C consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.04.515139", "rel_title": "Evasive spike variants elucidate the preservation of T cell immune response to the SARS-CoV-2 omicron variant", @@ -152323,69 +152799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2022.11.04.22281855", - "rel_title": "Disproportionate impacts of COVID-19 in a large US city", - "rel_date": "2022-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281855", - "rel_abs": "COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 16.9% (95% CrI: 16.1-17.8%) infection rate and 34.1% (95% CrI: 32.4-35.8%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (8.0% [95% CrI: 7.5-8.6%] vs 18.1% [95% CrI: 17.2-19.2%]), but more likely to be hospitalized (1,381 per 100,000 vs 319 per 100,000) and have their infections reported (51% [95% CrI: 48-55%] vs 33% [95% CrI: 31-35%]). Children under 18, who make up 20.3% of the local population, accounted for only 5.5% (95% CrI: 3.8-7.7%) of all infections between March 1 and May 1, 2020 compared with 20.4% (95% CrI: 17.3-23.9%) between December 1, 2020 and February 1, 2021. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 61%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. For example, the ratio in infection rates between the more and less vulnerable communities declined from 12.3 (95% CrI: 8.8-17.1) to 4.0 (95% CrI: 3.0-5.3) to 2.7 (95% CrI: 2.0-3.6), from April to August to December of 2020, respectively. Our results suggest that public health efforts to mitigate COVID-19 disparities were only partially effective and that the CDCs social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Spencer J Fox", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Emily Javan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Remy Pasco", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Graham C Gibson", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Briana Betke", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jos\u00e9 L Herrera Diestra", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Spencer Woody", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kelly Pierce", - "author_inst": "The Texas Advanced Computing Center" - }, - { - "author_name": "Kaitlyn E Johnson", - "author_inst": "The Rockefeller Foundation" - }, - { - "author_name": "Maureen Johnson-Le\u00f3n", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "The Santa Fe Institute" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.04.22281943", "rel_title": "Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income", @@ -152879,6 +153292,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.07.22282029", + "rel_title": "Changes in Alcohol Consumption during the COVID-19 Pandemic: Evidence from Wisconsin", + "rel_date": "2022-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282029", + "rel_abs": "IntroductionThe COVID-19 pandemic increased stress levels broadly in the general population. Patterns of alcohol consumption are known to increase in times of increased stress like natural disasters, disease outbreaks, and economic turmoil. Wisconsin is an important place to study changes in alcohol consumption because it is one of the heaviest-drinking states in the United States. The primary aim of this study is to identify changes in alcohol use at three distinct timepoints during the COVID-19 pandemic in a statewide sample.\n\nMethodsAn online survey was sent to 5,502 previous Survey of the Health of Wisconsin (SHOW) participants to ask about a wide range of topics related to COVID-19. The timepoints were taken May through June 2020 (Wave 1), January to February 2021 (Wave 2), and June 2021 (Wave 3) The sample included 1,290, 1,868, and 1,585 participants in each of the three waves respectively. Changes in alcohol consumption (whether they drank more, about the same, or less) were examined by race, age, gender, educational attainment, annual income, anxiety and depression status, remote work status, whether the participant experienced employment changes due to COVID-19, and whether there were children present in the home. Within-wave univariate changes in alcohol consumption were evaluated by demographics using a chi-squared test.\n\nResultsIn all three waves, those with anxiety, a bachelors degree or higher, two younger age groups, and those with children in the home were significantly more likely to increase alcohol consumption. Those reporting depression, those in the highest income quartile, and those working remotely were more likely to report increased drinking in the first two surveys, but not in the third survey. Participants reporting changes in employment due to COVID-19 were more likely to increase drinking in the first survey only. Non-white participants were more likely to report decreased drinking in the first survey only.\n\nConclusionsThere may be subpopulations in Wisconsin at higher risk for the negative effects of heavy drinking during the pandemic like those with anxiety, those with children in the home, those with a bachelors degree or higher, and those in younger age groups, as these groups had consistently higher alcohol use that did not subside 15 months after lockdowns began.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rachel Pomazal", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Laura McCulley", + "author_inst": "School of Medicine and Public Health, University of Wisconsin, Madison" + }, + { + "author_name": "Amy Schultz", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Noah Stafford", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Mikayla Schowalter", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Kristen Malecki", + "author_inst": "University of Illinois Chicago" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.04.22281935", "rel_title": "Effects of Different Mask Policies in 2020: A Comparative Analysis", @@ -153949,57 +154401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.11.03.22281925", - "rel_title": "Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative study: A systematic review and meta-analysis", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.03.22281925", - "rel_abs": "BackgroundPrior infection with SARS-CoV-2 can provide protection against infection and severe COVID-19. In settings with high pre-existing immunity, vaccine effectiveness (VE) should decrease with higher levels of immunity among unvaccinated individuals. Here, we conducted a systematic review and meta-analysis to understand the influence of prior infection on VE.\n\nMethodsWe included test-negative design (TND) studies that examined VE against infection or severe disease (hospitalization, ICU admission, or death) for primary vaccination series. To determine the impact of prior infections on VE estimates, we compared studies that excluded or included people with prior COVID-19 infection. We also compared VE estimates by the cumulative incidence of cases before the start of and incidence rates during each study in the study locations, as further measures of prior infections in the community.\n\nFindingsWe identified 67 studies that met inclusion criteria. Pooled VE among studies that included people with prior COVID-19 infection was lower against infection (pooled VE: 77%; 95% confidence interval (CI): 72%, 81%) and severe disease (pooled VE: 86%; 95% CI: 83%, 89%), compared with studies that excluded people with prior COVID-19 infection (pooled VE against infection: 87%; 95% CI: 85%, 89%; pooled VE against severe disease: 93%; 95% CI: 91%, 95%). There was a negative correlation between the cumulative incidence of cases before the start of the study and VE estimates against infection (spearman correlation ({rho}) = -0.32; 95% CI: -0.45, -0.18) and severe disease ({rho} = -0.49; 95% CI: -0.64, -0.30). There was also a negative correlation between the incidence rates of cases during the study period and VE estimates against infection ({rho} = - 0.48; 95% CI: -0.59, -0.34) and severe disease ({rho} = -0.42; 95% CI: -0.58, -0.23).\n\nInterpretationBased on a review of published VE estimates we found clear empirical evidence that higher levels of pre-existing immunity in a population were associated with lower VE estimates. Excluding previously infected individuals from VE studies may result in higher VE estimates with limited generalisability to the wider population. Prior infections should be treated as confounder and effect modificatory when the policies were targeted to whole population or stratified by infection history, respectively.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tim Tsang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "SheenaG Sullivan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Xiaotong Huang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "Can Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yifan Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joshua Nealon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Bingyi Yang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kylie E.C Ainslie", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ben J Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.02.22281821", "rel_title": "Screening COVID-19 by Swaasa AI Platform using cough sounds: A cross-sectional study", @@ -154581,6 +154982,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.01.22281810", + "rel_title": "Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants", + "rel_date": "2022-11-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.01.22281810", + "rel_abs": "The microbiome inherited at birth exerts marked effects on immune programming with long-term health consequences. Here, we demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition compared to healthy controls at the time of delivery. Accordingly, infants born to pregnant women with early SARS-CoV-2 infection exhibit a unique oral microbiota dominated by Streptococcus species. Together, we demonstrated that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infants microbiome-dependent immune programming.\n\nOne Sentence SummaryPregnant patients with SARS-CoV-2 infection early in pregnancy and with active infection exhibit an altered vaginal and oral microbiota that is passed on to infants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Heidi K. Leftwich", + "author_inst": "Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Medical Center, University of Massachusetts C" + }, + { + "author_name": "Daniela Vargas-Robles", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Mayra Rojas Correa", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Yan Rou Yap", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Shakti Bhattarai", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Doyle V. Ward", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Gavin Fujimori", + "author_inst": "Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Catherine S. Forconi", + "author_inst": "Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Tracy Yeboah", + "author_inst": "Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Medical Center, University of Massachusetts C" + }, + { + "author_name": "Acara Carter", + "author_inst": "Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Medical Center, University of Massachusetts C" + }, + { + "author_name": "Alyssa Kastrinakis", + "author_inst": "Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Medical Center, University of Massachusetts C" + }, + { + "author_name": "Alison M. Asirwatham", + "author_inst": "Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Massachusetts Memorial Medical Center, University of Massachusetts C" + }, + { + "author_name": "Vanni Bucci", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Ann M. Moormann", + "author_inst": "Department of Medicine. Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School" + }, + { + "author_name": "Ana Maldonado-Contreras", + "author_inst": "Department of Microbiology and Physiological Systems, Program of Microbiome Dynamics, University of Massachusetts Chan Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.02.22281825", "rel_title": "Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop", @@ -155231,20 +155707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.10.31.22281764", - "rel_title": "SARS-CoV-2 antibody prevalence among industrial livestock operation workers and nearby community residents, North Carolina, USA, 2021-2022", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281764", - "rel_abs": "Industrial livestock operations (ILOs), particularly processing facilities, emerged as centers of coronavirus disease 2019 (COVID-19) outbreaks in spring 2020. Confirmed cases of COVID-19 underestimate true prevalence. To investigate prevalence of antibodies against SARS-CoV-2, we enrolled 279 participants in North Carolina from February 2021 to July 2022: 90 from households with at least one ILO worker (ILO), 97 from high-ILO intensity areas (ILO neighbors - ILON), and 92 from metropolitan areas (Metro). Participants provided a saliva swab we analyzed for SARS-CoV-2 IgG using a multiplex immunoassay. Prevalence of infection-induced IgG (positive for nucleocapsid and receptor binding domain) was higher among ILO (63%) compared to ILON (42.9%) and Metro (48.7%) participants (prevalence ratio [PR] =1.38; 95% confidence interval [CI]: 1.06, 1.80; ref. ILON and Metro combined). Prevalence of infection-induced IgG was also higher among ILO participants compared to an Atlanta healthcare worker cohort (PR=2.45, 95% CI: 1.8, 3.3) and a general population cohort in North Carolina (PRs 6.37-10.67). Infection-induced IgG prevalence increased over the study period. Participants reporting not masking in public in the past two weeks had higher infection-induced IgG prevalence (78.6%) compared to participants reporting masking (49.3%) (PR=1.59; 95% CI: 1.19, 2.13). Lower education, more people per bedroom, Hispanic/Latino ethnicity, and more contact with people outside the home were also associated with higher infection-induced IgG prevalence. Similar proportions of ILO (51.6%), ILON (48.4%), and Metro (55.4%) participants completed the COVID-19 primary vaccination series; median completion was more than four months later for ILO compared to ILON and Metro participants.\n\nImportanceFew studies have measured COVID-19 seroprevalence in North Carolina, especially among rural, Black, and Hispanic/Latino communities that have been heavily affected. Antibody results show high rates of COVID-19 among industrial livestock operation workers and their household members. Antibody results add to evidence of health disparities in COVID-19 by socioeconomic status and ethnicity. Associations between masking and physical distancing with antibody results also add to evidence of the effectiveness of these prevention strategies. Delays in the timing of receipt of COVID-19 vaccination reinforce the importance of dismantling vaccination barriers, especially for industrial livestock operation workers and their household members.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.28.22281588", "rel_title": "A novel hospital-at-home model for patients with COVID-19 built by a team of local primary care clinics and clinical outcomes: A multi-center retrospective cohort study", @@ -155854,6 +156316,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.10.28.22281660", + "rel_title": "Seroprevalence, seroconversion, and seroreversion of infection-induced SARS-CoV-2 antibodies among a cohort of children and adolescents in Montreal, Canada", + "rel_date": "2022-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281660", + "rel_abs": "ImportanceRepeated serological testing for SARS-CoV-2 allows the monitoring of antibody dynamics in populations, including detecting infections that are missed by RT-PCR or antigen testing. Understanding the factors associated with seroconversion and seroreversion as well as the duration of infection-induced antibodies can also inform public health recommendations regarding disease prevention and mitigation efforts.\n\nObjectiveTo use serological testing to assess the prevalence, seroconversion, and seroreversion of infection-induced SARS-CoV-2 antibodies in children and adolescents in Montreal, Canada.\n\nDesignThis analysis reports on three rounds of data collection from a prospective cohort study (Enfants et COVID-19: Etude de seroprevalence [EnCORE]). The study rounds occurred as follows: Round 1 October 2020-March 2021, Round 2 May to July 2021, and Round 3 November 2021 to January 2022. Most Round 3 samples were collected prior to the spread of the Omicron BA.1 variant in Quebec.\n\nSettingPopulation-based sample.\n\nParticipantsChildren and adolescents aged 2 to 17 years in Montreal, Canada.\n\nExposurePotential exposure to SARS-CoV-2.\n\nMain Outcomes and MeasuresParticipants provided dried blood spots (DBS) for antibody detection and parents completed online questionnaires for sociodemographics and COVID-19 symptoms and testing history. The serostatus of participants was determined by enzyme-linked immunosorbent assays (ELISAs) using the receptor-binding domain (RBD) from the spike protein and the nucleocapsid protein (N) as antigens. We estimated seroprevalence for each round of data collection and by participant and household characteristics. Seroconversion rates were calculated as were the likelihoods of remaining seropositive at six months and one year.\n\nResultsThe study included DBS samples from 1 632, 936, and 723 participants in the first, second, and third rounds of data collection, respectively. The baseline seroprevalence was 5{middle dot}8% (95% CI 4{middle dot}8-7{middle dot}1), which increased to 10{middle dot}5% and 10{middle dot}9% for the respective follow-ups (95% CI 8{middle dot}6-12{middle dot}7; 95% CI 8{middle dot}8-13{middle dot}5). The overall average crude rate of seroconversion over the study period was 12{middle dot}7 per 100 person-years (95% CI 10{middle dot}9-14{middle dot}5). Adjusted hazard rates of seroconversion by child and household characteristics showed higher rates in children who were female, whose parent identified as a racial or ethnic minority, and in households with incomes less than 100K. The likelihood of remaining seropositive at six months was 67% (95% CI 59-76) and dropped to 19% (95% CI 11%-33%) at one year.\n\nConclusions and RelevanceThe data reported here provide estimates of pre-Omicron seroprevalence, seroconversion rates and time to seroreversion in a population-based cohort of children and adolescents. Serological studies continue to provide valuable contributions for infection prevalence estimates and help us better understand the dynamics of antibody levels following infection. Continued study of seroconversion and seroreversion can inform public health recommendations such as COVID-19 vaccination and booster schedules.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat was the rate of seroconversion and time to seroreversion for SARS-CoV-2 antibodies among children and adolescents in Montreal between October 2020 to January 2022?\n\nFindingsThe overall average crude rate of seroconversion was 12{middle dot}7 per 100 person-years (95% CI 10{middle dot}9-14{middle dot}5). We observed higher rates of seroconversion in children who were female, whose parent identified as a racial or ethnic minority, and in households with incomes less than 100K. Among all children who seroconverted, 71% had not been previously diagnosed with COVID-19. Median time to seroreversion was 7{middle dot}5 months.\n\nMeaningEven before the emergence of the Omicron variants, we observed a high rate of seroconversion for infection-induced SARS-CoV-2 antibodies along with widespread antibody waning by one year. Many children and adolescents seroconverted despite not receiving a prior COVID-19 diagnosis, indicating that RT-PCR and antigen testing continue to underestimate true disease prevalence.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kate Zinszer", + "author_inst": "University of Montreal, Montreal, Quebec, Canada; Centre for Public Health Research, University of Montreal, Quebec, Canada" + }, + { + "author_name": "Katia Charland", + "author_inst": "Centre for Public Health Research, University of Montreal, Quebec, Canada" + }, + { + "author_name": "Laura Pierce", + "author_inst": "Centre for Public Health Research, University of Montreal, Quebec, Canada" + }, + { + "author_name": "Adrien Saucier", + "author_inst": "University of Montreal, Montreal, Quebec, Canada; Centre for Public Health Research, University of Montreal, Quebec, Canada" + }, + { + "author_name": "Britt McKinnon", + "author_inst": "Centre for Public Health Research, University of Montreal, Quebec, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada" + }, + { + "author_name": "Marie-\u00c8ve Hamelin", + "author_inst": "Infectious Disease Research Center, Research Centre of Quebec-Universit\u00e9 Laval, Quebec City, Quebec, Canada" + }, + { + "author_name": "Islem Cheriet", + "author_inst": "University of Montreal, Montreal, Quebec, Canada" + }, + { + "author_name": "Margot Barbosa Da Torre", + "author_inst": "University of Montreal, Montreal, Quebec, Canada; Centre for Public Health Research, University of Montreal, Quebec, Canada" + }, + { + "author_name": "Julie Carbonneau", + "author_inst": "Infectious Disease Research Center, Research Centre of Quebec-Universit\u00e9 Laval, Quebec City, Quebec, Canada" + }, + { + "author_name": "Cat Tuong Nguyen", + "author_inst": "Minist\u00e8re de la sant\u00e9 et des services sociaux, Quebec City, Quebec, Canada" + }, + { + "author_name": "Gaston De Serres", + "author_inst": "National Institute of Public Health of Quebec, Quebec City, Quebec, Canada" + }, + { + "author_name": "Jesse Papenburg", + "author_inst": "Montreal Childrens Hospital of the McGill University Health Centre" + }, + { + "author_name": "Guy Boivin", + "author_inst": "Infectious Disease Research Center, Research Centre of Quebec-Universit\u00e9 Laval, Quebec City, Quebec, Canada" + }, + { + "author_name": "Caroline Quach", + "author_inst": "University of Montreal, Montreal, Quebec, Canada; Research Centre of the Sainte-Justine University Hospital, Montreal, Quebec, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.10.28.22281667", "rel_title": "Identifying trends in SARS-CoV-2 RNA in wastewater to infer changing COVID-19 incidence: Effect of sampling frequency", @@ -157240,53 +157773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.26.22281575", - "rel_title": "Impact of COVID-19 related maternal stress on fetal brain development: A Multimodal MRI study", - "rel_date": "2022-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22281575", - "rel_abs": "BackgroundDisruptions in perinatal care and support due to the COVID-19 pandemic was an unprecedented but significant stressor among pregnant women. Various neurostructural differences have been re-ported among fetuses and infants born during the pandemic compared to pre-pandemic counterparts. The relationship between maternal stress due to pandemic related disruptions and fetal brain is yet unexamined.\n\nMethodsPregnant participants with healthy pregnancies were prospectively recruited in 2020-2022 in the greater Los Angeles Area. Participants completed multiple self-report assessments for experiences of pandemic related disruptions, perceived stress, and coping behaviors and underwent fetal MRI. Maternal perceived stress exposures were correlated with quantitative multimodal MRI measures of fetal brain development using ltivariate models.\n\nResultsFetal brain stem volume increased with increased maternal perception of pandemic related stress positively correlated with normalized fetal brainstem volume (suggesting accelerated brainstem maturation). In contrast, increased maternal perception of pandemic related stress correlated with reduced global fetal brain temporal functional variance (suggesting reduced functional connectivity).\n\nConclusionsWe report alterations in fetal brainstem structure and global functional fetal brain activity associated with increased maternal stress due to pandemic related disruptions, suggesting altered fetal programming. Long term follow-up studies are required to better understand the sequalae of these early multi-modal brain disruptions among infants born during the COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vidya Rajagopalan", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "William T. Reynolds", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jeremy Zepeda", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Jeraldine Lopez", - "author_inst": "The Saban Research Institute" - }, - { - "author_name": "Skorn Ponrartana", - "author_inst": "Keck School of Medicine University of Southern California" - }, - { - "author_name": "John Wood", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Rafael Ceschin", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ashok Panigrahy", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.10.26.22278866", "rel_title": "Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID-19", @@ -158072,6 +158558,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.24.22281482", + "rel_title": "The pervasive association between political ideology and COVID-19 vaccine uptake in Brazil: an ecologic study", + "rel_date": "2022-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.24.22281482", + "rel_abs": "BackgroundStudies suggest vaccine hesitancy is an increasingly significant phenomenon in Brazil and other countries. Moreover, political ideologies have emerged as an influencing factor for vaccine hesitancy during the COVID-19 pandemic.\n\nMethodsIn this study, we use information from publicly available databases to investigate the association between political alignment, depicted by the percentage of Bolsonaro voters in the presidential elections of 2018 and 2022, and COVID-19 vaccination in Brazilian municipalities, adjusted for human development index (HDI) scores and basic sociodemographic characteristics of voters.\n\nFindingsFor both the 2018 and 2022 elections, higher percentages of Bolsonaro voters were significantly associated with a lower vaccination index after adjustment for voters sociodemographic characteristics. We also found a statistically significant interaction between the percentage of Bolsonaro voters and HDI, with a more significantly detrimental effect of the right-wing political stance in municipalities in the lower HDI quartile.\n\nInterpretationOur study highlights what may be the beginning of a new scenario with unforeseen challenges for vaccine programs: the politicization of vaccines. Strategies to face these challenges should include joint efforts from governments and civil society for a common public health goal.\n\nFundingThis manuscript received no specific funding", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gabriel J Seara-Morais", + "author_inst": "Faculdade Israelita de Ciencias da Saude Albert Einstein, Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Thiago J Avelino-Silva", + "author_inst": "Laboratorio de Investigacao Medica em Envelhecimento (LIM-66), Servico de Geriatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao P" + }, + { + "author_name": "Marcia Couto", + "author_inst": "Department of Preventive Medicine, Faculdade de Medicina, Universidade de Sao Paulo, SP, Brazil" + }, + { + "author_name": "Vivian I Avelino-Silva", + "author_inst": "Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de Sao Paulo, SP, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.10.25.22281489", "rel_title": "Effects of the COVID-19 pandemic on hospital admissions and inpatient mortality in Kenya", @@ -159646,125 +160163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.10.23.22281414", - "rel_title": "Impact of vaccination on the presence and severity of symptoms of hospitalised patients with an infection by the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1).", - "rel_date": "2022-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.23.22281414", - "rel_abs": "ObjectivesThe emergence of SARS-CoV-2 variants raised questions over the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalised patients.\n\nMethodsWe conducted an international, multicentric, retrospective study in 14 centres (Bulgaria, Croatia, France, Turkey). We collected data on patients hospitalised [≥]24 hours between 01/12/2021 and 03/03/2022, with PCR-confirmed infection at a time of exclusive Omicron circulation, with hospitalisation related or not to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least 2 injections of either mRNA and/or ChAdOx1-S, or 1 injection of Ad26.CoV2-S vaccines.\n\nResultsAmong the 1215 patients (median [IQR] age 73.0 [57.0; 84.0]; 51.3% males), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28-day mortality (RR=0.50 [0.32-0.77]), ICU admission (R=0.40 [0.26-0.62], and oxygen requirement (RR=0.34 [0.25-0.46]), independently of age and comorbidities. When co-analysing these Omicron patients with 948 Delta patients from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (RR=0.53 [0.37-0.76]), ICU admission (R=0.19 [0.12-0.28], and oxygen requirements (RR=0.50 [0.38-0.67]), independently of age, comorbidities and vaccination status.\n\nConclusionsmRNA- and adenovirus-based vaccines have remained effective on severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independently of vaccination and patient characteristics.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Guillaume Beraud", - "author_inst": "University Hospital of Poitiers" - }, - { - "author_name": "Laura Bouetard", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Rok Civljak", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia and University of Zagreb School of Medicine, Zagreb, Croatia." - }, - { - "author_name": "Jocelyn Michon", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Necla Tulek", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Lejeune", - "author_inst": "Infectious diseases, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France" - }, - { - "author_name": "Romain Millot", - "author_inst": "Infectious disease department, University Hospital of Poitiers, Poitiers, France" - }, - { - "author_name": "Aurelie Garchet-Beaudron", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Maeva Lefebvre", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France and INSERM UIC 1413 Nantes University," - }, - { - "author_name": "Petar Velikov", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Benjamin Festou", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France" - }, - { - "author_name": "Sophie Abgrall", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Ivan Kresimir Lizatovic", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia" - }, - { - "author_name": "Aurelie Baldolli", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Huseyin Esmer", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Blanchi", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Gabrielle Froidevaux", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France" - }, - { - "author_name": "Nikol Kapincheva", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Jean-Francois Faucher", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France and INSERM U1094, Limoges, France." - }, - { - "author_name": "Mario Duvnjak", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Elcin Afsar", - "author_inst": "Atilim University, Vocational School of Health Services, Ankara, Turkey" - }, - { - "author_name": "Luka Svitek", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Saliha Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Rafet Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Cecile Janssen", - "author_inst": "Infectious Disease Unit, Centre Hospitalier Annecy Genevois, Annecy, France" - }, - { - "author_name": "olivier EPAULARD", - "author_inst": "centre hospitalier universitaire Grenoble Alpes" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.24.513610", "rel_title": "Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2", @@ -160706,6 +161104,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.22.22281373", + "rel_title": "Comparative Effectiveness of Dexamethasone in Treatment of Hospitalized COVID-19 Patients during the First Year of the Pandemic: The N3C Data Repository", + "rel_date": "2022-10-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.22.22281373", + "rel_abs": "BackgroundDexamethasone, a widely available glucocorticoid, was approved for use in hospitalized COVID-19 patients early in the pandemic based on the RECOVERY trial; however, evidence is still needed to support its real-world effectiveness in patients with a wide range of comorbidities and in diverse care settings.\n\nObjectivesTo conduct a comparative effectiveness analysis of dexamethasone use with and without remdesivir in hospitalized COVID-19 patients using electronic health record data.\n\nMethodsWe conducted a retrospective real-world effectiveness analysis using the harmonized, highly granular electronic health record data of the National COVID Cohort Collaborative (N3C) Data Enclave. Analysis was restricted to COVID-19 patients in an inpatient setting, prior to vaccine availability. Primary outcome was in-hospital death; secondary outcome was combined in-hospital death and severe outcome as defined by use of ECMO or mechanical ventilation during stay. Missing data were imputed with single imputation. Matching of dexamethasone-treated patients to non-dexamethasone-treated controls was accomplished using propensity score (PS) matching, stratified by remdesivir treatment and based on demographics, baseline laboratory values, and comorbidities. Treatment benefit was quantified using logistic regression. Further sensitivity analyses were performed using clinical adjusters in matched groups and in strata defined by quartiles of PS.\n\nResultsRegression analysis revealed a statistically significant association between dexamethasone use and reduced risk of in-hospital mortality for those not receiving remdesivir (OR=0.77, 95% CI: 0.62 to 0.95, p=0.017), and a borderline statistically significant risk for those receiving remdesivir (OR=0.74, 95% CI: 0.53 to 1.02, p=0.054). Treatment also showed secondary outcome benefit. In sensitivity analyses, treatment effect size generally remained similar with some heterogeneity of benefit across strata of PS.\n\nConclusionsWe add evidence that dexamethasone provides benefit with respect to mortality and severe outcomes in a diverse, national hospitalized sample, prior to vaccine availability.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Richard Zhou", + "author_inst": "Department of Biomedical Engineering, University of Texas at Austin" + }, + { + "author_name": "Kaitlyn E Johnson", + "author_inst": "The Pandemic Prevention Institute, The Rockefeller Foundation" + }, + { + "author_name": "Justin F Rousseau", + "author_inst": "Dell Medical School at the University of Texas at Austin" + }, + { + "author_name": "Paul J Rathouz", + "author_inst": "Dell Medical School at the University of Texas at Austin" + }, + { + "author_name": "- The N3C Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.10.21.22281349", "rel_title": "Association of viral variant and vaccination status with the occurrence of symptoms compatible with post-acute sequelae after primary SARS-CoV-2 infection", @@ -161664,29 +162097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.10.18.22281063", - "rel_title": "Deep reinforcement learning framework for controlling infectious disease outbreaks in the context of multi-jurisdictions", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281063", - "rel_abs": "In the absence of pharmaceutical interventions, social distancing and lockdown have been key options for controlling new or reemerging respiratory infectious disease outbreaks. The timely implementation of these interventions is vital for effectively controlling and safeguarding the economy.\n\nMotivated by the COVID-19 pandemic, we evaluated whether, when, and to what level lockdowns are necessary to minimize epidemic and economic burdens of new disease outbreaks. We formulated the question as a sequential decision-making Markov Decision Process and solved it using deep Q-network algorithm. We evaluated the question under two objective functions: a 2-objective function to minimize economic burden and hospital capacity violations, suitable for diseases with severe health risks but with minimal death, and a 3-objective function that additionally minimizes the number of deaths, suitable for diseases that have high risk of mortality. A key feature of the model is that we evaluated the above questions in the context of two-geographical jurisdictions that interact through travel but make autonomous and independent decisions, evaluating under cross-jurisdictional cooperation and non-cooperation.\n\nIn the 2-objective function under cross-jurisdictional cooperation, the optimal policy was to aim for shutdowns at 50% and 25% per day. Though this policy avoided hospital capacity violations, the shutdowns extended until a large proportion of the population reached herd immunity. Delays in initiating this optimal policy or non-cooperation from an outside jurisdiction required shutdowns at a higher level of 75% per day, thus adding to economic burdens. In the 3-objective function, the optimal policy under cross-jurisdictional cooperation was to aim for shutdowns of up to 75% per day to prevent deaths by reducing infected cases. This optimal policy continued for the entire duration of the simulation, suggesting that, until pharmaceutical interventions such as treatment or vaccines become available, contact reductions through physical distancing would be necessary to minimize deaths. Deviating from this policy increased the number of shutdowns and led to several deaths.\n\nIn summary, we present a decision-analytic methodology for identifying optimal lockdown strategy under the context of interactions between jurisdictions that make autonomous and independent decisions. The numerical analysis outcomes are intuitive and, as expected, serve as proof of the feasibility of such a model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Seyedeh Nazanin khatami", - "author_inst": "MGH Institute for Technology Assessment, Harvard Medical School, Boston, MA 02114, , USA" - }, - { - "author_name": "Chaitra Gopalappa", - "author_inst": "University of Massachusetts Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.20.22281317", "rel_title": "The COVID-19 burnout scale: Development and initial validation", @@ -162620,6 +163030,41 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2022.10.21.513200", + "rel_title": "A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses", + "rel_date": "2022-10-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.21.513200", + "rel_abs": "T cell recognition of SARS-CoV-2 antigens after vaccination and/or natural infection has played a central role in resolving SARS-CoV-2 infections and generating adaptive immune memory. However, the clinical impact of SARS-CoV-2-specific T cell responses is variable and the mechanisms underlying T cell interaction with target antigens are not fully understood. This is especially true given the virus rapid evolution, which leads to new variants with immune escape capacity. In this study, we used the Omicron variant as a model organism and took a systems approach to evaluate the impact of mutations on CD8+ T cell immunogenicity. We computed an immunogenicity potential score for each SARS-CoV-2 peptide antigen from the ancestral strain and Omicron, capturing both antigen presentation and T cell recognition probabilities. By comparing ancestral vs. Omicron immunogenicity scores, we reveal a divergent and heterogeneous landscape of impact for CD8+ T cell recognition of mutated targets in Omicron variants. While T cell recognition of Omicron peptides is broadly preserved, we observed mutated peptides with deteriorated immunogenicity that may assist breakthrough infection in some individuals. We then combined our scoring scheme with an in-silico mutagenesis, to characterise the position- and residue-specific theoretical mutational impact on immunogenicity. While we predict many escape trajectories from the theoretical landscape of substitutions, our study suggests that Omicron mutations in T cell epitopes did not develop under cell-mediated pressure. Our study provides a generalisable platform for fostering a deeper understanding of existing and novel variant impact on antigen-specific vaccine- and/or infection-induced T cell immunity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Paul R Buckley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chloe Hyun-Jung Lee", + "author_inst": "University of Oxford" + }, + { + "author_name": "Agne Antanaviciute", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alison Simmons", + "author_inst": "University of Oxford" + }, + { + "author_name": "Hashem Koohy", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.10.21.513196", "rel_title": "SARS-CoV-2 nsp3-4 suffice to form a pore shaping replication organelles", @@ -163718,81 +164163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.18.22281172", - "rel_title": "Antibody-mediated protection against symptomatic COVID-19 can be achieved at low serum neutralizing titers", - "rel_date": "2022-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281172", - "rel_abs": "Multiple studies of vaccinated and convalescent cohorts have demonstrated that serum neutralizing antibody (nAb) titers correlate with protection against COVID-19. However, the induction of multiple layers of immunity following SARS-CoV-2 exposure has complicated the establishment of nAbs as a mechanistic correlate of protection (CoP) and hindered the definition of a protective nAb threshold. Here, we show that a half-life extended monoclonal antibody (adintrevimab) provides approximately 50% protection against symptomatic COVID-19 in SARS-CoV-2-naive adults at low serum nAb titers on the order of 1:30. Vaccine modeling supports a similar 50% protective nAb threshold, suggesting low levels of serum nAb can protect in both monoclonal and polyclonal settings. Extrapolation of adintrevimab pharmacokinetic data suggests that protection against susceptible variants could be maintained for approximately 3 years. The results provide a benchmark for the selection of next-generation vaccine candidates and support the use of broad, long-acting monoclonal antibodies as an alternative or supplement to vaccination in high-risk populations.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pete Schmidt", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Kristin Narayan", - "author_inst": "Invivyd, Inc." - }, - { - "author_name": "Yong Li", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Chengzi Kaku", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Michael Brown", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Elizabeth Champney", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "James Geoghegan", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Maximiliano Vasquez", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Eric Krauland", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Thomas Yockachonis", - "author_inst": "Washington State University" - }, - { - "author_name": "Shuangyi Bai", - "author_inst": "Washington State University" - }, - { - "author_name": "Bronwyn Gunn", - "author_inst": "Washington State University" - }, - { - "author_name": "Anthony Cammarata", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Chris Rubino", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Laura M Walker", - "author_inst": "Invivyd, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.17.22281161", "rel_title": "Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants", @@ -164774,6 +165144,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.17.512569", + "rel_title": "N6-Adenosine Methylation of SARS-CoV-2 5-UTR Regulates Translation", + "rel_date": "2022-10-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.17.512569", + "rel_abs": "The coronavirus disease 2019 (COVID19) continues to spread despite global vaccination efforts (1). This, alongside the rapid emergence of vaccine resistant variants, creates a need for orthogonal therapeutic strategies targeting more conserved facets of severe acute respiratory syndrome coronavirus (SARS-CoV-2) (2-4). One conserved feature of all coronaviruses is their ability to undergo discontinuous transcription wherein individual open reading frames fuse with the 5-UTR leader sequence during negative-strand RNA synthesis (5). As such all viral protein coding genes use the same 5-UTR for translation (6). Using in vitro reporter assays, we demonstrate that the SARS-CoV-2 5-UTR efficiently initiates protein translation despite its predicted structural complexity. Through a combination of bioinformatic and biochemical assays, we demonstrate that a single METTL3-dependent m6A methylation event in SARS-CoV-2 5-UTR regulates the rate of translation initiation. We show that m6A likely exerts this effect by destabilizing secondary structure in the 5-UTR, thereby facilitating access to the ribosomal pre-initiation complex. This discovery opens new avenues for novel therapeutic strategies aimed at controlling the ability of SARS-CoV-2 to replicate in host cells.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ammar Aly", + "author_inst": "The Buck Institute for Research Aging" + }, + { + "author_name": "Gary Scott", + "author_inst": "The Buck Institute for Research on Aging" + }, + { + "author_name": "Mario Calderon", + "author_inst": "The Buck Institute for Research on Aging" + }, + { + "author_name": "Pejmun Haghighi", + "author_inst": "The Buck Institute for Research on Aging" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.10.17.512637", "rel_title": "Deep learning-based Drug discovery of Mac domain of SARS-CoV-2 (WT) Spike inhibitors: using experimental ACE2 Inhibition TR-FRET Assay Screening and Molecular Dynamic Simulations.", @@ -165924,61 +166325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.16.22281142", - "rel_title": "Making use of an App (Tawakkalna) to track and reduce COVID transmission in KSA", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.16.22281142", - "rel_abs": "Since March 2020, the Kingdom of Saudi Arabia (KSA) has launched several digital applications to support the intervention response to reduce the spread of SARS-CoV-2. At the beginning of 2021, the KSA Government introduced a mandatory immunity passport to regulate access to public venues. The passport was part of the strategy of resuming public activities before reaching high vaccination coverage. The passport was implemented as a new service in the Tawakkalna mobile phone application (App). The immunity passport allowed access to public locations only for the users who recovered from COVID-19 or those who were double vaccinated. Our study aimed to evaluate the effectiveness of the immunity passport, implemented through the Tawakkalna App, on SARS-CoV-2 spread. We built a spatial-explicit individual-based model to represent the whole KSA population (IBM-KSA) and its dynamic on a national scale. The IBM-KSA was parameterized using country demographic, remote sensing, and epidemiological data. The model included non-pharmaceutical interventions and vaccination coverage. A social network was created to represent contact heterogeneity and interaction among age groups of the population. The IBM-KSA also simulated the movement of people across the country based on a gravity model. We used the IBM-KSA to evaluate the effect of the immunity passport on the COVID-19 epidemics outcomes. The IBM-KSA results showed that implementing the immunity passport through the Tawakkalna App mitigated the SARS-CoV2 spread. In a scenario without the immunity passport, the KSA could have reported 1,515,468 (95% confidence interval [CI]: 965,725-1,986,966) cases, and 30,309 (95% CI: 19,314-39,739) deaths from March 2021 to November 2021. The comparison of IBM-KSA results with COVID-19 official reporting estimated that the passport effectively reduced the number of cases, hospitalizations, and deaths by 8.7 times, 13.5 times, and 11.9 times, respectively. These results showed that the introduction of the immunity passport through the Tawakkalna App was able to control the spread of the SARS-COV-2 until vaccination reached high coverage. By introducing the immunity passport, The KSA was able to allow to resume most of public activities safely.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Donal Bisanzio", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Richard Reithinger", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Sami Almudarra", - "author_inst": "Saudi Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Reem F Alsukait", - "author_inst": "Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Di Dong", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Yi Zhang", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Sameh El-Saharty", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Hala Almossawi", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Christopher H Herbst", - "author_inst": "World Bank, Washington, D.C., USA" - }, - { - "author_name": "Ada Alqunaibet", - "author_inst": "Saudi Public Health Authority, Riyadh, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.14.512325", "rel_title": "The impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola", @@ -166508,6 +166854,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.13.22280957", + "rel_title": "Serology assays used in SARS-CoV-2 seroprevalence surveys worldwide: a systematic review and meta-analysis of assay features, testing algorithms, and performance", + "rel_date": "2022-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.13.22280957", + "rel_abs": "BackgroundMany serological assays to detect SARS-CoV-2 antibodies were developed during the COVID-19 pandemic. Differences in the detection mechanism of SARS-CoV-2 serological assays limited the comparability of seroprevalence estimates for populations being tested.\n\nMethodsWe conducted a systematic review and meta-analysis of serological assays used in SARS-CoV-2 population seroprevalence surveys, searching for published articles, preprints, institutional sources, and grey literature between January 1, 2020, and November 19, 2021. We described features of all identified assays and mapped performance metrics by the manufacturers, third-party head-to-head, and independent group evaluations. We compared the reported assay performance by evaluation source with a mixed-effect beta regression model. A simulation was run to quantify how biased assay performance affects population seroprevalence estimates with test adjustment.\n\nResultsAmong 1807 included serosurveys, 192 distinctive commercial assays and 380 self-developed assays were identified. According to manufacturers, 28.6% of all commercial assays met WHO criteria for emergency use (sensitivity [Sn.] >= 90.0%, specificity [Sp.] >= 97.0%). However, manufacturers overstated the absolute values of Sn. of commercial assays by 1.0% [0.1, 1.4%] and 3.3% [2.7, 3.4%], and Sp. by 0.9% [0.9, 0.9%] and 0.2% [-0.1, 0.4%] compared to third-party and independent evaluations, respectively. Reported performance data was not sufficient to support a similar analysis for self-developed assays. Simulations indicate that inaccurate Sn. and Sp. can bias seroprevalence estimates adjusted for assay performance; the error level changes with the background seroprevalence.\n\nConclusionsThe Sn. and Sp. of the serological assay are not fixed properties, but varying features depending on the testing population. To achieve precise population estimates and to ensure the comparability of seroprevalence, serosurveys should select assays with high performance validated not only by their manufacturers and adjust seroprevalence estimates based on assured performance data. More investigation should be directed to consolidating the performance of self-developed assays.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Xiaomeng Ma", + "author_inst": "Institute of Health Policy Management & Evaluation, University of Toronto" + }, + { + "author_name": "Zihan Li", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, University of California Berkeley" + }, + { + "author_name": "Mairead G. Whelan", + "author_inst": "Cumming School of Medicine, University of Calgary" + }, + { + "author_name": "Dayoung Kim", + "author_inst": "Cumming School of Medicine, University of Calgary" + }, + { + "author_name": "Christian Cao", + "author_inst": "Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Mercede Yanes-Lane", + "author_inst": "COVID-19 Immunity Task Force, McGill University" + }, + { + "author_name": "Tingting Yan", + "author_inst": "Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Thomas Jaenisch", + "author_inst": "Department of Epidemiology & Center for Global Health, Colorado School of Public Health" + }, + { + "author_name": "May C. Chu", + "author_inst": "Department of Epidemiology & Center for Global Health, Colorado School of Public Health" + }, + { + "author_name": "David A. Clifton", + "author_inst": "COVID-19 Immunity Task Force, McGill University" + }, + { + "author_name": "Lorenzo Subissi", + "author_inst": "World Health Organization" + }, + { + "author_name": "Niklas Bobrovitz", + "author_inst": "Temerty Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Rahul K. Arora", + "author_inst": "Institute of Biomedical Engineering, University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.10.13.512134", "rel_title": "Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1Omicron", @@ -167894,41 +168307,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.13.512053", - "rel_title": "SARS-CoV-2 infection in domestic rats after transmission from their infected owner", - "rel_date": "2022-10-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.13.512053", - "rel_abs": "We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur, Universite Paris Cite, Mouse Genetics Laboratory, Paris, France" - }, - { - "author_name": "Berenice Decaudin", - "author_inst": "Service NAC, Centre Hospitalier Veterinaire Advetia, Velizy-Villacoublay, France" - }, - { - "author_name": "Maxime Beretta", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Hugo Mouquet", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.12.512011", "rel_title": "Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic", @@ -168602,6 +168980,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.11.511764", + "rel_title": "SARS-CoV2 associated secretion of nanoLuciferase reports on virus and Virus-Like Particle production", + "rel_date": "2022-10-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.11.511764", + "rel_abs": "SARS-CoV2 is a positive-strand RNA virus in the Coronaviridae family that has caused world-wide morbidity and mortality. While much progress has been made we still need expanded rapid anti-virals. The top advanced antiviral candidates all target stages of RNA replication, leaving virus assembly an unexplored avenue of antiviral research. To address this gap, and explore the biochemical and cell biological features of viral assembly, we have employed an improved virus-like particle (VLP) system. We exploited the small nanoLuciferase protein for enhanced signal and surprisingly found that the protein itself appears to be packaged into both SARS CoV2 VLPs and virions and secreted from cells. Interestingly, nLuc is not co-secreted with dengue or Zika infection, suggesting the large virion of Coronavirus can encaspidate and secrete a cellularly expressed reporter protein. Our findings open the way for powerful new approaches to measure viral particle production, egress and viral entry mechanisms.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rebekah Gullberg", + "author_inst": "Stanford University" + }, + { + "author_name": "Judith Frydman", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.10.12.22280996", "rel_title": "Analysis of fatality among COVID-19 cases in Mexican pregnant women: a cross-sectional study", @@ -169908,29 +170309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.10.22280683", - "rel_title": "Sensitivity of endemic behaviour of Covid-19 under a multi-dose vaccination regime, to various biological parameters and control variables", - "rel_date": "2022-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280683", - "rel_abs": "For an infectious disease such as Covid-19, we present a new four-stage vaccination model (un-vaccinated, dose 1+2, booster, repeated boosters), which examines the impact of vaccination coverage, vaccination rate, generation interval, control reproduction number, vaccine efficacies, and rates of waning immunity, upon the dynamics of infection. We derive a single equation that allows computation of equilibrium prevalence and incidence of infection, given knowledge about these parameter and variable values. Based upon a 20 compartment model, we develop a numerical simulation of the associated differential equations. The model is not a forecasting or even predictive one, given the uncertainty about several biological parameter values. Rather, it is intended to aid qualitative understanding of how equilibrium levels of infection may be impacted upon, by the parameters of the system. We examine one at a time sensitivity analysis around a base case scenario. The key finding which should be of interest to policy makers, is that while factors such as improved vaccine efficacy, increased vaccination rates, lower waning rates, and more stringent non-pharmaceutical interventions might be thought to improve equilibrium levels of infection, this might only be done to good effect, if vaccination coverage on a recurrent basis, is sufficiently high.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "John S Dagpunar", - "author_inst": "School of Mathematical Sciences, University of Southampton" - }, - { - "author_name": "Chenchen Wu", - "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.09.22280878", "rel_title": "Associations Between Reported Post-COVID-19 Symptoms and Subjective Well-Being, Israel, July 2021 -April 2022", @@ -170784,6 +171162,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.07.22280607", + "rel_title": "Comparison of COVID-19 Antigen Rapid Test (Oral Fluid) and Real-Time RT-PCR in the laboratory diagnosis of SARS-CoV-2 infection", + "rel_date": "2022-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.07.22280607", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first diagnosed in December 2019. Since then this virus has caused an ongoing wide pandemic. Accurate diagnostic tests for SARS-CoV-2 are used to prevent the virus from spreading. However, these tests could not keep up with the demand and were not available in all places. Self-testing devices are easy-to-use-tests and reduce the demand in the diagnostic laboratories. The Antigen Rapid Test evaluated in this study uses oral fluid which is a non-invasive technique compared to nasopharyngeal swabs.\n\nIn this study the COVID-19 Antigen Rapid Test (Oral fluid) was evaluated with 150 SARS-CoV-2 positive saliva specimens and 350 SARS-CoV-2 negative saliva specimens. The Antigen Rapid Test was performed according to the instruction manual. SARS-CoV-2 Real-time RT-PCR was used as Golden Standard.\n\nAlthough the criteria of the WHO are specific to nasal / nasopharyngeal samples (and not saliva), the specificity of the Antigen Rapid Test meets the criteria of the World Health Organization (WHO; specificity [≥] 97%). The test meets the WHO sensitivity criteria in samples with higher viral loads (Ct<30), showing the better performance of the test in highly positive samples. For positive SARS-CoV-2 specimens with a Ct value lower than 30 a sensitivity of 83.8% (95% CI: 80.1%-86.8%) and an accuracy of 95.9% (95% CI: 93.7%-97.4%) was observed. This shows that this assay with saliva samples is able to meet the high standards set by the WHO. The performance of the test is comparable to other antigen rapid tests reported in meta-analyses. Furthermore, the test allows self-testing which is non-invasive, affordable and straightforward. This antigen rapid test may provide an affordable, quick, and easy to perform method to differentiate between individuals with high and low viral loads.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lotte M. Mense", + "author_inst": "Microbe&Lab BV" + }, + { + "author_name": "Sander Ouburg", + "author_inst": "Microbe&Lab BV" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.07.22280781", "rel_title": "THE IMPACT OF THE COVID-19 LOCKDOWN ON BIRTH WEIGHT AMONG SINGLETON TERM BIRTHS IN DENMARK", @@ -171850,41 +172251,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.04.510837", - "rel_title": "Community engagement through student-led science for dengue prevention during the COVID-19 pandemic in Cordoba, Argentina.", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510837", - "rel_abs": "BackgroundDuring 2019-2020 while COVID-19 pandemic, the Americas were facing the biggest dengue fever epidemic in recent history. Traditional vector control programs, based on insecticide application have been insufficient to control the spread of dengue fever. Several studies suggest refocusing on education with the aim of an integrated vector management strategy within the local ecological-community context. We aim to assess community perceptions, knowledge, attitude, preventive practice, and action through student-led science assignments regarding dengue fever, prevention, and socio-ecological factors in temperate Cordoba, Argentina.\n\nMethodsThe study was conducted during the COVID-19 quarantine when schools switched to online education for the first time. Several activities through Google Classroom platform included a survey to one students family member, and an outdoor activity to assess their attitudes and to clean the backyard and gardens.\n\nResultsSignificant number of respondents developed good preventive practices and increased their knowledge about the vector and disease highlighting that 75% of responders knew that dengue fever was transmitted by a mosquito, 81.96% declared having obtained knowledge regarding dengue and vector through television, 56% affirm that dengue is a severe illness, 67% of respondents admitted that individuals play an important role in the prevention of dengue. Regarding mosquito control activities, 90% of respondents reported turning containers.\n\nConclusionsThis highlights the need for school programs with curricula to address vector biology and the prevention of vector-borne diseases not only during activity periods when mosquitoes batter people but all year long to do real prevention.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elizabet Lilia Estallo", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Magali Madelon", - "author_inst": "Instituto Jesus Maria" - }, - { - "author_name": "Elisabet Benitez", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Anna Maria Stewart-Ibarra", - "author_inst": "InterAmerican Institute for Global Change Research" - }, - { - "author_name": "Francisco Felipe Luduena-Almeida", - "author_inst": "Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Cordoba." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2022.10.03.22280660", "rel_title": "Effectiveness and duration of a second COVID-19 vaccine booster", @@ -172458,6 +172824,53 @@ "type": "new results", "category": "physiology" }, + { + "rel_doi": "10.1101/483867", + "rel_title": "Optimal metabolic states in cells", + "rel_date": "2022-10-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/483867", + "rel_abs": "Cells, in order to thrive, make efficient use of metabolites, proteins, energy, membrane space, and time. How, for example, should they allocate the available amount of protein to different metabolic pathways or cell functions? To model metabolic behaviour as an economic problem, some flux analysis model, kinetic models, and cell models apply optimality principles. However, due to their different assumptions these models are hard to compare and combine. Benefits and costs of metabolic pathways - e.g. favouring high production fluxes and low metabolite and enzyme cost - can be derived from general fitness objectives such as fast cell growth. To define pathway objectives, we may assume \"optimistically\" that, given a pathway state, any cell variables outside the pathway will be chosen for maximal fitness. The resulting fitness defines an effective pathway objective as a function of the pathway variables. Here I propose a unified theory that considers kinetic models, describes the set of feasible states as a state manifold and score each state by cost and benefit functions for fluxes, metabolite concentrations, and enzyme levels. To screen the state manifold and to find optimal states, the problem can be projected into flux, metabolite, or enzyme space, where effective cost and benefit functions are used. We reobtain existing modelling approaches such as enzyme cost minimisation or nonlinear versions of Flux Balance Analysis. Due to their common origin, the different approaches share mathematical optimality conditions of the same form. A general theory of optimal metabolic states, as proposed here, provides a logical link between existing modelling approaches and can help justify, interconvert, and combine metabolic optimality problems.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Bingchen Yu", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Shanshan Li", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Takako Tabata", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Nanxi Wang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "G. Renuka Kumar", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Jun Liu", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Melanie M. Ott", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Lei Wang", + "author_inst": "University of California San Francisco" + } + ], + "version": "2", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2022.10.04.22280574", "rel_title": "A randomized, placebo-controlled trial of a nasal spray solution containing broadly potent neutralizing antibodies against SARS-CoV-2 variants in healthy volunteers", @@ -173896,41 +174309,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.03.22280646", - "rel_title": "Impact of Omicron Wave and Associated Infection Prevention and Control Measures in Shanghai on Health Management and Psychosocial Well-Being of Patients with Chronic Conditions", - "rel_date": "2022-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.03.22280646", - "rel_abs": "BackgroundCOVID-19 and associated controls may be particularly problematic in the context of chronic conditions. This study investigated health management, well-being, and pandemic-related perspectives in these patients in the context of stringent measures, and associated correlates.\n\nMethodsA self-report survey was administered via Wenjuanxing in Simplified Chinese between March-June 2022 during the Omicron wave lockdown in Shanghai, China. Items from the Somatic Symptom Scale (SSS) and Symptom Checklist-90 (SCL-90) were administered, as well as pandemic-related items created by a working group of the Chinese Preventive Medical Association. Chronic disease patients in this cross-sectional study were recruited through an associated community family physician group.\n\nResultsOverall, 1775 patients, mostly married females with hypertension, participated. Mean SSS scores were 36.1{+/-}10.5/80, with 41.5% scoring in the elevated range (i.e., above 36). In an adjusted model, female, diagnosis of coronary artery disease and arrhythmia, perceived impact of pandemic on life, duration can tolerate control measures, perception of future & control measures, impact of pandemic on health condition and change to exercise routine due to pandemic were significantly associated with greater distress. Approximately one-quarter (24.5%) perceived the pandemic had a permanent impact on their life, and 44.1% perceived at least a minor impact on their health. One-third (33.5%) discontinued exercise due to the pandemic. While 47.6% stocked up on their medications before the lockdown, their remaining supply was mostly only enough for a couple of weeks and 17.5% of participants discontinued use. Chief among their fears were inability to access healthcare (83.2%), and what they stated they most needed to manage their condition was medication access (65.6%).\n\nConclusionsSince 2020 when we assessed a similar cohort, distress and perceived impact of the pandemic has worsened. Greater access to cardiac rehabilitation in China could address these issues.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhimin Xu", - "author_inst": "Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Gabriela Lima de Melo Ghisi", - "author_inst": "Cardiovascular Prevention and Rehabilitation Program, Toronto Rehabilitation Institute, University Health Network, University of Toronto, Toronto" - }, - { - "author_name": "Xia Liu", - "author_inst": "Chengdu Wanda UPMC Hospital, Chengdu, China" - }, - { - "author_name": "Lixian Cui", - "author_inst": "Division of Arts and Sciences, NYU Shanghai, Shanghai, China" - }, - { - "author_name": "Sherry Grace", - "author_inst": "Faculty of Health, York University, Toronto M3J 1P3, Canada; and KITE-Toronto Rehabilitation Institute & Peter Munk Cardiac Centre, University Health Network, U" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.02.22280627", "rel_title": "Dynamics of Vaccine-Hesitant Parents' Considerations Regarding Covid-19 Vaccination", @@ -174668,6 +175046,33 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.10.01.510442", + "rel_title": "SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks", + "rel_date": "2022-10-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.01.510442", + "rel_abs": "With new daily discoveries about the long-term impacts of COVID-19 there is a clear need to develop in vitro models that can be used to better understand the pathogenicity and impact of COVID-19. Here we demonstrate the utility of developing a model of endothelial dysfunction that utilizes induced pluripotent stem cell-derived endothelial progenitors encapsulated in collagen hydrogels to study the effects of COVID-19 on the endothelium. We found that treating these cell-laden hydrogels with SARS-CoV-2 spike protein resulted in a significant decrease in the number of vessel-forming cells as well as vessel network connectivity. Following treatment with the anti-inflammatory drug dexamethasone, we were able to prevent SARS-CoV-2 spike protein-induced endothelial dysfunction. In addition, we confirmed release of inflammatory cytokines associated with the COVID-19 cytokine storm. In conclusion, we have demonstrated that even in the absence of immune cells, we are able to use this 3D in vitro model for angiogenesis to reproduce COVID-19 induced endothelial dysfunction seen in clinical settings.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Brett Stern", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Peter Monteleone", + "author_inst": "Dell Medical School" + }, + { + "author_name": "Janet Zoldan", + "author_inst": "University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.09.30.510331", "rel_title": "CiDRE+ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity", @@ -175962,77 +176367,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.09.30.510287", - "rel_title": "Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor", - "rel_date": "2022-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.30.510287", - "rel_abs": "Spike protein of SARS-CoV-2 variants play critical role in the infection and transmission through its interaction with hACE2 receptor. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with hACE2 receptor. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike proteins of Wild (Wuhan Hu-1), Delta, C.1.2 and Omicron variants. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptor expressing HEK-293T cell line and evaluated binding efficiencies of the variants and competitive binding of spike variants with D614G spike pseudotyped virus. In lines with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. From the analysis in receptor binding domain (RBD) revealed that a single common modification, N501Y, present in both Omicron and C.1.2 is driving the enhanced spike binding to the receptor and showed two-fold superior competitive binding than Delta. Our study using cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors and signifies the role of single common modification N501Y in RBD towards imparting superior binding efficiencies. Our approach would be instrumental in understanding the disease progression and developing therapeutics.\n\nAuthor SummarySpike proteins of evolving SARS-CoV2 variants demonstrated their signature binding to hACE2 receptor, in turn contributed to driving the infection and transmission. Prior studies to scale the binding efficiencies between the spike variant and the receptor had consensus in distinct variants, but discrepancies in the closely related ones. To this end, we compared spike variants-receptor interactions with ELISA, from cells expressing hACE2 receptor. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. More importantly, competitive binding studies in presence of pseudovirus, demonstrated that a single common modification, N501Y, present in both Omicron and C.1.2 showed two fold superior competitive binding than Delta. Collectively, our study suggests a precise approach to evaluate the binding interactions between spike sub-lineages to hACE2 receptor. This would be instrumental in understanding the disease progression and developing therapeutics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gokulnath Mahalingam", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Porkizhi Arjunan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Yogapriya Periasami", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ajay Kumar Dhyani", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Nivedhitha Devaraju", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Vignesh Rajendiran", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Abhisha Crystal Christopher", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ramya Devi KT", - "author_inst": "SRM University: SRM Institute of Science and Technology" - }, - { - "author_name": "Immanuel Darasingh", - "author_inst": "Vellore Institute of Technology: VIT University" - }, - { - "author_name": "Saravanabhavan Thangavel", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mohankumar Murugesan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mahesh Moorthy", - "author_inst": "CMCH: Christian Medical College Vellore" - }, - { - "author_name": "Alok Srivastava", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Srujan Marepally", - "author_inst": "CSCR: Center for Stem Cell Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.09.28.22280472", "rel_title": "Covid-19: Qualitative Change in the Behavior of the \"Virus vs Human\" System - From Limit Cycle to Sustained Focus", @@ -176550,6 +176884,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.29.510004", + "rel_title": "Sensitivity of diffusion-tensor and correlated diffusion imaging to white-matter microstructural abnormalities: application in COVID-19", + "rel_date": "2022-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.29.510004", + "rel_abs": "There has been growing attention on the effect of COVID-19 on white-matter microstructure, especially among those that self-isolated after being infected. There is also immense scientific interest and potential clinical utility to evaluate the sensitivity of single-shell diffusion MRI methods for detecting such effects. In this work, the sensitivities of three single-shell-compatible diffusion MRI modeling methods are compared for detecting the effect of COVID-19, including diffusion-tensor imaging, diffusion-tensor decomposition of orthogonal moments and correlated diffusion imaging. Imaging was performed on self-isolated patients at baseline and 3-month follow-up, along with age- and sex-matched controls. We demonstrate through simulations and experimental data that correlated diffusion imaging is associated with far greater sensitivity, being the only one of the three single-shell methods to demonstrate COVID-19-related brain effects. Results suggest less restricted diffusion in the frontal lobe in COVID-19 patients, but also more restricted diffusion in the cerebellar white matter, in agreement with several existing studies highlighting the vulnerability of the cerebellum to COVID-19 infection. These results, taken together with the simulation results, suggest that a significant proportion of COVID-19 related white-matter microstructural pathology manifests as a change in water diffusivity. Interestingly, different b-values also confer different sensitivities to the effects. No significant difference was observed in patients at the 3-month follow-up, likely due to the limited size of the follow-up cohort. To summarize, correlated diffusion imaging is shown to be a sensitive single-shell diffusion analysis approach that allows us to uncover opposing patterns of diffusion changes in the frontal and cerebellar regions of COVID-19 patients, suggesting the two regions react differently to viral infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nick Teller", + "author_inst": "Baycrest Health Sciences" + }, + { + "author_name": "Jordan A Chad", + "author_inst": "Baycrest Health Sciences" + }, + { + "author_name": "Alexander Wong", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Hayden Gunraj", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Xiang Ji", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "Bradley J MacIntosh", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "Eugenie Roudaia", + "author_inst": "Baycrest Health Sciences" + }, + { + "author_name": "Asaf Gilboa", + "author_inst": "Baycrest Health Sciences" + }, + { + "author_name": "Banjamin Lam", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "Allison Sekuler", + "author_inst": "Baycrest Health Sciences" + }, + { + "author_name": "Chris Heyn", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "Simon Graham", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "Sandra Black", + "author_inst": "Sunnybrook Health Sciences" + }, + { + "author_name": "J. Jean Chen", + "author_inst": "Baycrest Health Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.09.27.509649", "rel_title": "Mutational spectra distinguish SARS-CoV-2 replication niches", @@ -177852,97 +178257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.26.22280364", - "rel_title": "Clinical Subphenotypes of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280364", - "rel_abs": "BackgroundMulti-system inflammatory syndrome in children (MIS-C) represents one of the most severe post-acute sequelae of SARS-CoV-2 infection in children, and there is a critical need to characterize its disease patterns for improved recognition and management. Our objective was to characterize subphenotypes of MIS-C based on presentation, demographics and laboratory parameters.\n\nMethodsWe conducted a retrospective cohort study of children with MIS-C from March 1, 2020 - April 30, 2022 and cared for in 8 pediatric medical centers that participate in PEDSnet. We included demographics, symptoms, conditions, laboratory values, medications and outcomes (ICU admission, death), and grouped variables into eight categories according to organ system involvement. We used a heterogeneity-adaptive latent class analysis model to identify three clinically-relevant subphenotypes. We further characterized the sociodemographic and clinical characteristics of each subphenotype, and evaluated their temporal patterns.\n\nFindingsWe identified 1186 children hospitalized with MIS-C. The highest proportion of children (44{middle dot}4%) were aged between 5-11 years, with a male predominance (61.0%), and non- Hispanic white ethnicity (40{middle dot}2%). Most (67{middle dot}8%) children did not have a chronic condition. Class 1 represented children with a severe clinical phenotype, with 72{middle dot}5% admitted to the ICU, higher inflammatory markers, hypotension/shock/dehydration, cardiac involvement, acute kidney injury and respiratory involvement. Class 2 represented a moderate presentation, with 4-6 organ systems involved, and some overlapping features with acute COVID-19. Class 3 represented a mild presentation, with fewer organ systems involved, lower CRP, troponin values and less cardiac involvement. Class 1 initially represented 51{middle dot}1% of children early in the pandemic, which decreased to 33{middle dot}9% from the pre-delta period to the omicron period.\n\nInterpretationMIS-C has a spectrum of clinical severity, with degree of laboratory abnormalities rather than the number of organ systems involved providing more useful indicators of severity. The proportion of severe/critical MIS-C decreased over time.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint articles from December 2019, to July 2022, for studies published in English that investigated the clinical subphenotypes of MIS-C using the terms \"multi-system inflammatory syndrome in children\" or \"pediatric inflammatory multisystem syndrome\" and \"phenotypes\". Most previous research described the symptoms, clinical characteristics and risk factors associated with MIS-C and how these differ from acute COVID-19, Kawasaki Disease and Toxic Shock Syndrome. One single-center study of 63 patients conducted in 2020 divided patients into Kawasaki and non-Kawasaki disease subphenotypes. Another CDC study evaluated 3 subclasses of MIS-C in 570 children, with one class representing the highest number of organ systems, a second class with predominant respiratory system involvement, and a third class with features overlapping with Kawasaki Disease. However, this study evaluated cases from March to July 2020, during the early phase of the pandemic when misclassification of cases as Kawasaki disease or acute COVID-19 may have occurred. Therefore, it is not known from the existing literature whether the presentation of MIS-C has changed with newer variants such as delta and omicron.\n\nAdded value of this studyPEDSnet provides one of the largest MIS-C cohorts described so far, providing sufficient power for detailed analyses on MIS-C subphenotypes. Our analyses span the entire length of the pandemic, including the more recent omicron wave, and provide an update on the presentations of MIS-C and its temporal dynamics. We found that children have a spectrum of illness that can be characterized as mild (lower inflammatory markers, fewer organ systems involved), moderate (4-6 organ involvement with clinical overlap with acute COVID-19) and severe (higher inflammatory markers, critically ill, more likely to have cardiac involvement, with hypotension/shock and need for vasopressors).\n\nImplications of all the available evidenceThese results provide an update to the subphenotypes of MIS-C including the more recent delta and omicron periods and aid in the understanding of the various presentations of MIS-C. These and other findings provide a useful framework for clinicians in the recognition of MIS-C, identify factors associated with children at risk for increased severity, including the importance of laboratory parameters, for risk stratification, and to facilitate early evaluation, diagnosis and treatment.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Suchitra Rao", - "author_inst": "University of Colorado School of Medicine and Children's Hospital Colorado" - }, - { - "author_name": "Naimin Jing", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Xiaokang Liu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Vitaly Lorman", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Mitchell Maltenfort", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Julia Schuchard", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Qiong Wu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiayi Tong", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hanieh Razzaghi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Asuncion Mejias", - "author_inst": "Nationwide Children's Hospital and The Ohio State University" - }, - { - "author_name": "Grace M. Lee", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nathan M Pajor", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Grant S. Schulert", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Health" - }, - { - "author_name": "Ravi Jhaveri", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Dimitri A. Christakis", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "L. Charles Bailey", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Christopher B. Forrest", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Yong Chen", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.09.22.22280262", "rel_title": "Development and validation of a methodology to measure exhaled carbon dioxide (CO2) and control indoor air renewal", @@ -178476,6 +178790,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.26.22280233", + "rel_title": "Impact of COVID-19 pandemic on the incidence of suicidal behaviors: a retrospective analysis of integrated electronic health records in a 7.5-million population", + "rel_date": "2022-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280233", + "rel_abs": "The COVID-19 pandemic has caused a remarkable psychological overwhelming and an increase of stressors that may trigger suicidal behaviors. However, its impact on the rate of suicidal behaviors has been poorly reported. We conducted a population-based retrospective analysis of all suicidal behaviors attended in healthcare centers of Catalonia (North-East Spain; 7.5-million inhabitants) between January 2017 and June 2022. We retrieved data from the episode, including an assessment of suicide risk and the individuals socioeconomic and clinical characteristics. Data were summarized yearly and for the periods before and after the onset of the COVID-19 pandemic in Spain in March 2020. The analysis included 26,458 episodes of suicidal behavior (21,920 individuals); of them, 16,414 (62.0%) were suicide attempts. The monthly moving average ranged between 300 and 400 episodes until July 2020, and progressively increased to over 600 episodes monthly. In the post-pandemic period, suicidal ideation increased at the expense of suicidal attempts. Cases showed a lower suicide risk; the percentage of females and younger individuals increased, whereas the prevalence of classical risk factors, such as living alone or lacking a family network and a history of psychiatric diagnosis, decreased. In summary, suicidal behaviors have increased during the COVID-19 pandemic, with more episodes of suicidal ideations without attempt and younger and lower risk profiles.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Dami\u00e0 Valero-Bover", + "author_inst": "Catalan Health Service, Barcelona, Spain" + }, + { + "author_name": "Marc Fradera", + "author_inst": "Department of Mental Health, University Hospital ParcTaul\u00ed, Unitat Mixta de Neuroci\u00e8ncia Traslacional I3PT-INc-UAB, Institut d'Investigaci\u00f3 i Innovaci\u00f3 Parc Tau" + }, + { + "author_name": "Gerard Carot-Sans", + "author_inst": "Catalan Health Service, Barcelona, Spain" + }, + { + "author_name": "Isabel Parra", + "author_inst": "Department of Mental Health, University Hospital ParcTaul\u00ed, Unitat Mixta de Neuroci\u00e8ncia Traslacional I3PT-INc-UAB, Institut d'Investigaci\u00f3 i Innovaci\u00f3 Parc Tau" + }, + { + "author_name": "Jordi Piera-Jim\u00e9nez", + "author_inst": "Catalan Health Service, Barcelona, Spain" + }, + { + "author_name": "Caridad Pontes", + "author_inst": "Catalan Health Service, Barcelona, Spain" + }, + { + "author_name": "Diego Palao-Vidal", + "author_inst": "Department of Mental Health, University Hospital ParcTaul\u00ed, Unitat Mixta de Neuroci\u00e8ncia Traslacional I3PT-INc-UAB, Institut d'Investigaci\u00f3 i Innovaci\u00f3 Parc Tau" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.26.22280358", "rel_title": "Markers of blood-brain barrier disruption increase early and persistently in COVID-19 patients with neurological manifestations", @@ -179942,57 +180299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.23.22280278", - "rel_title": "Impact of COVID-19 on lifestyle and mental wellbeing in a drought-affected rural Australian population: A mixed method approach", - "rel_date": "2022-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280278", - "rel_abs": "BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented social and economic disruption, accompanied by the enactment of a multitude of public health measures to restrain disease transmission. These public health and social measures have had a considerable impact on lifestyle and mental wellbeing, which has been well-studied in metropolitan populations, but very little in rural populations. Additionally, the development and use of a standardised scoring system for an overall assessment of patient lifestyle management, and monitoring of changes in these, may be warranted in clinical practice.\n\nMethodsThe associations between psychological distress and changes in SNAPS health behaviours (smoking, nutrition, alcohol, physical activity, sleep) since the onset of COVID-19 in rural Australia were examined. A cross-sectional anonymous online survey was distributed among adults in the Western New South Wales Primary Health Network in August 2020. The survey included measures of psychological distress, income, disposition, lifestyle factors and behaviours during the pandemic, as well as changes in lifestyle due to COVID-19. A novel Global Lifestyle Score (GLS) was generated as a holistic assessment of lifestyle across multiple domains.\n\nResultsThe survey was completed by 308 individuals (modal age group: 45-54 years old, 86.4% female). High distress on the K5 scale was present in over one-third of respondents (n=98, 34.3%). Negative change was reported for sleep (24.4%), nutrition (14.3%), alcohol (17.8%), physical exercise (33.8%) and smoking (26.6%) since the onset of the pandemic. Additionally, changes in sleep, nutrition, physical activity and smoking were associated with distress. Respondents with a poor lifestyle (GLS) during the pandemic were significantly more distressed. Perceived COVID-19 impact was associated with high distress, level of drought impact and loss of income.\n\nConclusionHigh rates of distress amongst rural Australians during the COVID-19 pandemic was linked, worsening lifestyles as measured by the GLS and loss of income. Lifestyle promotion strategies should be considered by health professionals for the management of crisis-related distress. Further research may explore the impact of COVID-19 on a larger population, including a greater proportion of male respondents, and the impact of modifying lifestyle factors on the reduction of distress in the context of a stressor such as this pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jack Carlson", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Kevin Chan", - "author_inst": "University of Western Sydney: Western Sydney University" - }, - { - "author_name": "Jonah Gray", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Houston Xue", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Krista Reed", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Jannine K Bailey", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Tegan Dutton", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Uchechukwu L. Osuagwu", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Robyn Vines", - "author_inst": "Western Sydney University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.09.23.22279458", "rel_title": "Pan-Canadian survey on the impact of the COVID-19 pandemic on cervical cancer screening and management", @@ -181198,6 +181504,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.22.508962", + "rel_title": "Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism", + "rel_date": "2022-09-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.508962", + "rel_abs": "Inhibitors of bromodomain and extra-terminal proteins (iBETs), including JQ-1, have been suggested as potential therapeutics against SARS-CoV-2 infection. However, molecular mechanisms underlying JQ-1-induced antiviral activity and its susceptibility to viral antagonism remain incompletely understood. iBET treatment transiently inhibited infection by SARS-CoV-2 variants and SARS-CoV, but not MERS-CoV. Our functional assays confirmed JQ-1-mediated downregulation of ACE2 expression and multi-omics analysis uncovered induction of an antiviral NRF-2-mediated cytoprotective response as an additional antiviral component of JQ-1 treatment. Serial passaging of SARS-CoV-2 in the presence of JQ-1 resulted in predominance of ORF6-deficient variants. JQ-1 antiviral activity was transient in human bronchial airway epithelial cells (hBAECs) treated prior to infection and absent when administered therapeutically. We propose that JQ-1 exerts pleiotropic effects that collectively induce a transient antiviral state that is ultimately nullified by an established SARS-CoV-2 infection, raising questions on their clinical suitability in the context of COVID-19.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Baxolele Mhlekude", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Dylan Postmus", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "January Weiner III", + "author_inst": "Berlin Institute of Health at Charite - Universitatsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany" + }, + { + "author_name": "Saskia Stenzel", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Francisco J. Zapatero-Belinchon", + "author_inst": "Department of Biochemistry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany" + }, + { + "author_name": "Ruth Olmer", + "author_inst": "Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Cen" + }, + { + "author_name": "Jenny Jansen", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Anja Richter", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Julian Heinze", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Nicolas Heinemann", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Barbara Muhlemann", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Simon Schroeder", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Terry C. Jones", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Marcel Alexander Muller", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Andreas Pich", + "author_inst": "Institute of Toxicology, Hannover Medical School, Core Facility Proteomics, 30629 Hannover, Germany" + }, + { + "author_name": "Volker Thiel", + "author_inst": "Institute of Virology and Immunology (IVI), University of Bern, 3001 Bern, Switzerland" + }, + { + "author_name": "Ulrich Martin", + "author_inst": "Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Cen" + }, + { + "author_name": "Daniela Niemeyer", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + }, + { + "author_name": "Gisa Gerold", + "author_inst": "Department of Biochemistry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany" + }, + { + "author_name": "Dieter Beule", + "author_inst": "Berlin Institute of Health at Charite - Universitatsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany" + }, + { + "author_name": "Christine Goffinet", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, Chariteplatz 1, 10117" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.21.22280189", "rel_title": "Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022", @@ -182264,145 +182673,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.22.509040", - "rel_title": "SARS-CoV-2 Omicron boosting induces de novo B cell response in humans", - "rel_date": "2022-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.509040", - "rel_abs": "The primary two-dose SARS-CoV-2 mRNA vaccine series are strongly immunogenic in humans, but the emergence of highly infectious variants necessitated additional doses of these vaccines and the development of new variant-derived ones1-4. SARS-CoV-2 booster immunizations in humans primarily recruit pre-existing memory B cells (MBCs)5-9. It remains unclear, however, whether the additional doses induce germinal centre (GC) reactions where reengaged B cells can further mature and whether variant-derived vaccines can elicit responses to novel epitopes specific to such variants. Here, we show that boosting with the original SARS- CoV-2 spike vaccine (mRNA-1273) or a B.1.351/B.1.617.2 (Beta/Delta) bivalent vaccine (mRNA-1273.213) induces robust spike-specific GC B cell responses in humans. The GC response persisted for at least eight weeks, leading to significantly more mutated antigen-specific MBC and bone marrow plasma cell compartments. Interrogation of MBC-derived spike-binding monoclonal antibodies (mAbs) isolated from individuals boosted with either mRNA-1273, mRNA-1273.213, or a monovalent Omicron BA.1-based vaccine (mRNA-1273.529) revealed a striking imprinting effect by the primary vaccination series, with all mAbs (n=769) recognizing the original SARS-CoV-2 spike protein. Nonetheless, using a more targeted approach, we isolated mAbs that recognized the spike protein of the SARS-CoV-2 Omicron (BA.1) but not the original SARS-CoV-2 spike from the mRNA-1273.529 boosted individuals. The latter mAbs were less mutated and recognized novel epitopes within the spike protein, suggesting a naive B cell origin. Thus, SARS-CoV-2 boosting in humans induce robust GC B cell responses, and immunization with an antigenically distant spike can overcome the antigenic imprinting by the primary vaccination series.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Wafaa B. Alsoussi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sameer K. Malladi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Julian Q. Zhou", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Baoling Ying", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Wooseob Kim", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Aaron J. Schmitz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Tingting Lei", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Stephen C. Horvath", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Alexandria J. Sturtz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Katherine M. McIntire", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Birk Evavold", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Fangjie Han", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Suzanne M. Scheaffer", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Isabella F. Fox", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Luis Parra-Rodriguez", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Raffael Nachbagauer", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Biliana Nestorova", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Spyros Chalkias", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Christopher W. Farnsworth", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael K. Klebert", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Iskra Pusic", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Benjamin S. Strnad", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "William D. Middleton", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sharlene A. Teefey", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sean P.J. Whelan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Robert Paris", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Rachel M. Presti", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jackson S. Turner", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Ali H. Ellebedy", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.09.22.508999", "rel_title": "Triple COVID-19 vaccination induces humoral and cellular immunity to SARS-CoV-2 with cross-recognition of the Omicron variant and IgA secretion", @@ -183084,6 +183354,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.09.21.508870", + "rel_title": "Association of polymorphisms of IL-6 pathway genes (IL6, IL6R and IL6ST) with COVID-19 severity in an Amazonian population.", + "rel_date": "2022-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.21.508870", + "rel_abs": "Interleukin-6 have been recognized as a major role player in COVID-19 severity, being an important regulator of cytokine storm. Hence, the evaluation of the influence of polymorphisms in key genes of IL-6 pathway, namely IL6, IL6R and IL6ST, may provide valuable prognostic/predictive biomarkers on COVID-19. The present cross-sectional study genotyped three Single Nucleotide Polymorphisms - SNPs (rs1800795, rs2228145 and rs7730934) at IL6, IL6R and IL6ST genes, respectively, in 227 COVID-19 patients (132 hospitalized and 95 non-hospitalized). Genotype frequencies were compared between these groups. As control group, published data on gene and genotype frequencies was gathered from published studies from before the pandemic started. Our major results point to an association of IL6 C allele with COVID-19 severity. Moreover, IL-6 plasmatic levels were higher among IL6 CC genotype carriers. Additionally, the frequency of symptoms was higher at IL6 CC and IL6R CC genotypes. In conclusion the data suggest an important role of IL6 C allele and IL6R CC genotype on COVID-19 severity, in agreement with indirect evidences from literature about association of these genotypes with mortality rates, pneumonia, heightening of protein plasmatic levels proinflammatory driven effects.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Fab\u00edola Brasil Barbosa Rodrigues", + "author_inst": "Federal University of Para: Universidade Federal do Para" + }, + { + "author_name": "Malaya Sahoo", + "author_inst": "Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.09.21.508818", "rel_title": "Exposure to BA.4/BA.5 Spike glycoprotein drives pan-Omicron neutralization in vaccine-experienced humans and mice", @@ -184326,77 +184619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.18.22280022", - "rel_title": "Liquid biomarkers of macrophage dysregulation and circulating spike protein illustrate the biological heterogeneity in patients with post-acute sequelae of COVID-19", - "rel_date": "2022-09-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.18.22280022", - "rel_abs": "Post-acute sequelae of COVID-19 (PASC) are long-term consequences of SARS-CoV-2 infection that can substantially impair quality of life. Underlying mechanisms ranging from persistent virus to innate and adaptive immune dysregulation have been discussed. Here, we profiled plasma of 181 individuals from the cohort study for digital health research in Germany (DigiHero) including individuals after mild to moderate COVID-19 with or without PASC and uninfected controls. We focused on soluble factors related to monocyte/macrophage biology and on circulating SARS-CoV-2 spike (S1) protein as potential biomarker for persistent viral reservoirs. At a median time of eight months after infection, we found pronounced dysregulation in almost all tested soluble factors including both pro-inflammatory and pro-fibrotic cytokines. These perturbations were remarkably independent of ongoing symptoms, but further correlation and regression analyses suggested PASC specific patterns involving CCL2/MCP-1 and IL-8 as well as long-term persistence of high IL-5 and IL-17F levels. None of the analyzed factors correlated with the detectability or levels of circulating S1 indicating that this represents an independent subset of patients with PASC. This data confirms prior evidence of immune dysregulation and persistence of viral protein in PASC and illustrates its biological heterogeneity that still awaits correlation with clinically defined PASC subtypes.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Christoph Schultheiss", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Edith Willscher", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Lisa Paschold", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Cornelia Gottschick", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Bianca Klee", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Lidia Bosurgi", - "author_inst": "I. Department of Medicine, University Medical Center Hamburg-Eppendorf; Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine" - }, - { - "author_name": "Jochen Dutzmann", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Daniel Sedding", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Thomas Frese", - "author_inst": "Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Matthias Girndt", - "author_inst": "Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Jessica I. Hoell", - "author_inst": "Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Michael Gekle", - "author_inst": "Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Rafael Mikolajczyk", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Mascha Binder", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.19.22280079", "rel_title": "The impact of prior COVID-19 on vaccine response and the resultant hybrid immunity are age-dependent", @@ -184978,6 +185200,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.13.22279837", + "rel_title": "Hospital contact patterns and vulnerability to SARS-CoV-2 outbreaks", + "rel_date": "2022-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.13.22279837", + "rel_abs": "The transmission risk of SARS-CoV-2 within hospitals can exceed that in the general community because of more frequent close proximity interactions. However, epidemic risk across wards is still poorly described. We measured CPIs directly using wearable sensors given to all those present in a clinical ward over a 36-hour period, across 15 wards in three hospitals in spring 2020. Data were collected from 2114 participants. These data were combined with a simple transmission model describing the arrival of a single index case to the ward to estimate the risk of an outbreak. Estimated epidemic risk ranged four-fold, from 0.12 secondary infections per day in an adult emergency to 0.49 per day in general paediatrics. The risk presented by an index case in a patient varied twenty-fold across wards. Using simulation, we assessed the potential impact on outbreak risk of targeting the most connected individuals for prevention. We found that targeting those with the highest cumulative contact hours was most impactful (20% reduction for 5% of the population targeted), and on average resources were better spent targeting patients. This study reveals patterns of interactions between individuals in hospital during a pandemic and opens new routes for research into airborne nosocomial risk.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "George Shirreff", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur; UMR 1018, team \"Anti-infective Evasion and Pharmacoepidemiology\", Universite Paris-Saclay, U" + }, + { + "author_name": "Bich-Tram Huynh", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur; UMR 1018, team Anti-infective Evasion and Pharmacoepidemiology, Universite Paris-Saclay, UVS" + }, + { + "author_name": "Audrey Duval", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur" + }, + { + "author_name": "Lara Cristina Pereira", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur" + }, + { + "author_name": "Djillali Annane", + "author_inst": "Service de Reanimation Adulte, AP-HP. Paris Saclay, Hopital Raymond Poincare" + }, + { + "author_name": "Aurelien Dinh", + "author_inst": "Service de Maladies Infectieuses et Tropicales, AP-HP. Paris Saclay, Hopital Raymond Poincare" + }, + { + "author_name": "Olivier Lambotte", + "author_inst": "Service de Medecine Interne et Immunologie Clinique, AP-HP. Paris Saclay, Hopital de Bicetre; UMR1184, IMVA-HB, Inserm, CEA, Universite Paris Saclay" + }, + { + "author_name": "Sophie Bulifon", + "author_inst": "Service de Pneumologie, AP-HP. Paris Saclay, Hopital de Bicetre" + }, + { + "author_name": "Magali Guichardon", + "author_inst": "Service de Geriatrie, AP-HP. Paris Saclay, Hopital Paul Brousse" + }, + { + "author_name": "Sebastien Beaune", + "author_inst": "Service des Urgences Adultes, AP-HP. Paris Saclay, Hopital Ambroise Pare" + }, + { + "author_name": "Julie Toubiana", + "author_inst": "Service de Pediatrie Generale, AP-HP. Centre - Universite Paris Cite, Hopital Necker-enfants malades" + }, + { + "author_name": "Elsa Kermorvant-Duchemin", + "author_inst": "Service de Reanimation Neonatale, AP-HP. Centre - Universite Paris Cite, Hopital Necker-enfants malades" + }, + { + "author_name": "Gerard Cheron", + "author_inst": "Service des Urgences Pediatriques, AP-HP. Centre - Universite Paris Cite, Hopital Necker-enfants malades" + }, + { + "author_name": "Hugues Cordel", + "author_inst": "Service de Maladies Infectieuses et Tropicales, AP-HP. Hopitaux Universitaires Paris Seine-Saint-Denis, Hopital Avicenne" + }, + { + "author_name": "Laurent Argaud", + "author_inst": "Service de Reanimation Adulte, Hospices Civils de Lyon - Universite Claude Bernard, Hopital Edouard Herriot" + }, + { + "author_name": "Marion Douplat", + "author_inst": "Service des Urgences Adultes, Hospices Civils de Lyon - Universite Claude Bernard, Hopital Lyon Sud" + }, + { + "author_name": "Paul Abraham", + "author_inst": "Service d'Anesthesie-Reanimation, Hospices Civils de Lyon - Universite Claude Bernard, Hopital Edouard Herriot" + }, + { + "author_name": "Karim Tazarourte", + "author_inst": "Service des Urgences Adultes, Hospices Civils de Lyon - Universite Claude Bernard, Hopital Edouard Herriot" + }, + { + "author_name": "Geraldine Martin-Gaujard", + "author_inst": "Service de Geriatrie, Hospices Civils de Lyon - Universite Claude Bernard, Hopital Edouard Herriot" + }, + { + "author_name": "Philippe Vanhems", + "author_inst": "Service Hygiene, epidemiologie, Infectiovigilance et Prevention, Hospices Civils de Lyon - Universite Claude Bernard; Centre International de Recherche en Infec" + }, + { + "author_name": "Delphine Hilliquin", + "author_inst": "Service Hygiene, epidemiologie, Infectiovigilance et Prevention, Hospices Civils de Lyon - Universite Claude Bernard" + }, + { + "author_name": "Duc Nguyen", + "author_inst": "Service des Maladies Infectieuses et Tropicales, CHU de Bordeaux, Hopital Pellegrin" + }, + { + "author_name": "Guillaume Chelius", + "author_inst": "INRIA" + }, + { + "author_name": "Antoine Fraboulet", + "author_inst": "INRIA" + }, + { + "author_name": "- EMEA-MESuRS Working Group on Nosocomial SARS-CoV-2 Modelling", + "author_inst": "" + }, + { + "author_name": "Laura Temime", + "author_inst": "PACRI unit, Institut Pasteur, Conservatoire national des Arts et Metiers" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur; UMR 1018, team \"Anti-infective Evasion and Pharmacoepidemiology\", Universite Paris-Saclay, U" + }, + { + "author_name": "Didier Guillemot", + "author_inst": "Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur; UMR 1018, team \"Anti-infective Evasion and Pharmacoepidemiology\", Universite Paris-Saclay, U" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2022.09.15.22280009", "rel_title": "Neutralizing antibodies following three doses of BNT162b2 vaccine, breakthrough infection, and symptoms during the Omicron predominant wave", @@ -186220,25 +186569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.10.22279806", - "rel_title": "Cognitive status and rehabilitation outcomes of patients in acute rehabilitation post Covid-19", - "rel_date": "2022-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.10.22279806", - "rel_abs": "ObjectiveThis study aims to 1) characterize cognitive functioning in patients admitted for inpatient rehabilitation due to Covid-19 diagnosis and 2) examine how cognitive status at admission is associated with rehabilitation outcomes.\n\nDesignRetrospective chart review.\n\nSettingAn inpatient rehabilitation center located in Chicago, Illinois.\n\nParticipants80 participants in acute rehabilitation due to Covid-19 disease\n\nInterventionNot applicable.\n\nMain Outcome MeasuresCognitive functioning as measured by the Montreal Cognitive Assessment (MoCA) and rehabilitation outcomes as measured by Functional Index Measure (FIM) and Section GG items for self-care and mobility (GG-SC and GG-M respectively).\n\nResultsOn average, our sample presented with mild cognitive impairment as assessed by the (MoCA). The most significant deficits were demonstrated in executive function, attention, language, and delayed free recall measures. Higher levels of overall cognitive function were associated with higher cognitive measures of rehabilitation outcomes. Weaker associations were observed with outcome measures of self-care and motor functioning.\n\nConclusionCognitive impairments are common in patients in acute rehabilitation due to Covid-19 and cognitive performance may help predict rehabilitation outcomes.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Madli Vahtra", - "author_inst": "Ascension St Alexius" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.09.09.22279763", "rel_title": "COVID-19 induced birth sex ratio changes in England and Wales", @@ -187004,6 +187334,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.13.22279543", + "rel_title": "A Cross-Sectional Study of Quantitative CT Measurements Associated with the Diffusion Capacity of the Lung in Recovered COVID-19 Patients with Clear Chest CTs", + "rel_date": "2022-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.13.22279543", + "rel_abs": "Impairment of the diffusion capacity of the lung for carbon monoxide (DLco) is commonly reported in convalescent and recovered COVID-19 patients, although the cause is not fully understood especially in patients with no radiological sequelae. In a group of 47 patients at 7 - 51 weeks post infection with either none or minimal scarring or atelectasis on chest CT scans (total < 0.1% of lung volume), dispersions in DLco-adj % and total lung capacity (TLC) % of predicted were observed, with median(quartiles) of 87(78, 99)% and 84(78, 92)%, respectively. Thirteen(27.1%) patients had DLco-adj% < 80%. Although the DLco-adj% did not significantly correlate with the severity of the illness in the acute phase, time since the onset of symptoms, the volume of residual lesions on CT, age or sex, DLco-adj/alveolar volume (Kco-adj) % predicted was correlated with the measurements of small blood vessel volume fraction (diameter <= 5mm) and parenchyma density on CT. Multivariate analysis revealed that these two CT metrics significantly contributed to the variance in DLco-adj% independent of TLC%. Comparing to between-subject variability of DLco-adj in healthy individuals, patients in this cohort with DLco-adj% < 80% were likely abnormal with a degree of disease not visually detectable on CT. However, it is not clear whether the associated variance of parenchyma density and small vessel volume fraction were a consequence of the COVID-19 disease or a pre-existing background variance.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Han Wen", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Shreya M Kanth", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Julio A Huapaya Carrera", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Junfeng Sun", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Michael Do", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Marcus Y. Chen", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ashkan A Malayeri", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Anthony F Suffredini", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.09.12.22279779", "rel_title": "Evaluation of long-term sequelae by cardiopulmonary exercise testing 12 months after hospitalization for critical COVID-19", @@ -188018,125 +188395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.14.507842", - "rel_title": "Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants", - "rel_date": "2022-09-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507842", - "rel_abs": "There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Sergio Andre Rodriguez-Aponte", - "author_inst": "MIT" - }, - { - "author_name": "Neil Chandra Dalvie", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ting Y. Wong", - "author_inst": "West Virginia University" - }, - { - "author_name": "Ryan S. Johnston", - "author_inst": "MIT" - }, - { - "author_name": "Christopher A. Naranjo", - "author_inst": "MIT" - }, - { - "author_name": "Sakshi Bajoria", - "author_inst": "University of Kansas" - }, - { - "author_name": "Ozan S. Kumru", - "author_inst": "University of Kansas" - }, - { - "author_name": "Kawaljit Kaur", - "author_inst": "University of Kansas" - }, - { - "author_name": "Brynnan P. Russ", - "author_inst": "West Virginia University" - }, - { - "author_name": "Katherine S. Lee", - "author_inst": "West Virginia University" - }, - { - "author_name": "Holly A. Cyphert", - "author_inst": "West Virginia University" - }, - { - "author_name": "Mariette Barbier", - "author_inst": "West Virginia University" - }, - { - "author_name": "Harish D. Rao", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Meghraj P. Rajurkar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rakesh R. Lothe", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Umesh Shaligram", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Saurabh Batwal", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rahul Chandrasekaran", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Gaurav Nagar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Harry Kleanthous", - "author_inst": "Bill & Melinda Gates Foundation" - }, - { - "author_name": "Sumi Biswas", - "author_inst": "Spybiotech Limited" - }, - { - "author_name": "Justin R. Bevere", - "author_inst": "West Virginia University" - }, - { - "author_name": "Sangeeta B. Joshi", - "author_inst": "University of Kansas" - }, - { - "author_name": "David B. Volkin", - "author_inst": "University of Kansas" - }, - { - "author_name": "Fredrick Heath Damron", - "author_inst": "West Virginia University" - }, - { - "author_name": "J. Christopher Love", - "author_inst": "Koch Institute at MIT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.09.14.507985", "rel_title": "Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods", @@ -188818,6 +189076,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.12.505486", + "rel_title": "High throughput Bioluminescent assay to characterize and monitor the activity of SARS-CoV-2 Methyltransferases", + "rel_date": "2022-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.12.505486", + "rel_abs": "The fast rate of viral mutations of SARS CoV-2 result in decrease in the efficacy of the vaccines that have been developed before the emergence of these mutations. Thus, it is believed that using additional measures to combat the virus is not only advisable but also beneficial. Two antiviral drugs were authorized for emergency use by the FDA, namely Pfizers two-drug regimen sold under the brand name Paxlovid, and Mercks drug Lagevrio. Pfizers two-drug combination consists of nirmatrelvir, a protease inhibitor that blocks coronavirus ability to multiply and another antiviral, ritonavir, that lowers the rate of drug clearance to boost the longevity and activity of the protease inhibitor. Mercks drug Lagevrio (molnupiravir) is a nucleoside analogue with a mechanism of action that aims to introduce errors into the genetic code of the virus. We believe the armament against the virus can be augmented by the addition of another class of enzyme inhibitors that are required for viral survival and its ability to replicate. Enzymes like nsp14 and nsp10/16 methyltransferases represent another class of drug targets since they are required for viral RNA translation and evading the host immune system. In this communication, we have successfully verified that the Methyltransferase Glo, which is universal and homogeneous methyltransferase assay can be used to screen for inhibitors of the two pivotal enzymes nsp14 and nsp16 of SARS CoV-2. Furthermore, we have carried out extensive studies on those enzymes using different RNA substrates and tested their activity using various inhibitors and verified the utility of this assay for use in drug screening programs. We anticipate our work will be pursued further to screen for large libraries to discover new and selective inhibitors for the viral enzymes particularly that these enzymes are structurally different from their mammalian counterparts.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hicham Zegzouti", + "author_inst": "Promega Corporation" + }, + { + "author_name": "Said A. Goueli", + "author_inst": "Promega Corp." + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.09.11.22279815", "rel_title": "MAM: Flexible Monte-Carlo Agent-based Model for Modelling COVID-19 Spread", @@ -190132,65 +190413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.06.22279658", - "rel_title": "Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279658", - "rel_abs": "Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. Whole-genome sequencing of virus from an early case revealed a sub-consensus level of sequencing reads supporting a 17-nucleotide frameshift-inducing deletion in ORF7a that truncated the peptide sequence. The variant rapidly became represented at the consensus level (Delta-ORF7a{Delta}17del) in most of the outbreak cases in Australia. Retrospective analysis of ORF7a deletions in all GISAID clade GK Delta genomes showed that of 4,018,216 genomes, 134,751 ([~]3.35%) possessed a deletion in ORF7a, with the ORF7a{Delta}17del mutation by far the most common. Approximately 99.05% of Delta-ORF7a{Delta}17del genomes on GISAID originated from the Australian Delta outbreak, and comprised 87% of genomes in the outbreak. In vitro comparison of lineages in cell culture showed a significantly greater proportion of cells were infected with Delta-ORF7a{Delta}17del than with a contemporaneous Delta variant without ORF7a{Delta}17del (Delta-ORF7aintact), and the proportion was also measurably higher than an early SARS-CoV-2 strain (A.2.2). These results showed that Delta-ORF7a{Delta}17del potentially has a slight growth advantage compared to Delta-ORF7aintact. Delta-ORF7a{Delta}17del viruses still produced ORF7a protein, but significantly less than A.2.2, in a different cellular distribution with a more diffuse expression throughout the cytoplasm of infected cells. These data suggest that the proliferation of Delta-ORF7a{Delta}17del genomes during the Australian Delta outbreak was likely not a result of an intrinsic benefit of the ORF7a{Delta}17del mutation, but rather a chance founder effect. Nonetheless, the abundance of different ORF7a deletions in genomes worldwide suggests these have some benefit to virus transmission.\n\nIMPORTANCEDeletions in the ORF7a region of SARS-CoV-2 have been noted since early in the COVID-19 pandemic, but are generally reported as transient mutations that are quickly lost in the population. Consequently, ORF7a deletions are considered disadvantageous to the virus through possible loss-of-function effects. In constrast to these earlier reports, we present the first report of a SARS-CoV-2 variant with an ORF7a deletion that dominated for the entirety of a protracted outbreak, and found no associated fitness disadvantage or advantage in cell culture. The relatively common rise and fall of ORF7a deletion variants over time likely represent chance founder events followed by proliferation until a more fit variant(s) is introduced to the population. Our global clade-level survey of ORF7a deletions will be a useful resource for future studies into this gene region.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Charles S.P. Foster", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Rowena Bull", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Nicodemus Tedla", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Fernando Santiago", - "author_inst": "University of New South Wales" - }, - { - "author_name": "David Agapiou", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Anurag Adhikari", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Gregory J Walker", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Lok Bahadur Shrestha", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Sebastiaan van Hal", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Ki Wook Kim", - "author_inst": "University of New South Wales" - }, - { - "author_name": "William D Rawlinson", - "author_inst": "Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.09.08.22279729", "rel_title": "Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2", @@ -191132,6 +191354,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.08.22278709", + "rel_title": "Are primary care virtual visits associated with higher emergency department use? A cross-sectional analysis from Ontario, Canada", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.08.22278709", + "rel_abs": "ImportanceThe COVID-19 pandemic has resulted in increased use of virtual care, however, few studies have looked at the association between virtual primary care visits and other healthcare use.\n\nObjectiveTo determine whether there was an association between a high proportion of virtual visits in primary care and more emergency department visits\n\nDesignA cross-sectional study, using routinely collected data\n\nSettingOntario, Canada\n\nParticipantsOntario residents alive on March 31st 2021 and family physicians with at least 1 visit claim between February and October 2021.\n\nExposureFamily physicians stratified by the percentage of total visits that were virtual (phone or video) between February and October 2021\n\nMain outcome(s) and measure(s)We calculated the emergency department visit rate for each stratum of family physician virtual care use. We used multivariable logistic regression models to understand the relative rate of patient emergency department use after stratifying for rurality and adjusting first for patient characteristics and then the 2019 emergency department visit rate.\n\nResultsWe analyzed data for 15,155 family physicians and 12,951,063 Ontarians attached to these physicians. The mean number of emergency department visits was highest among patients whose physicians provided only in-person care (470.3 {+/-} 1918.8 per 1,000) and was lowest among physicians who provided >80 to <100% care virtually (242.0 {+/-} 800.3 per 1,000). After adjustment for patient characteristics patients seen by physicians with >20% of visits delivered virtually had lower rates of emergency department visits compared to patients of physicians who provided >0%-20% virtually (e.g. >80 to <100% vs >0%-20% virtual visits in Big Cities, Relative Rate (RR) 0.80 [95%CI 0.76-0.83]). This trend held across all rurality strata and after adjustment for 2019 emergency department visit rates. In urban areas, there was a gradient whereby physicians providing the highest level of virtual care had the lowest emergency department visit rates.\n\nConclusions and RelevancePhysicians who provided a high proportion of care virtually did not have higher emergency department visits than those who provided the lowest levels of virtual care. Our findings refute hypotheses that emergency department use is being driven by family physicians providing more care virtually.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSDo family physicians who provide more care virtually have higher emergency department visit rates among their patient panel?\n\nFindingsIn this cross-sectional study from Ontario, Canada, we examined data from February to October 2021 for 12,951,063 patients attached to 15,155 family doctors and found that physicians who provided a high proportion of virtual care did not have higher emergency department visits than those who provided the lowest levels of virtual care. This finding remained true after adjusting for patient characteristics.\n\nMeaningOur findings refute hypotheses that emergency department use is being driven by family physicians providing more care virtually.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Tara Kiran", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Michael E. Green", + "author_inst": "Queen's University" + }, + { + "author_name": "Rachel Strauss", + "author_inst": "University of Toronto" + }, + { + "author_name": "C. Fangyun Wu", + "author_inst": "ICES Central, Toronto, Ontario" + }, + { + "author_name": "Maryam Daneshvarfard", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Alexander Kopp", + "author_inst": "ICES Central, Toronto, Ontario" + }, + { + "author_name": "Lauren Lapointe-Shaw", + "author_inst": "University of Toronto and University Health Network" + }, + { + "author_name": "Lidija Latifovic", + "author_inst": "University of Toronto" + }, + { + "author_name": "Eliot Frymire", + "author_inst": "Queen's University" + }, + { + "author_name": "Richard H. Glazier", + "author_inst": "ICES Central, Toronto, Ontario" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2022.09.08.22279670", "rel_title": "The effects of COVID-19 on child mental and social health: biannual assessments up to April 2022 in a clinical and two general population samples", @@ -192146,57 +192423,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.08.507221", - "rel_title": "Use of the particle agglutination/particle agglutination-inhibition test for antigenic analysis of SARS-CoV-2", - "rel_date": "2022-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.08.507221", - "rel_abs": "The antigenicity of SARS-CoV-2 is a critical issue for the effectiveness of the vaccine, and thus it should be phenotypically evaluated by serological assays as new field isolates emerge. The hemagglutination/hemagglutination-inhibition (HA/HI) tests are well-known as a representative method for antigenic analysis of influenza viruses, but SARS-CoV-2 is unlikely to agglutinate to human or guinea pig red blood cells. Therefore, the antigenic analysis requires complicated enzyme-linked immunosorbent assay (ELISA) or cell-based assays such as the microneutralization assay. In this study, we developed the particle agglutination/particle agglutination-inhibition (PA/PAI) test to easily and rapidly quantify the virus and antibody using human angiotensin-converting enzyme 2 (hACE2)-bound latex beads. The PA titer was positively correlated with the plaque-forming units. The PAI titer using post-infection Syrian hamster antisera clearly revealed the antigenic difference between the omicron and previous variants. The results show the PAI test is useful for easy and rapid antigenic analysis of SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jun Kobayashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shutoku Matsuyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masayuki Shirakura", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tomoko Arita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yasushi Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Asanuma", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shinji Watanabe", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Hasegawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kazuya Nakamura", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.09.507257", "rel_title": "Cellular stress modulates severity of the acute respiratory distress syndrome in COVID-19", @@ -192926,6 +193152,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.09.05.22278731", + "rel_title": "Advanced Care Planning (ACP) in the early phase of COVID-19: A rapid review of the practice and policy lessons learned.", + "rel_date": "2022-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.05.22278731", + "rel_abs": "This rapid review of quantitative and qualitative publications of any design indexed in PUBMED between January 2020-April 2021 investigates barriers and enablers of advancecare planning (ACP) worldwide in the early stages of the life-threatening COVID-19 pandemic. Seventy-four papers were included: 35 primary research studies (cohorts, reviews, case studies, and cross-sectional designs) and 39 commentaries. Publications from hospitals, outpatient services, aged care and community indicated widespread interest in accelerating ACP documentation to facilitate management decisions and goal-aligned care. Enablers of ACP included targeted public awareness, availability of telehealth, access to online tools and a person-centered approaches. Barriers included uncertainty regarding clinical outcomes, cultural or communication difficulties, legal and ethical considerations, infection control restrictions, lack of time, and limited resources and support systems. The opportunities for rapid implementation of ACP offered by the social distancing restrictions and high demand for health services are valuable in informing future policy and practice.\n\nWhat this paper addsO_LIOur study adds to existing evidence by identifying emerging barriers and creative ways of overcoming them in response to a global crisis\nC_LIO_LIDiscussions on death prospects and care of the dying were feasible and a step towards normalisation of advance care planning\nC_LIO_LIDespite new and overwhelming challenges, policies and practices could be rapidly implemented to satisfy clinicians and families in need of advance care planning\nC_LI\n\nApplications of study findingsO_LIThe lessons learnt can be incorporated in future health service planning since the threat of other pandemics is real\nC_LIO_LIA formal evaluation of effectiveness of some of the emerging strategies would be a valuable addition to the evidence\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sarah Younan", + "author_inst": "Liverpool Hospital, Department of Geriatric Medicine" + }, + { + "author_name": "Magnolia Cardona", + "author_inst": "Bond University, Institute for Evidence Based Healthcare" + }, + { + "author_name": "Ashlyn Sahay", + "author_inst": "Central Queensland University, Mackay campus" + }, + { + "author_name": "Eileen Willis", + "author_inst": "Central Queensland University, Mackay campus" + }, + { + "author_name": "Danielle Ni Chroinin", + "author_inst": "Liverpool Hospital, Department of Geriatric Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "palliative medicine" + }, { "rel_doi": "10.1101/2022.09.05.22279602", "rel_title": "Persistent somatic symptoms are key to individual illness perception at one year after COVID-19", @@ -194324,45 +194585,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.03.506470", - "rel_title": "Optimization and deoptimization of codons in SARS-CoV-2 and the implications for vaccine development", - "rel_date": "2022-09-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.03.506470", - "rel_abs": "The spread of Coronavirus Disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has progressed into a global pandemic. To date, thousands of genetic variants have been identified across SARS-CoV-2 isolates from patients. Sequence analysis reveals that the codon usage of viral sequences decreased over time but fluctuated from time to time. In this study, through evolution modeling, we found that this phenomenon might result from the virus preference for mutations during transmission. Using dual luciferase assays, we further discovered that the deoptimization of codons on viruses might weaken protein expression during the virus evolution, indicating that the choice of codon usage might play important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccine, we designed several omicron BA.2.12.1 and BA.4/5 spike mRNA vaccine candidates based on codon optimization, and experimentally validated their high levels of expression. Our study highlights the importance of codon usage in virus evolution and mRNA vaccine development.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Xinkai Wu", - "author_inst": "Peking university" - }, - { - "author_name": "Kejia Shan", - "author_inst": "Peking University" - }, - { - "author_name": "Fuwen Zan", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xiaolu Tang", - "author_inst": "Peking University" - }, - { - "author_name": "Zhaohui Qian", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jian Lu", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.09.02.22279526", "rel_title": "Spatial determination of COVID-19 mortality", @@ -195040,6 +195262,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.01.22279517", + "rel_title": "Cardiac Magnetic Resonance Findings of COVID-19 Vaccine Associated Myocarditis at Intermediate Follow Up: a Comparison to Classic Myocarditis and MIS-C Related Myocarditis", + "rel_date": "2022-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.01.22279517", + "rel_abs": "ObjectiveTo report intermediate cardiac magnetic resonance (CMR) findings of COVID-19 vaccine associated myocarditis (C-VAM) and compare to classic myocarditis (CM) and multisystem inflammatory syndrome in children (MIS-C).\n\nStudy DesignRetrospective cohort study including children diagnosed with C-VAM from 5/2021 through 12/2021 with early and intermediate CMR. Patients with CM and MIS-C with intermediate CMR were included for comparison.\n\nResultsThere were 8 patients with C-VAM, 20 with CM, and 61 with MIS-C. Among those with C-VAM, CMR performed at median 3 days (IQR 3, 7) revealed 2/8 patients with left ventricular ejection fraction (LVEF)<55%, 7/7 patients with late gadolinium enhancement (LGE), and 5/8 patients with elevated native T1 values. Borderline T2 values suggestive of myocardial edema were present in 6/8. Follow-up CMRs performed at median 107 days (IQR 97, 177) showed normal ventricular systolic function, T1, and T2 values; 3/7 patients had LGE. At intermediate follow up the C-VAM group had a lower percentage of LVEF<55% compared to CM and MIS-C (0.0 vs 30.0 vs 6.6%, respectively, p=0.018) and an intermediate degree of LGE (42.9 vs 75.0 vs 3.3%, respectively, p<0.001). Pairwise comparisons showed fewer myocardial segments with LGE in the C-VAM group versus CM (4/119 vs 42/340, p=0.004) and more segments with LGE than MIS-C (4/119 vs 2/1020, p=0.0014).\n\nConclusionPatients with C-VAM had no evidence of active inflammation or ventricular dysfunction on intermediate CMR although a minority had persistent LGE. Intermediate findings in C-VAM may be favorable compared to CM though LGE is more common compared to MIS-C.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Matthew L Dove", + "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" + }, + { + "author_name": "Timothy C Slesnick", + "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" + }, + { + "author_name": "Matthew E Oster", + "author_inst": "Children's Healthcare of Atlanta" + }, + { + "author_name": "Sassan Hashemi", + "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" + }, + { + "author_name": "Trisha Patel", + "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" + }, + { + "author_name": "Hunter C Wilson", + "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.09.01.22279496", "rel_title": "The impact and progression of the COVID-19 pandemic in Bulgaria in its first two years", @@ -196030,33 +196291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.31.22279430", - "rel_title": "Periodic epidemic outbursts explained by local saturation of clusters", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279430", - "rel_abs": "Adding the notion of spatial locality to the susceptible-infected-recovered (or SIR) model, allows to capture local saturation of an epidemic. The resulting minimum model of an epidemic, consisting of five ordinary differential equations with constant model coefficients, reproduces slowly decaying periodic outbursts, as observed in the COVID-19 or Spanish flu epidemic. It is shown that if immunity decays, even slowly, the model yields a fully periodic dynamics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Louis Gostiaux", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Wouter Bos", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Jean-Pierre Bertoglio", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.31.22279444", "rel_title": "Effectiveness of the COVID-19 vaccines against severe disease with Omicron sub-lineages BA.4 and BA.5 in England", @@ -196754,6 +196988,89 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.08.30.505966", + "rel_title": "Impact of reinfection with SARS-CoV-2 Omicron variants in previously infected hamsters", + "rel_date": "2022-08-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.30.505966", + "rel_abs": "The diversity of SARS-CoV-2 mutations raises the possibility of reinfection of individuals previously infected with earlier variants, and this risk is further increased by the emergence of the B.1.1.529 Omicron variant. In this study, we used an in vivo, hamster infection model to assess the potential for individuals previously infected with SARS-CoV-2 to be reinfected with Omicron variant and we also investigated the pathology associated with such infections. Initially, Syrian hamsters were inoculated with a lineage A, B.1.1.7, B.1.351, B.1.617.2 or a subvariant of Omicron, BA.1 strain and then reinfected with the BA.1 strain 5 weeks later. Subsequently, the impact of reinfection with Omicron subvariants (BA.1 and BA.2) in individuals previously infected with the BA.1 strain was examined. Although viral infection and replication were suppressed in both the upper and lower airways, following reinfection, virus-associated RNA was detected in the airways of most hamsters. Viral replication was more strongly suppressed in the lower respiratory tract than in the upper respiratory tract. Consistent amino acid substitutions were observed in the upper respiratory tract of infected hamsters after primary infection with variant BA.1, whereas diverse mutations appeared in hamsters reinfected with the same variant. Histopathology showed no acute pneumonia or disease enhancement in any of the reinfection groups and, in addition, the expression of inflammatory cytokines and chemokines in the airways of reinfected animals was only mildly elevated. These findings are important for understanding the risk of reinfection with new variants of SARS-CoV-2.\n\nIMPORTANCEThe emergence of SARS-CoV-2 variants and the widespread use of COVID-19 vaccines has resulted in individual differences in immune status against SARS-CoV-2. A decay in immunity over time and the emergence of variants that partially evade the immune response can also lead to reinfection. In this study, we demonstrated that, in hamsters, immunity acquired following primary infection with previous SARS-CoV-2 variants was effective in preventing the onset of pneumonia after reinfection with the Omicron variant. However, viral infection and multiplication in the upper respiratory tract were still observed after reinfection. We also showed that more diverse nonsynonymous mutations appeared in the upper respiratory tract of reinfected hamsters that had acquired immunity from primary infection. This hamster model reveals the within-host evolution of SARS-CoV-2 and its pathology after reinfection, and provides important information for countermeasures against diversifying SARS-CoV-2 variants.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Nozomi Shiwa-Sudo", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yusuke Sakai", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Naoko Iwata-Yoshikawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shinji Watanabe", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Souichi Yamada", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yudai Kuroda", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Tsukasa Yamamoto", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Masayuki Shirakura", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Seiichiro Fujisaki", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Kaya Miyazaki", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Hideka Miura", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shiho Nagata", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shuetsu Fukushi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Ken Maeda", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Hideki Hasegawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Tadaki Suzuki", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Noriyo Nagata", + "author_inst": "National Institute of Infectious Diseases" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.31.506023", "rel_title": "The SARS-CoV-2 Spike S1 Protein Induces Global Proteomic Changes in ATII-Like Rat L2 Cells that are Attenuated by Hyaluronan", @@ -197748,77 +198065,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.08.29.505777", - "rel_title": "Can SARS-CoV-2 transmit from a dead body?", - "rel_date": "2022-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.29.505777", - "rel_abs": "Although it has been 2.5 years since the COVID-19 pandemic began, the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a dead infected body remains unclear, and often, in Japan bereaved family members are not allowed to view in-person a loved one who has died from COVID-19. In this study, we analyzed the possibility of SARS-CoV-2 transmission from a dead body by using the hamster model. We also analyzed the effect of Angel-care--in which the pharynx, nostril, and rectum are plugged--and embalming on reducing transmissibility from dead bodies. We found that SARS-CoV-2 could be transmitted from the body of animals that died within a few days of infection; however, Angel-care and embalming were effective in preventing transmission from the dead body. These results suggest that protection from infection is essential when in contact with a SARS-CoV-2-infected dead body, and that sealing the cavities of a dead body is an important infection control step if embalming is not done.\n\nImportanceWe found that SARS-CoV-2 could be transmitted from a dead body presumably via postmortem gases. However, we also found that postmortem care, such as plugging the pharynx, nostrils, and rectum, or embalming could prevent transmission from the dead body. These results indicate that protection from infection is essential when handling infected corpses, and that appropriate care of SARS-CoV-2-infected corpses is important.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Hiroshi Ueki", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Sayaka Nagasawa", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yuichiro Hirata", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenichiro Hashizume", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Kazuho Ushiwata", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Hirotaro Iwase", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yohsuke Makino", - "author_inst": "Graduate School of Medicine, University of Tokyo" - }, - { - "author_name": "Tetsuo Ushiku", - "author_inst": "Yokohama City University Hospital" - }, - { - "author_name": "Shinji Akitomi", - "author_inst": "Japan Medical Association Research Institute" - }, - { - "author_name": "Masaki Imai", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Hisako Saitoh", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin System" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.29.22279161", "rel_title": "Organizational impact of an ID NOW COVID-19 point-of-care testing for SARS-CoV2 detection in a maternity ward", @@ -198380,6 +198626,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.29.505649", + "rel_title": "Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR", + "rel_date": "2022-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.29.505649", + "rel_abs": "Coronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM).\n\nWe evaluated the performance of four transport media: locally manufactured (\"REVITAL\") Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy.\n\nFour vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80{degrees}C, 4{degrees}C, room temperature (25{degrees}C) and 37{degrees}C for 7 days. Viral Ribonucleic acid (RNA) extractions and qRT-PCR were done on the following days after inoculation with the cultured virus, days 1, 2, 3, 4 and 7 to assess virus stability and viral recovery.\n\nCT values fell over time at room temperature, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 viral RNA.\n\nOverall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Caroline Ngetsa", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Victor Osoti", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Dorcas Okanda", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Faith Marura", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Krupali Shah", + "author_inst": "Revital Healthcare (EPZ) Limited" + }, + { + "author_name": "Henry Karanja", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Daisy Mugo", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "John Gitonga", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Martin Mutunga", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Clement Lewa", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Bennedict Orindi", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Philip Bejon", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + }, + { + "author_name": "Lynette Isabella Ochola-Oyier", + "author_inst": "KEMRI-Wellcome Trust Collaborative Programme" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.08.25.22279201", "rel_title": "Effect of Pranayama on Perceived Stress, Well Being and Quality of Life of Frontline Healthcare Professionals on Covid-19 Duty: A Quasi- Randomized Clinical Trial", @@ -199678,49 +199991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.23.22279123", - "rel_title": "The Role of Modelling and Analytics in South African COVID-19 Planning and Budgeting", - "rel_date": "2022-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279123", - "rel_abs": "BackgroundThe South African COVID-19 Modelling Consortium (SACMC) was established in late March 2020 to support planning and budgeting for COVID-19 related healthcare in South Africa. We developed several tools in response to the needs of decision makers in the different stages of the epidemic, allowing the South African government to plan several months ahead of time.\n\nMethodsOur tools included epidemic projection models, several cost and budget impact models, and online dashboards to help government and the public visualise our projections, track case development and forecast hospital admissions. Information on new variants, including Delta and Omicron, were incorporated in real time to allow the shifting of scarce resources when necessary.\n\nResultsGiven the rapidly changing nature of the outbreak globally and in South Africa, the model projections were updated regularly. The updates reflected 1) the changing policy priorities over the course of the epidemic; 2) the availability of new data from South African data systems; and 3) the evolving response to COVID-19 in South Africa such as changes in lockdown levels and ensuing mobility and contact rates, testing and contact tracing strategies, and hospitalisation criteria. Insights into population behaviour required updates by incorporating notions of behavioural heterogeneity and behavioural responses to observed changes in mortality. We incorporated these aspects into developing scenarios for the third wave and developed additional methodology that allowed us to forecast required inpatient capacity. Finally, real-time analyses of the most important characteristics of the Omicron variant first identified in South Africa in November 2021 allowed us to advise policymakers early in the fourth wave that a relatively lower admission rate was likely.\n\nConclusionThe SACMCs models, developed rapidly in an emergency setting and regularly updated with local data, supported national and provincial government to plan several months ahead of time, expand hospital capacity when needed, allocate budgets, and procure additional resources where possible. Across four waves of COVID-19 cases, the SACMC continued to serve the planning needs of the government, tracking waves and supporting the national vaccine rollout.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gesine Meyer-Rath", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Rachel Hounsell", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Juliet Pulliam", - "author_inst": "University of Stellenbosch: Stellenbosch University" - }, - { - "author_name": "Lise Jamieson", - "author_inst": "University of the Witwatersrand Johannesburg" - }, - { - "author_name": "Brooke Nichols", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Harry Moultrie", - "author_inst": "NHLS: National Health Laboratory Service" - }, - { - "author_name": "Sheetal Prakash Silal", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.24.22279159", "rel_title": "Dynamics of anti-S IgG antibodies titers after the second dose of COVID 19 mRNA and non-mRNA vaccines in the manual and craft worker population of Qatar", @@ -200446,6 +200716,37 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.08.25.505249", + "rel_title": "Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding", + "rel_date": "2022-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.25.505249", + "rel_abs": "The binding affinity of the SARS-CoV-2 spike (S)-protein {Delta}{Delta}Gbind to the human membrane protein ACE2 is critical for virus function and evolution. Computational structure-based screening of new S-protein mutations for ACE2 binding lends promise to rationalize virus function directly from protein structure and ideally aid early detection of potentially concerning variants. We used a computational protocol based on cryo-electron microscopy structures of the S-protein to estimate the ACE2-binding that gave good trend agreement with experimental ACE2 affinities. We then expanded predictions to all possible S-protein mutations in 21 different S-protein-ACE2 complexes (400,000 {Delta}{Delta}Gbind data points in total), using mutation group comparisons to reduce systematic errors. We show that mutations that have arisen in major variants as a group maintain ACE2 affinity significantly more than random mutations in the total protein, at the interface, and at evolvable sites, with differences between variant mutations being small relative to these effects. Omicron mutations as a group had a modest change in binding affinity compared to mutations in other major variants. The single-mutation effects are consistent with ACE2 binding being optimized and maintained in omicron, despite increased importance of other selection pressures (antigenic drift). As epistasis, glycosylation and in vivo conditions will modulate these effects, computational predictive SARS-CoV-2 evolution remains far from achieved, but the feasibility of large-scale computation is substantially aided by using many structures and comparison of mutation groups rather than single mutation effects, which are very uncertain. Our results demonstrate substantial challenges but indicate ways to improve the quality of computer models for assessing SARS-CoV-2 mutation effects.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shivani Thakur", + "author_inst": "Indian Institute of Technology Bhilai" + }, + { + "author_name": "Rajaneesh Kumar Verma", + "author_inst": "Indian Institute of Technology Bhilai" + }, + { + "author_name": "Kasper Planeta Kepp", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Rukmankesh Mehra", + "author_inst": "Indian Institute of Technology Bhilai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.08.25.22279199", "rel_title": "Assessing glucose-6-phosphate dehydrogenase (G6PD) during COVID-19 requires caution: evidence on the impact of the infection upon enzyme activity", @@ -201428,185 +201729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.22.22279080", - "rel_title": "Humoral and cellular response induced by a second booster of an inactivated SARS-CoV-2 vaccine in adults", - "rel_date": "2022-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22279080", - "rel_abs": "The SARS-CoV-2 Omicron variant has challenged the control of the COVID-19 pandemic even in highly vaccinated countries. While a second booster of mRNA vaccines improved the immunity against SARS-CoV-2, the humoral and cellular responses induced by a second booster of an inactivated SARS-CoV-2 vaccine have not been studied. In the context of a phase 3 clinical study, we report that a second booster of CoronaVac(R) increased the neutralizing response against the ancestral virus yet showed poor neutralization against the Omicron variant. Additionally, isolated PBMCs displayed equivalent activation of specific CD4+ T cells and IFN-{gamma} production when stimulated with a mega-pool of peptides derived from the spike protein of the ancestral virus or the Omicron variant. In conclusion, a second booster dose of CoronaVac(R) does not improve the neutralizing response against the Omicron variant compared with the first booster dose, yet it helps maintaining a robust spike-specific CD4+ T cell response.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Felipe Melo-Gonzalez", - "author_inst": "Universidad Andres Bello, Santiago, Chile/Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Constanza Mendez", - "author_inst": "Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Hernan F Penaloza", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Barbara M Schultz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alejandro Pina-Iturbe", - "author_inst": "Pontificia Universidad Catolica Chile" - }, - { - "author_name": "Mariana Rios", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Moreno-Tapia", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Patricia Pereira-Sanchez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Diane Leighton", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Claudia Orellana", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Consuelo Covarrubias", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Nicolas MS Galvez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Jorge A Soto", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "LUISA F DUARTE", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Rivera-Perez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Yaneisi Vazquez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alex Cabrera", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Sergio Bustos", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Carolina Iturriaga", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Marcela Urzua", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Maria S Navarrete", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alvaro Rojas", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Rodrigo Fasce", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Jorge Fernandez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Judith Mora", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Eugenio Ramirez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Aracelly Gaete-Argel", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Monica Acevedo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Fernando Valiente-Echeverria", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Ricardo Soto-Rifo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Gang Zeng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "Weining Meng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "- CoronaVac03CL Study Group", - "author_inst": "-" - }, - { - "author_name": "Jose V Gonzalez-Aramundiz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Pablo A Gonzalez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Katia Abarca", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Susan M Bueno", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alexis M Kalergis", - "author_inst": "Pontificia Universidad Catolica de Chile" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.22.22279079", "rel_title": "Assessing Vulnerability to COVID-19 in High-Risk Populations: The Role of SARS-CoV-2 Spike-Targeted Serology", @@ -202196,6 +202318,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.22.504888", + "rel_title": "SARS-CoV-2 infects multiple species of North American deer mice and causes clinical disease in the California mouse", + "rel_date": "2022-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.22.504888", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that causes coronavirus disease-19 (COVID-19), emerged in late 2019 in Wuhan, China and its rapid global spread has resulted in millions of deaths. An important public health consideration is the potential for SARS-CoV-2 to establish endemicity in a secondary animal reservoir outside of Asia or acquire adaptations that result in new variants with the ability to evade the immune response and reinfect the human population. Previous work has shown that North American deer mice (Peromyscus maniculatus) are susceptible and can transmit SARS-CoV-2 to naive conspecifics, indicating its potential to serve as a wildlife reservoir for SARS-CoV-2 in North America. In this study, we report experimental SARS-CoV-2 susceptibility of two additional subspecies of the North American deer mouse and two additional deer mouse species, with infectious virus and viral RNA present in oral swabs and lung tissue of infected deer mice and neutralizing antibodies present at 15 days post-challenge. Moreover, some of one species, the California mouse (P. californicus) developed clinical disease, including one that required humane euthanasia. California mice often develop spontaneous liver disease, which may serve as a comorbidity for SARS-CoV-2 severity. The results of this study suggest broad susceptibility of rodents in the genus Peromyscus and further emphasize the potential of SARS-CoV-2 to infect a wide array of North American rodents.\n\nImportanceA significant concern is the spillback of SARS-CoV-2 into North American wildlife species. We have determined that several species of peromyscine rodents, the most abundant mammals in North America, are susceptible to SARS-CoV-2 and that infection is likely long enough that the virus may be able to establish persistence in local rodent populations. Strikingly, some California mice developed clinical disease that suggests this species may be useful for the study of human co-morbidities often associated with severe and fatal COVID-19 disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Juliette Lewis", + "author_inst": "Colorado State University" + }, + { + "author_name": "Shijun Zhan", + "author_inst": "Colorado State University" + }, + { + "author_name": "Allison Vilander", + "author_inst": "Colorado State University" + }, + { + "author_name": "Anna C Fagre", + "author_inst": "Bat Health Foundation" + }, + { + "author_name": "Hippokratis Kiaris", + "author_inst": "University of South Carolina" + }, + { + "author_name": "Tony Schountz", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.22.504904", "rel_title": "Isolation and characterization of SARS-CoV-2 in Kenya", @@ -203298,93 +203459,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.08.21.22279029", - "rel_title": "Humoral and cellular immune correlates of protection against COVID-19 in kidney transplant recipients", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279029", - "rel_abs": "As solid organ recipients are at high risk of severe COVID-19 and respond poorly to primary SARS-CoV-2 mRNA vaccination, they have been prioritized for booster vaccination. However, an immunological correlate of protection has not been identified in this vulnerable population. We conducted a prospective monocentric cohort study of 65 kidney transplant recipients who received three doses of SARS-CoV-2 BNT162b2 mRNA vaccination. Associations between symptomatic breakthrough infection (BTI) and vaccine responses, patient demographic and clinical characteristics were explored. Symptomatic COVID-19 was diagnosed in 32% of kidney transplant recipients during a period of six months after the administration of the third vaccine dose. During this period, SARS-CoV-2 delta and omicron were the dominant variants in the general population. Univariate analyzes identified avidity of SARS-CoV-2 receptor binding domain (RBD) binding IgG, neutralizing antibodies and SARS-CoV-2 S2 domain-specific IFN-{gamma} responses as correlates of protection against BTI. Some demographic and clinical parameters correlated with vaccine responses, but none correlated with the risk of BTI. In multivariate analysis, the risk of BTI was best predicted by neutralizing antibody and S2-specific IFN-{gamma} responses, adjusting for age, graft function and mycophenolate mofetil use. In conclusion, both antibody and T cell responses predict the risk of BTI in kidney transplant recipients who received three doses of SARS-CoV-2 mRNA vaccine. T cell responses may help compensate for the suboptimal antibody response to vaccination in this vulnerable population.\n\nOne Sentence SummaryAntibody and T cell responses to booster SARS-CoV-2 vaccination predict the risk of symptomatic breakthrough infection in kidney transplant recipients", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Delphine KEMLIN", - "author_inst": "Hopital Erasme, ULB, Bruxelles" - }, - { - "author_name": "Nicolas Gemander", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Stephanie Depickere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Veronique Olislagers", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Daphnee Georges", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Alexandra Waegemans", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Pieter Pannus", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Anne Lemy", - "author_inst": "Department of Nephrology, Hopital Marie Curie, Charleroi, Belgium" - }, - { - "author_name": "Maria E Goossens", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Isabelle Desombere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Johan Michiels", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Marylene Vandevenne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Kevin K Arien", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Andre Matagne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Thayer School of Engineering, Dartmouth College, Hanover, NH, USA" - }, - { - "author_name": "Alain Le Moine", - "author_inst": "Department of Nephrology, Dialysis and Transplantation, Erasme Hospital, Universite Libre de Bruxelles (ULB), Bruxelles, Belgium" - }, - { - "author_name": "Arnaud Marchant", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2022.08.20.22279023", "rel_title": "Brain microstructural changes and fatigue after COVID-19", @@ -203982,6 +204056,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.22.22278433", + "rel_title": "Knowledge practice gap of nurses towards COVID-19 patients dead body care in a tertiary care hospital.", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22278433", + "rel_abs": "AimTo know the dead body care of COVID-19 patients.\n\nObjectiveO_LITo determine health care professionals, knowledge, attitude, and practice towards Covid-19 dead body care.\nC_LIO_LITo find the association of knowledge, attitude, practice with selected demographic variables.\nC_LI\n\nBackgroundCOVID-19 was a global pandemic and it was a serious note for health care professionals from many aspects. The virus was infective and causes serious infectionsto patients which were easily transmitted, hence specific dead body care is required for such kinds of patients. To keep this background in mind the study was conducted to identify the knowledge, practice and attitude towards COVID-19 dead body care among nurses.\n\nMethodologyA cross sectional survey based study was done on 282 samples.Quantitative research design with purposive sampling technique data was collected for knowledge,attitude, and practice.\n\nResultKnowledge, attitude and practice were assessed and association was done with demographic profile. Hence the good knowledge, attitude and practicewere observed in experienced and trained nurses (p value<0.005. Whereas no significant changes were observed with age, gender and education qualification.\n\nConclusionOverall knowledge, attitude and practice regarding COVID-19 dead body care were moderate to good. But it was important to identify the gap as it was a global pandemic and higher chances of spreading of infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "GIRRAJ SAINI", + "author_inst": "AIIMS Rishikesh, Uttrakhand, India" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Mahendra Singh", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Maneesh Maneesh", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Pankaj Punjot", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Raviprakash Meshram", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Puneet Kumar Gupta", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.18.22278340", "rel_title": "A pilot study of 0.4% povidone-iodine nasal spray to eradicate SARS-CoV-2 in the nasopharynx", @@ -205748,6 +205865,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.16.22278820", + "rel_title": "Rapid waning of protection induced by prior BA.1/BA.2 infection against BA.5 infection", + "rel_date": "2022-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.16.22278820", + "rel_abs": "SARS-CoV-2 omicron subvariants BA.1 and BA.2 became dominant in many countries in early 2022. These subvariants are now being displaced by BA.4 and BA.5. While natural infection with BA.1/BA.2 provides some protection against BA.4/BA.5 infection, the duration of this protection remains unknown.\n\nWe used the national Portuguese COVID-19 registry to investigate the waning of protective immunity conferred by prior BA.1/BA.2 infection towards BA.5. We divided the individuals infected during the period of BA.1/BA.2 dominance (>90% of sample isolates) in successive 15-day intervals and determined the risk of subsequent infection with BA.5 over a fixed period.\n\nCompared with uninfected people, one previous infection conferred substantial protection against BA.5 re-infection at 3 months (RR=0.12; 95% CI: 0.11-0.12). However, although still significant, the protection was reduced by two-fold at 5 months post-infection (RR=0.24; 0.23-0.24).\n\nThese results should be interpreted in the context of vaccine breakthrough infections, as the vaccination coverage in the individuals included in the analyses is >98% since the end of 2021.\n\nThis waning of protection following BA.1/BA.2 infection highlights the need to assess the stability and durability of immune protection induced with the adapted vaccines (based on BA.1) over time.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joao Malato", + "author_inst": "Instituto de Medicina Molecular, Faculdade de Medicina, Centro Academico de Medicina de Lisboa, Universidade de Lisboa" + }, + { + "author_name": "Ruy M. Ribeiro", + "author_inst": "Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545" + }, + { + "author_name": "Eugenia Fernandes", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao Geral da Saude, Lisboa, Portugal" + }, + { + "author_name": "Pedro Pinto-Leite", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao Geral da Saude, Lisboa, Portugal" + }, + { + "author_name": "Pedro Casaca", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao Geral da Saude, Lisboa, Portugal" + }, + { + "author_name": "Carlos Antunes", + "author_inst": "Faculdade de Ciencias, Universidade de Lisboa, Lisboa, Portugal" + }, + { + "author_name": "Valter R. Fonseca", + "author_inst": "Instituto de Medicina Molecular, Faculdade de Medicina, Centro Academico de Medicina de Lisboa, Universidade de Lisboa; Direcao Geral da Saude, Lisboa, Portugal" + }, + { + "author_name": "Manuel Carmo Gomes", + "author_inst": "Faculdade de Ciencias, Universidade de Lisboa, Lisboa, Portugal" + }, + { + "author_name": "Luis Graca", + "author_inst": "Instituto de Medicina Molecular, Faculdade de Medicina, Centro Academico de Medicina de Lisboa, Universidade de Lisboa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.16.22278809", "rel_title": "Revealing geographic transmission pattern of COVID-19 using neighborhood-level simulation with human mobility data and SEIR model: A Case Study of South Carolina", @@ -206691,25 +206859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2022.08.14.503890", - "rel_title": "A pan-cancer analysis of the oncogenic role of COVID-19 risk gene Leucine Zipper Transcription Factor-Like Protein 1 (LZTFL1) in human tumors", - "rel_date": "2022-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.14.503890", - "rel_abs": "Population-based studies showed that COVID-19 infection causes higher death rate in cancer patients. However, the molecular mechanism of COVID-19 with cancer is still largely unknown. Here we analyzed the Leucine Zipper Transcription Factor-Like Protein 1 (LZTFL1) which is the most significant gene associated with COVID-19. First, we explored the potential oncogenic roles of LZTFL1 through transcriptome data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. LZTFL1 is significantly low expressed in 11 of 34 kinds of cancers we analyzed. Consistent with the mRNA expression data, the protein expression of LZTFL1 in lung adenocarcinoma (LUAD), clear cell renal cell carcinoma (ccRCC), Uterine corpus endometrial carcinoma (UCEC), and ovarian cancer (OV) patients are significantly decreased compared to healthy tissues. The survival analysis from the Kidney renal clear cell carcinoma (KIRC), Rectum adenocarcinoma (READ), and Uveal Melanoma (UVM), the LZTFL1 high expression group have a significantly higher survival rate compared to the low expression group. Taken together, LZTFL1 acts as a cancer suppressor gene for several cancers. Moreover, LZTFL1 expression was associated with the cancer-associated fibroblast infiltration in several tumors including Bladder Urothelial Carcinoma (BLCA), Breast invasive carcinoma (BRCA), Esophageal carcinoma (ESCA), Head and Neck squamous cell carcinoma (HNSC), Lung squamous cell carcinoma (LUSC), and Pancreatic adenocarcinoma (PAAD). Gene ontology analysis showed that cilium organization, positive regulation of establishment of protein localization to telomere and SRP-dependent cotranslational protein targeting to the membrane were involved in the function mechanisms related to LZTFL1. Our studies offer a relatively comprehensive understanding of the oncogenic roles of LZTFL1 across different kinds of tumors.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lei Wang", - "author_inst": "Chinese academy of sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.08.11.503706", "rel_title": "The P681H mutation in the Spike glycoprotein escapes IFITM restriction and is necessary for type I interferon resistance in the SARS-CoV-2 alpha variant", @@ -207434,6 +207583,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.11.503574", + "rel_title": "SARS-CoV-2 specific plasma cells acquire the phenotype of long-lived plasma cells in the human bone marrow", + "rel_date": "2022-08-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.11.503574", + "rel_abs": "Establishment of long-lived plasma cells (PC) in the bone marrow (BM) is important for the development of long-term specific humoral immunity. While SARS-CoV-2-specific, resting, affinity-matured, IgG-secreting plasma cells were described in human bone marrow approx. 6-7 months after infection or vaccination, the long-term durability of these PC remains unclear. We here show that approximately 20% of SARS-CoV-2-specific human BM plasma cells, including RBD-specific PC accommodate the phenotype of long-lived plasma cells, characterized by the lack of CD19 and/or CD45. This result provides evidence in support of the emergence of persistent SARS-CoV-2 specific plasma cells in humans sustaining the durable production of specific serum IgG protecting against severe courses of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Axel Ronald Schulz", + "author_inst": "Germany Rheumatism Research Center Berlin (DRFZ)" + }, + { + "author_name": "Heike Hirseland", + "author_inst": "Germany Rheumatism Research Center Berlin (DRFZ)" + }, + { + "author_name": "Lisa-Marie Diekmann", + "author_inst": "German Rheumatism Research Center Berlin (DRFZ)" + }, + { + "author_name": "Simon Reinke", + "author_inst": "Berlin Institute of Health (BIH)" + }, + { + "author_name": "Sebastian Hardt", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Antonia Niedobitek", + "author_inst": "German Rheumatism Research Center Berlin (DRFZ)" + }, + { + "author_name": "Henrik E Mei", + "author_inst": "German Rheumatism Research Center Berlin (DRFZ)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.08.11.503601", "rel_title": "Memory B cell responses to Omicron subvariants after SARS-CoV-2 mRNA breakthrough infection", @@ -208741,57 +208933,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.08.05.22278477", - "rel_title": "Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort study", - "rel_date": "2022-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278477", - "rel_abs": "BackgroundIn patients with COVID-19 and baseline soluble urokinase plasminogen receptor plasma (suPAR) levels [≥] 6ng/mL, early administration of anakinra, a recombinant interleukin-1 receptor antagonist, may prevent disease progression and death. In case of suPAR testing unavailability, the Severe COvid Prediction Estimate (SCOPE) score may be used as an alternative in guiding treatment decisions.\n\nMethodsWe conducted a monocenter, retrospective cohort study, including patients with SARS-CoV2 infection and respiratory failure. Patients treated with anakinra (anakinra group, AG) were compared to two control groups of patients who did not receive anakinra, respectively with [≥] 6 ng/mL (CG1) and < 6 ng/mL (CG2) baseline suPAR levels. Controls were paired by age, sex, date of admission and vaccination status. Primary endpoint of the study was disease progression at day 14 from admission, as defined by patient distribution on a simplified version of the 11-point World Health Organization Clinical Progression Scale (WHO-CPS).\n\nResultsBetween July, 2021 and January, 2022, 153 patients were included, among which 56 were treated with off-label anakinra, 49 retrospectively fulfilled prescriptive criteria for anakinra and were assigned to CG1, and 48 presented with suPAR levels < 6ng/mL and were assigned to CG2. At day 14, when comparing to CG1, patients who received anakinra had significantly reduced odds of progressing towards worse clinical outcome both in ordinal regression analysis (OR 0.25, 95% CI 0.11-0.54, p<0.001) and in multivariable analysis (OR 0.19, 95% CI 0.03-0.82, p=0.037), and these results were confirmed even when controlling for age, sex, BMI and vaccinal status. Sensitivities of baseline suPAR and SCOPE score in predicting progression towards severe disease or death at day 14 were similar (83% vs 100%, p=0.59).\n\nConclusionThis real-word, retrospective cohort study confirmed the safety and the efficacy of suPAR-guided, early use of anakinra in hospitalized COVID-19 patients with respiratory failure.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Francesco Vladimiro Segala", - "author_inst": "Universita Cattolica del Sacro Cuore Facolta di Medicina e Chirurgia" - }, - { - "author_name": "Emanuele Rando", - "author_inst": "Universit\u00e0 Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Federica Salvati", - "author_inst": "Universit\u00e0 Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Marcantonio Negri", - "author_inst": "Policlinico Universitario Agostino Gemelli Dipartimento di scienze mediche e chirurgiche" - }, - { - "author_name": "Francesca Catania", - "author_inst": "Universit\u00e0 Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Flavia Sanmartin", - "author_inst": "Universit\u00e0 Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Rita Murri", - "author_inst": "Universit\u00e0 Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Evangelos J. Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens Faculty of Medicine: Ethniko kai Kapodistriako Panepistemio Athenon Iatrike Schole" - }, - { - "author_name": "Massimo Fantoni", - "author_inst": "Fondazione Policlinico Universitario Agostino Gemelli IRCCS" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.05.22278483", "rel_title": "Antibody feedback regulation of memory B cell development in SARS-CoV-2 mRNA vaccination", @@ -209872,6 +210013,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.08.22278553", + "rel_title": "Early Detection of Emerging SARS-CoV-2 Variants of Interest for Experimental Evaluation", + "rel_date": "2022-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278553", + "rel_abs": "Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has demonstrated its ability to rapidly and continuously evolve, leading to the emergence of thousands of different sequence variants, many with distinctive phenotypic properties. Fortunately, the broad availability of next generation sequencing (NGS) technologies across the globe has produced a wealth of SARS- CoV-2 genome sequences, offering a comprehensive picture of how this virus is evolving so that accurate diagnostics and reliable therapeutics for COVID-19 can be maintained. The millions of SARS-CoV-2 sequences deposited into genomic sequencing databases, including GenBank, BV-BRC, and GISAID are annotated with the dates and geographical regions of sample collection, and can be aligned to the Wuhan-Hu-1 reference genome to extract the constellation of nucleotide and amino acid substitutions. By aggregating these data into concise datasets, the spread of variants through space and time can be assessed. Variant tracking efforts have focused on the spike protein due to its critical role in viral tropism and antibody neutralization. To identify emerging variants of concern as early as possible, we developed a computational pipeline to process the genomic data from public databases and assign risk scores based on both epidemiological and functional parameters. Epidemiological dynamics are used to identify variants exhibiting substantial growth over time and across geographical regions. In addition, experimental data that quantify Spike protein regions critical for adaptive immunity are used to predict variants with consequential immunogenic or pathogenic impacts. These growth assessment and functional impact scores are combined to produce a Composite Score for any set of Spike substitutions detected. With this systematic approach to routinely score and rank emerging variants, we have established a method to identify threatening variants early and prioritize them for experimental evaluation.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Zachary S Wallace", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "James Davis", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Anna Maria Niewiadomska", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "Robert D Olson", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Maulik Shukla", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Rick Stevens", + "author_inst": "University of Chicago" + }, + { + "author_name": "Yun Zhang", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "Christian M Zmasek", + "author_inst": "J. Craig Venter Institute" + }, + { + "author_name": "Richard H. Scheuermann", + "author_inst": "J. Craig Venter Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.08.10.22277939", "rel_title": "Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS", @@ -210939,81 +211131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.08.22278532", - "rel_title": "Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI)", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278532", - "rel_abs": "BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England.\n\nMethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence.\n\nResults14175 residents and 19973 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0-83 days after first booster, but no protection was apparent after 84 days. Additional protection following booster vaccination waned, but was still present at 84+ days for COVID-associated hospitalisation (aHR: 0.47, 0.24-0.89) and death (aHR: 0.37, 0.21-0.62). Most residents (64.4%) had received primary course of AstraZeneca, but this did not impact on pre- or post-booster risks. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalisations and no deaths.\n\nConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.\n\nSummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Oliver Stirrup", - "author_inst": "University College London" - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "University College London" - }, - { - "author_name": "Natalie L Adams", - "author_inst": "University College London" - }, - { - "author_name": "Maria Krutikov", - "author_inst": "University College London" - }, - { - "author_name": "Hadjer Nacer-Laidi", - "author_inst": "University College London" - }, - { - "author_name": "Borscha Azmi", - "author_inst": "University College London" - }, - { - "author_name": "Tom Palmer", - "author_inst": "University College London" - }, - { - "author_name": "Christopher Fuller", - "author_inst": "University College London" - }, - { - "author_name": "Aidan Irwin-Singer", - "author_inst": "Department of Health and Social Care" - }, - { - "author_name": "Verity Baynton", - "author_inst": "Department of Health and Social Care" - }, - { - "author_name": "Gokhan Tut", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Paul Moss", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Copas", - "author_inst": "University College London" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.07.22278506", "rel_title": "The prognostic value of transthoracic echocardiography findings in hospitalized adult patients with COVID-19: A single-center retrospective analysis", @@ -211766,6 +211883,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.04.22278439", + "rel_title": "Who is pregnant? defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C)", + "rel_date": "2022-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278439", + "rel_abs": "ObjectiveTo define pregnancy episodes and estimate gestational aging within electronic health record (EHR) data from the National COVID Cohort Collaborative (N3C).\n\nMaterials and MethodsWe developed a comprehensive approach, named Hierarchy and rule-based pregnancy episode Inference integrated with Pregnancy Progression Signatures (HIPPS) and applied it to EHR data in the N3C from 1 January 2018 to 7 April 2022. HIPPS combines: 1) an extension of a previously published pregnancy episode algorithm, 2) a novel algorithm to detect gestational aging-specific signatures of a progressing pregnancy for further episode support, and 3) pregnancy start date inference. Clinicians performed validation of HIPPS on a subset of episodes. We then generated three types of pregnancy cohorts based on the level of precision for gestational aging and pregnancy outcomes for comparison of COVID-19 and other characteristics.\n\nResultsWe identified 628,165 pregnant persons with 816,471 pregnancy episodes, of which 52.3% were live births, 24.4% were other outcomes (stillbirth, ectopic pregnancy, spontaneous abortions), and 23.3% had unknown outcomes. We were able to estimate start dates within one week of precision for 431,173 (52.8%) episodes. 66,019 (8.1%) episodes had incident COVID-19 during pregnancy. Across varying COVID-19 cohorts, patient characteristics were generally similar though pregnancy outcomes differed.\n\nDiscussionHIPPS provides support for pregnancy-related variables based on EHR data for researchers to define pregnancy cohorts. Our approach performed well based on clinician validation.\n\nConclusionWe have developed a novel and robust approach for inferring pregnancy episodes and gestational aging that addresses data inconsistency and missingness in EHR data.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Sara Jones", + "author_inst": "Office of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA" + }, + { + "author_name": "Katie R Bradwell", + "author_inst": "Palantir Technologies, Denver, CO, USA" + }, + { + "author_name": "Lauren E Chan", + "author_inst": "Oregon State University; College of Public Health and Human Sciences" + }, + { + "author_name": "Courtney Olson-Chen", + "author_inst": "Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY" + }, + { + "author_name": "Jessica Tarleton", + "author_inst": "Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Kenneth J Wilkins", + "author_inst": "Biostatistics Program, Office of the Director, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Qiuyuan Qin", + "author_inst": "Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY" + }, + { + "author_name": "Emily Groene Faherty", + "author_inst": "University of Minnesota School of Public Health, Minneapolis, MN" + }, + { + "author_name": "Yan Kwan Lau", + "author_inst": "Sema4, Stamford, CT" + }, + { + "author_name": "Catherine Xie", + "author_inst": "Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY" + }, + { + "author_name": "Yu-Han Kao", + "author_inst": "Sema4, Stamford, CT" + }, + { + "author_name": "Michael N Liebman", + "author_inst": "IPQ Analytics, LLC, Kennett Square, PA" + }, + { + "author_name": "Federico Mariona", + "author_inst": "Beaumont Hospital, Dearborn, MI, Wayne State University, Detroit, MI" + }, + { + "author_name": "Anup Challa", + "author_inst": "Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN" + }, + { + "author_name": "Li Li", + "author_inst": "Sema4, Stamford, CT" + }, + { + "author_name": "Sarah J Ratcliffe", + "author_inst": "Department of Public Health Sciences, University of Virginia, Charlottesville, VA" + }, + { + "author_name": "Julie A McMurry", + "author_inst": "Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO" + }, + { + "author_name": "Melissa A Haendel", + "author_inst": "Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO" + }, + { + "author_name": "Rena C Patel", + "author_inst": "Department of Medicine and Global Health, University of Washington, Seattle, WA" + }, + { + "author_name": "Elaine L Hill", + "author_inst": "Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY and Department of Public Health Sciences, University of Rochester" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.08.05.22278464", "rel_title": "Differential immune response induced by two immunization schedules with an inactivated SARS-CoV-2 vaccine in a randomized phase 3 clinical trial", @@ -212937,57 +213149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.03.22278351", - "rel_title": "A Reagent and Virus Benchmarking Panel for a Uniform Analytical Performance Assessment of N Antigen-Based Diagnostic Tests for COVID-19", - "rel_date": "2022-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278351", - "rel_abs": "Rapid diagnostic tests (RDTs) that detect antigen indicative of SARS-CoV-2 infection can help in making quick health care decisions and regularly monitoring groups at risk of infection. With many RDT products entering the market, it is important to rapidly evaluate their relative performance. Comparison of clinical evaluation study results is challenged by protocol design variations and study populations. Laboratory assays were developed to quantify nucleocapsid (N) and spike (S) SARS-CoV-2 antigens. Quantification of the two antigens in nasal eluates confirmed higher abundance of N than S antigen. The median concentration of N antigen was 10 times greater than S per genome equivalent. The N antigen assay was used in combination with quantitative RT-PCR to qualify a panel composed of recombinant antigens, inactivated virus, and clinical specimen pools. This benchmarking panel was applied to evaluate the analytical performance of the SD Biosensor STANDARD Q COVID-19 Ag test, Abbott Panbio COVID-19 Ag Rapid Test, Abbott BinaxNOW COVID-19 Ag test, and the LumiraDx SARS-CoV-2 Ag Test. The four tests displayed different sensitivities toward the different panel members, but all performed best with the clinical specimen pool. The concentration for a 90% probability of detection across the four tests ranged from 21 pg/mL to 102 pg/mL of N antigen in the extracted sample. Benchmarking panels provide a quick way to verify the baseline performance of a diagnostic and enable direct comparison between diagnostic tests.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Allison L Golden", - "author_inst": "PATH" - }, - { - "author_name": "Jason Cantera", - "author_inst": "PATH (currently GH Labs)" - }, - { - "author_name": "Lorraine Lillis", - "author_inst": "PATH" - }, - { - "author_name": "Thanh T Phan", - "author_inst": "PATH" - }, - { - "author_name": "Hannah Slater", - "author_inst": "PATH" - }, - { - "author_name": "Edwin J Webb", - "author_inst": "PATH (currently Lyell Immunopharma)" - }, - { - "author_name": "Roger B Peck", - "author_inst": "PATH" - }, - { - "author_name": "Gonzalo J Domingo", - "author_inst": "PATH" - }, - { - "author_name": "David S Boyle", - "author_inst": "PATH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.04.22278431", "rel_title": "Determining population-level allocation strategies for COVID-19 treatments in the United States using a quantitative framework, a case study using nirmatrelvir/ritonavir", @@ -213980,6 +214141,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.04.22278160", + "rel_title": "The effect of Omicron breakthrough infection and extended BNT162b2 booster dosing on neutralization breadth against SARS-CoV-2 variants of concern", + "rel_date": "2022-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278160", + "rel_abs": "COVID-19 vaccines are playing a vital role in controlling the COVID-19 pandemic. As SARS-CoV-2 variants encoding mutations in the surface glycoprotein, Spike, continue to emerge, there is increased need to identify immunogens and vaccination regimens that provide the broadest and most durable immune responses. We compared the magnitude and breadth of the neutralizing antibody response, as well as levels of Spike-reactive memory B cells, in individuals receiving a second dose of BNT126b2 at a short (3-4 week) or extended interval (8-12 weeks) and following a third vaccination approximately 6-8 months later. We show that whilst an extended interval between the first two vaccinations can greatly increase the breadth of the immune response and generate a higher proportion of Spike reactive memory B cells, a third vaccination leads to similar levels between the two groups. Furthermore, we show that the third vaccine dose enhances neutralization activity against omicron lineage members BA.1, BA.2 and BA.4/BA.5 and this is further increased following breakthrough infection during the UK omicron wave. These findings are relevant for vaccination strategies in populations where COVID-19 vaccine coverage remains low.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Carl Graham", + "author_inst": "King's College London" + }, + { + "author_name": "Thomas Lechmere", + "author_inst": "King's College London" + }, + { + "author_name": "Aisha Rehman", + "author_inst": "King's College London" + }, + { + "author_name": "Jeffrey Seow", + "author_inst": "King's College London" + }, + { + "author_name": "Ashwini Kurshan", + "author_inst": "King's College London" + }, + { + "author_name": "Isabella Huettner", + "author_inst": "King's College London" + }, + { + "author_name": "Thomas J.A. Maguire", + "author_inst": "King's College London" + }, + { + "author_name": "Jerry Tam", + "author_inst": "King's College London" + }, + { + "author_name": "Daniel Cox", + "author_inst": "King's College London" + }, + { + "author_name": "Christopher Ward", + "author_inst": "King's College London" + }, + { + "author_name": "Mariusz Racz", + "author_inst": "Guy's and St Thomas NHS Trust" + }, + { + "author_name": "Anele Waters", + "author_inst": "Guy's and St Thomas' NHS Trust" + }, + { + "author_name": "Christine Mant", + "author_inst": "King's College London" + }, + { + "author_name": "Michael H Malim", + "author_inst": "King's College London" + }, + { + "author_name": "Julie Fox", + "author_inst": "King's College London" + }, + { + "author_name": "Katie J Doores", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.04.22278274", "rel_title": "Finding a Needle in the Haystack: Design and Implementation of a Digital Site-less Clinical Study of Serial Rapid Antigen Testing to Identify Asymptomatic SARS-CoV-2 Infection", @@ -215227,101 +215467,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.02.22278317", - "rel_title": "Healthcare workers' worries and Monkeypox vaccine advocacy during the first month of the WHO Monkeypox alert: Cross-sectional survey in Saudi Arabia", - "rel_date": "2022-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278317", - "rel_abs": "BackgroundMonkeypox virus re-surged in May 2022 as a new potential global health threat with outbreaks bursting in multiple countries across different continents. This study was conducted during the first month of the WHO announcement to assess the healthcare workers (HCWs) within Saudi Arabia, exploring their perception, worries, and vaccine acceptance for Monkeypox in-line with the resolving COVID-19 pandemic.\n\nMethodsA national cross-sectional survey was conducted between May 27 and June 10, 2022, in Saudi Arabia. Data were collected on the sociodemographic and job-related characteristics, COVID-19 infection status, HCWs worry levels of Monkeypox compared to COVID-19 and its sources, their perceptions, awareness, and HCWs Monkeypox vaccination advocacy.\n\nResultsAmong the 1130 HCWs who completed survey, 41.6% already developed COVID-19. Still, 56.5% were more worried from COVID-19 compared to Monkeypox, while the rest were more worried of Monkeypox disease. The main reason for their worry among 68.8% of the participants was development of another worldwide pandemic post COVID-19, followed by their worry of acquiring the infection themselves or their families (49.6%). Most HCWs (60%) rated their self-awareness of Monkeypox disease as moderate to high.\n\nMales and those who previously developed COVID-19 were significantly less likely to worry about Monkeypox. The worry about Monkeypox developing into a pandemic and the perception of Monkeypox being a severe disease correlated significantly positively with the odds of high worry from the disease.\n\nRegarding participants advocacy for HCWs vaccination against Monkeypox disease, those who developed COVID-19 previously and those who supported application of tighter infection control measures compared to the current ones to combat the disease were significantly predicted to agree for vaccination. 74.2% of the surveyed HCWs perceived that they need to read more about the Monkeypox disease after the survey.\n\nConclusionDuring the first month of the WHOs Monkeypox international alert, about half of HCWs in this study were more worried about Monkeypox disease as compared to COVID-19, and its possible progression into another pandemic. In addition, the majority were in favor of applying tighter infection prevention measures to combat the disease. The current study highlights areas needed for healthcare administrative about the HCWs perceptions and readiness for Monkeypox especially in the event of any occurrence of local or international pandemic.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Fadi Aljamaan", - "author_inst": "King Saud University" - }, - { - "author_name": "Shuliweeh Alenezi", - "author_inst": "King Saud University" - }, - { - "author_name": "Khalid Alhasan", - "author_inst": "King Saud University" - }, - { - "author_name": "Basema Saddik", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Ali Alhaboob", - "author_inst": "King Saud University" - }, - { - "author_name": "Esraa S. Altawil", - "author_inst": "King Saud University Medical City" - }, - { - "author_name": "Fatimah Alshahrani", - "author_inst": "King Saud University" - }, - { - "author_name": "Abdulkarim Alrabiaah", - "author_inst": "King Saud University" - }, - { - "author_name": "Ali Alaraj", - "author_inst": "Qassim University" - }, - { - "author_name": "Khaled Alkriadees", - "author_inst": "King Saud University" - }, - { - "author_name": "Yousef Alshammari", - "author_inst": "King Saud University Medical City" - }, - { - "author_name": "Homood Alharbi", - "author_inst": "King Saud University" - }, - { - "author_name": "Amr Jamal", - "author_inst": "King Saud Univesrity" - }, - { - "author_name": "Rabih Halwani", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Fahad AlZamil", - "author_inst": "King Saud University" - }, - { - "author_name": "Sarah Al-Subaie", - "author_inst": "King Saud University" - }, - { - "author_name": "Mazin Barry", - "author_inst": "King Saud University" - }, - { - "author_name": "Ziad A Memish", - "author_inst": "Alfaisal University" - }, - { - "author_name": "Jaffar A. Al-Tawfiq", - "author_inst": "Johns Hopkins Aramco Healthcare" - }, - { - "author_name": "Mohamad Hani Temsah", - "author_inst": "King Saud University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.02.22278349", "rel_title": "Geospatial disparities in federal COVID-19 test-to-treat program", @@ -215898,6 +216043,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.07.31.22278258", + "rel_title": "Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome", + "rel_date": "2022-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.31.22278258", + "rel_abs": "Expansion of the SARS-CoV-2 BA.4 and BA.5 Omicron subvariants in populations with prevalent immunity from prior infection and vaccination, and associated burden of severe COVID-19, has raised concerns about epidemiologic characteristics of these lineages including their association with immune escape or severe clinical outcomes. Here we show that BA.4/BA.5 cases had 15% (95% confidence interval: 9-21%) and 38% (27-49%) higher adjusted odds of having received 3 and [≥]4 COVID-19 vaccine doses, respectively, than time-matched BA.2 cases, as well as 55% (43-69%) higher adjusted odds of prior documented infection. However, after adjusting for differences in epidemiologic characteristics among cases with each lineage, BA.4/BA.5 infection was not associated with differential risk of emergency department presentation, hospital admission, or intensive care unit admission following an initial outpatient diagnosis. This finding held in sensitivity analyses correcting for potential exposure misclassification resulting from unascertained prior infections. Our results demonstrate that the reduced severity associated with prior (BA.1 and BA.2) Omicron lineages, relative to the Delta variant, has persisted with BA.4/BA.5, despite the association of BA.4/BA.5 with increased risk of breakthrough infection among previously vaccinated or infected individuals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Joseph A Lewnard", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Vennis Hong", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Jeniffer S Kim", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Sally F Shaw", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Bruno Lewin", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Harpreet Takhar", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Sara Y Tartof", + "author_inst": "Kaiser Permanente Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.30.22278161", "rel_title": "Changes in COVID-19-related mortality across key demographic and clinical subgroups: an observational cohort study using the OpenSAFELY platform on 18 million adults in England", @@ -217005,29 +217193,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.30.502143", - "rel_title": "Evolution to increased positive charge on the viral spike protein may be part of the adaptation of SARS-CoV-2 to human transmission", - "rel_date": "2022-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.30.502143", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, continues to evolve and infect individuals. The exterior surface of the SARS-CoV-2 virion is dominated by the spike protein and the current work examined spike protein biochemical features that have changed during the 2 years that SARS-CoV-2 has infected humans. These biochemical properties may influence virion survival and promote movement through the environment and within the human airway to reach target cells to bind, enter and establish the next round of infection. In addition to selective pressure to avoid immune recognition of viral proteins, we hypothesised that SARS-CoV-2 emerged from an animal reservoir capable of human infection and transmission but in a sub-optimum state and a second level of selective pressure is acting on these biochemical features. Our analysis identified a striking change in spike protein charge, from -8.3 in the original Lineage A and B viruses to -1.26 in the current Omicron viruses. In summary, we conclude that in addition to immune selection pressure, the evolution of SARS-CoV-2 has also altered viral spike protein biochemical properties. Future vaccine and therapeutic development should also exploit and target these biochemical properties.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew Cotten", - "author_inst": "MRC/UVRI & London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "My V.T. Phan", - "author_inst": "MRC/UVRI & London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.07.31.500554", "rel_title": "Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variant.", @@ -217768,6 +217933,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.29.22278190", + "rel_title": "SARS-CoV-2 IgG seroprevalence surveys in blood donors before the vaccination campaign, France 2020-2021", + "rel_date": "2022-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.29.22278190", + "rel_abs": "We conducted a cross-sectional study for SARS-CoV-2 anti-S1 IgG prevalence in French blood donors (n=32605), from May-2020 to January-2021. A mathematical model combined seroprevalence with daily number of hospital admissions to estimate the probability of hospitalization upon infection and determine the number of infections while correcting for antibody decay. There was an overall seroprevalence increase over the study period and we estimate that [~]15% of the French population had been infected by SARS-CoV-2 by January-2021. The infection/hospitalization ratio increased with age, from 0.56% (18-30yo) to 6.75% (61-70yo). Half of the IgG-S1 positive individuals had no detectable antibodies 4 to 5 months after infection. The seroprevalence in group O donors (7.43%) was lower (p=0.003) than in A, B and AB donors (8.90%). We conclude, based on seroprevalence data and mathematical modelling, that the overall immunity in the French population before the vaccination campaign started was too low to achieve herd immunity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Pierre Gallian", + "author_inst": "Etablissement Francais du Sang, La Plaine Saint Denis, 93218, France" + }, + { + "author_name": "Nathana\u00ebl Hoz\u00e9", + "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, UMR2000, CNRS, Paris, 75015, France" + }, + { + "author_name": "Nad\u00e8ge Brisbarre", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + }, + { + "author_name": "Paola Mariela Saba Villarroel", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + }, + { + "author_name": "Elif Nurtop", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + }, + { + "author_name": "Christine Isnard", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + }, + { + "author_name": "Boris Pastorino", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + }, + { + "author_name": "Pascale Richard", + "author_inst": "Etablissement Francais du Sang, La Plaine Saint Denis, 93218, France" + }, + { + "author_name": "Pascal Morel", + "author_inst": "Etablissement Francais du Sang, La Plaine Saint Denis, 93218, France" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, UMR2000, CNRS, Paris, 75015, France" + }, + { + "author_name": "Xavier de Lamballerie", + "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207), Marseille, 13005, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.28.22278153", "rel_title": "The Efficacy of Facemasks in the Prevention of COVID-19: A Systematic Review", @@ -218815,49 +219039,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.26.22277799", - "rel_title": "The COVID-19 pandemic impact on continuity of care provision on rare brain diseases and on Ataxia, Dystonia and PKU. A scoping review protocol", - "rel_date": "2022-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22277799", - "rel_abs": "One of the most relevant challenges for healthcare providers during the COVID - 19 pandemic has been assuring the continuity of care to patients with complex health needs such as people living with rare diseases (RDs). The COVID-19 pandemic accelerated the healthcare sectors digital transformation agenda. The delivery of telemedicine services instead of many face-to-face procedures has been expanded and, many healthcare services not directly related to COVID-19 treatments shifted online remotely. Many hospitals, specialist centres, patients and families started to use telemedicine because they were forced to. This trend could directly represent a good practice on how care services could be organized and continuity of care could be ensured for patients. If done properly, it could boast improved patient outcomes and become a post COVID-19 major shift in the care paradigm. There is a fragmented stakeholders spectrum, as many questions arise on: how is e-health interacting with traditional healthcare providers; about the role of the European Reference Networks (ERNs); if can remote care retain a human touch and stay patient centric. Here, we outline a protocol for a scoping review that investigates this topic, focusing on continuity of care and novel methods (e.g., digital approaches) used to reduce the care disruption. This scoping review protocol was designed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews (PRISMA-ScR) standards and will culminate in a narrative synthesis of evidence.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sara Cannizzo", - "author_inst": "Sant'Anna School of Advanced Studies, Institute of Management, Pisa, Italy" - }, - { - "author_name": "Vinciane Quoidbach", - "author_inst": "European Brain Council, Brussels, Belgium" - }, - { - "author_name": "Paola Giunti", - "author_inst": "University College London Hospital, United Kingdom" - }, - { - "author_name": "Wolfgang Oertel", - "author_inst": "Philipps-Universitat Marburg, Germany" - }, - { - "author_name": "Gregory Pastores", - "author_inst": "National Centre for inherited Metabolic Disorders, Mater Misericordiae University Hospital, Dublin, Ireland" - }, - { - "author_name": "Maja Relja", - "author_inst": "University of Zagreb Medical School, Croatia" - }, - { - "author_name": "Giuseppe Turchetti", - "author_inst": "Sant'Anna School of Advanced Studies, Institute of Management, Pisa, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.07.26.22277958", "rel_title": "Induction of poxviral immunity by synthetic MVA-based dual-antigen COVID-19 vaccine COH04S1", @@ -219546,6 +219727,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.26.22278002", + "rel_title": "SARS-CoV-2 infection is associated with anti-desmoglein 2 autoantibody detection.", + "rel_date": "2022-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22278002", + "rel_abs": "Post-acute cardiac sequelae, following SARS-CoV-2 infection, are well recognised as complications of COVID-19. We have previously shown the persistence of autoantibodies against antigens in skin, muscle, and heart in individuals following severe COVID-19; the most common staining on skin tissue displayed an inter-cellular cement pattern consistent with antibodies against desmosomal proteins. Desmosomes play a critical role in maintaining the structural integrity of tissues. For this reason, we analysed desmosomal protein levels and the presence of anti-desmoglein (DSG) 1, 2 and 3 antibodies in acute and convalescent sera from patients with COVID 19 of differing clinical severity. We find increased levels of DSG2 protein in sera from acute COVID patients. Furthermore, we find that DSG2 autoantibody levels are increased significantly in convalescent sera following severe COVID-19 but not in hospitalised patients recovering from influenza infection or healthy controls. Levels of autoantibody in sera from patients with severe COVID-19 were comparable to levels in patients with non-COVID-19-associated cardiac disease, potentially identifying DSG2 autoantibodies as a novel biomarker for cardiac damage. To determine if there was any association between severe COVID-19 and DSG2, we stained post-mortem cardiac tissue from patients who died from COVID-19 infection. This revealed disruption of the intercalated disc between cardiomyocytes that was consistent with separation of the DSG2 protein homodimer. Our results reveal the potential for DSG2 protein and autoimmunity to DSG2 to contribute to unexpected pathologies associated with COVID-19 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kerensa E Ward", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Lora Steadman", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Abid R Karim", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Gary M Reynolds", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Matthew Pugh", + "author_inst": "Institute of Cancer and Genomic Sciences, University of Birmingham, United Kingdom" + }, + { + "author_name": "Sian E Faustini", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Tonny Veenith", + "author_inst": "Department of Critical Care, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom" + }, + { + "author_name": "Ryan S Thwaites", + "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" + }, + { + "author_name": "Peter JM Openshaw", + "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" + }, + { + "author_name": "Mark T Drayson", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Adrian M Shields", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Adam F Cunningham", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom" + }, + { + "author_name": "David C Wraith", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + }, + { + "author_name": "Alex G Richter", + "author_inst": "Institution of Immunology and Immunotherapy, University of Birmingham, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.07.27.22278118", "rel_title": "Risk factors among Black and White COVID-19 patients from a Louisiana Hospital System, March, 2020-August, 2021", @@ -220677,49 +220929,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.07.26.501658", - "rel_title": "Environmental Stability of Enveloped Viruses is Impacted by the Initial Volume and Evaporation Kinetics of Droplets", - "rel_date": "2022-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.26.501658", - "rel_abs": "Efficient spread of respiratory viruses requires the virus to maintain infectivity in the environment. Environmental stability of viruses can be influenced by many factors, including temperature and humidity. Our study measured the impact of initial droplet volume (50, 5, and 1 {micro}L) and relative humidity (RH: 40%, 65%, and 85%) on the stability of influenza A virus, bacteriophage, Phi6, a common surrogate for enveloped viruses, and SARS-CoV-2 under a limited set of conditions. Our data suggest that the drying time required for the droplets to reach quasi-equilibrium (i.e. a plateau in mass) varied with RH and initial droplet volume. The macroscale physical characteristics of the droplets at quasi-equilibrium varied with RH but not with initial droplet volume. We observed more rapid virus decay when the droplets were still wet and undergoing evaporation, and slower decay after the droplets had dried. Initial droplet volume had a major effect on virus viability over the first few hours; whereby the decay rate of influenza virus was faster in smaller droplets. In general, influenza virus and SARS-CoV-2 decayed similarly. Overall, this study suggests that virus decay in media is closely correlated with the extent of droplet evaporation, which is controlled by RH. Taken together, these data suggest that decay of different viruses is more similar at higher RH and in smaller droplets and is distinct at lower RH and in larger droplets. Importantly, accurate assessment of transmission risk requires use of physiologically relevant droplet volumes and careful consideration of the use of surrogates.\n\nFundingNational Institute of Allergy and Infectious Diseases, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Department of Health and Human Services; Flu Lab.\n\nImportanceDuring the COVID-19 pandemic, policy decisions were being driven by virus stability experiments involving SARS-CoV-2 applied to surfaces in large droplets at various humidity conditions. The results of our study indicate that determination of half-lives for emerging pathogens in large droplets likely over-estimates transmission risk for contaminated surfaces, as occurred during the COVID-19 pandemic. Our study implicates the need for the use of physiologically relevant droplet sizes with use of relevant surrogates in addition to what is already known about the importance of physiologically relevant media for risk assessment of future emerging pathogens.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Seema Lakdawala", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Andrea Janie French", - "author_inst": "University of Pittsburgh School of Medicine" - }, - { - "author_name": "Alexandra K Longest", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Jin Pan", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Peter Vikesland", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Nisha K Duggal", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Linsey Marr", - "author_inst": "Virginia Tech" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.20.22277848", "rel_title": "Virtual care use among older immigrant adults in Ontario, Canada during the COVID-19 pandemic: a repeated cross-sectional analysis", @@ -221396,6 +221605,25 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2022.07.25.22278017", + "rel_title": "Transfer learning for Covid-19 detection in medical images", + "rel_date": "2022-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.25.22278017", + "rel_abs": "As of late, the Covid infection 2019 (COVID-19) has caused a pandemic sickness in more than 200 nations, therefore impacting billions of people. To control the spread of the coronavirus, it is crucial to detect infected individuals and ensure their complete isolation to prevent further infection. Chest X-rays and CT-scans have been proven to be very promising as signals of the infection can be clearly shown in lung areas. Transfer learning from ImageNet dataset has become the latent trend in medical imaging applications. However, there are major differences between ImageNet and medical imaging datasets. Therefore, the feasibility of transfer learning in medical applications remains questionable. This paper investigates the performance of five fine-tuned pre-trained models for chest x-rays and CT-scans classification in contrast with a deep CNN model built from scratch. DenseNet121, Resnet-50, Inception v2, Resnet101-V2 and VGG16 are selected and initialized with either random or pre-trained weights to classify augmented images into two classes: Covid and non-Covid. The performance evaluation proves the minuscule impact of training transfer learning models for good quality results, as all CNN models contribute almost equally to the classification and achieve considerable results in terms of precision, accuracy, recall and F1 score.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Maryam El Azhari", + "author_inst": "LISTI" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.07.25.22278009", "rel_title": "Beta-Thalassemia minor and SARS-CoV-2, prevalence, severity, morbidity and mortality: a systematic review study", @@ -222535,33 +222763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.23.22277952", - "rel_title": "Vaccination strategies impact the probability of outbreak extinction: a case study of COVID-19 transmission", - "rel_date": "2022-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.23.22277952", - "rel_abs": "Mass vaccination has been one of the effective control measures for mitigating infectious disease transmission. Several vaccination strategies have been introduced throughout history to control infections and terminate the outbreak. Here, we employed the coronavirus disease 2019 (COVID-19) transmission as a case study and constructed a stochastic age-structured compartmental model to investigate the effectiveness of different vaccination strategies. We estimated the outbreak extinction probability under different vaccination scenarios in homogeneous and heterogeneous populations. We found that population heterogeneity could enhance the likelihood of outbreak extinction at various vaccine coverage. In addition, prioritizing vaccines for people with higher infection risk could maximize the outbreak extinction probability and reduce more infections. In contrast, allocating vaccines to individuals with higher mortality risk provides better results in reducing deaths. We also found that as the vaccine effectiveness wane over time, a booster dose of vaccine could significantly enhance the extinction probability and mitigate disease transmission.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Natcha C. Jitsuk", - "author_inst": "Mahidol University" - }, - { - "author_name": "Sudarat Chadsuthi", - "author_inst": "Naresuan University" - }, - { - "author_name": "Charin Modchang", - "author_inst": "Mahidol University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.23.22277948", "rel_title": "Predicting intention to vaccinate against COVID-19 in older Syrian refugees in Lebanon: findings from a multi-wave study", @@ -223242,6 +223443,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.20.22277849", + "rel_title": "Changes in mobility patterns during the COVID-19 pandemic in Zambia: implications for the effectiveness of NPIs in Sub-Saharan Africa", + "rel_date": "2022-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277849", + "rel_abs": "The COVID-19 pandemic has impacted many facets of human behavior, including human mobility partially driven by the implementation of non-pharmaceutical interventions (NPIs) such as stay at home orders, travel restrictions, and workplace and school closures. Given the importance of human mobility in the transmission of SARS-CoV-2, there have been an increase in analyses of mobility data to understand the COVID-19 pandemic to date. However, despite an abundance of these analyses, few have focused on Sub-Saharan Africa (SSA). Here, we use mobile phone calling data to provide a spatially refined analysis of sub-national human mobility patterns during the COVID-19 pandemic from March 2020-July 2021 in Zambia. Overall, among highly trafficked intra-province routes, mobility decreased up to 52% from March-May 2020 compared to baseline, which was also the time period of the strictest NPIs. However, despite dips in mobility during the first wave of COVID-19 cases, mobility returned to baseline levels and did not drop again suggesting COVID-19 cases did not influence mobility in subsequent waves.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Stacie Loisate", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Simon Mutembo", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Rohan Arambepola", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Kabondo Makungo", + "author_inst": "Zamtel" + }, + { + "author_name": "Elliot N Kabalo", + "author_inst": "Information and Communications University Zambia" + }, + { + "author_name": "Nyambe B. Sinyange", + "author_inst": "Zambia National Public Health Institute" + }, + { + "author_name": "Nathan Kapata", + "author_inst": "Zambia National Public Health Institute" + }, + { + "author_name": "Mazyanga Liwewe", + "author_inst": "Zambia National Public Health Institute" + }, + { + "author_name": "Andrew Silumezi", + "author_inst": "Directorate of Public Health Research" + }, + { + "author_name": "Gershom Chongwe", + "author_inst": "Tropical Diseases Research Centre" + }, + { + "author_name": "Natalya Kostandova", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Amy Wesolowski", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.19.22277827", "rel_title": "Active safety surveillance of COVID-19 mRNA vaccines in children aged 5-15 years in Australia", @@ -224105,101 +224373,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.07.20.22277839", - "rel_title": "Risk factors for severe COVID-19 among HIV-infected and-uninfected individuals in South Africa, April 2020- March 2022:data from sentinel surveillance.", - "rel_date": "2022-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277839", - "rel_abs": "BackgroundData on risk factors for COVID-19-associated hospitalisation and mortality in high HIV prevalence settings are limited.\n\nMethodsUsing existing syndromic surveillance programs for influenza-like-illness and severe respiratory illness at sentinel sites in South Africa, we identified factors associated with COVID-19 hospitalisation and mortality.\n\nResultsFrom April 2020 through March 2022, SARS-CoV-2 was detected in 24.0% (660/2746) of outpatient and 32.5% (2282/7025) of inpatient cases. Factors associated with COVID-19-associated hospitalisation included: older age (25-44 [adjusted odds ratio (aOR) 1.8, 95% confidence interval (CI) 1.1-2.9], 45-64 [aOR 6.8, 95%CI 4.2-11.0] and [≥]65 years [aOR 26.6, 95%CI 14.4-49.1] vs 15-24 years); black race (aOR 3.3, 95%CI 2.2-5.0); obesity (aOR 2.3, 95%CI 1.4-3.9); asthma (aOR 3.5, 95%CI 1.4-8.9); diabetes mellitus (aOR 5.3, 95%CI 3.1-9.3); HIV with CD4 [≥]200/mm3 (aOR 1.5, 95%CI 1.1-2.2) and CD4<200/mm3 (aOR 10.5, 95%CI 5.1-21.6) or tuberculosis (aOR 12.8, 95%CI 2.8-58.5). Infection with Beta (aOR 0.5, 95%CI 0.3-0.7) vs Delta variant and being fully vaccinated (aOR 0.1, 95%CI 0.1-0.3) were less associated with COVID-19 hospitalisation.\n\nIn-hospital mortality was increased in older age (45-64 years [aOR 2.2, 95%CI 1.6-3.2] and [≥]65 years [aOR 4.0, 95%CI 2.8-5.8] vs 25-44 years) and male sex (aOR1.3, 95%CI 1.0-1.6) and was lower in Omicron -infected (aOR 0.3, 95%CI 0.2-0.6) vs Delta-infected individuals.\n\nConclusionActive syndromic surveillance encompassing clinical, laboratory and genomic data identified setting-specific risk factors associated with COVID-19 severity that will inform prioritization of COVID-19 vaccine distribution. Elderly, people with tuberculosis or people living with HIV, especially severely immunosuppressed should be prioritised for vaccination.\n\nSummary of articles viewpointCompared to the Delta variant, the Omicron variant was associated with reduced risk of mortality and Beta associated with decreased risk of hospitalisation. Active syndromic surveillance combining clinical, laboratory and genomic data can be used to describe the epidemic timing, epidemiological characteristics of cases, early detection of variants of concern and how these impact disease severity and outcomes; and presents a viable surveillance approach in settings where national surveillance is not possible.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sibongile Walaza", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Stefano Tempia", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "Centre for Respiratory Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service; School of pathology, University of Witw" - }, - { - "author_name": "Jinal N Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Laboratory services" - }, - { - "author_name": "Amelia Buys", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory service" - }, - { - "author_name": "Daniel Amoako", - "author_inst": "National Institute for Communicable Diseases of the National Health service" - }, - { - "author_name": "Fahima Moosa", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service" - }, - { - "author_name": "Mignon du Plessis", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Diseases; School of pathology, University of Witwatersrand" - }, - { - "author_name": "Jocelyn Moyes", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service; School of public Health, University of Witwatersrand" - }, - { - "author_name": "Meredith L McMorrow", - "author_inst": "Influenza Program, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" - }, - { - "author_name": "Halima Dawood", - "author_inst": "Department of Medicine, Greys Hospital; Caprisa, University of KwaZulu - Natal" - }, - { - "author_name": "Ebrahim Variava", - "author_inst": "Klerksdorp-Tshepong Hospital, North West Province, South Africa; Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand" - }, - { - "author_name": "Gary Reubenson", - "author_inst": "Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Rahima Moosa Mother & Child Hospital, Johannesburg South " - }, - { - "author_name": "Jeremy Nel", - "author_inst": "Helen Joseph Hospital, Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Heather J Zar", - "author_inst": "Department of Paediatrics, Red cross war Memorial hospital, and SA-Medical Research Council on Child & Adolescent Health, University of Cape Town, South Africa" - }, - { - "author_name": "Mvuyo Makhasi", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Susan Meiring", - "author_inst": "Divison of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South " - }, - { - "author_name": "Vanessa Quan", - "author_inst": "Divison of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South " - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.19.22277248", "rel_title": "COVID-19 could cause long term peripheral nerve demyelination and axonal loss: A One Year Prospective Cohort Study", @@ -224964,6 +225137,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.18.22277434", + "rel_title": "Adaptive sentinel testing in workplace for COVID-19 pandemic", + "rel_date": "2022-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277434", + "rel_abs": "Testing and isolation of infectious employees is one of the critical strategies to make the workplace safe during the pandemic for many organizations. Adaptive testing frequency reduces cost while keeping the pandemic under control at the workplace. However, most models aimed at estimating test frequencies were structured for municipalities or large organizations such as university campuses of highly mobile individuals. By contrast, the workplace exhibits distinct characteristics: employee positivity rate may be different from the local community because of rigorous protective measures at workplace, or self-selection of co-workers with common behavioral tendencies for adherence to pandemic mitigation guidelines. Moreover, dual exposure to COVID19 occurs at work and home that complicates transmission modelling, as does transmission tracing at the workplace. Hence, we developed bi-modal SEIR model and R-shiny tool that accounts for these differentiating factors to adaptively estimate the testing frequency for workplace. Our tool uses easily measurable parameters: community incidence rate, risks of acquiring infection from community and work-place, workforce size, and sensitivity of testing. Our model is best suited for moderate-sized organizations with low internal transmission rates, no-outward facing employees whose position demands frequent in-person interactions with the public, and low to medium population positivity rates. Simulations revealed that employee behavior in adherence to protective measures at work and in their community, and the onsite workforce size have large effects on testing frequency. Reducing workplace transmission rate through workplace mitigation protocols and higher sensitivity of the test deployed, though to a lesser extent. Furthermore, our simulations showed that sentinel testing leads to only marginal increase in the number of infections even for high community incidence rates, suggesting that this may be a cost-effective approach in future pandemics. We used our model to accurately guide testing regimen for three campuses of The Jackson Laboratory.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yi Li", + "author_inst": "The Jackson Laboratory, USA" + }, + { + "author_name": "Mandy Chen", + "author_inst": "The Jackson Laboratory, USA" + }, + { + "author_name": "Joshy George", + "author_inst": "The Jackson Laboratory, USA" + }, + { + "author_name": "Edison T Liu", + "author_inst": "The Jackson Laboratory, USA" + }, + { + "author_name": "R. Krishna Murthy Karuturi", + "author_inst": "The Jackson Laboratory, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.17.22277729", "rel_title": "Adjusting non-pharmaceutical interventions based on hospital bed capacity using a multi-operator differential evolution", @@ -225979,33 +226187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.18.22277757", - "rel_title": "COVID-19 Vaccine Booster Dose Willingness Among Patients with Inflammatory Bowel Disease on Infliximab and Vedolizumab: A Cross-Sectional Study", - "rel_date": "2022-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277757", - "rel_abs": "BackgroundVaccination has been effective in preventing COVID-19 infections and related mortality. However, waning immunity after the two-dose vaccination prompted health authorities to recommend a third dose of COVID-19 vaccine to boost immunity. The aim of our study was to assess willingness to receive a third (booster) dose among patients with IBD.\n\nMethodsA cross-sectional study was performed at a tertiary care inflammatory bowel disease center. Patients were recruited at the infusion room from January 1st, 2022, until March 31st, 2022. The primary outcome was the prevalence of BNT162b2 third (booster) dose in infliximab- or vedolizumab-treated patients with IBD. The secondary outcome evaluated whether the prevalence of BNT162b2 third (booster) dose differed based on type of COVID-19 vaccine, gender, age, type of biologic therapy and citizenship.\n\nResultsIn total, 499 patients with IBD were included in this study. The median age was 34.5 years, and 60% had ulcerative colitis (UC). Among the study participants, 302 (60.5%) patients were vaccinated with BNT162b2, and 197 (39.5%) were vaccinated with ChAdOx1 nCoV-19. Of the total number of participants, 400 (80.2%) were receiving infliximab, and 99 (19.8%) were receiving vedolizumab. Overall, 290 (58.1%) of the included patients were willing to receive the third (booster) dose. Patients vaccinated with BNT162b2 were more likely to receive booster dose compared to patients vaccinated with ChAdOx1 nCoV-19 [201 (66.5%) vs 101 (33.5%), p = 0.014]. Infliximab-treated patients were more likely to receive booster dose compared to patients receiving vedolizumab [310 (77.5%) vs 62 (62.6%), p = 0.002]. There was no statistical difference in willingness to receive booster dose in terms of age, nationality, or gender.\n\nConclusionThe percentage of patients with IBD willing or have received a third (booster) dose of BNT162b2 vaccine was lower compared to general population. In addition, patients who received two doses of BNT162b2 vaccines were more likely to receive a third (booster) dose compared to patients who received ChAdOx1 nCoV-19. Patients treated with infliximab were more likely to receive a third (booster) dose of COVID-19 vaccine.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Fatema Alrashed", - "author_inst": "Kuwait University" - }, - { - "author_name": "Ahmad Alfadhli", - "author_inst": "Mubarak Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2022.07.18.22276918", "rel_title": "Drivers and prevalence of COVID-19 vaccine uptake among homeless and precariously housed people in France: a cross-sectional population-based study", @@ -226866,6 +227047,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.18.500430", + "rel_title": "Experimental infection of Mexican free-tailed bats (Tadarida brasiliensis) with SARS-CoV-2.", + "rel_date": "2022-07-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.18.500430", + "rel_abs": "The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus originated in wild bats from Asia, and as the resulting pandemic continues into its third year, concerns have been raised that the virus will expand its host range and infect North American wildlife species, including bats. Mexican free-tailed bats (Tadarida brasiliensis: TABR) live in large colonies in the southern United States, often in urban areas, and as such, could be exposed to the virus from infected humans. We experimentally challenged wild TABR with SARS-CoV-2 to determine the susceptibility, reservoir potential, and population impacts of infection in this species. Of nine bats oronasally inoculated with SARS-CoV-2, five became infected and orally excreted moderate amounts of virus for up to 18 days post inoculation. These five subjects all seroconverted and cleared the virus before the end of the study with no obvious clinical signs of disease. We additionally found no evidence of viral transmission to uninoculated subjects. These results indicate that while TABR are susceptible to SARS-CoV-2 infection, infection of wild populations of TABR would not likely cause mortality. However, the transmission of SARS-CoV-2 from TABR to or from humans, or to other animal species, is a distinct possibility requiring further investigation to better define.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jeffrey Hall", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Erik Hofmeister", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Hon Ip", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Sean Nashold", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Ariel Leon", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Carly Malave", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Elizabeth Falendysz", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Tonie Rocke", + "author_inst": "USGS National Wildlife Health Center" + }, + { + "author_name": "Mariano Carossino", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Udeni Balasuriya", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Susan Knowles", + "author_inst": "USGS National Wildlife Health Center" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.07.15.22277666", "rel_title": "From The Plague Horrors of Cholera, What Partnership Lessons Can Be Learnt in Addressing COVID-19 In Zambia", @@ -227945,41 +228185,6 @@ "type": "new results", "category": "animal behavior and cognition" }, - { - "rel_doi": "10.1101/2022.07.13.499991", - "rel_title": "SARS-CoV-2 causes brain inflammation via impaired neuro-immune interactions", - "rel_date": "2022-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.13.499991", - "rel_abs": "The brain inflammation that frequently occurs in SARS-CoV-2 is the cause of neurological complications1,2 and long COVID 3,4,5. However, many aspects of its pathogenesis mechanism remain unknown 6, 7 and no method of treatment has been established 8. By administering a non-proliferating adenovirus vector expressing SARS-CoV-2 S1 protein into the nasal cavity of mice, we developed a mouse model (S1 mouse) reproducing brain inflammation, fatigue, depressive symptoms, and lung inflammation. Having intracellular calcium elevating activity, S1 protein increased olfactory bulb apoptosis, and reduced the number of acetylcholine producing cells in the medial septal and the diagonal band of Broca as well as the amount of acetylcholine in the brain. This resulted in disrupting the cholinergic anti-inflammatory pathway (CAP) 9 and enhancing inflammation in the brain. Previously, nothing was known about anti-inflammatory factors in the CAP but we discovered that, in the inflammation occurring in the S1 mouse brain, the action of the RNA binding protein ZFP36 10 in degrading inflammatory cytokine mRNA was impaired.\n\nThe symptoms exhibited by the S1 mouse were improved by administering donepezil, a drug with a cholinergic action used in the treatment of dementia. These findings clarify the mechanism of brain inflammation in COVID-19 and indicate the possibility of applying donepezil in the treatment of neurological complications in COVID-19 and long COVID.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Naomi Oka", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kazuya Shimada", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Azusa Ishii", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Nobuyuki Kobayashi", - "author_inst": "The Jikei University School of Medicine" - }, - { - "author_name": "Kazuhiro Kondo", - "author_inst": "The Jikei University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.12.22277450", "rel_title": "Effect of Vitamin D3 supplementation vs. dietary-hygienic measures on SARS-COV-2 infection rates in hospital workers with 25-hydroxyvitamin D3 levels >20 ng/mL", @@ -228944,6 +229149,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.13.22277113", + "rel_title": "SARS-CoV-2 exhibits extreme differences in early viral loads among specimen types suggesting improved detection of pre-infectious and infectious individuals using combination specimen types", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277113", + "rel_abs": "SARS-CoV-2 viral load measurements from a single specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 109 copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise up to 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single specimen types have low clinical sensitivity, whereas a combined throat-nasal swab, and assays with high analytical sensitivity, were inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.\n\nSignificance StatementIn a longitudinal study of SARS-CoV-2 Omicron viral loads in three paired specimen types (saliva, anterior-nares swabs, and oropharyngeal swabs), we found extreme differences among paired specimen types collected from a person at the same timepoint, and that viral loads in different specimen types from the same person often do not correlate throughout infection. Individuals often exhibited high, presumably infectious viral loads in oral specimen types before nasal viral loads remained low or even undetectable. Combination oropharyngeal-nasal swabs were inferred to have superior clinical sensitivity to detect infected and infectious individuals. This demonstrates that single specimen type reference standard tests for SARS-CoV-2, such as in clinical trials or diagnostics evaluations may miss infected and even infectious individuals.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Alexander Viloria Winnett", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Reid Akana", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Natasha Shelby", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Hannah Davich", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Saharai Caldera", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Taikun Yamada", + "author_inst": "Pangea Laboratory, LLC; Zymo Research Corp." + }, + { + "author_name": "John Raymond B. Reyna", + "author_inst": "Pangea Laboratory LLC" + }, + { + "author_name": "Anna E. Romano", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Alyssa M. Carter", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Mi Kyung Kim", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Matt Thomson", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Colten Tognazzini", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Matthew Feaster", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Ying-Ying Goh", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Yap Ching Chew", + "author_inst": "Zymo Research Corp.; Pangea Laboratory, LLC" + }, + { + "author_name": "Rustem F. Ismagilov", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.12.22276726", "rel_title": "Upregulation of Activation Induced Cell Markers (AIM) among Severe COVID-19 patients in Bangladesh", @@ -229783,101 +230067,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.14.500042", - "rel_title": "Fc effector activity and neutralization against SARS-CoV-2 BA.4 is compromised in convalescent sera, regardless of the infecting variant", - "rel_date": "2022-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500042", - "rel_abs": "The SARS-CoV-2 Omicron BA.1 variant, which exhibits high level neutralization resistance, has since evolved into several sub-lineages including BA.4 and BA.5, which have dominated the fifth wave of infection in South Africa. Here we assessed the sensitivity of BA.4 to neutralization and antibody dependent cellular cytotoxicity (ADCC) in convalescent donors infected with four previous variants of SARS-CoV-2, as well as in post-vaccination breakthrough infections (BTIs) caused by Delta or BA.1. We confirm that BA.4 shows high level resistance to neutralization, regardless of the infecting variant. However, breakthrough infections, which trigger potent neutralization, retained activity against BA.4, albeit at reduced titers. Fold reduction of neutralization in BTIs was lower than that seen in unvaccinated convalescent donors, suggesting maturation of neutralizing responses to become more resilient against VOCs in hybrid immunity. BA.4 sensitivity to ADCC was reduced but remained detectable in both convalescent donors and in BTIs. Overall, the high neutralization resistance of BA.4, even to antibodies from BA.1 infections, provides an immunological mechanism for the rapid spread of BA.4 immediately after a BA.1-dominated wave. Furthermore, although ADCC activity against BA.4 was reduced, residual activity may nonetheless contribute to the protection from disease.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Simone Richardson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Prudence Kgagudi", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Nelia P Manamela", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Haajira Kaldine", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Elizabeth Venter", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Thanusha Pillay", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Bronwen E. Lambson", - "author_inst": "NICD: National Institute for Communicable Diseases" - }, - { - "author_name": "Mieke van der Mescht", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Tandile Hermanus", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Zelda de Beer", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Talita de Villier", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Annie Bodenstein", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Gretha van den Berg", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Marizane du Pisanie", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Wendy Burgers", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Ntobeko A.B. Ntusi", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Theresa Rossouw", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Michael Boswell", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Penny Moore", - "author_inst": "University of the Witwatersrand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.14.500039", "rel_title": "SARS-CoV-2 BA.4 infection triggers more cross-reactive neutralizing antibodies than BA.1", @@ -230542,6 +230731,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.12.499813", + "rel_title": "Inducible Bronchus-Associated Lymphoid Tissue in SARS-CoV-2 Infected Rhesus Macaques", + "rel_date": "2022-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.12.499813", + "rel_abs": "Pulmonary immunity against SARS-CoV-2 infection has not been well studied. This study investigated the distribution of immune cells int the lungs of 8 rhesus macaques experimentally infected with SARS-CoV-2, and euthanized 11-14 days later. Using immunohistochemistry, inducible bronchus-associated lymphoid tissue was found in all animals. The inducible bronchus-associated lymphoid tissues were composed of B cells, T cells, and follicular dendritic cells with evidence of lymphocyte priming and differentiation. This suggests local immunity plays an important role in the SARS-CoV-2 infection. Further study of local immunity in the lung would benefit our understanding of SARS-CoV-2 pathogenesis and could lead to new interventions to control the SARS-CoV-2 infection and disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Zhong-Min Ma", + "author_inst": "UC Davis" + }, + { + "author_name": "Katherine J Olstad", + "author_inst": "UC Davis" + }, + { + "author_name": "Koen K. A. Van Rompay", + "author_inst": "UC Davis" + }, + { + "author_name": "Smita S. Iyer", + "author_inst": "UC Davis" + }, + { + "author_name": "Christopher J Miller", + "author_inst": "UC Davis" + }, + { + "author_name": "J. Rachel Reader", + "author_inst": "UC Davis" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.07.13.499851", "rel_title": "Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2", @@ -231537,41 +231765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.07.11.22277508", - "rel_title": "Multi-site disease analytics with applications to estimating COVID-19 undetected cases in Canada", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277508", - "rel_abs": "Even with daily case counts, the true scope of the COVID-19 pandemic in Canada is unknown due to undetected cases. We estimate the pandemic scope through a new multi-site model using publicly available disease count data including detected cases, recoveries among detected cases, and total deaths. These counts are used to estimate the case detection probability, the infection fatality rate through time, as well as the probability of recovery, and several important population parameters including the rate of spread, and importation of external cases. We also estimate the total number of active COVID-19 cases per region of Canada for each reporting interval. We applied this multi-site model Canada-wide to all provinces and territories, providing an estimate of the total COVID-19 burden for the 90 weeks from 23 Apr 2020 to 6 Jan 2022. We also applied this model to the five Health Authority regions of British Columbia, Canada, describing the pandemic in B.C. over the 31 weeks from 2 Apr 2020 to 30 Oct 2020.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matthew RP Parker", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Jiguo Cao", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Laura LE Cowen", - "author_inst": "University of Victoria" - }, - { - "author_name": "Lloyd T Elliott", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Junling Ma", - "author_inst": "University of Victoria" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.11.22277368", "rel_title": "Structural epitope profiling identifies antibodies associated with critical COVID-19 and long COVID", @@ -232528,6 +232721,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.07.22277367", + "rel_title": "Non-hospitalised, vaccinated adults with COVID-19 caused by Omicron BA.1 and BA.2 present with changing symptom profiles compared to those with Delta despite similar viral kinetics", + "rel_date": "2022-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277367", + "rel_abs": "BackgroundSARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC).\n\nMethodsIn a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive PCR or lateral flow test, self-swabbed on alternate days until day 10. We compared symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 and BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR Ct value as a proxy for viral load.\n\nResults555 infection episodes were reported among 483 participants. Across VOCs, symptom burden and duration were similar, however symptom profiles differed among infections caused by Delta compared to Omicron sub-variants; symptoms of all Omicron sub-variants BA.1, BA.2 and BA.4/5 were very similar. Anosmia was reported in 7-13% of participants with Omicron sub-variants, compared to 25/60 (42%) with Delta infection (P= 1.31e-08 or 1.03e-05 or 5.63e-05; {chi}2 test d2+Delta vs. Omicron BA.1 or vs. BA.2, or BA.5, respectively), fever was more common with Omicron BA.5 (30/55, 55%) than Delta (20/60, 33%) (p 0.03). Amongst infections with all Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. Ct values were negatively associated with time since vaccination in participants infected with BA.1; however, this trend was not observed in BA.2/BA.4/5 infections.\n\nConclusionOur study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults.\n\nTrial registrationNCT04750356", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Hermaleigh Townsley", + "author_inst": "Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini" + }, + { + "author_name": "Joshua Gahir", + "author_inst": "Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini" + }, + { + "author_name": "Timothy W Russell", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Edward J Carr", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Matala Dyke", + "author_inst": "Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini" + }, + { + "author_name": "Murad Miah", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Bobbi Clayton", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Callie Smith", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Mauro Miranda", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Nicola O'Reilly", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Lorin Adams", + "author_inst": "Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK" + }, + { + "author_name": "Harriet V Mears", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Christopher Bailey", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "James RM Black", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Ashley S Fowler", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Katalin Wilkinson", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Matthew Hutchinson", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "Francis Crick Institute, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London, UK" + }, + { + "author_name": "Bobbi Clayton", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Gavin Kelly", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Rupert Beale", + "author_inst": "Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)" + }, + { + "author_name": "Padmasayee Papineni", + "author_inst": "London Northwest University Healthcare NHS Trust, London" + }, + { + "author_name": "Tumena Corrah", + "author_inst": "London Northwest University Healthcare NHS Trust, London" + }, + { + "author_name": "Simon Caidan", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Jerome Nicod", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "George Kassiotis", + "author_inst": "Francis Crick Institute, Department of Infectious Disease, St Mary's Hospital, Imperial College London, London" + }, + { + "author_name": "Vincenzo Libri", + "author_inst": "National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo" + }, + { + "author_name": "Bryan Williams", + "author_inst": "National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, Lo" + }, + { + "author_name": "Sonia Gandhi", + "author_inst": "Francis Crick Institute, University College London, Gower Street, London" + }, + { + "author_name": "Adam J Kucharski", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Charles Swanton", + "author_inst": "Francis Crick Institute, University College London, Gower Street, London" + }, + { + "author_name": "David LV Bauer", + "author_inst": "Francis Crick Institute, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)" + }, + { + "author_name": "Emma C Wall", + "author_inst": "Francis Crick Institute, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clini" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.06.22277313", "rel_title": "Seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naive adult Nigerians", @@ -233783,45 +234127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.08.22277413", - "rel_title": "Medical complaints after 3 vs 2 doses SARS-CoV-2 mRNA vaccination", - "rel_date": "2022-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.08.22277413", - "rel_abs": "AimsTo examine whether individuals vaccinated with three doses of mRNA SARS-CoV-2 vaccines have an altered incidence of medical complaints compared to individuals not vaccinated with three doses.\n\nMethodsUsing longitudinal exact 1:1 matching on days since 2nd dose, calendar month and a set of covariates, we obtained a matched sample with 138 581 individuals aged 18-70 years that had the 3rd dose at 20-30 weeks after the 2nd dose and an equally large control group that did not. Main outcomes were medical records of common complaints seen in primary care for up to 90 days after the treatment.\n\nResultsDepending on type of complaint, the estimated 90-day cumulative incidence varied between 70 and 5000 per 100 000 individuals. Among individuals aged 18-44 years, the number of medical complaints was lower for individuals with three doses: Fatigue: 662, 95% confidence interval=473-850, shortness of breath: 160 (90-230) and brain fog: 65 (22-108) fewer per 100 000 vaccinated. No decrease in incidence was observed for musculoskeletal pain, cough or heart palpitations. When individuals where censored from the analysis from the date of positive SARS-CoV-2 test, these absolute differences were smaller. Similar analyses gave higher estimates among individuals aged 45-70 years, yet more ambiguous results when censored at positive test.\n\nConclusionIndividuals vaccinated with dose 3 had reduced incidence of complaints compared to matched controls with only 2 doses. Analyses with vs without censoring at positive test implied that this reduction might be explained by a reduced COVID-19 incidence among the 3-dose-vaccinated.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fredrik Methi", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Jon Michael Gran", - "author_inst": "University of Oslo" - }, - { - "author_name": "Morten Valberg", - "author_inst": "University of Oslo" - }, - { - "author_name": "Jonas Minet Kinge", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Elias Telle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Karin Magnusson", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.08.22277388", "rel_title": "Manifestations Associated with Post Acute Sequelae of SARS-CoV2 Infection (PASC) Predict Diagnosis of New-Onset Psychiatric Disease: Findings from the NIH N3C and RECOVER Studies", @@ -234750,6 +235055,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.06.22277306", + "rel_title": "Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar", + "rel_date": "2022-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277306", + "rel_abs": "BACKGROUNDThe future of the SARS-CoV-2 pandemic hinges on virus evolution and duration of immune protection of natural infection against reinfection. We investigated duration of protection afforded by natural infection, the effect of viral immune evasion on duration of protection, and protection against severe reinfection, in Qatar, between February 28, 2020 and June 5, 2022.\n\nMETHODSThree national, matched, retrospective cohort studies were conducted to compare incidence of SARS-CoV-2 infection and COVID-19 severity among unvaccinated persons with a documented SARS-CoV-2 primary infection, to incidence among those infection-naive and unvaccinated. Associations were estimated using Cox proportional-hazard regression models.\n\nRESULTSEffectiveness of pre-Omicron primary infection against pre-Omicron reinfection was 85.5% (95% CI: 84.8-86.2%). Effectiveness peaked at 90.5% (95% CI: 88.4-92.3%) in the 7th month after the primary infection, but waned to [~]70% by the 16th month. Extrapolating this waning trend using a Gompertz curve suggested an effectiveness of 50% in the 22nd month and <10% by the 32nd month. Effectiveness of pre-Omicron primary infection against Omicron reinfection was 38.1% (95% CI: 36.3-39.8%) and declined with time since primary infection. A Gompertz curve suggested an effectiveness of <10% by the 15th month. Effectiveness of primary infection against severe, critical, or fatal COVID-19 reinfection was 97.3% (95% CI: 94.9- 98.6%), irrespective of the variant of primary infection or reinfection, and with no evidence for waning. Similar results were found in sub-group analyses for those [≥]50 years of age.\n\nCONCLUSIONSProtection of natural infection against reinfection wanes and may diminish within a few years. Viral immune evasion accelerates this waning. Protection against severe reinfection remains very strong, with no evidence for waning, irrespective of variant, for over 14 months after primary infection.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Nico Nagelkerke", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al-Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Maria K. Smatti", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohammad R. Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Zaina Al-Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al-Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul-Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al-Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al-Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al-Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.05.22277237", "rel_title": "PERSISTENT IMMUNITY AFTER MILD SARS CoV-2 INFECTION - THE CoNAN-LONG TERM STUDY -", @@ -235769,45 +236185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.05.22277273", - "rel_title": "Knowledge, attitudes, and practices regarding COVID-19 among university students and employees in Massachusetts, USA: a qualitative study", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.05.22277273", - "rel_abs": "BackgroundAt the time of this study, Massachusetts had recorded a total of 352,558 COVID-19 cases and 12,076 deaths. Few qualitative studies have been conducted that investigate the experiences of university students and employees during the COVID-19 pandemic. The objective of this study was to explore the knowledge, attitudes, and practices regarding COVID-19 in university affiliates to inform future COVID-19 policies.\n\nMethodsSemi-structured focus groups and interviews were conducted via Zoom between December 14, 2020 and January 15, 2021. Twenty-two focus group participants included undergraduate students, graduate students and university employees who had not experienced isolation or quarantine during the Fall 2020 semester. Fourteen participants who had experienced quarantine or isolation were interviewed individually to protect confidentiality. Data were analyzed using Dedoose software via inductive thematic analysis, with reporting as per Consolidated Criteria for Reporting Qualitative Studies (COREQ) guidelines.\n\nResultsFive major themes emerged from these data: COVID-19 knowledge, stress and coping, trust, decision-making, and institutional feedback. Misinformation regarding COVID-19 was common, compounding high levels of stress reported by many participants. Reported direct sources of stress included physical illness, fear of infection, and lack of access to resources while in quarantine or isolation settings. Reported indirect sources of stress included social isolation and financial constraints. Levels of trust were generally high regarding mainstream news media, scientific journals, and university-related information sources. For decision-making processes, participants described altered behaviors to socialize safely during the pandemic, which included increased testing, gathering outdoors, and limiting group sizes. Conversely, some undergraduate students reported increases in socialization behaviors after testing negative for COVID-19, while most university employees did not report altered behaviors after negative test results. While some participants described negative feedback regarding university decisions, most feedback for the institution was positive, with participants reporting appreciation for the universitys asymptomatic testing program and other on-campus health response activities.\n\nConclusionThe universitys investment in COVID-related resources, including the asymptomatic testing program and the on-campus quarantine and isolation spaces, were reported to greatly reduce stress and increase perceived safety. Key findings from this research could guide institutional communication, public health protocols, and support for university community members.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Johanna Ravenhurst", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts- Amherst, Amherst MA" - }, - { - "author_name": "Teah Snyder", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts- Amherst, Amherst MA" - }, - { - "author_name": "Kate F. Wallace", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts- Amherst, Amherst MA" - }, - { - "author_name": "Sheila Pennell", - "author_inst": "Elaine Marieb College of Nursing, University of Massachusetts- Amherst, Amherst MA" - }, - { - "author_name": "Sarah L. Goff", - "author_inst": "Department of Health Promotion and Policy, School of Public Health and Health Sciences, University of Massachusetts- Amherst, Amherst MA" - }, - { - "author_name": "Andrew A. Lover", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts- Amherst, Amherst MA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.04.22277239", "rel_title": "Drivers of Mortality in COVID ARDS Depend on Patient Sub-Type", @@ -236692,6 +237069,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.07.02.22277178", + "rel_title": "CD19+ B cell numbers predict the increase of anti-SARS CoV2 antibodies in fingolimod-treated and COVID-19-vaccinated patients with multiple sclerosis", + "rel_date": "2022-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.02.22277178", + "rel_abs": "Treatment with fingolimod for multiple sclerosis (MS) reduces the efficacy of COVID-19 vaccination. We evaluated by a multivariate linear regression model whether main lymphocyte subsets and demographic feature correlated to the subsequent increase in anti-SARS-CoV2 antibodies following the third dose of COVID-19 vaccination in fingolimod-treated MS patients. We found that number and proportion of peripheral blood CD19+ B lymphocytes before the third dose of vaccination in MS patients treated with fingolimod, predict the subsequent increase of anti-SARS-CoV2 antibodies (respectively p = 0.013; p = 0.015). This work suggests that evaluating the numbers of CD19+ B cells may be important to identify patients at risk of not producing SARS-CoV-2 antibodies, with possible reduced protection from COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Irene Schiavetti", + "author_inst": "University of Genoa" + }, + { + "author_name": "Lucrezia Barcellini", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy" + }, + { + "author_name": "Caterina Lapucci", + "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, Italy" + }, + { + "author_name": "Francesco Tazza", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy" + }, + { + "author_name": "Maria Cellerino", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy" + }, + { + "author_name": "Elisabetta Capello", + "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, Italy" + }, + { + "author_name": "Diego Franciotta", + "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, Italy" + }, + { + "author_name": "Matilde Inglese", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy; IRCCS Ospedale Policlinico San M" + }, + { + "author_name": "Maria Pia Sormani", + "author_inst": "Department of Health Sciences, Section of Biostatistics, University of Genova, Genova, Italy; IRCCS Ospedale Policlinico San Martino, Genova, Italy" + }, + { + "author_name": "Antonio Uccelli", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy; IRCCS Ospedale Policlinico San Mart" + }, + { + "author_name": "Alice Laroni", + "author_inst": "Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child University of Genova, Genova, Italy; IRCCS Ospedale Policlinico San Mart" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.07.03.22277195", "rel_title": "Impact of age-structure and vaccine prioritization on COVID-19 in West Africa", @@ -239039,85 +239475,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.07.03.22277201", - "rel_title": "Clinical characteristics and factors associated with COVID-19-related mortality and hospital admission in 5 rural provinces in Indonesia: a retrospective cohort study", - "rel_date": "2022-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.03.22277201", - "rel_abs": "BackgroundData on COVID-19 clinical characteristics and severity from resource-limited settings are limited. This study examined clinical characteristics and factors associated with COVID-19 mortality and hospitalisation in rural settings of Indonesia, from 1 January to 31 July, 2021.\n\nMethodsThis retrospective cohort included individuals diagnosed with COVID-19 based on polymerase chain reaction or rapid antigen diagnostic test, from Lampung, Gorontalo, Central Sulawesi, Southeast Sulawesi, and East Nusa Tenggara Provinces. We extracted demographic and clinical data, including hospitalisation and mortality from COVID-19 surveillance records. We used mixed-effect logistic regression to examine factors associated with COVID-19-related mortality and hospitalisation.\n\nResultsOf 6,583 confirmed cases, 205 (3.1%) died, and 1,727 (26%) were hospitalised. The median age was 37 years (IQR 26-52), with 825 (12{middle dot}53%) under 20 years, and 3,371 (51.21%) females. 4,533 (68.86%) cases were symptomatic, 319 (4.85%) had a clinical diagnosis of pneumonia, and 945 (14.36%) with at least one pre-existing comorbidity. The mortality and hospitalisation rate ranged from 2.0% and 13.4% in East Nusa Tenggara to 4.3% and 36{middle dot}1% in Lampung. Age-specific mortality rates were 0.9% (2/340) for 0-4 years; 0% (0/112) for 5-9 years; 0.2% (1/498) for 10-19 years; 0.8% (11/1,385) for 20-29 years; 0.9% (12/1,382) for 30-39 years; 2% (23/1,095) for 40-49 years; 5% (57/1,064) for 50-59 years; 11% (62/576) for 60-69 years; 16% (37/232) for [≥]70 years. Older age, pre-existing diabetes, liver diseases, malignancy, and pneumonia were associated with higher risk of mortality and hospitalisation. Pre-existing hypertension, cardiac diseases, chronic kidney disease, COPD, and immunocompromised condition were associated with risk of hospitalisation but not with mortality.\n\nConclusionClinical characteristics and risk factors of severe COVID-19 outcomes in rural provinces were broadly similar to those in urban settings. The risk of COVID-19-related mortality and hospitalisation was associated with higher age, pre-existing chronic comorbidities, and clinical presentation of pneumonia.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Henry Surendra", - "author_inst": "Oxford University Clinical Research Unit, Jakarta, Indonesia" - }, - { - "author_name": "C Yekti Praptiningsih", - "author_inst": "US Centers for Disease Control and Prevention, Jakarta, Indonesia" - }, - { - "author_name": "Arina M Ersanti", - "author_inst": "Perhimpunan Ahli Epidemiologi Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Mariati Rahmat", - "author_inst": "Dinas Kesehatan Kabupaten Sinjai, Sinjai, Indonesia" - }, - { - "author_name": "Widia Noviyanti", - "author_inst": "Perhimpunan Ahli Epidemiologi Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Joshua AD Harmani", - "author_inst": "Perhimpunan Ahli Epidemiologi Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Erni NA Mansur", - "author_inst": "Dinas Kesehatan Provinsi Gorontalo, Gorontalo, Indonesia" - }, - { - "author_name": "Yana Y Suleman", - "author_inst": "Dinas Kesehatan Provinsi Gorontalo, Gorontalo, Indonesia" - }, - { - "author_name": "Sitti Sudrani", - "author_inst": "Dinas Kesehatan Provinsi Sulawesi Tengah, Manado, Indonesia" - }, - { - "author_name": "Rosalina Rosalina", - "author_inst": "Dinas Kesehatan Provinsi Sulawesi Tenggara, Kendari, Indonesia" - }, - { - "author_name": "Ismen Mukhtar", - "author_inst": "Dinas Kesehatan Provinsi Lampung, Bandar Lampung, Indonesia" - }, - { - "author_name": "Dian Rosadi", - "author_inst": "Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, Indonesia" - }, - { - "author_name": "Lukman Fauzi", - "author_inst": "Public Health Science Department, Universitas Negeri Semarang, Semarang, Indonesia" - }, - { - "author_name": "Iqbal RF Elyazar", - "author_inst": "Oxford University Clinical Research Unit, Jakarta, Indonesia" - }, - { - "author_name": "William A Hawley", - "author_inst": "US Centers for Disease Control and Prevention, Jakarta, Indonesia" - }, - { - "author_name": "Hariadi Wibisono", - "author_inst": "Perhimpunan Ahli Epidemiologi Indonesia, Jakarta, Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.28.22276786", "rel_title": "Hybrid immunity expands the functional humoral footprint of both mRNA and vector-based SARS-CoV-2 vaccines", @@ -239718,6 +240075,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2022.06.30.22277105", + "rel_title": "Real World Evidence of Effectiveness of COVID-19 Vaccines and Anti SARS-CoV-2 Monoclonal Antibodies Against Post-Acute Sequelae of SARS-CoV-2 Infection", + "rel_date": "2022-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277105", + "rel_abs": "BackgroundWe evaluated the effectiveness of COVID-19 vaccines and monoclonal antibodies (mAb) against Post-Acute Sequelae of SARS-CoV-2 infection (PASC), an emerging public health problem.\n\nMethods and FindingsIn a retrospective cohort study, we identified patients with clinically significant PASC using a COVID-19 specific, electronic medical record-based surveillance and outcomes registry from an 8-hospital tertiary healthcare system in the greater Houston metropolitan (primary analyses). Analyses were then replicated across a global research network database. We included all adults (>= 18) who survived beyond 28-days of their index infection. PASC was defined as experiencing constitutional (palpitations, malaise / fatigue, headache) or systemic (sleep disorder, shortness of breath, mood / anxiety disorders, cough, and cognitive impairment) symptoms beyond 28-day post-infection period. Instances of PASC were excluded if the symptoms were present pre-COVID or if they resolved within four weeks of initial infection. We fit multivariable logistic regression models and report estimated likelihood of PASC associated with vaccination or mAb treatment as adjusted odds ratios (aOR) with 95% confidence intervals (CI).\n\nPrimary analyses included 53,239 subjects (54.9% female), of whom 5,929, 11.1% (CI: 10.9 - 11.4), experienced PASC. Both, vaccinated breakthrough cases (vs. unvaccinated) and mAb treated patients (vs. untreated) had lower likelihoods for developing PASC, aOR (CI): 0.58 (0.52, 0.66), and 0.77 (0.69, 0.86), respectively. Vaccination was associated with decreased odds of developing all constitutional and systemic symptoms except for taste and smell changes. For all symptoms, vaccination was associated with lower likelihood of experiencing PASC compared to mAb treatment. Replication analysis found almost identical frequency of PASC (11.2%) and similar protective effects against PASC for the COVID-19 vaccine: aOR (CI) 0.25 (0.21 - 0.30) and mAb treatment: 0.62 (0.59 - 0.66).\n\nDiscussionAlthough both COVID-19 vaccines and mAbs decreased the likelihood of PASC, at present, vaccination is the most effective tool to potentially prevent long-term clinical and socio-economic consequences of COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jonika Tannous", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Alan Pan", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Thomas Potter", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Abdulaziz Bako", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Katharine Dlouhy", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Ashley Drews", + "author_inst": "Houston Methodist" + }, + { + "author_name": "H Dirk Sostman", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Farhaan Vahidy", + "author_inst": "Houston Methodist Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.29.22276868", "rel_title": "Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection", @@ -240721,29 +241125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.30.22277091", - "rel_title": "Limitations of models for guiding policy in the COVID-19 pandemic", - "rel_date": "2022-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277091", - "rel_abs": "At the outset of the COVID-19 epidemic in the UK, infectious disease modellers advised the government that unless a lockdown was imposed, most of the population would be infected within a few months and critical care capacity would be overwhelmed. This paper investigates the quantitative arguments underlying these predictions, and draws lessons for future policy.\n\nThe modellers assumed that within age bands all individuals were equally susceptible and equally connected, leading to predictions that more than 80% of the population would be infected in the first wave of an unmitigated epidemic. Models that relax this unrealistic assumption to allow for selective removal of the most susceptible and connected individuals predict much smaller epidemic sizes. In most European countries no more than 10% of the population was infected in the first wave, irrespective of what restrictions were imposed. The modellers assumed that about 2% of those infected would require critical care, far higher than the proportion who entered critical care in the first wave, and failed to identify the key role of nosocomial transmission in overloading health systems. Model-based forecasts that only a lockdown could suppress the epidemic relied on a survey of contact rates in 2006, with no information on the types of contact most relevant to aerosol transmission or on heterogeneity of contact rates.\n\nIn future epidemics, modellers should communicate the uncertainties associated with their assumptions and data, especially when these models are used to recommend policies that have high societal costs and are hard to reverse. Recognition of the gap between models and reality also implies a need to rebalance in favour of greater reliance on rapid studies of real-world transmission, robust model criticism, and acceptance that when measurements contradict model predictions it is the model that needs to be changed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Paul M McKeigue", - "author_inst": "Usher Institute, University of Edinburgh" - }, - { - "author_name": "Simon N Wood", - "author_inst": "School of Mathematics, University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.29.498158", "rel_title": "Vitamin D and the ability to produce 1,25(OH)2D are critical for protection from viral infection of the lungs.", @@ -241332,6 +241713,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.28.22277015", + "rel_title": "Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021-22: a status-based multi-variant model", + "rel_date": "2022-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22277015", + "rel_abs": "BackgroundSARS-CoV-2 is a rapidly spreading disease affecting human life and the economy on a global scale. The disease has caused so far more then 5.5 million deaths. The omicron outbreak that emerged in Botswana in the south of Africa spread around the globe at further increased rates, and caused unprecedented SARS-CoV-2 infection incidences in several countries. At the start of December 2021 the first omicron cases were reported in France.\n\nMethodsIn this paper we investigate the contagiousness of this novel variant relatively to the delta variant that was also in circulation in France at that time. Using a dynamic multi-variant model accounting for cross-immunity through a status-based approach, we analyze screening data reported by Sante Publique France over 13 metropolitan French regions between 1st of December 2021 and the 30th of January 2022. During the investigated period, the delta variant was replaced by omicron in all metropolitan regions in approximately three weeks. The analysis conducted retrospectively allows us to consider the whole replacement time window and compare regions with different times of omicron introduction and baseline levels of variants transmission potential. As large uncertainties regarding cross-immunity among variants persist, uncertainty analyses were carried out to assess its impact on our estimations.\n\nResultsAssuming that 80% of the population was immunized against delta, a cross delta/omicron cross-immunity of 25% and omicron generation time was 3.5 days, the relative strength of omicron to delta, expressed as the ratio of their respective reproduction rates,[Formula], was found to range between 1.51 and 1.86 across regions. Uncertainty analysis on epidemiological parameters led [Formula] ranging over 1.57-2.13 when averaged over the metropolitan French regions, weighting by population size.\n\nConclusionsUpon introduction, omicron spread rapidly through the French territory and showed a high fitness relative to delta. We documented considerable geographical heterogeneities on the spreading dynamics. The historical reconstruction of variant emergence dynamics provide valuable ground knowledge to face future variant emergence events.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Thomas Haschka", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Elisabeta Vergu", + "author_inst": "INRAE" + }, + { + "author_name": "Benjamin Roche", + "author_inst": "Institut de recherche pour le developpement France-Sud: Montpellier, Languedoc-Roussillon, FR" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "INSERM and Sorbonne Universite" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Univ Versailles Saint Quentin / Institut pasteur / Inserm" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.28.22276549", "rel_title": "Understanding reported COVID-19 cases in England following changes to testing, between November 2021 and April 2022", @@ -242471,77 +242887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.27.22276955", - "rel_title": "Impact of COVID-19 on the management and outcomes of ureteric stones in the UK: a multicentre retrospective study", - "rel_date": "2022-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276955", - "rel_abs": "ObjectivesTo determine if management of ureteric stones in the United Kingdom changed during the COVID-19 pandemic and whether this affected patient outcomes.\n\nPatients and methodsWe conducted a multicentre retrospective study of adults with CT-proven ureteric stone disease at 39 UK hospitals during a pre-pandemic period (23/3/19 to 22/6/19) and a period during the pandemic (the 3-month period after the first SARS-CoV-2 case at individual sites). The primary outcome was success of primary treatment modality, defined as no further treatment required for the index ureteric stone. Our study protocol was published prior to data collection.\n\nResultsA total of 3735 patients were included (pre-pandemic=1956 patients; pandemic=1779 patients). Stone size was similar between groups (p>0.05). During the pandemic, patients had lower hospital admission rates (pre-pandemic=54.0% vs pandemic=46.5%, p<0.001), shorter length of stay (mean=4.1 vs. 3.3 days, p=0.02), and higher rates of use of medical expulsive therapy (17.4% vs. 25.4%, p<0.001). In patients who received interventional management (pre-pandemic n=787 vs. pandemic n=685), rates of ESWL (22.7% vs. 34.1%, p<0.001) and nephrostomy were higher (7.1% vs. 10.5%, p=0.03); and rates of ureteroscopy (57.2% vs. 47.5%, p<0.001), stent insertion (68.4% vs. 54.6%, p<0.001), and general anaesthetic (92.2% vs. 76.2%, p<0.001) were lower.\n\nThere was no difference in success of primary treatment modality between patient cohorts (pre-pandemic=73.8% vs. pandemic=76.1%, P=0.11), nor when patients were stratified by treatment modality or stone size. Rates of operative complications, 30-day mortality, and readmission and renal function at 6 months did not differ between the data collection periods.\n\nConclusionsDuring the COVID-19 pandemic, there were lower admission rates and fewer invasive procedures performed. Despite this, there were no differences in treatment success or outcomes. Our findings indicate that clinicians can safely adopt management strategies developed during the pandemic to treat more patients conservatively and in the community.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Matthew H V Byrne", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fanourios Georgiades", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alexander Light", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Catherine Lovegrove", - "author_inst": "University of Oxford" - }, - { - "author_name": "Catherine Dominic", - "author_inst": "Barts and the London School of Medicine, Queen Mary University of London, UK" - }, - { - "author_name": "Josephine Rahman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Senthooran Kathiravelupillai", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Tobias Klatte", - "author_inst": "Department of Urology, Charite - Universitatsmedizin Berlin, Germany" - }, - { - "author_name": "Kasra Saeb-Parsy", - "author_inst": "Cambridge University Hospitals" - }, - { - "author_name": "Rajeev Kumar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Grant D Stewart", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ben Turney", - "author_inst": "University of Oxford" - }, - { - "author_name": "Oliver Wiseman", - "author_inst": "Cambridge University Hospitals" - }, - { - "author_name": "- COVID Stones Collaborative", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "urology" - }, { "rel_doi": "10.1101/2022.06.27.22276790", "rel_title": "BNT162b2 effectiveness against Delta & Omicron variants in teens by dosing interval and duration", @@ -243350,6 +243695,53 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2022.06.23.22276832", + "rel_title": "Patients with affective disorders profit most from telemedical treatment: Evidence from a naturalistic patient cohort during the COVID-19 pandemic", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.23.22276832", + "rel_abs": "BackgroundDuring the COVID-19 pandemic telemedicine became essential in maintaining diagnostic procedures and treatment in psychiatry. However, it is still an open question if telemedicine is a feasible treatment option for all groups of psychiatric patients alike. This prospective monocentric observational trial was conducted to assess the general applicability of telemedical treatment in a naturalistic psychiatric outpatient cohort and to identify groups of disorders and clusters of psychopathology that respond particularly well to telemedical treatment considering sociodemographic characteristics and patients perspectives.\n\nMethodsPatients were recruited April 2020 - April 2021 and asked to fill out the WHO-5 and the SCL-90R at baseline, after 4-6 and 8-12 weeks and a feedback-survey. Additionally, medical records, psychopathology, psychosocial functioning and sociodemographic data were analyzed. Primary outcomes were well-being, psychopathology and functioning during treatment. Secondly, diagnostic groups and psychopathology linked to a superior treatment-response were determined with respect to patients subjective experiences.\n\nResultsOut of 1.385 patients, 254 - mostly with hyperkinetic (35.3%) and depressive disorders (24.6%) - took part. Well-being and SCL-90R total scores improved substantially (both p<0.001). CGI and GAF scores were worse in depressed subjects (both p<0.05). Improvement was mainly seen in depressed patients; chronic disorders experienced a decline in well-being. Sociodemographic characteristics could not explain this difference. Particularly female (r=0.413) patients found telepsychiatry equivalent to conventional treatment. The more virtual sessions participants attended the more likely they were to find telepsychiatry equal to conventional treatment (r=0.231).\n\nConclusionsTelemedicine is an effective treatment for patients with depression under naturalistic conditions. Telemedical consultations are a simple and reliable way of monitoring symptom severity and directing treatment choices during the treatment of depressive disorders. Patients with depression benefited more from telemedical treatment compared to participants with chronic non episodic psychiatric disorders. Future research needs to concentrate on improving telemedical treatment options suited for the latter conditions. Psychiatric telemedicine yielded overall high degrees of satisfaction among users.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tobias Rohrmann", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Peter Praus", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Tanja Proctor", + "author_inst": "Institute of Medical Biometry (IMBI), University of Heidelberg, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany" + }, + { + "author_name": "Anastasia Benedyk", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Heike Tost", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Oliver Hennig", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Andreas Meyer-Lindenberg", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Anna-Sophia Wahl", + "author_inst": "Central Institute of Mental Health, University of Heidelberg, J5, 68159 Mannheim, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.06.23.22276821", "rel_title": "HEART rate variability biofeedback for LOng Covid symptoms (HEARTLOC): protocol for a feasibility study", @@ -244185,45 +244577,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.27.22276377", - "rel_title": "Digitalization impacts the COVID-19 pandemic and the stringency of government measures", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276377", - "rel_abs": "COVID-19 poses a significant burden to populations worldwide. Although the pandemic has accelerated digital transformation, little is known about the influence of digitalization on pandemic developments. Therefore, this country-level study aims to explore the impact of digital adoption on COVID-19 outcomes and government measures. Using the Digital Adoption Index (DAI), we examined the association between countries digital preparedness levels and COVID-19 cases, deaths, and stringency indices (SI) of government measures during the early phase of the pandemic. Gradient Tree Boosting pinpointed essential features related to COVID-19 trends, such as digital adoption, populations smoker fraction, age, and poverty. Subsequently, regression analyses indicated that higher DAI was associated with significant declines in new cases ({beta}=-362.25/pm; p<0.001) and attributed deaths ({beta}=-5.53/pm; p<0.001) months after the peak. When plotting DAI against the SI normalized for the starting day, countries with higher DAI adopted slightly more stringent government measures ({beta}=4.86; p<0.01). Finally, a scoping review identified 70 publications providing valuable arguments for our findings. Digital adoption shows a positive trend in handling the current pandemic and facilitates the implementation of more decisive governmental measures. Improving the distribution of digital adoption may have the potential to attenuate the impact of COVID-19 cases and deaths.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Helen Heinrichs", - "author_inst": "Institute for Experimental Molecular Imaging, RWTH Aachen University Clinic" - }, - { - "author_name": "Florian Mueller", - "author_inst": "Department of Physics of Molecular Imaging Systems, Institute for Experimental Molecular Imaging, RWTH Aachen University Clinic" - }, - { - "author_name": "Lucia Rohfleisch", - "author_inst": "Institute for Experimental Molecular Imaging, RWTH Aachen University Clinic" - }, - { - "author_name": "Volkmar Schulz", - "author_inst": "Department of Physics of Molecular Imaging Systems, Institute for Experimental Molecular Imaging, RWTH Aachen University Clinic" - }, - { - "author_name": "Steven R. Talbot", - "author_inst": "Institute for Laboratory Animal Science, Hannover Medical School" - }, - { - "author_name": "Fabian Kiessling", - "author_inst": "Institute for Experimental Molecular Imaging, RWTH Aachen University Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.26.22276861", "rel_title": "The burden of respiratory conditions in the emergency department of Muhimbili National Hospital in Tanzania in the first two years of the COVID-19 pandemic", @@ -244916,6 +245269,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.24.22276144", + "rel_title": "Humoral Responses in the Omicron Era following Three-Dose SARS-CoV-2 Vaccine Series in Kidney Transplant Recipients", + "rel_date": "2022-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276144", + "rel_abs": "BackgroundKidney transplant recipients (KTR) have a diminished response to SARS-CoV-2 vaccination in comparison to immunocompetent individuals. Deeper understanding of the antibody response in KTRs following third-dose vaccination would enable identification of those who remain unprotected against Omicron and require additional treatment strategies.\n\nMethodsWe profiled antibody responses in KTRs pre- and at one and three months post-third-dose SARS-CoV2 mRNA-based vaccine. Anti-spike and anti-RBD IgG levels were determined by ELISA. Neutralization against wild-type, Beta, Delta and Omicron (BA.1) variants was determined using a SARS-CoV-2 spike pseudotyped lentivirus assay.\n\nResults44 KTRs were analysed at 1 and 3 months (n=26) post-third-dose. At one month, the proportion of participants with a robust antibody response had increased significantly from baseline, but Omicron-specific neutralizing antibodies were detected in just 45% of KTRs. Median binding antibody levels declined at 3 months, but the proportion of KTRs with a robust antibody response was unchanged. 38.5% KTRs maintained Omicron-specific neutralization at 3 months. No clinical variables were significantly associated with detectable Omicron neutralizing antibodies, but anti-RBD titres appeared to identify those with Omicron-specific neutralizing capacity.\n\nConclusionOver 50% of KTRs lack an Omicron-specific neutralization response 1 month following a third mRNA-vaccine dose. Among responders, binding and neutralizing antibody responses were well preserved at 3 months. Anti-RBD antibody titres may be a useful identifier of patients with detectable Omicron neutralizing antibody response.\n\nTrial registrationClinical Trials Ontario: ID 3604\n\nFundingFunded by the St. Michaels Hospital Foundation (CMM, DAY) and the Public Health Agency of Canada, through the COVID-19 Immunity Task Force (MAH, MJO, AL).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Caitriona M. McEvoy", + "author_inst": "St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Queenie Hu", + "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON, Canada" + }, + { + "author_name": "Kento T. Abe", + "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON, Canada" + }, + { + "author_name": "Kevin Yau", + "author_inst": "Division of Nephrology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada" + }, + { + "author_name": "Matthew J. Oliver", + "author_inst": "Division of Nephrology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada" + }, + { + "author_name": "Adeera Levin", + "author_inst": "UBC Division of Nephrology, St. Paul's Hospital, Vancouver, BC, Canada" + }, + { + "author_name": "Anne-Claude M. Gingras", + "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital; Sinai Health System" + }, + { + "author_name": "Michelle Hladunewich", + "author_inst": "University of Toronto" + }, + { + "author_name": "Darren Yuen", + "author_inst": "Unity Health Tororonto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2022.06.24.22276854", "rel_title": "Effect of hybrid immunity, school reopening, and the Omicron variant on trajectory of COVID-19 epidemic in India: A modelling study", @@ -245931,69 +246335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.21.22276659", - "rel_title": "Pre-Omicron vaccine breakthrough infection induces superior cross-neutralization against SARS-CoV-2 Omicron BA.1 than primo infection", - "rel_date": "2022-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276659", - "rel_abs": "SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here we compared the ability of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and from 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta to neutralize the ancestral B.1 strain, and the Gamma, Delta and Omicron BA.1 variants using live virus. We further determined antibody levels against the Spike protein, the Receptor Binding Domain (RBD) and the N-terminal domain (NTD) of Spike. Convalescent sera featured considerable variability in neutralization of B.1 and in cross-neutralization of different strains, and neutralizing capacity moderately correlated with antibody levels against Spike and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed higher neutralizing ability against all strains than patients with mild or severe forms of disease. Sera from BTI cases fell into one of two categories: half the sera had high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or very low neutralizing activity against all strains. Although antibody levels against Spike and the RBD were lower in BTI cases than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, indicative of cross-neutralization between B.1, Delta and Omicron and suggestive of higher affinity, as confirmed by the IC50:Ab level ratios. Neutralizing activity of BTI sera was strongly correlated with antibodies against Spike and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further suggest that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross neutralizing antibodies against different strains, including Omicron BA.1.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Eveline Santos da Silva Dr", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Michel Kohnen Dr", - "author_inst": "Centre Hospitalier de Luxembourg" - }, - { - "author_name": "Georges Gilson Dr", - "author_inst": "Centre Hospitalier de Luxembourg" - }, - { - "author_name": "Therese Staub Dr", - "author_inst": "Centre Hospitalier de Luxembourg" - }, - { - "author_name": "Victor Arendt Dr", - "author_inst": "Centre Hospitalier de Luxembourg" - }, - { - "author_name": "Jean-Yves Servais Mr", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Emilie Charpentier Ms", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Olivia Domingues Ms", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Chantal J Snoeck Dr", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Markus Ollert Prof", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Carole Seguin-Devaux Dr", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Danielle Perez-Bercoff Dr", - "author_inst": "Luxembourg Institute of Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.22.22276298", "rel_title": "Mathematical modelling of COVID-19 with periodic transmission: The case of South Africa", @@ -246894,6 +247235,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.23.22276809", + "rel_title": "Effectiveness of vaccination against SARS-CoV-2 Omicron variant infection, symptomatic disease, and hospitalisation: a systematic review and meta-analysis.", + "rel_date": "2022-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.23.22276809", + "rel_abs": "BackgroundThe rapid rise of Sars-Cov2 B.1.1.529 variant (named Omicron) in the late November 2021 prompted the health authorities to estimate the potential impact on the existing countermeasures, including vaccines. This meta-analysis aims to assess the effectiveness of the current Sars-Cov2 vaccine regimens against laboratory-confirmed Omicron infection. A secondary endpoint aims to investigate the waning effectiveness of primary vaccination against symptomatic Omicron infection and related hospitalization.\n\nMethodsThe systematic review started on December 1, 2021 and was concluded on March 1, 2022. Random-effects (RE) frequentist meta-analyses are performed to estimate the primary vaccination course and the booster dose effectiveness against Omicron. Multiple meta-regressions are performed under mixed-effects model. This study is registered with PROSPERO, CRD42021240143.\n\nFindingsIn total, 15 out of 502 records are included in the quantitative synthesis. The meta-analysis on B.1.1.529 infection risk produces an OR=0{middle dot}69 (95%CI: 0{middle dot}57 to 0{middle dot}83; {tau}2=0{middle dot}225; I2=99{middle dot}49%) after primary vaccination and an OR=0{middle dot}30 (95%CI: 0{middle dot}23 to 0{middle dot}39; {tau}2=0{middle dot}469; I2=99{middle dot}33%) after one additional booster dose. According to the multiple meta-regression models, one booster dose significantly decreases by 69% the risk of symptomatic Omicron infection (OR=0{middle dot}31; 95%CI: 0{middle dot}23 to 0{middle dot}40) and by 88% the risk of hospitalization (OR=0{middle dot}12; 95%CI: 0{middle dot}08 to 0{middle dot}19) with respect to unvaccinated. Six months after primary vaccination, the average risk reduction declines to 22% (OR=0{middle dot}78; 95%CI: 0{middle dot}69 to 0{middle dot}88) against symptomatic infection and to 55% against hospitalization (OR=0{middle dot}45; 95%CI: 0{middle dot}30 to 0{middle dot}68).\n\nInterpretationDespite the high heterogeneity, this study confirms that primary vaccination does not provide sufficient protection against symptomatic Omicron infection. Although the effectiveness of the primary vaccination against hospitalization due to Omicron remains significantly above 50% after 3 months, it dramatically fades after 6 months. Therefore, the administration of one additional booster dose is recommended within 6 months and provides a 76% decrease in the odds of symptomatic Omicron after five months.\n\nFundingThere was no funding source for this study.\n\nARTICLE HIGHLIGHTSO_LIthe primary vaccination decreases the risk of Omicron infection by 31%, while one additional booster dose decreases the risk by 70%\nC_LIO_LIthe primary vaccination course reduces the risk of symptomatic Omicron infection by 24% and the risk of hospitalization by 50%\nC_LIO_LIone additional booster dose decreases by 69% the risk of symptomatic Omicron infection and the risk of hospitalization by 88%\nC_LIO_LIthe effectiveness of the primary vaccination against hospitalization dramatically wanes after 3 months from vaccination, reaching a minimum of 45% in risk reduction after more than 6 months\nC_LI\n\nPANEL: research in contextO_ST_ABSEvidence before this studyC_ST_ABSOmicron variants higher transmissibility combined with an increased risk of infection among individuals vaccinated with primary vaccination have prompted health authorities to introduce a booster vaccination. The systematic review including \"vaccine effectiveness\", \"Covid-19\", \"SARS-CoV-2\", and \"Omicron\" search terms, is performed over three web engines and one early stage research platform (i.e., WHO COVID-19 DATABASE, PubMed, medRxiv + bioRxiv) Additionally, all relevant web sources reporting living data on vaccine effectiveness (i.e., https://view-hub.org/covid-19/ and https://covid-nma.com/), electronic databases and grey literature are considered. The last search update was on March 1, 2022. No country, language, study design restrictions are applied.\n\nAdded value of this studyPrimary vaccination provides relatively low protection against the Omicron VOC, while one additional booster dose decreased substantially the risk of symptomatic Omicron infection and of hospitalization.\n\nImplications of all the available evidenceThe booster dose should be recommended after three months and no later than six months after the primary course vaccination, in order to avoid severe consequences, in particular among the elderly population.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Angela Meggiolaro", + "author_inst": "General Directorate for Health Prevention, Italian Ministry of Health, Viale Ribotta 5, 00144 Rome, Italy" + }, + { + "author_name": "Monica Sane Schepisi", + "author_inst": "General Directorate for Health Prevention, Italian Ministry of Health, Viale Ribotta 5, 00144 Rome, Italy" + }, + { + "author_name": "Sara Farina", + "author_inst": "Departament of Life Sciences and Public Health, Section of Hygiene, Universita Cattolica del Sacro Cuore, 00168 Rome, Italy" + }, + { + "author_name": "Carolina Castagna", + "author_inst": "Department of Life Sciences and Public Health, Section of Hygiene, Universita Cattolica del Sacro Cuore, 00168 Rome, Italy" + }, + { + "author_name": "Alessia Mammone", + "author_inst": "General Directorate for Health Prevention, Italian Ministry of Health, Viale Ribotta 5, 00144 Rome, Italy." + }, + { + "author_name": "Andrea Siddu", + "author_inst": "General Directorate for Health Prevention, Italian Ministry of Health, Viale Ribotta 5, 00144 Rome, Italy." + }, + { + "author_name": "Paola Stefanelli", + "author_inst": "Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Elena 299,00161, Rome, Italy" + }, + { + "author_name": "Stefania Boccia", + "author_inst": "Department of Life Sciences and Public Health, Section of Hygiene, Universita Cattolica del Sacro Cuore; Department of Woman and Child Health and Public Health-" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "General Directorate for Health Prevention, Italian Ministry of Health, Viale Ribotta 5, 00144 Rome, Italy." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.23.22276807", "rel_title": "Hill numbers at the edge of a pandemic: rapid SARS-COV2 surveillance without alignments or trees", @@ -247821,145 +248213,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.06.21.496751", - "rel_title": "Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.", - "rel_date": "2022-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.21.496751", - "rel_abs": "The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from COVID-19-convalescent patients, and identified antibodies that exhibited comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced, and showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Masaru Takeshita", - "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Hidehiro Fukuyama", - "author_inst": "RIKEN Center for Integrative Medical Sciences, Infectious Diseases Research unit, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Katsuhiko Kamada", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Takehisa Matsumoto", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Chieko Makino-Okamura", - "author_inst": "RIKEN Center for Integrative Medical Sciences, Infectious Diseases Research unit, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Tomomi Uchikubo-Kamo", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Yuri Tomabechi", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Kazuharu Hanada", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Saya Moriyama", - "author_inst": "Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan" - }, - { - "author_name": "Yoshimasa Takahashi", - "author_inst": "Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan" - }, - { - "author_name": "Hirohito Ishigaki", - "author_inst": "Department of Pathology, Shiga University of Medical Science, Shiga 520-2192, Japan" - }, - { - "author_name": "Misako Nakayama", - "author_inst": "Department of Pathology, Shiga University of Medical Science, Shiga 520-2192, Japan" - }, - { - "author_name": "Cong Thanh Nguyen", - "author_inst": "Department of Pathology, Shiga University of Medical Science, Shiga 520-2192, Japan" - }, - { - "author_name": "Yoshinori Kitagawa", - "author_inst": "Division of Microbiology and Infectious Diseases, Department of pathology, Shiga University of Medical Science, Shiga 520-2192, Japan" - }, - { - "author_name": "Yasushi Itoh", - "author_inst": "Department of Pathology, Shiga University of Medical Science, Shiga 520-2192, Japan" - }, - { - "author_name": "Masaki Imai", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Tadashi Maemura", - "author_inst": "Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA" - }, - { - "author_name": "Yuri Furusawa", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Hiroshi Ueki", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Seiya Yamayoshi", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan" - }, - { - "author_name": "Mikako Shirouzu", - "author_inst": "RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan" - }, - { - "author_name": "Makoto Ishii", - "author_inst": "Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Hideyuki Saya", - "author_inst": "Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo 162-8640, Japan" - }, - { - "author_name": "Yasushi Kondo", - "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Yuko Kaneko", - "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Katsuya Suzuki", - "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Koichi Fukunaga", - "author_inst": "Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - }, - { - "author_name": "Tsutomu Takeuchi", - "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.22.497134", "rel_title": "Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries", @@ -248724,6 +248977,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2022.06.21.496991", + "rel_title": "Identification of a guanine-specific pocket in the protein N of SARS-CoV-2", + "rel_date": "2022-06-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.21.496991", + "rel_abs": "The SARS-CoV-2 nucleocapsid protein (N) is responsible for RNA binding. Here we report the crystal structure of the C-terminal domain (NCTD) in open and closed conformations and in complex with guanine triphosphate, GTP. The crystal structure and biochemical studies reveals a specific interaction between the guanine, a nucleotide enriched in the packaging signals regions of coronaviruses, and a highly conserved tryptophan residue (W330). In addition, EMSA assays with SARS-CoV-2 derived RNA hairpin loops from a putative viral packaging sequence showed the preference interaction of the N-CTD to RNA oligonucleotides containing G and the loss of the specificity in the mutant W330A. Here we propose that this interaction may facilitate the viral assembly process. In summary we have identified a specific guanine-binding pocket in the N protein that may be used to design viral assembly inhibitors.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rafael Ciges-Tomas", + "author_inst": "Instituto de Biomedicina de Valencia CSIC" + }, + { + "author_name": "Maria Luisa Franco", + "author_inst": "Instituto de Biomedicina de Valencia. CSIC" + }, + { + "author_name": "Marcal Vilar", + "author_inst": "Instituto de Biomedicina de Valencia. CSIC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.06.20.22275744", "rel_title": "Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia", @@ -249759,101 +250039,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2022.06.20.22276205", - "rel_title": "Cohort Profile: Longitudinal population-based study of COVID-19 in UK adults (COVIDENCE UK)", - "rel_date": "2022-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276205", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is estimated to have caused more than 18 million deaths worldwide as of end-May 2022.\n\nMethodsCOVIDENCE UK is a longitudinal population-based study that investigates risk factors for, and impacts of, COVID-19 in UK residents aged [≥]16 years. A unique feature is the capacity to support trial-within-cohort studies to evaluate interventions for prevention of COVID-19 and other acute respiratory illnesses. Participants complete a detailed online baseline questionnaire capturing self-reported information relating to their socio-demographic characteristics, occupation, lifestyle, quality of life, weight, height, longstanding medical conditions, medication use, vaccination status, diet and supplemental micronutrient intake. Follow-up on-line questionnaires capturing incident symptoms of COVID-19 and other acute respiratory infections, incident swab test-confirmed COVID-19, doses of SARS-CoV-2 vaccine received, and quality of life are completed at monthly intervals.\n\nResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19.\n\nConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Hayley Holt", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Clare Relton", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Mohammad Talaei", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Jane Symons", - "author_inst": "Jane Symons Media" - }, - { - "author_name": "Molly R Davies", - "author_inst": "King's College London" - }, - { - "author_name": "David A Jolliffe", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Giulia Vivaldi", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Florence Tydeman", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Anne Williamson", - "author_inst": "Blizard Institute" - }, - { - "author_name": "Paul E Pfeffer", - "author_inst": "Barts Health NHS Trust" - }, - { - "author_name": "Christopher Orton", - "author_inst": "Swansea University" - }, - { - "author_name": "David Ford", - "author_inst": "Swansea University" - }, - { - "author_name": "Gwyneth A Davies", - "author_inst": "Swansea University" - }, - { - "author_name": "Ronan A Lyons", - "author_inst": "Swansea University" - }, - { - "author_name": "Chris J Griffiths", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Frank Kee", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "Aziz Sheikh", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Gerome Breen", - "author_inst": "King's College London" - }, - { - "author_name": "Seif Shaheen", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Adrian R Martineau", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.20.22275994", "rel_title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", @@ -250454,6 +250639,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.17.22276576", + "rel_title": "How do Urban Factors Control the Severity of COVID-19?", + "rel_date": "2022-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.17.22276576", + "rel_abs": "Human health in urban environment has emerged as a primary focus of sustainable development during the time of global pandemic caused by a severe acute respiratory syndrome due to the SARS-CoV-2 coronavirus, COVID-19. It has reshaped the world with the way our communities interact, people work, commute, and spend their leisure time. While different mitigation solutions for controlling COVID-19 virus transmission have already been established, global models that would explain and predict the impact of urban environments on the case fatality ratio CFR of COVID-19 (defined as the number of deaths divided by the number of cases over a time window) are missing. Here, with readily available data from public sources, we study the CFR of the coronavirus for 118 locations (city zip-codes, city boroughs, and cities) worldwide to identify the links between the CFR and outdoor, indoor and personal urban factors. We show that a probabilistic model, optimized on the sample of 20 districts from 4 major US cities, provides an accurate predictive tool for the CFR of COVID-19 regardless of the geographical location. When adjusted for the population, our model can be used to evaluate risk and severity of the disease at multi-geospatial scales worldwide ranging from zip-codes and neighborhoods to cities and countries for different waves of the pandemic. Our results suggest that although disease screening and vaccination policies to containment and lockdowns remain critical in controlling the spread of airborne diseases, urban factors such as population density, humidity, or order of buildings, should all be taken into consideration when identifying resources and planning targeted responses to mitigate the impact and severity of the viruses transmitted through air. We advocate the study of urban factors as a path towards facilitating timely deployment of targeted countermeasures and confinement strategies where sharing of personal information and availability of tests may be restricted or limited.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jacob Roxon", + "author_inst": "EpiDaPo Lab CNRS at George Washington University Children National Medical Center" + }, + { + "author_name": "Marie-Sophie Dumont", + "author_inst": "EpiDaPo Lab CNRS at George Washington University Children National Medical Center" + }, + { + "author_name": "Eric Vilain", + "author_inst": "EpiDaPo Lab CNRS at George Washington University Children National Medical Center" + }, + { + "author_name": "Roland Pellenq", + "author_inst": "EpiDaPo Lab CNRS at George Washington University Children National Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.11.22276273", "rel_title": "Epidemiological characteristics and transmission dynamics of the outbreak caused by the SARS-CoV-2 Omicron variant in Shanghai, China: a descriptive study", @@ -251725,97 +251941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.15.22276432", - "rel_title": "Viral load and timing of infection define neutralization diversity to SARS-CoV-2 infection", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276432", - "rel_abs": "AbstractImmunity to SARS-CoV-2 in COVID-19 cases has diversified due to complex combinations of exposure to vaccination and infection. Elucidating the drivers for upgrading neutralizing activity to SARS-CoV-2 in COVID-19 cases with pre-existing immunity will aid in understanding immunity to SARS-CoV-2 and improving COVID-19 booster vaccines with enhanced cross-protection against antigenically distinct variants. This study revealed that the magnitude and breadth of neutralization responses to SARS-CoV-2 infection in breakthrough infections are determined by upper respiratory viral load and vaccination-infection time interval, but not by the lineage of infecting viruses. Notably, the time interval, but not the viral load, may play a critical role in expanding the breadth of neutralization to SARS-CoV-2. This illustrates the importance of dosing interval optimization in addition to antigen design in the development of variant-proof booster vaccines.\n\nOne-Sentence SummaryViral load and infection timing define the magnitude and breadth of SARS-CoV-2 neutralization after breakthrough infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Sho Miyamoto", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takeshi Arashiro", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Akira Ueno", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takayuki Kanno", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shinji Saito", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Harutaka Katano", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shun Iida", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Akira Ainai", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Seiya Ozono", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takuya Hemmi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yuichiro Hirata", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Saya Moriyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Ryutaro Kotaki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hitomi Kinoshita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Souichi Yamada", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masaharu Shinkai", - "author_inst": "Tokyo Shinagawa Hospital" - }, - { - "author_name": "Shuetsu Fukushi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yoshimasa Takahashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.15.22276427", "rel_title": "Efficacy and Safety of Nebulized Ethanol Inhalation in COVID-19 Treatment. A Randomized, Clinical Trial", @@ -252424,6 +252549,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.06.13.22276325", + "rel_title": "Sensitivity of rapid antigen tests for COVID-19 during the Omicron variant outbreak", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276325", + "rel_abs": "BackgroundRapid antigen tests have been used to prevent the spread of the coronavirus disease 2019 (COVID-19); however, there have been concerns about their decreased sensitivity to the Omicron variant.\n\nAimsIn this study, we compared the sensitivity and specificity of the rapid antigen and the polymerase chain reaction (PCR) tests among the players and staff members of the Japan Professional Football League and clubs. Furthermore, we evaluated the relationship between the sensitivity and the duration from the onset of the symptoms to testing, the manufacturer of the rapid antigen test kits, and the PCR test analyte.\n\nDesign and methodsThis was a retrospective observational study. We used 656 results from both the rapid antigen and PCR tests for COVID-19 using the analytes collected on the same day from January 12 to March 2, 2022, during the Omicron variant outbreak in Japan.\n\nResultsThe sensitivity of the rapid antigen test compared with the PCR test was 0.63 (95% confidence interval: 0.54-0.72) and the specificity was 0.998 (95% confidence interval: 0.995-1.000). There were no significant associations between the sensitivity and the duration from the onset of the symptoms to testing (including asymptomatic cases in the category), vaccination status, manufacturer of the rapid antigen test kit or PCR analyte (P > 0.05) with small effect sizes (Cramers V or {varphi}: [≤] 0.22).\n\nConclusionsEven during the Omicron outbreak, the sensitivity of the rapid antigen tests did not depend on the duration from the onset of the symptoms to testing.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michio Murakami", + "author_inst": "Osaka University" + }, + { + "author_name": "Hitoshi Sato", + "author_inst": "Japan Professional Football League" + }, + { + "author_name": "Tomoko Irie", + "author_inst": "Japan Professional Football League" + }, + { + "author_name": "Masashi Kamo", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Wataru Naito", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Tetsuo Yasutaka", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Seiya Imoto", + "author_inst": "The University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.12.22276088", "rel_title": "Effect of Opaganib on Supplemental Oxygen and Mortality in Patients with Severe SARS-CoV-2 Pneumonia", @@ -253603,513 +253771,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.16.22276024", - "rel_title": "Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276024", - "rel_abs": "BackgroundShort-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022.\n\nMethodsWe used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported from a standardised source over the next one to four weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models past predictive performance.\n\nResultsOver 52 weeks we collected and combined up to 28 forecast models for 32 countries. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 84% of participating models forecasts of incident cases (with a total N=862), and 92% of participating models forecasts of deaths (N=746). Across a one to four week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over four weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models.\n\nConclusionsOur results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than two weeks.\n\nCode and data availabilityAll data and code are publicly available on Github: covid19-forecast-hub-europe/euro-hub-ensemble.", - "rel_num_authors": 123, - "rel_authors": [ - { - "author_name": "Katharine Sherratt", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Hugo Gruson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rok Grah", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Helen Johnson", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Rene Niehus", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Bastian Prasse", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Frank Sandman", - "author_inst": "European Centre for Disease Prevention and Control (ECDC)" - }, - { - "author_name": "Jannik Deuschel", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Daniel Wolffram", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Alexander Ullrich", - "author_inst": "Robert Koch Institute" - }, - { - "author_name": "Graham Gibson", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Evan L Ray", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Nicholas G Reich", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Daniel Sheldon", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Yijin Wang", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Nutcha Wattanachit", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Lijing Wang", - "author_inst": "Boston Children's Hospital and Harvard Medical School" - }, - { - "author_name": "Jan Trnka", - "author_inst": "Charles University" - }, - { - "author_name": "Guillaume Obozinski", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "Tao Sun", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "Dorina Thanou", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "Loic Pottier", - "author_inst": "Education nationale" - }, - { - "author_name": "Ekaterina Krymova", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Maria Vittoria Barbarossa", - "author_inst": "Frankfurt Institute for Advanced Studies" - }, - { - "author_name": "Neele Leithauser", - "author_inst": "Fraunhofer Institute for Industrial Mathematics" - }, - { - "author_name": "Jan Mohring", - "author_inst": "Fraunhofer Institute for Industrial Mathematics" - }, - { - "author_name": "Johanna Schneider", - "author_inst": "Fraunhofer Institute for Industrial Mathematics" - }, - { - "author_name": "Jaroslaw Wlazlo", - "author_inst": "Fraunhofer Institute for Industrial Mathematics" - }, - { - "author_name": "Jan Fuhrmann", - "author_inst": "Heidelberg University" - }, - { - "author_name": "Berit Lange", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Isti Rodiah", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Prasith Baccam", - "author_inst": "IEM, Inc." - }, - { - "author_name": "Heidi Gurung", - "author_inst": "IEM, Inc." - }, - { - "author_name": "Steven Stage", - "author_inst": "IEM, Inc." - }, - { - "author_name": "Bradley Suchoski", - "author_inst": "IEM, Inc." - }, - { - "author_name": "Jozef Budzinski", - "author_inst": "Independent" - }, - { - "author_name": "Robert Walraven", - "author_inst": "Independent" - }, - { - "author_name": "Inmaculada Villanueva", - "author_inst": "Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Universitat Pompeu Fabra" - }, - { - "author_name": "Vit Tucek", - "author_inst": "Institute of Computer Science of the CAS" - }, - { - "author_name": "Martin Smid", - "author_inst": "Institute of Information Theory and Automation of the CAS" - }, - { - "author_name": "Milan Zajicek", - "author_inst": "Institute of Information Theory and Automation of the CAS" - }, - { - "author_name": "Cesar Perez Alvarez", - "author_inst": "Inverence" - }, - { - "author_name": "Borja Reina", - "author_inst": "Inverence" - }, - { - "author_name": "Nikos I Bosse", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sophie Meakin", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Pierfrancesco Alaimo Di Loro", - "author_inst": "LUMSA University" - }, - { - "author_name": "Antonello Maruotti", - "author_inst": "LUMSA University" - }, - { - "author_name": "Veronika Eclerova", - "author_inst": "Masaryk University" - }, - { - "author_name": "Andrea Kraus", - "author_inst": "Masaryk University" - }, - { - "author_name": "David Kraus", - "author_inst": "Masaryk University" - }, - { - "author_name": "Lenka Pribylova", - "author_inst": "Masaryk University" - }, - { - "author_name": "Bertsimas Dimitris", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Michael Lingzhi Li", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Soni Saksham", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Jonas Dehning", - "author_inst": "Max-Planck-Institut fur Dynamik und Selbstorganisation" - }, - { - "author_name": "Sebastian Mohr", - "author_inst": "Max-Planck-Institut fur Dynamik und Selbstorganisation" - }, - { - "author_name": "Viola Priesemann", - "author_inst": "Max-Planck-Institut fur Dynamik und Selbstorganisation" - }, - { - "author_name": "Grzegorz Redlarski", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Benjamin Bejar", - "author_inst": "Paul Scherrer Institute" - }, - { - "author_name": "Giovanni Ardenghi", - "author_inst": "Politecnico di Milano" - }, - { - "author_name": "Nicola Parolini", - "author_inst": "Politecnico di Milano" - }, - { - "author_name": "Giovanni Ziarelli", - "author_inst": "Politecnico di Milano" - }, - { - "author_name": "Wolfgang Bock", - "author_inst": "Technical University of Kaiserlautern" - }, - { - "author_name": "Stefan Heyder", - "author_inst": "Technische Universitat Ilmenau" - }, - { - "author_name": "Thomas Hotz", - "author_inst": "Technische Universitat Ilmenau" - }, - { - "author_name": "David E. Singh", - "author_inst": "Universidad Carlos III de Madrid" - }, - { - "author_name": "Miguel Guzman-Merino", - "author_inst": "Universidad Carlos III de Madrid" - }, - { - "author_name": "Jose L Aznarte", - "author_inst": "Universidad Nacional de Educacion a Distancia (UNED)" - }, - { - "author_name": "David Morina", - "author_inst": "Universitat de Barcelona" - }, - { - "author_name": "Sergio Alonso", - "author_inst": "Universitat Politecnica de Catalunya" - }, - { - "author_name": "Enric Alvarez", - "author_inst": "Universitat Politecnica de Catalunya" - }, - { - "author_name": "Daniel Lopez", - "author_inst": "Universitat Politecnica de Catalunya" - }, - { - "author_name": "Clara Prats", - "author_inst": "Universitat Politecnica de Catalunya" - }, - { - "author_name": "Jan Pablo Burgard", - "author_inst": "Universitat Trier" - }, - { - "author_name": "Arne Rodloff", - "author_inst": "University of Cologne" - }, - { - "author_name": "Tom Zimmermann", - "author_inst": "University of Cologne" - }, - { - "author_name": "Alexander Kuhlmann", - "author_inst": "University of Halle" - }, - { - "author_name": "Janez Zibert", - "author_inst": "University of Ljubljana" - }, - { - "author_name": "Fulvia Pennoni", - "author_inst": "University of Milano-Bicocca" - }, - { - "author_name": "Fabio Divino", - "author_inst": "University of Molise" - }, - { - "author_name": "Marti Catala", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gianfranco Lovison", - "author_inst": "University of Palermo" - }, - { - "author_name": "Paolo Giudici", - "author_inst": "University of Pavia" - }, - { - "author_name": "Barbara Tarantino", - "author_inst": "University of Pavia" - }, - { - "author_name": "Francesco Bartolucci", - "author_inst": "University of Perugia" - }, - { - "author_name": "Giovanna Jona Lasinio", - "author_inst": "University of Rome \"\"La Sapienza\"\"" - }, - { - "author_name": "Marco Mingione", - "author_inst": "University of Rome \"\"La Sapienza\"\"" - }, - { - "author_name": "Alessio Farcomeni", - "author_inst": "University of Rome \"\"Tor Vergata\"\"" - }, - { - "author_name": "Ajitesh Srivastava", - "author_inst": "University of Southern California" - }, - { - "author_name": "Pablo Montero-Manso", - "author_inst": "University of Sydney" - }, - { - "author_name": "Aniruddha Adiga", - "author_inst": "University of Virginia" - }, - { - "author_name": "Benjamin Hurt", - "author_inst": "University of Virginia" - }, - { - "author_name": "Bryan Lewis", - "author_inst": "University of Virginia" - }, - { - "author_name": "Madhav Marathe", - "author_inst": "University of Virginia" - }, - { - "author_name": "Przemyslaw Porebski", - "author_inst": "University of Virginia" - }, - { - "author_name": "Srinivasan Venkatramanan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Rafal Bartczuk", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Filip Dreger", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Anna Gambin", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Krzysztof Gogolewski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Magdalena Gruziel-Slomka", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Bartosz Krupa", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Antoni Moszynski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Karol Niedzielewski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Jedrzej Nowosielski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Maciej Radwan", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Franciszek Rakowski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Marcin Semeniuk", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Ewa Szczurek", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Jakub Zielinski", - "author_inst": "University of Warsaw" - }, - { - "author_name": "Jan Kisielewski", - "author_inst": "University of Warsaw, University of Bialystok" - }, - { - "author_name": "Barbara Pabjan", - "author_inst": "University of Wroclaw" - }, - { - "author_name": "Kirsten Holger", - "author_inst": "Universtat Leipzig" - }, - { - "author_name": "Yuri Kheifetz", - "author_inst": "Universtat Leipzig" - }, - { - "author_name": "Markus Scholz", - "author_inst": "Universtat Leipzig" - }, - { - "author_name": "Marcin Bodych", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Maciej Filinski", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Radoslaw Idzikowski", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Tyll Krueger", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Tomasz Ozanski", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Johannes Bracher", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.13.22276312", "rel_title": "Quantifying Inequities in COVID-19 Vaccine Distribution Over Time by social vulnerability, race and ethnicity, and location: A Population-Level Analysis in St. Louis and Kansas City, Missouri", @@ -254834,6 +254495,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.08.22275684", + "rel_title": "Relation of spice consumption with COVID-19 first wave statistics (infection, recovery and mortality) across India", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.08.22275684", + "rel_abs": "Background & ObjectivesThe recovery and mortality statistics for COVID-19 first wave considerably differed in different states & Union territories (UT) of India. Though dependent on several factors, relation of diet and immunity is well-established. Spices are an essential part of Indian cuisine. Apart from adding flavors and colors to the food, their importance has been traditionally known in disease prevention and cure. Thus, present study was carried out to assess relation of spice consumption with COVID-19 first wave statistics in India.\n\nMethodsThe spice consumption data were retrieved from Household Consumption of Various Goods and Services in India from 68th round (2011-12) of survey conducted by National Sample Survey Organization (NSSO). Spices for which, consumption data was available, viz., ginger (Zingiber officinale), garlic (Allium sativum), cumin (Cuminum cyminum), coriander (Coriandrum sativum), turmeric (Curcuma longa), black pepper (Piper nigrum), chili (Capsicum annuuam), tamarind (Tamarandus indica) and other spices were selected for analysis. The COVID-19 first wave data for individual states and UTs were retrieved as total number of cases, number of cured/discharged/migrated cases and total number of deaths due to COVID-19, in a cumulative form. It was normalized per million population of respective states and UT. The correlation of individual spice consumption and COVID-19 statistics was analyzed.\n\nResults and ConclusionsSpices were consumed across all India with a varied range. The highest consumed spice was ginger. Its highest consumption was in Mizoram (185 gm/30 days) and least in Jammu & Kashmir (23gm/30 days). The highest consumption of Other spices were observed in Lakshadweep (149 gm/30 days), which incidentally reported zero COVID-19 cases. Tamarind consumption showed positive correlation (r = 0.4724) with total number of cases per million population, recovered/migrated/cured cases (r = 0.4948). The consumption of cumin exhibited a weak positive correlation (r = 0.5011) with total deaths per million population. However, most of these correlations were statistically insignificant. The findings from this study provide a basic framework and understanding for future studies. These findings can help to predict preventive/ mitigating or curative usage of these spices. Should similar scenario occur in future, these findings can provide some vital base to act as adjuvant management. As the unspecified and under-explored Other spices category showed promising correlation, more attention needs to be given to them too, along with mostly studied spices like ginger and turmeric.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Vedvati Bhapkar", + "author_inst": "D. Y. Patil deemed to be University School of Ayurveda, Nerul, Navi Mumbai" + }, + { + "author_name": "Supriya Bhalerao", + "author_inst": "IRSHA, Pune" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.10.22276234", "rel_title": "The impact of Test Positivity on Surveillance with Asymptomatic Carriers", @@ -255977,49 +255661,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.09.22276129", - "rel_title": "Side effects of Covishield vaccine among frontline healthcare workers of a tertiary health care center", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276129", - "rel_abs": "ObjectivesCOVID disease started in the late 2019 and within a short time became a pandemic disease. With the increasing morbidity and mortality all over the world and the therapeutics not doing wonders, scientists were in the attempt to develop vaccines as a mitigating measure. With continuous efforts and developments, different vaccines were developed and rolled out gradually in different countries. Concerns were notable for occurrence of side effects. Hence this study was done to assess the side effects following Covishield vaccination in Nepal at the initial stage.\n\nMethodsThis was a cross-sectional study done via snowball sampling method among healthcare workers at a tertiary medical college hospital in Pokhara, Nepal after obtaining ethical consent from the institutional review committee of the concerned hospital. The proforma was sent via online means through different social media platforms and also printed forms were also given to the respondents. A total of 139 respondents were obtained after removing duplications. The data were entered into SPSS and analyzed using descriptive and inferential statistics. P-value [≤] 0.05 was considered statistically significant.\n\nResultsMajority (64.7%) were female healthcare workers. More than half (52.3%) used pre-medication in an attempt to avoid the side effects of vaccine. Most (90.6%) reported at least one side effect-local or systemic to the first dose and approximately three-quarter (74.3%) reported side effect to the second dose. Common side effects were pain at injection site, muscle pain, headache, fatigue and weakness. Most of the side effects were higher with the first dose as compared to the second dose.\n\nConclusionSide effects are common with Covishield vaccination, significantly more with the first dose as compared to the second dose. Female gender, younger age and past covid infection were associated with slightly more occurrence of side effects; however were not found to be statistically significant.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Durga Dhungana", - "author_inst": "MCOMS: Manipal College of Medical Sciences" - }, - { - "author_name": "Yukta Narayan Regmi", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - }, - { - "author_name": "Deependra Shrestha", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - }, - { - "author_name": "Krishna Thapa", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - }, - { - "author_name": "Chandra Bahadur Pun", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - }, - { - "author_name": "Tirthalal Upadhaya", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - }, - { - "author_name": "Gopi Hirachan", - "author_inst": "Gandaki Medical College Teaching Hospital and Research Center Pvt Ltd: Gandaki Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.09.22276209", "rel_title": "Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection", @@ -256804,6 +256445,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2022.06.09.22276142", + "rel_title": "Clinical sensitivity and specificity of a high-throughput microfluidic nano-immunoassay combined with capillary blood microsampling for the identification of anti-SARS-CoV-2 Spike IgG serostatus", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276142", + "rel_abs": "BackgroundWe evaluate the diagnostic performance of dried blood microsampling combined with a high-throughput microfluidic nano-immunoassay (NIA) for the identification of anti-SARS-CoV-2 Spike IgG seropositivity.\n\nMethodsWe conducted a serological study among 192 individuals with documented prior SARS-CoV-2 infection and 44 SARS-CoV-2 negative individuals. Participants with prior SARS-CoV-2 infection had a long interval of 11 months since their qRT-PCR positive test. Serum was obtained after venipuncture and tested with an automated electrochemiluminescence anti-SARS-CoV-2 S total Ig reference assay, a commercial ELISA anti-S1 IgG assay, and the index test NIA. 109 participants from the positive cohort and 44 participants from the negative cohort also participated in capillary blood collection using three microsampling devices: Mitra, repurposed glucose test strips, and HemaXis. Samples were dried, shipped by regular mail, extracted, and measured with NIA.\n\nFindingsUsing serum samples, we achieve a clinical sensitivity of 98{middle dot}33% and specificity of 97{middle dot}62% on NIA, affirming the high performance of NIA in participants 11 months post infection. Combining microsampling with NIA, we obtain a clinical sensitivity of 95{middle dot}05% using Mitra, 61{middle dot}11% using glucose test strips, 83{middle dot}16% using HemaXis, and 91{middle dot}49% for HemaXis after automated extraction, without any drop in specificity.\n\nInterpretationHigh sensitivity and specificity was demonstrated when testing micro-volume capillary dried blood samples using NIA, which is expected to facilitate its use in large-scale studies using home-based sampling or samples collected in the field.\n\nFundingSwiss National Science Foundation NRP 78 Covid-19 grant 198412 and Private Foundation of the Geneva University Hospital.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSerological surveillance is of importance to better understand the evolution and spread of SARS-CoV-2 and adapt public health measures. We identified multiple studies conducting such serological surveys using decentralized collection of capillary blood, facilitating the logistics and reducing burden on participants and healthcare facilities. To perform the detection of anti-SARS-CoV-2 antibodies with a high-throughput and at low-cost, a microfluidic nano-immunoassay (NIA) was developed which requires ultra-low sample volumes and minimizes reagent consumption.\n\nAdded value of this studyIn this study we showed the possibility of combining capillary microsampling with NIA. We validated the use of NIA in serum samples obtained 11 months after infection and show the good clinical performance of the assay in samples with waning antibody titers. Using three different microsampling device, namely Mitra, repurposed glucose test strips, and HemaXis, we implemented a protocol using dried blood sample collection, shipping, extraction, and testing on the microfluidic assay. The sensitivity and specificity were measured and are presented when using the different microsampling devices.\n\nImplications of all the available evidenceWe show that the performance of NIA is good when using serum samples, but also in combination with microsampling. Facilitated logistics and increased convenience of microsampling, together with high-throughput and low-cost testing on a microfluidic assay should facilitate the conduction of serological surveys.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Gr\u00e9goire Michielin", + "author_inst": "\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne" + }, + { + "author_name": "Fatemeh Arefi", + "author_inst": "\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne" + }, + { + "author_name": "Olha Puhach", + "author_inst": "University of Geneva" + }, + { + "author_name": "Mathilde Bellon", + "author_inst": "University of Geneva" + }, + { + "author_name": "Pascale Sattonnet", + "author_inst": "University of Geneva" + }, + { + "author_name": "Arnaud L'Huillier", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Benjamin Meyer", + "author_inst": "University of Geneva" + }, + { + "author_name": "Sebastian J Maerkl", + "author_inst": "\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.14.495413", "rel_title": "Optimized intramuscular immunization with VSV-vectored spike protein triggers a superior protective humoral immune response to SARS-CoV-2", @@ -257687,81 +257379,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.12.22276307", - "rel_title": "Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study", - "rel_date": "2022-06-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.12.22276307", - "rel_abs": "BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status.\n\nMethodsWe used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure.\n\nFindingsVaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses).\n\nInterpretationDifferential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Rachel Burns", - "author_inst": "University College London" - }, - { - "author_name": "Isobel Braithwaite", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Edward Byrne", - "author_inst": "University College London" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - }, - { - "author_name": "Cyril Geismar", - "author_inst": "University College London" - }, - { - "author_name": "Susan J Hoskins", - "author_inst": "University College London" - }, - { - "author_name": "Jana Kovar", - "author_inst": "University College London" - }, - { - "author_name": "Annalan Mathew Dwight Navaratnam", - "author_inst": "University College London" - }, - { - "author_name": "Parth Patel", - "author_inst": "University College London" - }, - { - "author_name": "Alexei Yavlinsky", - "author_inst": "University College London" - }, - { - "author_name": "Martie J Van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.10.495677", "rel_title": "The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice", @@ -258322,6 +257939,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.09.495422", + "rel_title": "SARS-CoV-2-neutralizing humoral IgA response occurs earlier but modest and diminishes faster compared to IgG response.", + "rel_date": "2022-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.09.495422", + "rel_abs": "Secretory immunoglobulin A (IgA) plays a crucial role in the mucosal immunity for preventing the invasion of the exogenous antigens, however, little has been understood about the neutralizing activity of serum IgA. Here, to examine the role of IgA antibodies against COVID-19 illnesses, we determined the neutralizing activity of serum/plasma IgG and IgA purified from previously SARS-CoV-2-infected and COVID-19 mRNA-vaccine-receiving individuals. We found that serum/plasma IgA possesses substantial but rather modest neutralizing activity against SARS-CoV-2 compared to IgG with no significant correlation with the disease severity. Neutralizing IgA and IgG antibodies achieved the greatest activity at approximately 25 and 35 days after symptom onset, respectively. However, neutralizing IgA activity quickly diminished and went down below the detection limit approximately 70 days after onset, while substantial IgG activity was observed till 200 days after onset. The total neutralizing activity in sera/plasmas of those with COVID-19 largely correlated with that in purified-IgG and purified-IgA and levels of anti-SARS-CoV-2-S1-binding IgG and anti-SARS-CoV-2-S1-binding IgA. In individuals who were previously infected with SARS-CoV-2 but had no detectable neutralizing IgA activity, a single dose of BNT162b2 or mRNA-1273 elicited potent serum/plasma neutralizing IgA activity but the second dose did not further strengthen the neutralization antibody response. The present data show that the systemic immune stimulation with natural infection and COVID-19 mRNA-vaccines elicit both SARS-CoV-2-specific neutralizing IgG and IgA response in serum, but the IgA response is modest and diminishes faster compared to IgG response.\n\nAuthor SummaryImmunoglobulin A (IgA) is the most abundant type of antibody in the body mostly located on mucosal surfaces as a dimeric secretory IgA. Such secretory IgA plays an important role in preventing the adherence and invasions of foreign objects by its neutralizing activity, while monomeric serum IgA is thought to relate to the phagocytic immune system activation. Here, we report that individuals with the novel coronavirus disease (COVID-19) developed both systemic neutralizing IgG and IgA active against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the neutralizing IgA response was quick and reached the highest activity 25 days post-symptom-onset, compared to 35 days for IgG response, neutralizing IgA activity was modest and diminished faster than neutralizing IgG response. In individuals, who recovered from COVID-19 but had no detectable neutralizing IgA activity, a single dose of COVID-19 mRNA-vaccine elicited potent neutralizing IgA activity but the second dose did not further strengthen the antibody response. Our study provides novel insights into the role and the kinetics of serum IgA against the viral pathogen both in naturally-infected and COVID-19 mRNA-vaccine-receiving COVID-19-convalescent individuals.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuki Takamatsu", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Kazumi Omata", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Yosuke Shimizu", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Noriko Kinoshita-Iwamoto", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Mari Terada", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Tetsuya Suzuki", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Shinichiro Morioka", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Yukari Uemura", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Kenji Maeda", + "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + }, + { + "author_name": "Hiroaki Mitsuya", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.08.495396", "rel_title": "Binding and unbinding pathways of peptide substrate on SARS-CoV-2 3CL protease", @@ -259345,65 +259021,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.06.22276070", - "rel_title": "Hospitalization, death, and probable reinfection in Peruvian healthcare workers infected with SARS-CoV-2: a national retrospective cohort study", - "rel_date": "2022-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.06.22276070", - "rel_abs": "OBJECTIVETo determine if occupation is a risk factor for probable reinfection, hospitalization, and death from COVID-19 in Peruvian healthcare workers infected with SARS-CoV-2.\n\nMATERIAL AND METHODSRetrospective cohort study. Healthcare workers who presented SARS-CoV-2 infection between March 1, 2020 and August 9, 2021 were included. Occupational cohorts were reconstructed from the following sources of information: the National Epidemiological Surveillance System, molecular tests (NETLAB), results of serology and antigen tests (SICOVID-19), National Registry of Health Personnel (INFORHUS) and National Information System of Deaths (SINADEF). The incidence of probable reinfection, hospitalization, and death from COVID-19 was obtained in the cohorts of health auxiliaries and technicians, nursing staff, obstetricians, physicians, and other healthcare workers. We evaluated whether occupation was a risk factor for probable reinfection, hospitalization, and death from COVID-19 using a log-binomial generalized linear model, obtaining the adjusted relative risk (RR AJ).\n\nRESULTS90,672 healthcare workers were included. 8.1% required hospitalization, 1.7% died from COVID-19, and 2.0% had probable reinfection. A similar incidence of probable reinfection was found in the 5 cohorts (1.9%-2.2%). Physicians had a higher incidence of hospitalization (13.2%) and death (2.6%); however, they were also those who presented greater susceptibility linked to non-occupational variables such as age and comorbidities. The multivariate analysis found that physicians (RR=1.691; CI 95: 1.556-1.837) had a higher risk of hospitalization and that the occupation of health technician and assistant was the only one that constituted a risk factor for mortality from COVID-19 (RR =1.240; 95% CI: 1.052-1.463).\n\nCONCLUSIONSPeruvian health technicians and auxiliaries have a higher risk of death from COVID-19 linked to their occupation, while doctors have higher mortality due to non-occupational factors. Physicians had a higher risk of hospitalization independent of the presence of comorbidities and age; likewise, all occupations had a similar risk of probable reinfection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Willy Ramos", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru. Universidad Ricardo Palma." - }, - { - "author_name": "Nadia Guerrero", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - }, - { - "author_name": "Omar Napanga Saldana", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - }, - { - "author_name": "Jose Medina", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - }, - { - "author_name": "Manuel Loayza", - "author_inst": "Universidad Ricardo Palma. Instituto de Investigaciones en Ciencias Biomedicas." - }, - { - "author_name": "Jhony A. De La Cruz-Vargas", - "author_inst": "Instituto de Investigaciones en Ciencias Biomedicas, Universidad Ricardo Palma." - }, - { - "author_name": "Maria Vargas", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - }, - { - "author_name": "Luis Ordones", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - }, - { - "author_name": "Yovanna Seclen", - "author_inst": "Post Graduate Unit. Faculty of Medicine, National University of San Marcos. Lima Peru." - }, - { - "author_name": "Carlos Alvarez", - "author_inst": "Center for Disease Control and Prevention, Loreto Regional Health Directorate. Iquitos, Peru." - }, - { - "author_name": "Juan Arrasco", - "author_inst": "National Center for Epidemiology, Disease Prevention and Control. Lima Peru." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.05.22276023", "rel_title": "Modeling the Omicron Dynamics and Development in China: with a Deep Learning Enhanced Compartmental Model", @@ -260372,6 +259989,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.06.22276060", + "rel_title": "COVID-19 and per capita green tea consumption: update", + "rel_date": "2022-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.06.22276060", + "rel_abs": "PurposeIn spite of the development of numerous vaccines for the prevention of COVID-19 and approvement of several drugs for its treatment, there is still a great need in effective and inexpensive therapy of this disease. Pharmacological evidence suggesting the therapeutic potential of green tea catechins in amelioration/treatment of COVID19 is growing rapidly, however, there are only a few epidemiological studies addressing this possibility. The aim of this study was to provide update regarding ecological study assessing this issue as of January 2021.\n\nMethodsThe methodological approach used in this report is similar to that described previously. Briefly, information about COVID-19 morbidity (defined as a total number of cases per million population) and mortality (defined as a total number of deaths per million population) for a specific date was directly obtained from Worldometers info. Coronavirus. Analysis was restricted to 134 countries or territories with at least 3 million population. Twenty-one of these countries/territories, with estimated per/capita green tea consumption above 150 g (annually), were considered as a group with the high consumption. Countries/territories with the estimated per/capita green tea consumption below 150 g (N=82) were considered as the group with low the consumption.\n\nResultsPronounced differences in COVID-19 morbidity and mortality between groups of countries with high and low green tea consumption were found as of February 20, 2022. These differences were still observed in a subset of countries with HDI above 0.55. Moreover, in this restricted subset of countries, weak but statistically significant correlations between COVID-19 morbidity (or mortality) and per/capita green tea consumption were observed in a multiple regression model accounting for: population density, percentage of population aged above 65, and percentage of urban population.\n\nConclusionThe obtained results provide additional, though indirect, support of the idea that green tea catechins can be useful for treatment/amelioration of COVID-19. These results are in line with emerging evidence from other studies, including pharmacological. Nevertheless, further research is necessary to directly validate or reject this idea.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Maksim Storozhuk", + "author_inst": "Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.06.22276026", "rel_title": "Effectiveness of BNT162b2 booster doses in England: an observational study in OpenSAFELY-TPP", @@ -261507,57 +261143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.03.494777", - "rel_title": "NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.03.494777", - "rel_abs": "Noncoding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing signaling pathway databases do not include information on miRNA and lncRNA. Here, we redesigned a novel pathway database named NcPath by integrating and visualizing a total of 178,308 human experimentally-validated miRNA-target interactions (MTIs), 36,537 experimentally-verified lncRNA target interactions (LTIs), and 4,879 experimentally-validated human ceRNA networks across 222 KEGG pathways (including 27 sub-categories). To expand the application potential of the redesigned NcPath database, we identified 553,523 reliable lncRNA-PCG interaction pairs by integrating co-expression relations, ceRNA relations, co-TF-binding interactions, co-Histone-modification interactions, cis-regulation relations and lncPro Tool predictions between lncRNAs and protein-coding genes. In addition, to determine the pathways in which miRNA/lncRNA targets are involved, we performed a KEGG enrichment analysis using an hypergeometric test. The NcPath database also provides information on MTIs/LTIs/ceRNA networks, PubMed IDs, gene annotations and the experimental verification method used. In summary, the NcPath database will serve as an important and continually updated platform that provides annotation and visualization of the pathways on which noncoding RNAs (miRNA and lncRNA) are involved, and provide support to multimodal noncoding RNAs enrichment analysis. The NcPath database is freely accessible at http://ncpath.pianlab.cn/.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Zutan Li", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Yuanyuan Chen", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Yuan Zhang", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Jingya Fang", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Zhihui Xu", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Hao Zhang", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Minfang Mao", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Liangyun Zhang", - "author_inst": "Nanjing Agricultural University" - }, - { - "author_name": "Cong Pian", - "author_inst": "Nanjing Agricultural University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.06.05.494906", "rel_title": "Implications of Spike Protein Interactions with Zn-bound form of ACE2: A Computational Structural Study", @@ -262254,6 +261839,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.02.22275916", + "rel_title": "Long COVID is associated with extensive in-vivo neuroinflammation on DPA-714 PET", + "rel_date": "2022-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275916", + "rel_abs": "A significant number of COVID-19 patients develop long COVID, a condition defined by long-lasting debilitating, often neurological, symptoms. The pathophysiology of long COVID is unknown. Here we present in-vivo evidence of widespread neuroinflammation in long COVID, using a quantitative assessment, [18F]DPA-714 PET, in two long COVID patients. We reanalyzed historical data from three matched healthy control subjects, for comparison purposes. Both patients with long COVID had widespread increases in [18F]DPA-714 binding throughout the brain. Quantitative measures of binding (BPND values) were increased on average by 121% and 76%, respectively. This implicates profound neuroinflammation in the pathophysiology of long COVID.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Denise Visser", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Sandeep S.V. Golla", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Sander C.J. Verfaillie", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Emma M. Coomans", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Roos M. Rikken", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Elsmarieke M. van de Giessen", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Marijke E. den Hollander", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Anouk Verveen", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Maqsood Yaqub", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Frederik Barkhof", + "author_inst": "Amsterdam UMC & University College London" + }, + { + "author_name": "Janneke Horn", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Bart Koopman", + "author_inst": "OLVG" + }, + { + "author_name": "Patrick Schober", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Dook W. Koch", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Robert C. Schuit", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Albert D. Windhorst", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Michael Kassiou", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Ronald Boellaard", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Michele van Vugt", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Hans Knoop", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Nelleke Tolboom", + "author_inst": "University Medical Centre Utrecht" + }, + { + "author_name": "Bart N.M. van Berckel", + "author_inst": "Amsterdam UMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.01.494451", "rel_title": "A Big Data COVID-19 literature pattern discovery using NLP", @@ -263233,73 +262921,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.01.494373", - "rel_title": "Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis", - "rel_date": "2022-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.01.494373", - "rel_abs": "A deeper understanding of the molecular determinants that drive humoral responses to coronaviruses, and in particular severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is critical for improving and developing diagnostics, therapies and vaccines. Moreover, viral mutations can change key antigens in a manner that alters the ability of the immune system to detect and clear infections. In this study, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses of asymptomatic or recovered COVID-19-positive patients relative to COVID-19-negative patients. We made use of a novel high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses to rapidly identify B cell epitopes recognized by distinct antibody isotypes in patients blood sera. Using our integrated computational pipeline, we then evaluated the fine immunological properties of detected SARS-CoV-2 epitopes and relate them to their evolutionary and structural properties. While some epitopes are common across all CoVs, others are private to specific hCoVs. We also highlight the existence of hotspots of pre-existing immunity and identify a subset of cross-reactive epitopes that contributes to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves and SARS-CoV-2 variants, which have important implications for genomic surveillance and vaccine design. Lastly, we show that mutations in Spike and Nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Senthilkumar Kailasam", - "author_inst": "McGill University" - }, - { - "author_name": "Fatima Mostefai", - "author_inst": "University of Montreal" - }, - { - "author_name": "Raphael Poujol", - "author_inst": "University of Montreal" - }, - { - "author_name": "Jean-Christophe Grenier", - "author_inst": "University of Montreal" - }, - { - "author_name": "Paola Contini", - "author_inst": "University of Genoa" - }, - { - "author_name": "Raffaele De Palma", - "author_inst": "University of Genoa" - }, - { - "author_name": "Carsten Haber", - "author_inst": "PEPperPRINT" - }, - { - "author_name": "Volker Stadler", - "author_inst": "PEPperPRINT" - }, - { - "author_name": "Guillaume Bourque", - "author_inst": "McGill University" - }, - { - "author_name": "Julie Hussin", - "author_inst": "University of Montreal" - }, - { - "author_name": "B. Jesse Shapiro", - "author_inst": "McGill University" - }, - { - "author_name": "J\u00f6rg H Fritz", - "author_inst": "McGill University" - }, - { - "author_name": "Ciriaco A Piccirillo", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.06.02.22275908", "rel_title": "Asymptotic Analysis of Optimal Vaccination Policies", @@ -264036,6 +263657,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2022.06.02.22275894", + "rel_title": "Development and Validation of Multivariable Prediction Models of Serological Response to SARS-CoV-2 Vaccination in Kidney Transplant Recipients", + "rel_date": "2022-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275894", + "rel_abs": "BackgroundRepeated vaccination against SARS-CoV-2 increases serological response in kidney transplant recipients (KTR) with high interindividual variability. No decision support tool exists to predict SARS-CoV-2 vaccination response in KTR.\n\nMethodsWe developed, internally and externally validated five different multivariable prediction models of serological response after the third and fourth vaccine dose against SARS-CoV-2 in KTR. Using 27 candidate predictor variables, we applied statistical and machine learning approaches including logistic regression (LR), LASSO-regularized LR, random forest, and gradient boosted regression trees. For development and internal validation, data from 585 vaccinations were used. External validation was performed in four independent, international validation datasets comprising 191, 184, 254, and 323 vaccinations, respectively.\n\nFindingsLASSO-regularized LR performed on the whole development dataset yielded a 23- and 11- variable model, respectively. External validation showed AUC-ROC of 0.855, 0.749, 0.828, and 0.787 for the sparser 11-variable model, yielding an overall performance 0.819.\n\nInterpretationAn 11-variable LASSO-regularized LR model predicts vaccination response in KTR with good overall accuracy. Implemented as an online tool, it can guide decisions when choosing between different immunization strategies to improve protection against COVID-19 in KTR.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Bilgin Osmanodja", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + }, + { + "author_name": "Johannes Stegbauer", + "author_inst": "Department of Nephrology, University Hospital D\u00fcsseldorf, Heinrich-Heine-University, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Marta Kantauskaite", + "author_inst": "Department of Nephrology, University Hospital D\u00fcsseldorf, Heinrich-Heine-University D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lars Christian Rump", + "author_inst": "Deparment of Nephrology, University Hospital D\u00fcsseldorf, Heinrich-Heine-University D\u00fcsseldorf, Germany" + }, + { + "author_name": "Andreas Heinzel", + "author_inst": "Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Roman Reindl-Schwaighofer", + "author_inst": "Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Rainer Oberbauer", + "author_inst": "Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria" + }, + { + "author_name": "Ilies Benotmane", + "author_inst": "Department of Nephrology and Transplantation, University Hospitals of Strasbourg, INSERM Unit 1109, Strasbourg, France" + }, + { + "author_name": "Sophie Caillard", + "author_inst": "Department of Nephrology and Transplantation, University Hospitals of Strasbourg, INSERM Unit 1109, Strasbourg, France" + }, + { + "author_name": "Christophe Masset", + "author_inst": "Institut de Transplantation Urologie N\u00e9phrologie, Centre Hospitalier Universitaire de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, I" + }, + { + "author_name": "Clarisse Kerleau", + "author_inst": "Institut de Transplantation Urologie N\u00e9phrologie, Centre Hospitalier Universitaire de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, I" + }, + { + "author_name": "Gilles Blancho", + "author_inst": "Institut de Transplantation Urologie N\u00e9phrologie, Centre Hospitalier Universitaire de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, I" + }, + { + "author_name": "Klemens Budde", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + }, + { + "author_name": "Fritz Grunow", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + }, + { + "author_name": "Michael Mikhailov", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + }, + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + }, + { + "author_name": "Simon Ronicke", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charit\u00e9 University Hospital, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2022.06.01.22275889", "rel_title": "Impact of the Pandemic: Screening for Social Risk Factors in the Intensive Care Unit", @@ -264899,93 +264603,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.05.30.493765", - "rel_title": "Potent and pan-neutralization of SARS-CoV-2 variants of concern by DARPins", - "rel_date": "2022-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.30.493765", - "rel_abs": "We report the engineering and selection of two synthetic proteins - FSR16m and FSR22 - for possible treatment of SARS-CoV-2 infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon and exhibit broad spectrum neutralization of SARS-Cov-2 strains. The IC50 values of FSR16m against authentic B.1.351, B.1.617.2 and BA.1.1 variants are 3.4 ng/mL, 2.2 ng/mL and 7.4 ng/mL, respectively, comparable to currently used therapeutic antibodies. Despite the use of the spike protein from a now historical wild-type virus for design, FSR16m and FSR22 both exhibit increased neutralization against newly-emerged variants of concern (39- to 296-fold) in pseudovirus assays. Cryo-EM structures revealed that these DARPins recognize a region of the receptor binding domain (RBD, residues 455-456, 486-489) overlapping a critical portion of the ACE2-binding surface. K18-hACE2 transgenic mice inoculated with a B.1.617.2 variant and receiving intranasally-administered FSR16m were protected as judged by less weight loss and 10-100-fold reductions in viral burden in the upper and lower respiratory tracts. The strong and broad neutralization potency make FSR16m and FSR22 promising candidates for prevention and treatment of infection by current and potential future strains of SARS-CoV-2.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Vikas Kariyappa Chonira", - "author_inst": "Texas A&M University Health Science Center" - }, - { - "author_name": "Young-Do Kwon", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jason Gorman", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Zhiqiang Ku", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Rudo Simeon", - "author_inst": "Texas A&M University Health Science Center" - }, - { - "author_name": "Ryan G Casner", - "author_inst": "Columbia University" - }, - { - "author_name": "Darcy R Harris", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Adam S Olia", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Tyler Stevens", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Columbia University" - }, - { - "author_name": "Hannah Boyd", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Yaroslav Tsybovsky", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Peter D Kwong", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Zhiqiang An", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Zhilei Chen", - "author_inst": "Texas A&M University Health Science Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.05.31.22275802", "rel_title": "SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern", @@ -265710,6 +265327,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.30.22275753", + "rel_title": "Safety and superior immunogenicity of heterologous boosting with an RBD-based SARS-CoV-2 mRNA vaccine in Chinese adults", + "rel_date": "2022-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.30.22275753", + "rel_abs": "Homologous and heterologous booster with COVID-19 mRNA vaccines represent the most effective strategy to prevent the ongoing Omicron pandemic. The additional protection from these prototype SARS-CoV-2 S-targeting vaccine was attributed to the increased RBD-specific memory B cells with expanded potency and breadth. Herein, we show the safety and immunogenicity of heterologous boosting with the RBD-targeting mRNA vaccine AWcorna (also term ARCoV) in Chinese adults who have received two doses inactivated vaccine. The superiority over inactivated vaccine in neutralization antibodies, as well as the safety profile, support the use of AWcorna as heterologous booster in China.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Xiaoqiang Liu", + "author_inst": "Yunnan Province Centre for Disease Control and Prevention" + }, + { + "author_name": "Yuhua Li", + "author_inst": "National Institutes for Food and Drug Control" + }, + { + "author_name": "Zhongfang Wang", + "author_inst": "Guangzhou Institute of Respiratory Health" + }, + { + "author_name": "Shouchun Cao", + "author_inst": "National Institutes for Food and Drug Control" + }, + { + "author_name": "Weijin Huang", + "author_inst": "National Institutes for Food and Drug Control" + }, + { + "author_name": "Lin Yuan", + "author_inst": "Walvax Biotechnology Co., Ltd." + }, + { + "author_name": "Yi-Jiao Huang", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Yan Zheng", + "author_inst": "Yunnan Province Centre for Disease Control and Prevention" + }, + { + "author_name": "Jingjing Chen", + "author_inst": "Walvax Biotechnology Co., Ltd." + }, + { + "author_name": "Bo Ying", + "author_inst": "Suzhou Abogen Biosciences Co., Ltd." + }, + { + "author_name": "Zuoyun Xiang", + "author_inst": "Walvax Biotechnology Co., Ltd." + }, + { + "author_name": "Jin Shi", + "author_inst": "Walvax Biotechnology Co., Ltd." + }, + { + "author_name": "Jincun Zhao", + "author_inst": "Guangzhou Institute of Respiratory Health" + }, + { + "author_name": "Zhen Huang", + "author_inst": "Walvax Biotechnology Co., Ltd." + }, + { + "author_name": "Cheng-Feng Qin", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.29.22275748", "rel_title": "SARS-CoV-2 neutralising antibody activity in a highly vaccinated population: Longitudinal serology studies in Singapore", @@ -266545,49 +266237,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.05.27.22275037", - "rel_title": "Corticosteroids in COVID-19: Optimizing Observational Research through Target Trial Emulations", - "rel_date": "2022-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275037", - "rel_abs": "ImportanceCommunication and adoption of modern study design and analytical techniques is of high importance for the improvement of clinical research from observational data.\n\nObjectiveTo compare (1) a modern method for causal inference including a target trial emulation framework and doubly robust estimation to (2) approaches common in the clinical literature such as Cox proportional hazards models. To do this, we estimate the effect of corticosteroids on mortality for moderate-to-severe coronavirus disease 2019 (COVID-19) patients. We use the World Health Organizations (WHO) meta-analysis of corticosteroid randomized controlled trials (RCTs) as a benchmark.\n\nDesignRetrospective cohort study using longitudinal electronic health record data for 28 days from time of hospitalization.\n\nSettingsMulti-center New York City hospital system.\n\nParticipantsAdult patients hospitalized between March 1-May 15, 2020 with COVID-19 and not on corticosteroids for chronic use.\n\nInterventionCorticosteroid exposure defined as >0.5mg/kg methylprednisolone equivalent in a 24-hour period. For target trial emulation, interventions are (1) corticosteroids for six days if and when patient meets criteria for severe hypoxia and (2) no corticosteroids. For approaches common in clinical literature, treatment definitions used for variables in Cox regression models vary by study design (no time frame, one-, and five-days from time of severe hypoxia).\n\nMain outcome28-day mortality from time of hospitalization.\n\nResults3,298 patients (median age 65 (IQR 53-77), 60% male). 423 receive corticosteroids at any point during hospitalization, 699 die within 28 days of hospitalization. Target trial emulation estimates corticosteroids to reduce 28-day mortality from 32.2% (95% CI 30.9-33.5) to 25.7% (24.5-26.9). This estimate is qualitatively identical to the WHOs RCT meta-analysis odds ratio of 0.66 (0.53-0.82)). Hazard ratios using methods comparable to current corticosteroid research range in size and direction from 0.50 (0.41-0.62) to 1.08 (0.80-1.47).\n\nConclusion and RelevanceClinical research based on observational data can unveil true causal relationships; however, the correctness of these effect estimates requires designing the study and analyzing the data based on principles which are different from the current standard in clinical research.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow do modern methods for causal inference compare to approaches common in the clinical literature when estimating the effect of corticosteroids on mortality for moderate-to-severe coronavirus disease 2019 (COVID-19) patients?\n\nFindingsIn an analysis using retrospective data for 3,298 hospitalized COVID-19 patients, target trial emulation using a doubly robust estimation procedure successfully recovers a randomized controlled trial (RCT) meta-analysis benchmark. In contrast, analytic approaches common in the clinical research literature generally cannot recover the benchmark.\n\nMeaningClinical research based on observational data can unveil true causal relations. However, the correctness of these effect estimates requires designing and analyzing the data based on principles which are different from the current standard in clinical research. Widespread communication and adoption of these analytical techniques are of high importance for the improvement of clinical research.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Katherine L Hoffman", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Edward J. Schenck", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Michael Joseph Satlin", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Will Whalen", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Di Pan", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Nicholas Williams", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Ivan Diaz", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2022.05.24.22275504", "rel_title": "The connection between COVID-19 vaccine abundance, vaccination coverage, and public trust in government across the globe", @@ -267124,6 +266773,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.26.22275645", + "rel_title": "How is the COVID-19 pandemic impacting our life, mental health, and well-being? Design and preliminary findings of the pan-Canadian longitudinal COHESION Study", + "rel_date": "2022-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.26.22275645", + "rel_abs": "With the advent of the COVID-19 pandemic, in-person social interactions and opportunities for accessing resources that sustain health and well-being have drastically reduced. We therefore designed the pan-Canadian population-based prospective COVID-19: HEalth and Social Inequities across Neighbourhoods (COHESION) cohort to provide deeper understanding of how the COVID-19 pandemic context affects mental health and well-being, key determinants of health, and health inequities.\n\nThis paper presents the design of the two-phase COHESION Study, and descriptive results from the first phase conducted between May 2020 and September 2021. During that period, the COHESION research platform collected monthly data linked to COVID-19 such as infection and vaccination status, perceptions and attitudes regarding pandemic-related measures, and information on participants physical and mental health, well-being, sleep, loneliness, resilience, substances use, living conditions, social interactions, activities, and mobility.\n\nThe 1,268 people enrolled in the Phase 1 COHESION Study are for the most part from Ontario (47%) and Quebec (33%), aged 48 {+/-} 16 years [mean {+/-} standard deviation (SD)], and mainly women (78%), White (85%), with a university degree (63%), and living in large urban centers (70%). According to the 298 {+/-} 68 (mean {+/-} SD) prospective questionnaires completed each month in average, the first year of follow-up reveals significant temporal variations in standardized indexes of well-being, loneliness, anxiety, depression, and psychological distress.\n\nThe COHESION Study will allow identifying trajectories of mental health and well-being while investigating their determinants and how these may vary by subgroup, over time, and across different provinces in Canada, in the unique context of the COVID-19 pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Stephan Gabet", + "author_inst": "ESPUM: Universite de Montreal Ecole de Sante Publique" + }, + { + "author_name": "Benoit Thierry", + "author_inst": "Universit\u00e9 de Montr\u00e9al: Universite de Montreal" + }, + { + "author_name": "Rania Wasfi", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Margaret De Groh", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Guido Simonelli", + "author_inst": "University of Montreal: Universite de Montreal" + }, + { + "author_name": "Catherine Hudon", + "author_inst": "Universit\u00e9 de Sherbrooke: Universite de Sherbrooke" + }, + { + "author_name": "Lily Lessard", + "author_inst": "Universit\u00e9 du Qu\u00e9bec \u00e0 Rimouski: Universite du Quebec a Rimouski" + }, + { + "author_name": "Eve Dube", + "author_inst": "INSPQ: Institut national de sante publique du Quebec" + }, + { + "author_name": "Bouchra Nasri", + "author_inst": "ESPUM: Universite de Montreal Ecole de Sante Publique" + }, + { + "author_name": "Yan Kestens", + "author_inst": "ESPUM: Universite de Montreal Ecole de Sante Publique" + }, + { + "author_name": "Gregory Moullec", + "author_inst": "University of Montreal School of Public Health: Universite de Montreal Ecole de Sante Publique" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.25.22275516", "rel_title": "Facing the Omicron variant - How well do vaccines protect against mild and severe COVID-19? Third interim analysis of a living systematic review", @@ -268451,97 +268159,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.27.22275672", - "rel_title": "Profiling of immune responses to COVID-19 and vaccination uncovers potent adjuvant capacities of SARS CoV-2 infection to vaccination leading to memory T cell responses with a Th17 signature in cancer patients", - "rel_date": "2022-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275672", - "rel_abs": "It is unclear whether cancer patients show impaired responses to COVID-19 and vaccination. Immune profiling was performed in three cohorts of healthy donors and oncologic patients: infected with SARS CoV-2, BNT162b2-vaccinated, and with previous COVID-19 and subsequently vaccinated. Vaccination was a poor inductor of T cell responses compared to infection, which significantly potentiated vaccination in antibody and T cell responses. T cell major targets in natural infection were the M and S protein, but not the N protein. T cell responses quickly decayed after 6 months post-vaccination, and T cell profiling showed that vaccination expanded effector T cells rather than memory T cell subsets unless the subjects had previous COVID-19. Cancer patients with previous COVID-19 and vaccinated exhibited potent IL-17+ CD4 and CD8 responses and increased neutrophils. Concluding, COVID-19 infection had potent adjuvant effects for vaccination leading to memory T cell differentiation, but with enhanced IL-17 inflammation signatures.\n\nTeaserAdjuvancy of SARS CoV-2 in cancer patients.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Miriam Echaide", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Ibone Labiano", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Marina Delgado", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "Angela Fernandez de Lascoiti", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "Patricia Ochoa", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "Maider Garnica", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Pablo Ramos", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Luisa Chocarro de Erauso", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Leticia Fernandez", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Hugo Arasanz", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "Ana Bocanegra", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Ester Blanco", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Sergio Pineiro", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Miren Zuazo", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Pilar Morente", - "author_inst": "Navarrabiomed" - }, - { - "author_name": "Ruth Vera", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "Maria Alsina", - "author_inst": "Hospital Universitario de Navarra" - }, - { - "author_name": "David Escors", - "author_inst": "Fundacion Miguel Servet" - }, - { - "author_name": "Grazyna Kochan", - "author_inst": "Navarrabiomed" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2022.05.27.493693", "rel_title": "Development of a Novel SARS-CoV-2 Immune Complex Vaccine Candidate (CRCx) with Broad Immune Responses: A Preclinical Trial in Animal Model", @@ -269662,6 +269279,37 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.05.25.22275006", + "rel_title": "Overuse in US Medicare during the COVID-19 pandemic", + "rel_date": "2022-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22275006", + "rel_abs": "BackgroundThe COVID-19 pandemic and March 2020 shutdown in the US reduced the volume of healthcare services, but the impact on overuse has not been investigated.\n\nObjectiveTo examine the change in overuse rates and volumes through 2020.\n\nDesignA retrospective cohort study using Medicare fee-for-service claims.\n\nSettingOutpatient and inpatient claims.\n\nParticipantsPatients who met the criteria for one of 10 overuse measures with a claim between January 1 2019 to December 31 2020.\n\nMeasurementsOveruse volumes were reported as patients with claims meeting overuse metric criteria per 100,000 Medicare beneficiaries. Overuse rates were measured by the same overuse cohort per 100 patients meeting the denominator criteria of the metric. Rates in 2020 were compared to the same date period in 2019 using incidence rate ratios (IRRs) estimated from Poisson regressions.\n\nResultsIn 2019, 302,379 patients had an overuse claim (14.72% of 2,053,792 patients in the cohort) versus 234,481 (13.79% of 1,699,807) in 2020. The overall cohort included 2,112,904 (61.0%) women and a mean (SD) age of 76.5 (8.1) years. There was a 52.3% decrease in overall cohort volume during the COVID-19 shutdown; 2,341,017 patients in 2020 versus 4,912,453 in 2019. There was a 72.57% decrease in patients with an overuse procedure between April 2019 (N = 11,794) and 2020 (N = 3,220) (IRR 0.27 (95% CI 0.25 to 0.3; p <0.001)), including spinal fusion/laminectomy, carotid endarterectomy, knee arthroscopy, hysterectomy and vertebroplasty.\n\nLimitationsThis study uses claim-based measures of overuse and is limited to the first ten months of the COVID-19 pandemic.\n\nConclusionsThe shutdown period during March through May in 2020 had a drastic impact on both the overuse volume and rates for these 10 overuse metrics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kelsey Chalmers", + "author_inst": "Lown Institute" + }, + { + "author_name": "Shannon Brownlee", + "author_inst": "Lown Institute" + }, + { + "author_name": "Val\u00e9rie Gopinath", + "author_inst": "Lown Institute" + }, + { + "author_name": "VIKAS SAINI", + "author_inst": "Lown Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2022.05.24.22275467", "rel_title": "Omicron BA.1 and BA.2 Neutralizing Activity Following Pre-Exposure Prophylaxis with Tixagevimab plus Cilgavimab in Vaccinated Solid Organ Transplant Recipients", @@ -270801,61 +270449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.22.22275323", - "rel_title": "Initial protection against Omicron in children and adolescents by BNT162b2", - "rel_date": "2022-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.22.22275323", - "rel_abs": "BACKGROUNDThe BNT162b2 (Pfizer-BioNTech) 2-dose vaccine for children and the BNT162b2 3rd dose for adolescents were approved shortly before the Omicron outbreak in Israel. The effects of these vaccines on the rates of Omicron confirmed infection are not yet clear.\n\nMETHODSWe extracted data for the Omicron-dominated (sub-lineage BA.1) period December 26, 2021 through January 8, 2022. We compared rates of confirmed Covid-19 infection between children 5-10 years old 14-35 days after receiving the 2nd dose to an internal control group of children 3-7 days after receiving the 1st dose (when the vaccine is not yet effective). Similarly, we compared confirmed infection rates in adolescents 12-15 years old 14-60 days after receiving a booster dose to an internal control group of adolescents 3-7 days after receiving the booster dose. We used Poisson regression, adjusting for age, sex, socioeconomic status, calendar week, and exposure.\n\nRESULTSIn the 5-10 age group, the estimated rate of confirmed infection was 2.3 fold (95% CI, 2.0 to 2.5) lower in the 2nd dose group than in the internal control group. In adolescents, the third dose decreased confirmed infection rates by 3.3-fold (95% CI, 2.8 to 4.0).\n\nCONCLUSIONSA recent 2-dose BNT162b2 vaccination in children and a recent booster dose in adolescents reduced the rate of confirmed infection compared to the respective internal control groups. Future studies are needed to assess the duration of this protection and protection against other outcomes such as PIMS and long-COVID.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ofra Amir", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Yair Goldberg", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Micha Mandel", - "author_inst": "The Hebrew University of Jerusalem, Israel" - }, - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - }, - { - "author_name": "Omri Bodenheimer", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Laurence Freedman", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Nachman Ash", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Sharon Alroy-Preis", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Amit Huppert", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Ron Milo", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.24.493187", "rel_title": "Hemin shows antiviral activity in vitro, possibly through suppression of viral entry mediators.", @@ -271584,6 +271177,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.24.22275549", + "rel_title": "Population-weighted greenspace exposure tied to lower COVID-19 mortality rates: A nationwide dose-response study", + "rel_date": "2022-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275549", + "rel_abs": "The COVID-19 outbreak has caused enormous deaths and profound social and economic disruption globally. Accumulating evidence suggests exposure to greenspace may reduce the risk of COVID-19 mortality. Greenspace exposure enhances immune functioning, reduces inflammation, and replenishes gut microbiota may protect against the risk of mortality among those with COVID-19. However, previous studies often fail to distinguish the health effect of different types of greenspace, explore the dose-response association and optimal buffer distance, and consider the spatial dynamics of population distribution and geographic locations of greenspace.\n\nThis study examined the associations among ratio of different types of greenspaces, population- weighted exposure to different types of greenspaces, and COVID-19 mortality rates using a negative binomial generalized linear mixed effects model across 3,025 counties in the United States, adjusted for socioeconomic, demographic, pre-existing chronic disease, policy and regulation, behavioral, and environmental factors. The population-weighted measure gave proportionally greater weight to greenspace near areas of higher population density.\n\nExposure to forest and pasture was negatively associated with COVID-19 mortality rates, while developed open space has insignificant or positive associations with mortality rates. Forest outside park has the largest effect size across all buffer distances, followed by forest inside park. The optimal exposure buffer distance is 1km for forest outside park, with 1 unit of increase in exposure associated with a 9.9% decrease in mortality rates (95% confidence interval: 6.9% -12.8%). The optimal exposure buffer distance of forest inside park is 400m, with 1 unit of increase in exposure, associated with a 4.7% decrease in mortality rates (95% confidence interval: 2.4% - 6.9%).\n\nGreenspaces, especially nearby forest, may be effective at lowering the mortality risk of COVID-19 patients. Our findings suggest that policymakers and planners should prioritize forestry within walking distance of residential clusters to mitigate mortality rates during current and future respiratory pandemics.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yuwen Yang", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Yi Lu", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Bin Jiang", + "author_inst": "University of Hong Kong" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.24.22275552", "rel_title": "Clearing the Fog: A Systematic Review on Cognitive Dysfunction in COVID-19", @@ -272751,49 +272371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.05.21.22274939", - "rel_title": "Patient satisfaction with telemedicine in the Philippines during the COVID-19 pandemic", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22274939", - "rel_abs": "IntroductionThe capacity to deliver essential health services has been negatively impacted by the COVID-19 pandemic particularly due to lockdown restrictions. Telemedicine provides a safe, efficient, and effective solution that addresses the needs of patients and the health system. However, there remain implementation challenges and barriers to patient adoption in resource-limited settings as in the Philippines. This study thus aimed to describe patient perspectives and experiences with telemedicine services, and explore the factors that influence telemedicine use and satisfaction.\n\nMethodsThis study used a mixed-methods design through online surveys and in-depth interviews. An online survey using Consumer Assessment of Healthcare Providers and Systems (CAHPS) Clinician & Group Adult Visit Survey 4.0 (beta) and Telehealth Usability Questionnaire (TUQ) was accomplished by 200 participants aged 18 to 65 years. A subsample of 16 participants was interviewed to provide insights to the quantitative data. We used descriptive statistics to analyze survey data and grounded theory to analyze data from interviews.\n\nResultsParticipants were generally satisfied with telemedicine services, with most reporting that this was an efficient and convenient alternative to face-to-face consultations. However, only 2 in 5 perceived telemedicine as affordable. Our quantitative findings suggest that participants preferred telemedicine services rather than in-person consultations, especially in cases where they feel that their condition is not urgent and does not need extensive physical examination. Safety against COVID-19, and the availability of multiple communication platforms contributed to patient satisfaction with telemedicine. Negative perceptions of patients on their telemedicine provider, perceived higher costs, poor connectivity and other technological issues were found to be barriers to patient satisfaction.\n\nDiscussionTelemedicine is viewed as a safe and efficient alternative to receiving care. Continued adoption of telemedicine will require improvements in technology and better patient communication related to their telemedicine provider and the associated costs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alicia Victoria G. Noceda", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "Lianne Margot M. Acierto", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "Morvenn Chaimek C. Bertiz", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "David Emmanuel H. Dionisio", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "Chelsea Beatrice L. Laurito", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "Girrard Alphonse T. Sanchez", - "author_inst": "Ateneo School of Medicine and Public Health" - }, - { - "author_name": "Arianna Maever L. Amit", - "author_inst": "Ateneo School of Medicine and Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.21.22275368", "rel_title": "Variant-specific symptoms of COVID-19 among 1,542,510 people in England", @@ -273774,6 +273351,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.05.19.22275149", + "rel_title": "SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan", + "rel_date": "2022-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275149", + "rel_abs": "Identification and monitoring of SARS-CoV-2 Variants of Concern/Interest (VOC/VOIs) is essential to guide public health measures. We report the surveillance of VOCs circulating in Karachi during the pandemic between April 2021 and February 2022. We screened 2150 SARS-CoV-2 PCR positive samples received at the AKUH Clinical Laboratories. VOC was identified using a PCR-based approach targeting lineage-specific mutations using commercially available assays. Of the SARS-CoV-2 PCR positive samples, 81.7% had VOC/VOI, while 18.3% were undetermined. Alpha variants were predominant at 82.5% and 40.3% of the cases in April and May 2021. Beta variants increased in May (29%) and June (42%) and then reduced to 6% by July. Gamma variant cases were at 14.5% and 9% in May and June, respectively. Delta variants first detected in May, increased to comprise 66% of all variants by July, remaining dominant in August, September, October, and November 2021 at 88%, 91%, 91% and 85% respectively. Omicron (BA.1) variants emerged in December, rising to 42% of cases with an increase to 81% by January 2022 and then reducing to 45% in February 2022. Delta variant prevalence was coincident with increased hospital admissions and mortality. The Omicron variant surge was associated with increased daily infections but limited COVID-19 severity. We highlight the predominance of the VOCs identified through a rapid PCR based approach. As this is important to inform a public health response, we propose that a mutation targeted approach can be a rapid, lower cost solution to aid tracking of known VOCs during pandemic waves.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Asghar Nasir", + "author_inst": "Aga Khan University, Pakistan" + }, + { + "author_name": "Uzma Bashir Aamir", + "author_inst": "WHO, Pakistan" + }, + { + "author_name": "Akbar Kanji", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Azra Samreen", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Zeeshan Ansar", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Najia Ghanchi", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Ali Raza Bukhari", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Kiran Iqbal Masood", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Nazneen Islam", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Samina Ghanic", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Muhammad Asif Syed", + "author_inst": "Government of Sindh" + }, + { + "author_name": "Mansoor Wassan", + "author_inst": "Government of Sindh" + }, + { + "author_name": "Syed Faisal Mahmood", + "author_inst": "Aga Khan University" + }, + { + "author_name": "Zahra Hasan", + "author_inst": "Aga Khan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.20.22275356", "rel_title": "Assessing the knowledge and practices of primary healthcare workers on malaria diagnosis and related challenges in view of COVID-19 outbreak in a Nigerian Southwestern Metropolis", @@ -274801,33 +274449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.19.492636", - "rel_title": "A social media-based framework for quantifying temporal changes to wildlife viewing intensity: Case study of sea turtles before and during COVID-19", - "rel_date": "2022-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.19.492636", - "rel_abs": "Documenting how human pressure on wildlife changes over time is important to minimise potential adverse effects through implementing appropriate management and policy actions; however, obtaining objective measures of these changes and their potential impacts is often logistically challenging, particularly in the natural environment. Here, we developed a modular stochastic model that infers the ratio of actual viewing pressure on wildlife in consecutive time periods (years) using social media, as this medium is widespread and easily accessible. Pressure was calculated from the number of times individual animals appeared in social media in pre-defined time windows, accounting for time-dependent variables that influence them (e.g. number of people with access to social media). Formulas for the confidence intervals of viewing pressure ratios were rigorously developed and validated, and corresponding uncertainty was quantified. We applied the developed framework to calculate changes to wildlife viewing pressure on loggerhead sea turtles (Caretta caretta) at Zakynthos island (Greece) before and during the COVID-19 pandemic (2019-2021) based on 2646 social media entries. Our model ensured temporal comparability across years of social media data grouped in time window sizes, by correcting for the interannual increase of social media use. Optimal sizes for these windows were delineated, reducing uncertainty while maintaining high time-scale resolution. The optimal time window was around 7-days during the peak tourist season when more data were available in all three years, and >15 days during the low season. In contrast, raw social media data exhibited clear bias when quantifying changes to viewing pressure, with unknown uncertainty. The framework developed here allows widely-available social media data to be used objectively when quantifying temporal changes to wildlife viewing pressure. Its modularity allowed viewing pressure to be quantified for all data combined, or subsets of data (different groups, situations or locations), and could be applied to any site supporting wildlife exposed to tourism.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kostas Papafitsoros", - "author_inst": "Weierstrass Institute for Applied Analysis and Stochastics" - }, - { - "author_name": "Lukas Adam", - "author_inst": "Artificial Intelligence Center, Czech Technical University in Prague, Karlovo Namesti 13, 120 00 Praha 2" - }, - { - "author_name": "Gail Schofield", - "author_inst": "School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2022.05.19.22275339", "rel_title": "Covid-19 Vaccine Acceptance Among People Incarcerated in Connecticut State Jails", @@ -275632,6 +275253,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2022.05.19.22275291", + "rel_title": "Real-world effectiveness of molnupiravir and nirmatrelvir/ritonavir among COVID-19 inpatients during Hong Kong's Omicron BA.2 wave: an observational study", + "rel_date": "2022-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275291", + "rel_abs": "BackgroundEffectiveness of oral antivirals in mild-to-moderate COVID-19 patients is urgently needed. This retrospective cohort study aims to evaluate the clinical and virologic outcomes associated with molnupiravir and nirmatrelvir/ritonavir use in COVID-19 patients during a pandemic wave dominated by the Omicron BA.2 subvariant.\n\nMethodsWe analyzed data from a territory-wide retrospective cohort of hospitalized patients with confirmed diagnosis of SARS-CoV-2 infection from 26th February 2022 to 26th April 2022 in Hong Kong. Oral antiviral users were matched with controls using propensity-score matching in a ratio of 1:1. Study outcomes were all-cause mortality, a composite outcome of disease progression (all-cause mortality, initiation of invasive mechanical ventilation [IMV], intensive care unit admission, or the need for oxygen therapy) and their individual outcomes, and time to achieving lower viral burden of cycle threshold (Ct) value [≥]30 cycles. Hazard ratios (HR) of event outcomes were estimated using Cox regression models.\n\nResultsAmong 40,776 hospitalized patients with SARS-CoV-2 infection over a mean follow-up of 41.3 days with 925,713 person-days, this study included 1,856 molnupiravir users, 890 nirmatrelvir/ritonavir users and 2,746 control patients not initially requiring oxygen therapy at baseline after propensity-score matching. Oral antiviral use was associated with significantly lower risks of all-cause mortality (molnupiravir: HR=0.48, 95%CI=0.40-0.59, p<0.0001; nirmatrelvir/ritonavir: HR=0.34, 95%CI=0.23-0.50, p<0.0001), the composite outcome of disease progression (molnupiravir: HR=0.60, 95%CI=0.52-0.69, p<0.0001; nirmatrelvir/ritonavir: HR=0.57, 95%CI=0.45-0.72, p<0.0001), and the need for oxygen therapy (molnupiravir: HR=0.69, 95%CI=0.57-0.83, p=0.00011; nirmatrelvir/ritonavir: HR=0.73, 95%CI=0.54-0.97, p=0.032) than non-use. Time to achieving lower viral burden was significantly shorter among oral antiviral users than matched controls (molnupiravir: HR=1.38, 95%CI=1.15-1.64, p=0.0046; nirmatrelvir/ritonavir: HR=1.38, 95%CI=1.07-1.78, p=0.013).\n\nConclusionsAgainst Omicron BA.2, initiation of novel oral antiviral treatment in hospitalized patients not requiring any oxygen therapy was associated with lower risks of all-cause mortality and disease progression, in addition to achieving low viral burden faster. Our findings support the early use of oral antivirals in COVID-19 patients who do not require supplemental oxygen on admission.\n\nFundingHealth and Medical Research Fund, Food and Health Bureau, Government of the Hong Kong SAR\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe medical and research community are actively exploring the use of oral antivirals in COVID-19 patients to lower their risks of hospitalization and death, and to reduce the burden on healthcare systems. We searched Scopus and PubMed for studies until 13th May 2022 using the search terms \"SARS-CoV-2 OR COVID-19\" AND \"molnupiravir OR Lagevrio OR EIDD-2801\" OR \"nirmatrelvir OR Paxlovid OR PF-07321332\". Major studies examining the safety and efficacy of molnupiravir include MOVe-IN and MOVe-OUT trials conducted in hospitalized and non-hospitalized COVID-19 patients, respectively. Clinical evidence for the use of ritonavir-boosted nirmatrelvir came from the EPIC-HR trial conducted among non-hospitalized adults with COVID-19. While no clinical benefits have been observed with molnupiravir use in the inpatient setting among patients with moderate-to-severe COVID-19, early initiation of molnupiravir or nirmatrelvir/ritonavir within 5 days of symptom onset in non-hospitalized patients with mild-to-moderate COVID-19 and risk factors for progression to severe disease has been associated with relative risk reduction of hospitalization or death by 30% and 88%, respectively. Notably, these clinical trials were conducted prior to the prevalence of Omicron variant, and the efficacy of oral antivirals against this current variant of concern can only be inferred from experimental evidence to date. Real-world evidence of oral antiviral use in patients with SARS-CoV-2 infection of Omicron variant is lacking.\n\nAdded value of this studyTo the best of our knowledge, this is the first real-world study exploring the inpatient use of oral antivirals during a pandemic wave dominated by SARS-CoV-2 Omicron variant. We conducted a territory-wide, retrospective cohort study to examine the effectiveness of molnupiravir and nirmatrelvir/ritonavir in COVID-19 patients who did not require supplemental oxygen on admission in Hong Kong. Early initiation of oral antivirals within 2 days of admission was associated with significantly lower risks of all-cause mortality and disease progression, in addition to achieving low viral burden faster than their respective matched controls. Oral antiviral use was also associated with a reduced need for oxygen therapy than non-use.\n\nImplications of all the available evidenceCurrent guidelines are now prioritizing the distribution of oral antivirals to those who do not require supplemental oxygen, but who are at the highest risk of disease progression. Our study cohort reflected such prescription pattern in real-world clinical practice, consisting of mostly the elderly with multiple pre-existing comorbidities and who had not been fully vaccinated. The antiviral effect and mortality benefit observed in this patient cohort support the use of oral antivirals in COVID-19 patients who do not require supplemental oxygen on admission during a pandemic wave of Omicron variant. Ongoing research will inform the safety and effectiveness of oral antivirals in specific patient populations (by vaccination status and viral variants), drug combinations, and different healthcare settings.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Carlos KH Wong", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Ivan CH Au", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Kristy TK Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Eric Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Benjamin J Cowling", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Gabriel M Leung", + "author_inst": "University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2022.05.19.22275325", "rel_title": "Medication Safety Incidents Associated with the Remote Delivery of Primary Care: A Rapid Review", @@ -276659,121 +276319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.17.22275235", - "rel_title": "Reduced Exercise Capacity, Chronotropic Incompetence, Inflammation and Symptoms in Post-Acute COVID-19", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275235", - "rel_abs": "BACKGROUNDMechanisms underlying persistent cardiopulmonary symptoms following SARS-CoV-2 infection (post-acute sequelae of COVID-19 \"PASC\" or \"Long COVID\") remain unclear. This study sought to elucidate mechanisms of cardiopulmonary symptoms and reduced exercise capacity using advanced cardiac testing.\n\nMETHODSWe performed cardiopulmonary exercise testing (CPET), cardiac magnetic resonance imaging (CMR) and ambulatory rhythm monitoring among adults > 1 year after confirmed SARS-CoV-2 infection in Long-Term Impact of Infection with Novel Coronavirus cohort (LIINC; substudy of NCT04362150). Adults who completed a research echocardiogram (at a median 6 months after SARS-CoV-2 infection) without evidence of heart failure or pulmonary hypertension were asked to complete additional cardiopulmonary testing approximately 1 year later. Although participants were recruited as a prospective cohort, to account for selection bias, the primary analyses were as a case-control study comparing those with and without persistent cardiopulmonary symptoms. We also correlated findings with previously measured biomarkers. We used logistic regression and linear regression models to adjust for potential confounders including age, sex, body mass index, time since SARS-CoV-2 infection, and hospitalization for acute SARS-CoV-2 infection, with sensitivity analyses adjusting for medical history.\n\nRESULTSSixty participants (unselected for symptoms, median age 53, 42% female, 87% non- hospitalized) were studied at median 17.6 months following SARS-CoV-2 infection. On maximal CPET, 18/37 (49%) with symptoms had reduced exercise capacity (peak VO2<85% predicted) compared to 3/19 (16%) without symptoms (p=0.02). The adjusted peak VO2 was 5.2 ml/kg/min (95%CI 2.1-8.3; p=0.001) or 16.9% lower actual compared to predicted (95%CI 4.3- 29.6; p=0.02) among those with symptoms compared to those without symptoms. Chronotropic incompetence was present among 12/21 (57%) with reduced VO2 including 11/37 (30%) with symptoms and 1/19 (5%) without (p=0.04). Inflammatory markers (hsCRP, IL-6, TNF-) and SARS-CoV-2 antibody levels measured early in PASC were negatively correlated with peak VO2 more than 1 year later. Late-gadolinium enhancement on CMR and arrhythmias on ambulatory monitoring were not present.\n\nCONCLUSIONSWe found evidence of objectively reduced exercise capacity among those with cardiopulmonary symptoms more than 1 year following COVID-19, which was associated with elevated inflammatory markers early in PASC. Chronotropic incompetence may explain exercise intolerance among some with cardiopulmonary phenotype Long COVID.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC=\"FIGDIR/small/22275235v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@981366org.highwire.dtl.DTLVardef@21ca5dorg.highwire.dtl.DTLVardef@6cde4forg.highwire.dtl.DTLVardef@1773594_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsLong COVID symptoms were associated with reduced exercise capacity on cardiopulmonary exercise testing more than 1 year after SARS-CoV-2 infection. The most common abnormal finding was chronotropic incompetence. Reduced exercise capacity was associated with early elevations in inflammatory markers.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Matthew S Durstenfeld", - "author_inst": "University of California, San Francisco & Zuckerberg San Francisco General Hospital" - }, - { - "author_name": "Michael J Peluso", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Punita Kaveti", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Christopher Hill", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Danny Li", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Erica Sander", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Shreya Swaminathan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Victor M Arechiga", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Scott Lu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sarah A Goldberg", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Rebecca Hoh", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ahmed Chenna", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "Brandon C Yee", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "John W Winslow", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "Christos J Petropoulos", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "J. Daniel Kelly", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "David V Glidden", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Timothy J Henrich", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jeffrey N Martin", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Yoo Jin Lee", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mandar A Aras", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Carlin S Long", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Donald J Grandis", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Steven G Deeks", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Priscilla Y Hsue", - "author_inst": "University of California, San Francisco & Zuckerberg San Francisco General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.05.19.22275053", "rel_title": "Evaluating the impact on health outcomes of an event that resulted in a delay in contact tracing of COVID-19 cases", @@ -277378,6 +276923,29 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.05.18.492443", + "rel_title": "Using unsupervised learning algorithms to identify essential genes associated with SARS-CoV-2 as potential therapeutic targets for COVID-19", + "rel_date": "2022-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.18.492443", + "rel_abs": "MotivationSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide concern. Several genes associated with the SARS-CoV-2, which are essential for its functionality, pathogenesis, and survival, have been identified. These genes, which play crucial roles in SARS-CoV-2 infection, are considered potential therapeutic targets. Developing drugs against these essential genes to inhibit their regular functions could be a good approach for COVID-19 treatment. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data and can assist in finding fast explanations and cures.\n\nResultsWe propose a method to highlight the essential genes that play crucial roles in SARS-CoV-2 pathogenesis. For this purpose, we define eleven informative topological and biological features for the biological and PPI networks constructed on gene sets that correspond to COVID-19. Then, we use three different unsupervised learning algorithms with different approaches to rank the important genes with respect to our defined informative features. Finally, we present a set of 18 important genes related to COVID-19.\n\nAvailabilityMaterials and implementations are available at: https://github.com/MahnazHabibi/Gene_analysis.\n\nContactm_habibi@qiau.ac.ir\n\nSupplementary informationSupplementary data are available at Bioinformatics online.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Golnaz Taheri", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Mahnaz Habibi", + "author_inst": "Department of Mathematics, Qazvin Branch, Islamic Azad University, Qazvin, Iran." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.05.18.492452", "rel_title": "SARS-CoV-2 Subunit Virus-Like Vaccine Demonstrates High Safety Profile and Protective Efficacy: Preclinical Study", @@ -278285,41 +277853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.16.492068", - "rel_title": "Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction", - "rel_date": "2022-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.16.492068", - "rel_abs": "Transmission of SARS-CoV-2 from humans to other species threatens wildlife conservation and may create novel sources of viral diversity for future zoonotic transmission. A variety of computational heuristics have been developed to pre-emptively identify susceptible host species based on variation in the ACE2 receptor used for viral entry. However, the predictive performance of these heuristics remains unknown. Using a newly-compiled database of 96 species we show that, while variation in ACE2 can be used by machine learning models to accurately predict animal susceptibility to sarbecoviruses (accuracy = 80.2%, binomial confidence interval [CI]: 70.8 - 87.6%), the sites informing predictions have no known involvement in virus binding and instead recapitulate host phylogeny. Models trained on host phylogeny alone performed equally well (accuracy = 84.4%, CI: 75.5 - 91.0%) and at a level equivalent to retrospective assessments of accuracy for previously published models. These results suggest that the predictive power of ACE2-based models derives from strong correlations with host phylogeny rather than processes which can be mechanistically linked to infection biology. Further, biased availability of ACE2 sequences misleads projections of the number and geographic distribution of at-risk species. Models based on host phylogeny reduce this bias, but identify a very large number of susceptible species, implying that model predictions must be combined with local knowledge of exposure risk to practically guide surveillance. Identifying barriers to viral infection or onward transmission beyond receptor binding and incorporating data which are independent of host phylogeny will be necessary to manage the ongoing risk of establishment of novel animal reservoirs of SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nardus Mollentze", - "author_inst": "MRC - University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Deborah Keen", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Uuriintuya Munkhbayar", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Roman Biek", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Daniel G. Streicker", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.05.17.492198", "rel_title": "SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression", @@ -279016,6 +278549,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.15.22273945", + "rel_title": "COVID-19 vaccines effectiveness against SARS-CO-V-2 infection among persons attending RT-PCR centre at a medical College Hospital in Telangana: A case control study", + "rel_date": "2022-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.15.22273945", + "rel_abs": "BackgroundIn January 2021, India drug regulator issued restricted emergency approval for COVAXIN and COVISHIELD which were manufactured in India. On mid-January 2021, in India, there were 10.5million confirmed cases and 0.15 million deaths.\n\nObjectivesThe objectives were to evaluate vaccine effectiveness (VE) of India made Covid-19 vaccines against SARS-CoV-2 infection.\n\nMethodsA test negative case control study was conducted from May 2021 to December 2021 for duration of 8months among people attending an RT-PCR centre at a medical college Hospital for RT-PCR test. The baseline characteristics and RT-PCR report; and preliminary data about vaccine status were collected from the RT-PCR centre. The exposure to vaccination was enquired via Phone call or was checked with data available with the health authorities.\n\nResultsAfter applying inclusion exclusion criteria, case and control definitions, a total of 380 participants (95cases and 285 controls) were included. The adjusted VE of two doses of COVISHIED vaccine against symptomatic SARS-CoV-2 infection was 52.2% (95% CI, 41.7 to 62.1) and single dose was 40.88% (95% CI, 31.26 to 51.29). The adjusted VE of two doses of COVAXIN vaccine against SARS-CoV-2 infection was 39% (95% CI, 29.40 to 49.27). The overall VE was 48.20% (95% CI, 37.90 to 58.22) for two doses of any vaccines.\n\nConclusionsIndia made vaccines were nearly 50% effective. Similar results show by different studies with a margin of 10-25% difference. Further new studies should be conducted as new variants of SARS-CoV-2 are emerging, and we dont know how the vaccine works against the variants and booster doses were required or not.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Nagapraveen Veerapu", + "author_inst": "Mamata Medical College, Telangana" + }, + { + "author_name": "Dhanashree P Inmdar", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Baer P Ravi Kumar", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Basavaraju Anuradha", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Pavitra Guddanti", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Sree D Issapuri", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Nikhita S Ganta", + "author_inst": "Mamata Medical College" + }, + { + "author_name": "Arun Gopi", + "author_inst": "JSS Medical College, Mysuru" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.05.13.22275056", "rel_title": "Humoral immune responses against SARS-CoV-2 Spike variants after mRNA vaccination in solid organ transplant recipients", @@ -279947,49 +279527,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.16.22275120", - "rel_title": "Representation of evidence-based clinical practice guideline recommendations on FHIR", - "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275120", - "rel_abs": "BackgroundVarious formalisms have been developed to represent clinical practice guideline recommendations in a computer-interpretable way. However, none of the existing formalisms leverage the structured and computable information that emerge from the evidence-based guideline development process. Thus, we here propose a FHIR-based guideline representation format that is structurally aligned to the knowledge artifacts emerging during the process of evidence-based guideline development.\n\nMethodsWe identified the information required to represent evidence-based clinical practice guideline recommendations and reviewed the knowledge artifacts emerging during the evidence-based guideline development process. Then we conducted a consensus-based design process with domain experts to develop an information model for guideline recommendation representation that is structurally aligned to the evidence-based guideline recommendation development process and a corresponding representation based on evidence-based medicine (EBM)-on-FHIR resources.\n\nResultsThe information model of clinical practice guideline recommendations and its EBMonFHIR-based representation contain the clinical contents of individual guideline recommendations, a set of metadata for the recommendations, the ratings for the recommendations (e.g., strength of recommendation, certainty of overall evidence), the ratings of certainty of evidence for individual outcomes (e.g., risk of bias) and links to the underlying evidence (systematic reviews based on primary studies). We created profiles and an implementation guide for all FHIR resources required to represent a complete clinical practice guideline and used the profiles to implement an exemplary clinical guideline recommendation.\n\nConclusionsOur EBMonFHIR-based representation of clinical practice guideline recommendations allows to directly link the evidence assessment process through systematic reviews and evidence grading, and the underlying evidence from primary studies to the resulting guideline recommendations. This not only allows to evaluate the evidence on which recommendations are based on transparently and critically, but also allows for a more direct and in future automatable way to generate computer-interpretable guideline recommendations based on computable evidence.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gregor Lichtner", - "author_inst": "Universitaetsmedizin Greifswald, Department of Anesthesia, Critical Care, Emergency and Pain Medicine, Greifswald, Germany" - }, - { - "author_name": "Carlo Jurth", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Departmen" - }, - { - "author_name": "Brian S Alper", - "author_inst": "Computable Publishing LLC, Ipswich, Massachusetts USA" - }, - { - "author_name": "Claudia Spies", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Departmen" - }, - { - "author_name": "Martin Boeker", - "author_inst": "Institute for Artificial Intelligence and Informatics in Medicine, Chair of Medical Informatics, Medical Center rechts der Isar, Technical University of Munich," - }, - { - "author_name": "Joerg J Meerpohl", - "author_inst": "Institute for Evidence in Medicine, Medical Center & Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Falk von Dincklage", - "author_inst": "Universitaetsmedizin Greifswald, Department of Anesthesia, Critical Care, Emergency and Pain Medicine, Greifswald, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.05.16.22275147", "rel_title": "Quantifying the information in noisy epidemic curves", @@ -280634,6 +280171,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.13.491706", + "rel_title": "Three-doses of BNT162b2 COVID-19 mRNA vaccine establishes long-lasting CD8+ T cell immunity in CLL and MDS patients", + "rel_date": "2022-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.13.491706", + "rel_abs": "Patients with hematological malignancies are prioritized for COVID-19 vaccine due to their high risk for severe SARS-CoV-2 infection related disease and mortality. To understand T cell immunity, its long-term persistence, and correlation with antibody response, we evaluated the BNT162b2 COVID-19 mRNA vaccine-specific immune response in chronic lymphocytic leukemia (CLL) and myeloid dysplastic syndrome (MDS) patients. Longitudinal analysis of CD8+ T cells using DNA-barcoded peptide-MHC multimers covering the full SARS-CoV-2 Spike-protein (415 peptides) showed vaccine-specific T cell activation and persistence of memory T cells up to six months post-vaccination. Surprisingly, a higher frequency of vaccine-induced antigen-specific CD8+ T cell was observed in the patient group compared to a healthy donor group. Furthermore, and importantly, immunization with the second booster dose significantly increased the frequency of antigen-specific CD8+ T cells as well as the total number of T cell specificities. Altogether 59 BNT162b2 vaccine-derived immunogenic epitopes were identified, of which 23 established long-term CD8+ T cell memory response with a strong immunodominance for NYNYLYRLF (HLA-A24:02) and YLQPRTFLL (HLA-A02:01) epitopes. In summary, we mapped the vaccine-induced antigen-specific CD8+ T cells and showed a booster-specific activation and enrichment of memory T cells that could be important for long-term disease protection in this patient group.\n\nKey PointsO_LICOVID-19 mRNA vaccine induced an early and persistent activation of antigen-specific CD8+ T cells in this patient group.\nC_LIO_LIVaccination with a booster dose is required to maintain vaccine-specific CD8+ T cells.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Susana Patricia Amaya Hernandez", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Ditte Stampe Hersby", + "author_inst": "University Hospital of Copenhagen, Rigshospitalet" + }, + { + "author_name": "Kamilla Kjaergaard Munk", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Tripti Tamhane", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Darya Trubach", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Maria Tagliamonte", + "author_inst": "National Cancer Institute Pascale Foundation, IRCCS, Napoli, Italy" + }, + { + "author_name": "Luigi Buonaguro", + "author_inst": "National Cancer Institute Pascale Foundation, IRCCS, Napoli, Italy" + }, + { + "author_name": "Anne Ortved Gang", + "author_inst": "University Hospital of Copenhagen, Rigshospitalet" + }, + { + "author_name": "Sine Reker Hadrup", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Sunil Kumar Saini", + "author_inst": "Technical University of Denmark" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.05.13.491823", "rel_title": "Humoral immunity to SARS-CoV-2 elicited by combination COVID-19 vaccination regimens", @@ -281633,65 +281225,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.09.22274623", - "rel_title": "COVID-19 Vaccine effectiveness against symptomatic infection and hospitalization in Belgium, July 2021-April 2022", - "rel_date": "2022-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274623", - "rel_abs": "1.The COVID-19 vaccination campaign in Belgium aimed to reduce disease spread and severity. We quantified the observed vaccine effectiveness (VE) against symptomatic infection (VEi) and hospitalization (VEh).\n\nExhaustive data on testing and vaccination was combined with a clinical hospital survey. We estimated VEi using a test negative design and VEh using a proportional hazard analysis. We controlled for prior infection, age, sex, province of residence and calendar week of sampling. Variant of concern specific VE-estimates were obtained by time since vaccination from July 2021 to April 2022.\n\nWe included 1,433,135 persons. VEi against Delta waned from an initial estimate of 81% (95%CI 80- 82) to 56% (95%CI 56-57) 100-150 days after primary-vaccination. Booster-vaccination increased initial VEi to 84% (95%CI 83-85). Against Omicron, an initial VEi of 37% (95%CI 34-40) waned to 18% (95%CI 17-20) 100-150 days after primary-vaccination. Booster-vaccination increased VEi to 52% (95%CI 51-53) and waned to 25% (95%CI 24-27) 100-150 days after vaccination. Hybrid immunity conferred by prior infection and booster-vaccination outperformed booster-vaccination only even if the infection was over one year ago, 67% (95%CI 66-68). Initial VEh for booster-vaccination decreased from 93% (95%CI 93-94) against Delta to 87% (95%CI 85-89) against Omicron. VEh for Omicron waned to 66% (95%CI 63-70) 100-150 days after booster-vaccination.\n\nIn conclusion, we report significant immune-escape by Omicron. VEh was less affected than VEi and immune-escape was attenuated by booster-vaccination. Waning further reduced VEi- and VEh- estimates. Infection-acquired immunity offered additional protection against symptomatic infection in vaccinated persons which lasted at least one year.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Toon Braeye", - "author_inst": "Sciensano" - }, - { - "author_name": "Joris A.F. van Loenhout", - "author_inst": "Sciensano" - }, - { - "author_name": "Ruben Brondeel", - "author_inst": "Sciensano" - }, - { - "author_name": "Veerle Stouten", - "author_inst": "Sciensano" - }, - { - "author_name": "Pierre Hubin", - "author_inst": "Sciensano" - }, - { - "author_name": "Matthieu Billuart", - "author_inst": "Sciensano" - }, - { - "author_name": "Jenny Chung", - "author_inst": "Sciensano" - }, - { - "author_name": "Mathil Vandromme", - "author_inst": "Sciensano" - }, - { - "author_name": "Chlo\u00e9 Wyndham-Thomas", - "author_inst": "Sciensano" - }, - { - "author_name": "Koen Blot", - "author_inst": "Sciensano" - }, - { - "author_name": "Lucy Catteau", - "author_inst": "Sciensano" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.09.22274769", "rel_title": "COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study", @@ -282456,6 +281989,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.08.22274797", + "rel_title": "mRNA-based COVID-19 booster vaccination is highly effective and cost-effective in Australia", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.08.22274797", + "rel_abs": "BackgroundAustralia implemented an mRNA-based booster vaccination strategy against the COVID-19 Omicron variant in November 2021. We aimed to evaluate the effectiveness and cost-effectiveness of the booster strategy over 180 days.\n\nMethodsWe developed a decision-analytic Markov model of COVID-19 to evaluate the cost-effectiveness of a booster strategy (administered 3 months after 2nd dose) in those aged [≥]16 years in Australia from a healthcare system perspective. The willingness-to-pay threshold was chosen as A$ 50,000.\n\nFindingsCompared with 2-doses of COVID-19 vaccines without a booster, Australias booster strategy would incur an additional cost of A$0.88 billion but save A$1.28 billion in direct medical cost and gain 670 quality-adjusted life years (QALYs) in 180 days of its implementation. This suggested the booster strategy is cost-saving, corresponding to a benefit-cost ratio of 1.45 and a net monetary benefit of A$0.43 billion. The strategy would prevent 1.32 million new infections, 65,170 hospitalisations, 6,927 ICU admissions and 1,348 deaths from COVID-19 in 180 days. Further, a universal booster strategy of having all individuals vaccinated with the booster shot immediately once their eligibility is met would have resulted in a gain of 1,599 QALYs, a net monetary benefit of A$1.46 billion and a benefit-cost ratio of 1.95 in 180 days.\n\nInterpretationThe COVID-19 booster strategy implemented in Australia is likely to be effective and cost-effective for the Omicron epidemic. Universal booster vaccination would have further improved its effectiveness and cost-effectiveness.\n\nFundingNational Natural Science Foundation of China. Bill and Melinda Gates Foundation", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Rui Li", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Hanting Liu", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Christopher K Fairley", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Jason J Ong", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Yuming Guo", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Zhuoru Zou", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Li Xie", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Guihua Zhuang", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Yan Li", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mingwang Shen", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Lei Zhang", + "author_inst": "Melboune Sexual Health Centre" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.08.22274803", "rel_title": "Clinical characteristics of COVID-19 patients admitted to Intensive Care Unit in Panama during the first pandemic wave admissions in 2020.", @@ -283687,65 +283279,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.10.22274906", - "rel_title": "BA.2 omicron differs immunologically from both BA.1 omicron and pre-omicron variants", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274906", - "rel_abs": "BackgroundSeveral studies have shown that SARS-CoV-2 BA.1 omicron is an immune escape variant and current vaccines and infection with pre-omicron variants provide limited protection against BA.1. Meanwhile, however, omicron BA.2 has become the dominant variant in many countries and has replaced BA.1. As BA.2 has several mutations especially in the receptor binding and the N terminal domain compared to BA.1, we analyzed whether BA.2 shows further immune escape relative to BA.1.\n\nMethodsWe characterized neutralization profiles against the new BA.2 omicron variant in plasma samples from a variety of individuals with different numbers of exposures to infection/vaccination, including samples from previously virus-naive, BA.2 omicron-infected individuals. To illustrate antigenic differences of the two omicron sub-variants and pre-omicron variants we performed antigenic cartography and generated antibody landscapes.\n\nResultsUnvaccinated individuals after a single exposure to BA.2 had limited cross-neutralizing antibodies to pre-omicron variants and to BA.1. Consequently, our antigenic map, which included all Variants of Concern and both BA.1 and BA.2 omicron sub-variants, showed that both omicron sub-variants are distinct to pre-omicron variants, but that the two omicron variant are also antigenically distinct from each other. The antibody landscapes illustrate that cross-neutralizing antibodies against the whole antigenic space, as described in our maps, are generated only after three or more exposures to antigenically close variants but also after two exposures to antigenically distinct variants.\n\nConclusionsHere, we describe the antigenic space inhabited by the relevant SARS-CoV-2 variants, the understanding of which will have important implications for further vaccine strain adaptations.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Annika Roessler", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Antonia Netzl", - "author_inst": "University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK" - }, - { - "author_name": "Ludwig Knabl", - "author_inst": "Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria" - }, - { - "author_name": "Helena Schaefer", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Samuel H Wilks", - "author_inst": "University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK" - }, - { - "author_name": "David Bante", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Barbara Falkensammer", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Wegene Borena", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Dorothee von Laer", - "author_inst": "Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria" - }, - { - "author_name": "Derek Smith", - "author_inst": "University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK" - }, - { - "author_name": "Janine Kimpel", - "author_inst": "Medical University of Innsbruck" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.10.22274918", "rel_title": "Unrealistic optimism in the eye of the storm: Positive bias towards the consequences of COVID-19 during the second and third waves of the pandemic.", @@ -284546,6 +284079,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.06.490927", + "rel_title": "Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites.", + "rel_date": "2022-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.06.490927", + "rel_abs": "Since December 2019 the SARS-CoV-2 virus has infected billions of people around the world and caused millions of deaths. The ability for this RNA virus to mutate has produced variants that have been responsible for waves of infections across the globe. The spike protein on the surface of the SARS-CoV-2 virion is responsible for cell entry in the infection process. Here we have studied the spike proteins from the Original, Alpha (B.1.1.7), Delta (B1.617.2), Delta-plus (B1.617.2-AY1), Omicron BA.1 and Omicron BA.2 variants. Using models built from cryo-EM structures with linoleate bound (6BZ5.pdb) and the N-terminal domain from 7JJI.pdb, each is built from the first residue, with missing loops modelled and 45 disulphides per trimer. Each spike variant was modified from the same Original model framework to maximise comparability. Three replicate, 200 ns atomistic molecular dynamics simulations were performed for each case. (These data also provide the basis for further, non-equilibrium molecular dynamics simulations, published elsewhere.) The analysis of our equilibrium molecular dynamics reveals that sequence variation at the closed receptor binding domain interface particularly for Omicron BA.2 has implications for the avidity of the locked conformation, with potential effects on Omicron BA.1 and Delta-plus. Linoleate binding has a mildly stabilizing effect on furin cleavage site motions in the Original and Alpha variants, but has no effect in Delta, Delta-plus and slightly increases motions at this site for Omicron BA.1, but not BA.2, under these simulation conditions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Deborah Karen Shoemark", + "author_inst": "University of Bristol" + }, + { + "author_name": "AnaSofia F Oliveira", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew D. Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Imre Berger", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christiane Schaffitzel", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adrian J Mulholland", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.05.07.491022", "rel_title": "Cell cycle independent role of cyclin D3 in host restriction of SARS-CoV-2 infection", @@ -285513,61 +285085,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.06.22274719", - "rel_title": "Antibody responses to known and unknown SARS-CoV-2 infections after mRNA vaccine booster", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274719", - "rel_abs": "We followed a fully-vaccinated (two mRNA vaccine doses) community cohort (n=41) without prior COVID-19 diagnosis from September 2021 through March 2022 through the Omicron wave following a booster mRNA vaccination. 19.5% of participants reported a known SARS-CoV-2 infection during the Omicron wave, which was confirmed by anti-nucleocapsid IgG. An additional 36.5% also developed anti-nucleocapsid IgG after the boost, consistent with unknown, asymptomatic SARS-CoV-2 infection during this period. Infection defined by anti-nucleocapsid IgG, whether known to participant or not, increased anti-spike IgG levels, relative to those lacking anti-nucleocapsid IgG, at 120 days post-booster.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alexis R. Demonbreun", - "author_inst": "Northwestern University" - }, - { - "author_name": "Amelia Sancilio", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lauren A. Vaught", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nina L. Reiser", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lorenzo Pesce", - "author_inst": "Northwestern University" - }, - { - "author_name": "Eoin P. Sode", - "author_inst": "Northwestern University" - }, - { - "author_name": "Brian Mustanski", - "author_inst": "Northwestern University" - }, - { - "author_name": "Richard T D'Aquila", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elizabeth M McNally", - "author_inst": "Northwestern University" - }, - { - "author_name": "Thomas W McDade", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.04.22274677", "rel_title": "A statistical definition of epidemic waves", @@ -286224,6 +285741,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.06.490907", + "rel_title": "GDF15 and ACE2 stratify COVID19 patients according to severity while ACE2 mutations increase infection susceptibility.", + "rel_date": "2022-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.06.490907", + "rel_abs": "Coronavirus disease 19 (COVID-19) is a persistent global pandemic with a very heterogeneous disease presentation ranging from a mild disease to dismal prognosis. Early detection of sensitivity and severity of COVID-19 is essential for the development of new treatments. In the present study, we measured the levels of circulating growth differentiation factor 15 (GDF15) and angiotensin-converting enzyme 2 (ACE2) in plasma of severity-stratified COVID-19 patients and healthy control patients and characterized the in vitro effects and cohort frequency of ACE2 SNPs. Our results show that while circulating GDF15 and ACE2 stratify COVID-19 patients according to disease severity, ACE2 missense SNPs constitute a risk factor linked to infection susceptibility.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Margalida Torrens-Mas", + "author_inst": "Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Catalina M Perello-Reus", + "author_inst": "Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Neus Trias-Ferrer", + "author_inst": "Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain." + }, + { + "author_name": "Lesly Ibarguen-Gonzalez", + "author_inst": "Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Catalina Crespi", + "author_inst": "Cell Culture and Flow Cytometry Facility, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Aina Maria Galmes-Panades", + "author_inst": "Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Cayetano Navas-Enamorado", + "author_inst": "Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Andres Sanchez-Polo", + "author_inst": "Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain" + }, + { + "author_name": "Javier Pierola-Lopetegui", + "author_inst": "Microscopy Facility, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain." + }, + { + "author_name": "Lluis Masmiquel", + "author_inst": "Vascular and Metabolic Pathologies Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain." + }, + { + "author_name": "Lorenzo Socias Crespi", + "author_inst": "Intensive Care Unit, Son Llatzer University Hospital, Balearic Islands, Palma de Mallorca, Spain" + }, + { + "author_name": "Carles Barcelo", + "author_inst": "Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain." + }, + { + "author_name": "Marta Gonzalez-Freire", + "author_inst": "Health Research Institute of the Balearic Islands" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.05.05.490776", "rel_title": "Allelic gene polymorphisms suspected to diversify the individual early metabolic response upon influenza H3N2 and SARS-CoV-2 infections", @@ -287415,41 +286999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.05.04.22274692", - "rel_title": "The spread and burden of the COVID-19 pandemic in sub-Saharan Africa: comparison between predictions and actual data and lessons learned.", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274692", - "rel_abs": "IntroductionSub-Saharan Africa (SSA) was predicted to be severely affected by the coronavirus disease 2019 (COVID-19) pandemic, but the actual data seem to have contradicted these forecasts. This study attempted to verify this observation by comparing predictions against actual data on the spread and burden of the COVID-19 pandemic in SSA.\n\nMethodsFocused on the period from March 1st to September 30th, 2020, we compared (1) the predicted interval dates when each SSA country would report 1 000 and 10 000 COVID-19 cases, to the actual dates when these numbers were attained, as well as (2) the daily number of predicted versus actual COVID-19 cases.\n\nFurther, we calculated the case fatality ratio of the COVID-19 infection in SSA, and the correlation coefficient between the weekly average number of confirmed COVID-19 cases reported by each country and the weekly average stringency index of its anti-COVID-19 policy measures.\n\nResults84.61% (33) and 100% (39) of the 39 SSA countries for which predictions were made did not reach a total of 1 000 and 10 000 confirmed COVID-19 cases at the predicted interval dates. The daily number of confirmed COVID-19 cases was lower than the one projected for all SSA countries. The case fatality ratio of the COVID-19 infection in SSA was 3.42%. Among the 44 SSA countries for which the correlation could be estimated, it was negative for 17 (38.6 %) of them.\n\nConclusionsThe natural characteristics of SSA and the public health measures implemented might partly explain that the actual data were lower than the predictions on the COVID-19 pandemic in SSA, but the low case ascertainment and the numerous asymptomatic cases did significantly influence this observation.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christophe Dongmo Fokoua-Maxime", - "author_inst": "University of New York State - University at Albany" - }, - { - "author_name": "Yahia Bellouche", - "author_inst": "University Hospital Centre Brest: CHRU de Brest" - }, - { - "author_name": "Dillonne Ngonpong Tchigui-Ariolle", - "author_inst": "Catholic University of Health and Allied Sciences" - }, - { - "author_name": "Tchana Loic Tchato-Yann", - "author_inst": "Universite de Yaounde I FMSB: Universite de Yaounde I Faculte de Medecine et des Sciences Biomedicales" - }, - { - "author_name": "Simeon Pierre Choukem", - "author_inst": "University of Dschang: Universite de Dschang" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.04.22274647", "rel_title": "Protection against omicron severe disease 0-7 months after BNT162b2 booster", @@ -288150,6 +287699,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2022.05.03.490428", + "rel_title": "Protection from Omicron and other VOCs by Bivalent S-Trimer COVID-19 Vaccine", + "rel_date": "2022-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.03.490428", + "rel_abs": "The Omicron variant of SARS-COV-2 (GISAID GRA clade [B.1.1.529, BA.1 and BA.2]) is now the single dominant Variant of Concern (VOC). The high number of mutations in the Omicron Spike (S) protein promotes humoral immunological escape. Although a third homologous boost with S, derived from the ancestral strain, was able to increase neutralizing antibody titers and breadth including to Omicron, the magnitude of virus neutralization could benefit from further optimization. Moreover, combining SARS-COV-2 strains as additional valences may address the current antigenicity range occupied by VOCs.\n\nUsing Trimer-Tag platform we have previously demonstrated phase 3 efficacy and safety of a prototypic vaccine SCB-2019 in the SPECTRA trial and have submitted applications for licensure. Here, we successfully generated a bivalent vaccine candidate including both Ancestor and Omicron variant S-proteins. Preclinical studies demonstrate this SARS-CoV-2 bivalent S-Trimer subunit vaccine elicits high titers of neutralizing antibodies against all VOCs, with markedly enhanced Omicron specific neutralizing antibody responses.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Danmei Su", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Xingling Li", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Xueqin Huang", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Cui He", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Cheng Zeng", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Qiang Wang", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Zhongquan Mu", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Wenchang Qin", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Donna Ambrosino", + "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "George Siber", + "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Ralf Clemens", + "author_inst": "Scientific Advisory Board, Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Joshua G. Liang", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Peng Liang", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Nick Jackson", + "author_inst": "Clover Biopharmaceuticals, Chengdu, China" + }, + { + "author_name": "Rong Xu", + "author_inst": "Clover Biopharmaceuticals" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.05.03.490381", "rel_title": "Spatiotemporal landscape of SARS-CoV-2 pulmonary infection reveals Slamf9+Spp1+ macrophages promoting viral clearance and inflammation resolution", @@ -289621,45 +289245,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.29.22274483", - "rel_title": "Effectiveness of ChAdOx1-S COVID-19 Booster Vaccination against the Omicron and Delta variants in England", - "rel_date": "2022-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274483", - "rel_abs": "BackgroundDespite the potential widespread global use of the ChAdOx1-S booster, to date there are no published data on the real-world effectiveness. VE studies have found one and two doses of the ChAdOx1-S vaccine to be highly effective, and clinical trial data have demonstrated enhanced immunity following a ChAdOx1-S booster. In England, some individuals received a ChAdOx1-S booster where vaccination with mRNA vaccines was clinically contraindicated.\n\nMethodsThe demographic characteristics of those who received a ChAdOx1-S booster were compared to those who received a BNT162b2 booster. A test-negative case control design was used to estimate vaccine effectiveness of the ChAdOx1-S booster against symptomatic disease and hospitalisation in England.\n\nFindingsThose who received a ChAdOx1-S booster were more likely to be female (adjusted odds ratio (OR) 1.67 (1.64-1.71)), in a clinical risk group (adjusted OR 1.58 (1.54-1.63)), in the CEV group (adjusted OR 1.84 (1.79-1.89)) or severely immunosuppressed (adjusted OR 2.05 (1.96-2.13)).\n\nProtection against symptomatic disease in those aged 65 years and older peaked at 66.1% (16.6 to 86.3%) and 68.5% (65.7 to 71.2%) amongst those who received the ChAdOx1-S and BNT162b2 booster vaccines, respectively. Protection waned to 44.5% (22.4 to 60.2%) and 54.1% (50.5 to 57.5%) after 5-9 weeks. Protection against hospitalisation following Omicron infection peaked at 82.3% (64.2 to 91.3%) after receiving a ChAdOx1-S booster, as compared to 90.9% (88.7 to 92.7%) for those who received a BNT162b2 booster.\n\nInterpretationDifferences in the population boosted with ChAdOx1-S in England renders direct comparison of vaccine effectiveness by manufacturer challenging. Nonetheless, this study supports the use of the ChAdOx1-S booster for protection against severe disease with COVID-19 in settings that have not yet offered booster doses and suggests that those who received ChAdOx1-S as a booster in England do not require re-vaccination ahead of others.\n\nFundingUKHSA", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Freja Kirsebom", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Nick Andrews", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Ruchira Sachdeva", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Julia Stowe", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.29.22274494", "rel_title": "Forecast Intervals for Infectious Disease Models", @@ -290376,6 +289961,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.04.28.22274442", + "rel_title": "A Solution to the Kermack and McKendrick Integro-Differential Equations", + "rel_date": "2022-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274442", + "rel_abs": "In this manuscript, we derive a closed form solution to the full Kermack and McKendrick integro-differential equations (Kermack and McKendrick 1927) which we call the KMES. We demonstrate the veracity of the KMES using independent data from the Covid 19 pandemic and derive many previously unknown and useful analytical expressions for characterizing and managing an epidemic. These include expressions for the viral load, the final size, the effective reproduction number, and the time to the peak in infections. The KMES can also be cast in the form of a step function response to the input of new infections; and that response is the time series of total infections.\n\nSince the publication of Kermack and McKendricks seminal paper (1927), thousands of authors have utilized the Susceptible, Infected, and Recovered (SIR) approximations; expressions putatively derived from the integro-differential equations to model epidemic dynamics. Implicit in the use of the SIR approximation are the beliefs that there is no closed form solution to the more complex integro-differential equations, that the approximation adequately reproduces the dynamics of the integro-differential equations, and that herd immunity always exists. However, the KMES demonstrates that the SIR models are not adequate representations of the integro-differential equations, and herd immunity is not guaranteed. We suggest that the KMES obsoletes the need for the SIR approximations; and provides a new level of understanding of epidemic dynamics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Theodore G Duclos", + "author_inst": "The Entropy Research Institute" + }, + { + "author_name": "Thomas Alan Reichert", + "author_inst": "Entropy Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.28.22274344", "rel_title": "Understanding Definitions and Reporting of Deaths Attributed to COVID-19 in the UK - Evidence from FOI Requests", @@ -291347,89 +290955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.25.22274294", - "rel_title": "Effects of boosted mRNA and adenoviral-vectored vaccines on immune responses to omicron BA.1 and BA.2 following the heterologous CoronaVac/AZD1222 vaccination", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274294", - "rel_abs": "BackgroundThe coronavirus 2019 omicron variant has surged rapidly and raises concerns about immune evasion because it harbors mutations even in individuals with complete vaccination. Here, we examine the capability of the booster vaccination to induce neutralizing antibodies (NAbs) against omicron (BA.1 and BA.2) and T-cell responses.\n\nMethodsA total of 167 participants primed with heterologous CoronaVac/AZD1222 were enrolled to receive AZD1222, BNT162b2, or mRNA-1273 as a booster dose. Reactogenicity was recorded. Binding antibody, neutralizing antibody (NAb) titers against omicron BA.1 and BA.2, and total interferon gamma (IFN-{gamma}) post-booster responses were measured.\n\nResultsA substantial loss in neutralizing potency to omicron variant was found at 4 to 5 months after receiving the heterologous CoronaVac/AZD1222. Following booster vaccination, a significant increase in binding antibodies and neutralizing activities toward delta and omicron variants was observed. Neutralization to omicron BA.1 and BA.2 were comparable, showing the highest titers after boosted mRNA-1273 followed by BNT162b2 and AZD1222. Notably, boosted individuals with mRNA vaccines could induce T cell response. Reactogenicity was mild to moderate without serious adverse events.\n\nConclusionsOur findings highlight that the booster vaccination could overcome immunity wanes and provide adequate NAbs coverage against omicron BA.1 and BA.2.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Chompoonut Auphimai", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thaneeya Duangchinda", - "author_inst": "Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development" - }, - { - "author_name": "Warangkana Chantima", - "author_inst": "Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Ma" - }, - { - "author_name": "Pattarakul Pakchotanon", - "author_inst": "Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Jiratchaya Puenpa", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "yong Poovorawan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.04.26.22274273", "rel_title": "COVID-19 third wave experience in India, a survey of 5971 adults", @@ -292322,6 +291847,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.28.22274370", + "rel_title": "Neuropsychological assessments for dementia research in the COVID-19 era: comparing remote and face-to-face testing", + "rel_date": "2022-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.28.22274370", + "rel_abs": "ObjectivesWe explored whether adapting traditional neuropsychological tests for online administration against the backdrop of COVID-19 was feasible for people with diverse forms of dementia and healthy older controls. We compared face-to-face and remote settings to ascertain whether remote administration affected performance.\n\nDesignWe used a longitudinal design for healthy older controls who completed face-to-face neuropsychological assessments between three and four years before taking part remotely. For patients, we used a cross-sectional design, contrasting a prospective remote cohort with a retrospective face-to-face cohort matched in age, education, and disease duration.\n\nSettingRemote assessments were performed using video-conferencing and online testing platforms, with participants using a personal computer or tablet and situated in a quiet room in their own home. Face-to-face assessments were carried out in dedicated testing rooms in our research centre.\n\nParticipantsThe remote cohort comprised ten healthy older controls (also seen face-to-face 3-4 years previously) and 25 patients (n=8 Alzheimers disease (AD); n=3 behavioural variant frontotemporal dementia (bvFTD); n=4 semantic dementia (SD); n=5 progressive nonfluent aphasia (PNFA); n=5 logopenic aphasia (LPA)). The face-to-face patient cohort comprised 64 patients (n=25 AD; n=12 bvFTD; n=9 SD; n=12 PNFA; n=6 LPA).\n\nPrimary and secondary outcome measuresThe outcome measures comprised the strength of evidence under a Bayesian analytic framework for differences in performances between face-to-face and remote testing environments on a general neuropsychological (primary outcomes) and neurolingustic battery (secondary outcomes).\n\nResultsThere was evidence to suggest comparable performance across testing environments for all participant groups, for a range of neuropsychological tasks across both batteries.\n\nConclusionsOur findings suggest that remote delivery of neuropsychological tests for dementia research is feasible.\n\nStrengths and limitations of this studyO_ST_ABSMethodological strengths of this study includeC_ST_ABSO_LIDiverse patient cohorts representing rare dementias with specific communication difficulties\nC_LIO_LISampling of diverse and relevant neuropsychological domains\nC_LIO_LIUse of Bayesian statistics to quantify the strength of evidence for the putative null hypothesis (no effect between remote and face-to-face testing)\nC_LI\n\nLimitations includeO_LIRelatively small cohort sizes\nC_LIO_LILack of direct head-to-head comparisons of test environment in the same patients\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mai-Carmen Requena-Komuro", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Jessica Jiang", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Lucianne Dobson", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Elia Benhamou", + "author_inst": "MRC Cognition and Brain Sciences Unit, University of Cambridge" + }, + { + "author_name": "Lucy Russell", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Rebecca L Bond", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Emilie V Brotherhood", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Caroline Greaves", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Suzie Barker", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Jonathan D Rohrer", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Sebastian J Crutch", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Jason D Warren", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + }, + { + "author_name": "Chris JD Hardy", + "author_inst": "Dementia Research Centre, Queen Square Institute of Neurology, University College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.04.26.22274330", "rel_title": "Interest of seroprevalence surveys for the epidemiological surveillance of the SARS-CoV-2 pandemic in African populations: insights from the ARIACOV Project in Benin", @@ -293389,101 +292981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.23.22274112", - "rel_title": "Real-world study of the effectiveness of BBIBP-CorV (Sinopharm) COVID-19 vaccine in the Kingdom of Morocco", - "rel_date": "2022-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.23.22274112", - "rel_abs": "The Kingdom of Morocco approved BBIBP-CorV (Sinopharm) COVID-19 vaccine for emergency use on 22 January 2021 in a two-dose, three-to-four-week interval schedule. We conducted a case-control study to determine real-world BBIBP-CorV vaccine effectiveness (VE) against serious or critical hospitalization of individuals RT-PCR-positive for SARS-CoV-2 during the first five months of BBIBP-CorV use in Morocco.\n\nThe study was conducted among adults 18-99 years old who were tested by RT-PCR for SARS-CoV-2 infection between 1 February and 30 June 2021. RT-PCR results were individually linked with outcomes from the COVID-19 severe or critical hospitalization dataset and with vaccination histories from the national vaccination registration system. Individuals with partial vaccination (<2 weeks after dose two) or in receipt of any other COVID-19 vaccine were excluded. Unadjusted and adjusted VE estimates against hospitalization for serious or critical illness were made by comparing two-dose vaccinated and unvaccinated individuals in logistic regression models, calculated as (1-odds ratio) * 100%.\n\nThere were 348,190 individuals able to be matched across the three databases. Among these, 140,892 were fully vaccinated, 206,149 were unvaccinated, and 1,149 received homologous BBIBP-CorV booster doses. Unadjusted, full-series, unboosted BBIBP-CorV VE against hospitalization for serious or critical illness was 90.2% (95%CI: 87.8% - 92.0%). Full-series, unboosted VE, adjusted for age, sex, and calendar day of RT-PCR test, was 88.5% (95%CI: 85.8% - 90.7%). Calendar day- and sex-adjusted VE ranged from 93.9% to 100% for individuals <60 years, and was 53.3% for individuals 60 years and older. There were no serious or critical illnesses among BBIBP-CorV-boosted individuals.\n\nEffectiveness of Sinopharms BBIBP-CorV was consistent with phase III clinical trial results. Two doses of BBIBP-CorV was highly protective against COVID-19-associated serious or critical hospitalization in working-age adults under real-world conditions and moderately effective in older adults. Booster dose VE should be evaluated, as booster doses of BBIBP-CorV are recommended and are being used.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Yaowen Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Jihane Belayachi", - "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco" - }, - { - "author_name": "Yunkai Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Qiang Fu", - "author_inst": "China Sinopharm International Corporation, Beijing, P.R. China" - }, - { - "author_name": "Lance Rodewald", - "author_inst": "National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, P.R. China" - }, - { - "author_name": "Hongling Li", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Bing Yan", - "author_inst": "China Sinopharm International Corporation, Beijing, P.R. China" - }, - { - "author_name": "Ying Wang", - "author_inst": "China Sinopharm International Corporation, Beijing, P.R. China" - }, - { - "author_name": "Yanna Shen", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Qian Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Weiyun Mu", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Rong Tang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Chen Su", - "author_inst": "China Sinopharm International Corporation, Beijing, P.R. China" - }, - { - "author_name": "Tianfang Xu", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Majdouline Obtel", - "author_inst": "Laboratory of Biostatistics, Clinical, and Epidemiological Research, Department of Public Health, Faculty of Medicine and Pharmacy-Mohamed V University in Rabat" - }, - { - "author_name": "Abdelkader Mhayi", - "author_inst": "Department of informatics; Ministry of health and social protection, Rabat, Morocco" - }, - { - "author_name": "Rachid Razine", - "author_inst": "Laboratory of Biostatistics, Clinical, and Epidemiological Research, Department of Public Health, Faculty of Medicine and Pharmacy-Mohamed V University in Rabat" - }, - { - "author_name": "Redouane Abouqal", - "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco; Laboratory of Biostatistics, Clinical, and Epidemiological Research, Department of Publ" - }, - { - "author_name": "Yuntao Zhang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - }, - { - "author_name": "Xiaoming Yang", - "author_inst": "China National Biotec Group Company Limited, Beijing, P.R. China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.25.22274291", "rel_title": "Epidemiological behavior of the contamination curve by COVID-19 in Brazil: a time series study", @@ -294012,6 +293509,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.21.22274152", + "rel_title": "Health care use attributable to COVID-19: A propensity matched national electronic health records cohort study of 249,390 people in Wales, UK.", + "rel_date": "2022-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274152", + "rel_abs": "BackgroundTo determine the extent and nature of changes in infected patients healthcare utilization, we studied healthcare contact in the 1-4 weeks and 5-24 weeks following a COVID-19 diagnosis compared to propensity matched controls.\n\nMethodsSurvival analysis was used for time to death and first clinical outcomes including clinical terminology concepts for post-viral illness, fatigue, embolism, respiratory conditions, mental and developmental conditions, fit note, or hospital attendance. Increased instantaneous risk for the occurrence of an outcome for positive individuals was quantified using hazard ratios (HR) from Cox Regression and absolute risk was quantified using relative risk (RR) from life table analysis.\n\nResultsCompared to matched individuals testing negative, surviving positive community-tested patients had a higher risk of post-viral illness (HR: 4.57, 95%CI: 1.77-11.80, p=0.002), fatigue (HR: 1.47, 95%CI: 1.24-1.75, p<0.001) and embolism (HR: 1.51, 95%CI: 1.13-2.02, p=0.005) at 5-24 weeks post-diagnosis. In the four weeks after COVID-19 higher rates of sick notes were being issued for community-tested (HR: 3.04, 95%CI: 0.88 to 10.50, p<0.079); the risk was reduced after four weeks, compared to controls. Overall healthcare attendance for anxiety, depression was less likely in those with COVID-19 in the first four weeks (HR: 0.83, 95%CI: 0.73-1.06, p=0.007). After four weeks, anxiety, depression is less likely to occur for the positive community-tested individuals (HR: 0.87, 95%CI: 0.77-1.00, p=0.048), but more likely for positive hospital-tested individuals (HR: 1.16, 95%CI: 1.00-1.45, p=0.053). Although statistical associations between positive infection and post-infection healthcare use are clear, the absolute use of healthcare is very.\n\nConclusionsCommunity COVID-19 disease is associated with increased risks of post-viral illness, fatigue, embolism, depression, anxiety and respiratory conditions. Despite these elevated risks, the absolute healthcare burden is low. Either very small proportions of people experience adverse outcomes following COVID-19 or they are not presenting to healthcare.\n\nTrial registrationData held in SAIL databank are anonymised and therefore, no ethical approval is required. All data in SAIL has the permission from the relevant Caldicott Guardian or Data Protection Officer and SAIL-related projects are required to obtain Information Governance Review Panel (IGRP) approval. The IGRP approval number for this study is 1259.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jonathan Kennedy", + "author_inst": "Swansea University" + }, + { + "author_name": "Michael Parker", + "author_inst": "Swansea University" + }, + { + "author_name": "Michael Seaborne", + "author_inst": "Swansea University" + }, + { + "author_name": "Mohamed Mhereeg", + "author_inst": "Swansea University" + }, + { + "author_name": "Alex J Walker", + "author_inst": "Datalab, Nuffield Dept of Primary Care Health Science, Radcliffe Primary Care Building, Oxford, OX2 6GG." + }, + { + "author_name": "Venexia Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Spiros Denaxas", + "author_inst": "University College London" + }, + { + "author_name": "Natasha Kennedy", + "author_inst": "Swansea University" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Sinead Brophy", + "author_inst": "Swansea University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.24.22274237", "rel_title": "Hospitalized patients with severe COVID-19 during the Omicron wave in Israel - benefits of a fourth vaccine dose", @@ -295035,45 +294587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.20.22270880", - "rel_title": "Whole-Genome Sequencing Of Omicron Identified Multiple Outbreaks And Introduction Events In India During November 2021 and January 2022", - "rel_date": "2022-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22270880", - "rel_abs": "The variant of Concern(VOC), Omicron is the predominant variant circulating throughout the world of the SARS COV2 pandemic during the third wave including India. The World Health Organisation has designated this highly mutated variant as a VOC due to its high transmissibility and risk of reinfection. Whole-genome sequencing and analysis were performed for SARS-CoV2 PCR positive samples between Dec21 to Jan22. From the 133 omicron variants detected, genomic analysis was carried out by contextualizing them with 1586 complete genomes of Omicron from India obtained from GISAID.\n\nThe Omicron variant prevalence in India has increased in a log phase within 3 months in most of the metropolitan cities. The sublineage BA.1 was first observed in the country, while the BA.2 sublineage was introduced to Delhi in the mid of December 2021. The two outbreaks observed were of BA.2 variant and were observed to spread to multiple cities in a short time. The rapid spread and specific mutations in the outbreak samples of Omicron indicate that the variant is highly transmissible when compared to previous variants. The study shows the importance of genomic sequence to identify the emergence of clusters and take actions to prevent further spreading events.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shreedhanya Marathe", - "author_inst": "Central Research Laboratory" - }, - { - "author_name": "Geetha Nagaraj", - "author_inst": "Central Research Laboratory" - }, - { - "author_name": "Varun Shamanna Sr.", - "author_inst": "Central Research Laboratory" - }, - { - "author_name": "Muthumeenakshi Bhaskaran", - "author_inst": "Central Research Laboratory" - }, - { - "author_name": "Nischita S", - "author_inst": "Central Research Laboratory" - }, - { - "author_name": "Ravikumar Kadahalli Lingegowda", - "author_inst": "Central Research laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.22.22274198", "rel_title": "Estimation of the Ascertainment Bias in Covid Case Detection During the Omicron Wave", @@ -295802,6 +295315,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.04.21.22274110", + "rel_title": "Prosocial motivation for vaccination", + "rel_date": "2022-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274110", + "rel_abs": "Both private and public benefits result from vaccination for transmissible diseases, such as seasonal influenza, measles, and COVID-19. To help inform vaccination efforts for such diseases, we ask whether social preferences--concerns for the well-being of other people--influence ones decision regarding vaccination. We measure these social preferences for 549 online subjects: We give each subject $4 to play a public-good game and make contributions to public welfare. To the extent that one gets vaccinated out of concern for the health of others, contribution in this game is analogous to an individuals decision to obtain vaccination. We proxy vaccine demand with individuals delay to initially vaccinate for COVID-19. We collect COVID-19 vaccination history separately to avoid experimenter-demand effects. We find a strong result: Contribution in the public-good game is associated with greater demand to voluntarily receive a first dose, and thus also to vaccinate earlier. Compared to a subject who contributes nothing, one who contributes the maximum ($4) is 48% more likely to obtain a first dose voluntarily in the four-month period that we study (April through August 2021). People who are more pro-social are indeed more likely to take a voluntary COVID-19 vaccination. We thus recommend further research on the use of pro-social preferences to help motivate individuals to vaccinate for transmissible diseases, such as the flu and HPV.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jonathan Lucas Reddinger", + "author_inst": "University of Wisconsin, La Crosse" + }, + { + "author_name": "Gary Charness", + "author_inst": "University of California, Santa Barbara" + }, + { + "author_name": "David Levine", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.21.22274150", "rel_title": "Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya", @@ -296709,125 +296249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.21.22274025", - "rel_title": "Determinants of SARS-CoV-2 anti-spike antibody levels following BNT162b2 vaccination: cross-sectional analysis of 6,000 SIREN study participants", - "rel_date": "2022-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274025", - "rel_abs": "BackgroundUnderstanding immunological responses to SARS-CoV-2 vaccinations is integral to the management of SARS-CoV-2. We aimed to investigate determinants of antibody response to the BNT162b2 vaccine.\n\nMethodsA cross-sectional analysis of anti-spike binding antibodies in serum samples from healthcare workers after one or two doses. Post-vaccination interval was restricted to [≥]21 days after dose 1, [≥]14 days after dose 2. The primary outcome was anti-S titres with explanatory variables dose, previous infection, dosing interval, age, ethnicity, and comorbidities. Multivariable linear regression was also conducted.\n\nResultsParticipants (n=5,871) included 3,989 post-dose 1, 1,882 post-dose 2. In SARS-CoV-2 infection naive, 99.65% seroconverted after dose 1 and >99.9% seroconverted after dose 2. Geometric mean anti-S titre in the naive cohort was 75.48 Binding Antibody Units/ml after dose 1, 7,049 BAU/ml after dose 2. Anti-S titres were higher in those with previous infection (2,111 BAU/ml post-dose 1, 16,052 BAU/ml post-dose 2), and increased with time between infection and vaccination: 3 months 1,970 (1,506-2,579) vs 9 months; 13,759 (8,097-23,379). Longer dosing intervals increased antibody response post-dose 2: 11-fold higher with a longer interval (>10 weeks) than those with shorter intervals, across all age-groups. Younger participants had higher mean titres (>2.2-fold higher). Multivariable regression modelling corroborated the above associations, and also found higher titres associated with being female or from an ethnic minority but lower titres among immunocompromised participants.\n\nConclusionThe number of antigen exposures and timing between vaccinations plays a significant role in the magnitude of the post-vaccination antibody response, with implications for long-term protection and post-booster antibody responses.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Ashley David Otter", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Silvia D'Arcangelo", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Heather Whitaker", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jacqueline Hewson", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Sarah Foulkes", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Ana Atti", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Michelle Cole", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Ezra Linley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Simon Tonge", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Nipunadi Hettiarachchi", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Noshin Sajedi", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Davina Calbraith", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Chris Norman", - "author_inst": "Health and Care Research Wales" - }, - { - "author_name": "Elen de Lacy", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Lesley Price", - "author_inst": "Glasgow Caledonian University and Public Health Scotland" - }, - { - "author_name": "Sally Stewart", - "author_inst": "Glasgow Caledonian University and Public Health Scotland" - }, - { - "author_name": "Lisa Cromey", - "author_inst": "Public Health Agency Northern Ireland" - }, - { - "author_name": "Diane Corrigan", - "author_inst": "Public Health Agency Northern Ireland" - }, - { - "author_name": "- SIREN study group", - "author_inst": "" - }, - { - "author_name": "Cathy Rowe", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Colin Brown", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Jasmin Islam", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Amanda Semper", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Victoria Hall", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Tim Brooks", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.20.22274046", "rel_title": "Elevated plasma Complement Factor H Regulating Protein 5 is associated with venous thromboembolism and COVID-19 severity", @@ -297576,6 +296997,45 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.04.18.22273983", + "rel_title": "Modeling the initial phase of COVID-19 epidemic: The role of age and disease severity in the Basque Country, Spain", + "rel_date": "2022-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273983", + "rel_abs": "Declared a pandemic by the World Health Organization (WHO), COVID-19 has spread rapidly around the globe. With eventually substantial global underestimation of infection, by the end of March 2022, more than 470 million cases were confirmed, counting more than 6.1 million deaths worldwide.\n\nCOVID-19 symptoms range from mild (or no) symptoms to severe illness, with disease severity and death occurring according to a hierarchy of risks, with age and pre-existing health conditions enhancing risks of disease severity. In order to understand the dynamics of disease severity during the initial phase of the pandemic, we propose a modeling framework stratifying the studied population into two groups, older and younger, assuming different risks for severe disease manifestation.\n\nThe deterministic and the stochastic models are parametrized using epidemiological data for the Basque Country population referring to confirmed cases, hospitalizations and deaths, from February to the end of March 2020. Using similar parameter values, both models were able to describe well the existing data. A detailed sensitivity analysis was performed to identify the key parameters influencing the transmission dynamics of COVID-19 in the population. We observed that the population younger than 60 years old of age would contribute more to the overall force of infection than the older population, as opposed to the already existing age-structured models, opening new ways to understand the effect of population age on disease severity during the COVID-19 pandemic.\n\nWith mild/asymptomatic cases significantly influencing the disease spreading and control, our findings support the vaccination strategy prioritising the most vulnerable individuals to reduce hospitalization and deaths, as well as the non-pharmaceutical intervention measures to reduce disease transmission.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Akhil Kumar Srivasrav", + "author_inst": "Basque Center for Applied Mathematics: Centro Vasco de Matematicas Aplicadas" + }, + { + "author_name": "Nico Stollenwerk", + "author_inst": "Basque Center for Applied Mathematics: Centro Vasco de Matematicas Aplicadas" + }, + { + "author_name": "Joseba Bidaurrazaga Van-Dierdonck", + "author_inst": "Basque Government: Gobierno Vasco" + }, + { + "author_name": "Javier Mar", + "author_inst": "Osakidetza Servicio Vasco de Salud Comarca Araba" + }, + { + "author_name": "Oliver Ibarrondo", + "author_inst": "Osakidetza Servicio Vasco de Salud Comarca Araba" + }, + { + "author_name": "Maira Aguiar", + "author_inst": "Basque Center for Applied Mathematics: Centro Vasco de Matematicas Aplicadas" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.17.22273906", "rel_title": "The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.", @@ -300255,45 +299715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.19.22273818", - "rel_title": "Predictors of COVID-19 vaccine uptake: An online longitudinal study of US Veterans and non-Veterans", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22273818", - "rel_abs": "BackgroundTo effectively promote vaccine uptake, it is important to understand which people are most and least inclined to be vaccinated and why.\n\nPurposeTo identify predictors of COVID-19 vaccine uptake and reasons for non-vaccination.\n\nDesignA longitudinal English-language survey study.\n\nSettingOnline in December-2020, January-2021, and March-2021. Participants. 930 US respondents (63% Veterans).\n\nMeasurementsSurveys included questions about respondents behaviors, well-being, healthcare experiences, and attitudes regarding the pandemic.\n\nResultsThe proportion of respondents who received [≥]1-dose of a COVID-19 vaccine increased from 18% in January to 67% in March. Older age predicted vaccine uptake in January (OR=2.02[95%CI=1.14-3.78], p<.001) and March (10.92[6.76-18.05], p<.001). In January, additional predictors of vaccine uptake were higher numeracy (1.48[1.20-1.86], p<.001), COVID-19 risk perceptions (1.35[1.03-1.78], p=.029), and believing it is important that adults get the COVID-19 vaccine (1.66[1.05-2.66], p=.033). In March, additional predictors of vaccine uptake were believing it is important that adults get the COVID-19 vaccine (1.63[1.15-2.34], p=.006), previous (January) COVID-19 vaccine intentions (1.37[1.10-1.72], p=.006), and belief in science (0.84[0.72-0.99], p=.041). Concerns about side effects and the vaccine development process were the most common reasons for non-vaccination. Unvaccinated respondents with no interest in getting a COVID-19 vaccine were younger (0.27[0.09-0.77], p=.016), held negative views about COVID-19 vaccines for adults (0.15[0.08-0.26], p<.001), had lower trust in healthcare (0.59[0.36-0.95], p=.032), and preferred to watch and wait in clinically ambiguous medical situations (0.66[0.48-0.89], p=.007).\n\nLimitationsReliance on the accuracy and consistency of self-reported data.\n\nConclusionThese findings offer important insights regarding key predictors of vaccine uptake during the early stages of the COVID-19 vaccine rollout in the US, which can help guide health communications and public outreach. Evidence that attitudes and intentions towards COVID-19 vaccines are important predictors of uptake provides validation for studies which have used these measures and reinforces the need to develop effective strategies for addressing concerns about vaccine safety and development which continue to be at the forefront of vaccine hesitancy.\n\nRegistrationThe pre-registration document associated with this manuscript is available at: https://aspredicted.org/MKS_HRZ.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alistair Thorpe", - "author_inst": "Spencer Fox Eccles School of Medicine at University of Utah, Salt Lake City, UT." - }, - { - "author_name": "Angela Fagerlin", - "author_inst": "(1) Spencer Fox Eccles School of Medicine at University of Utah, Salt Lake City, UT. (2) Salt Lake City VA Informatics Decision-Enhancement and Analytic Science" - }, - { - "author_name": "Frank A Drews", - "author_inst": "(2) Salt Lake City VA Informatics Decision-Enhancement and Analytic Sciences (IDEAS) Center for Innovation, Salt Lake City, UT. (3) University of Utah College o" - }, - { - "author_name": "Holly Shoemaker", - "author_inst": "(1) Spencer Fox Eccles School of Medicine at University of Utah, Salt Lake City, UT. (2) Salt Lake City VA Informatics Decision-Enhancement and Analytic Science" - }, - { - "author_name": "Federica S Brecha", - "author_inst": "Spencer Fox Eccles School of Medicine at University of Utah, Salt Lake City, UT." - }, - { - "author_name": "Laura D Scherer", - "author_inst": "(4) Division of Cardiology, University of Colorado, School of Medicine, Aurora, CO. (5) Denver VA Center of Innovation." - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.18.22273978", "rel_title": "Effectiveness of BBIBP-CorV, BNT162b2 and mRNA-1273 vaccines against hospitalisations among children and adolescents during the Omicron outbreak in Argentina", @@ -300942,6 +300363,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.04.13.22273788", + "rel_title": "The Dawn is Coming -- the Description and Prediction of Omicron SARS-CoV-2 Epidemic Outbreak in Shanghai by Mathematical Modeling", + "rel_date": "2022-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22273788", + "rel_abs": "The COVID-19 Omicron outbreak in Shanghai has been going on for >1 month and 25 million population is subjected to strict lock-down quarantine. Until now, it is not clear how long this epidemic might end. Here, we present a time-delayed differentiation equation model to evaluate and forecast the spreading trend. Our model provides important parameters such as the average quarantine ratio, the detection interval from being infected to being tested positive, and the spreading coefficient to better understand the omicron progression. After data fitting, we concluded on 11 April that the maximum overall number infected in Shanghai would exceed 300,000 on 14 April and the turning point would be in the coming days around 13-15 April, 2022, which is perfectly in line with the real-life infection number. Furthermore, the quarantine ratio in Shanghai was found to be greater than 1, supportive of the effectiveness of the strict lockdown policy. Altogether, our mathematical model helps to define how COVID-19 epidemic progresses under the Shanghai lock-down unprecedented in human history and the Chinese zero tolerance policy.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Minghao Jiang", + "author_inst": "Shanghai Institute of Hematology, Ruijin Hospital" + }, + { + "author_name": "Guoyu Meng", + "author_inst": "Rujin Hospital, Shanghai" + }, + { + "author_name": "Geng Wu", + "author_inst": "Shanghai Jiaotong University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.18.488695", "rel_title": "An intranasal nanoparticle STING agonist has broad protective immunity against respiratory viruses and variants", @@ -301921,49 +301369,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.17.22273949", - "rel_title": "Effect of SARS-CoV-2 digital droplet RT-PCR assay sensitivity on COVID-19 wastewater based epidemiology", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.17.22273949", - "rel_abs": "We developed and implemented a framework for examining how molecular assay sensitivity for a viral RNA genome target affects its utility for wastewater-based epidemiology. We applied this framework to digital droplet RT-PCR measurements of SARS-CoV-2 and Pepper Mild Mottle Virus genes made using 10 replicate wells, and determined how using fewer wells affected assay sensitivity and its performance for wastewater-based epidemiology applications. We used a computational, downsampling approach. When percent of positive droplets was between 0.024% and 0.5% (as was the case for SARS-CoV-2 genes during the Delta surge), measurements obtained with 3 or more wells were similar to those obtained using 10. When percent of positive droplets was less than 0.024%, then 6 or more wells were needed to obtain similar results as those obtained using 10 wells. When COVID-19 incidence is low, as it was before the Delta surge and SARS-CoV-2 gene concentrations are <104 cp/g, using 6 wells will yield a detectable concentration 90% of the time. Overall, results support an adaptive approach where assay sensitivity is increased by running 6 or more wells during periods of low SARS-CoV-2 gene concentrations, and 3 or more wells during periods of high SARS-CoV-2 gene concentrations.\n\nSynopsisAdaptive approaches developed with assay sensitivity in consideration may reduce cost and increase sensitivity for wastewater-based epidemiology.\n\nAbstract Art\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC=\"FIGDIR/small/22273949v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@19cebdaorg.highwire.dtl.DTLVardef@14054d0org.highwire.dtl.DTLVardef@80286eorg.highwire.dtl.DTLVardef@1de7e3a_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Suzy Kim", - "author_inst": "Stanford University" - }, - { - "author_name": "Marlene K Wolfe", - "author_inst": "Emory University" - }, - { - "author_name": "Craig Criddle", - "author_inst": "Stanford University" - }, - { - "author_name": "Dorothea Duong", - "author_inst": "Verily Life Sciences" - }, - { - "author_name": "Vikram Chan-Herur", - "author_inst": "Verily Life Sciences" - }, - { - "author_name": "Bradley White", - "author_inst": "Verily Life Sciences" - }, - { - "author_name": "Alexandria Boehm", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.17.22273854", "rel_title": "Characterization of SARS-CoV-2 vaccine waning in Mexico", @@ -302692,6 +302097,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.17.488607", + "rel_title": "Ocular tropism of SARS-CoV-2 with retinal inflammation through neuronal invasion in animal models", + "rel_date": "2022-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.17.488607", + "rel_abs": "Although ocular manifestations are commonly reported in patients with coronavirus disease 2019 (COVID-19), there is currently no consensus on ocular tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To investigate this, we infected K18-hACE2 mice with SARS-CoV-2 using various routes. We observed ocular manifestation and retinal inflammation with cytokine production in the eyes of intranasally (IN) infected mice. An intratracheal (IT) injection resulted in virus spread from the lungs to the brain and eyes via trigeminal and optic nerves. Ocular and neuronal invasion were confirmed by an intracerebral (IC) infection. Notably, eye-dropped (ED) virus did not infect the lungs and was undetectable with time. Using infectious SARS-CoV-2-mCherry clones, we demonstrated the ocular and neurotropic distribution of the virus in vivo by a fluorescence-imaging system. Evidence for the ocular tropic and neuroinvasive characteristics of SARS-CoV-2 was confirmed in wild-type Syrian hamsters. Our data provides further understanding of the viral transmission; SARS-CoV-2 clinical characteristics; and COVID-19 control procedures.\n\nSummarySARS-CoV-2 can spread from the respiratory tract to the brain and eyes via trigeminal and optic nerves in animal models. This ocular tropism of SARS-CoV-2 through neuronal invasion likely causes ocular manifestation and retinal inflammation.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC=\"FIGDIR/small/488607v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (44K):\norg.highwire.dtl.DTLVardef@151c2d5org.highwire.dtl.DTLVardef@ce3aeforg.highwire.dtl.DTLVardef@17f453aorg.highwire.dtl.DTLVardef@99e9c2_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Gi Uk Jeong", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Hyung-Jun Kwon", + "author_inst": "Korea Research Institute of Bioscience and Biotechnology" + }, + { + "author_name": "Hyun Woo Moon", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Gun Young Yoon", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Hye Jin Shin", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Ji Soo Chae", + "author_inst": "PerkinElmer" + }, + { + "author_name": "Seong-Jun Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "In-Chul Lee", + "author_inst": "Korea Research Institute of Bioscience and Biotechnology" + }, + { + "author_name": "Kyun-Do Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Dae-Gyun Ahn", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Suresh Mahalingam", + "author_inst": "Griffith University" + }, + { + "author_name": "Young-Chan Kwon", + "author_inst": "Korea Research Institute of Chemical Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.04.18.488614", "rel_title": "Antibody escape and cryptic cross-domain stabilization in the SARS CoV-2 Omicron spike protein", @@ -303739,81 +303207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.04.09.22273653", - "rel_title": "Disease profile and plasma neutralizing activity of post-vaccination Omicron BA.1 infection in Tianjin, China: a retrospective study", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.09.22273653", - "rel_abs": "BackgroundSARS-CoV-2 Omicron variant BA.1 first emerged on the Chinese mainland in January 2022 in Tianjin and caused a large wave of infections. During mass PCR testing, a total of 430 cases infected with Omicron were recorded between January 8 and February 7, 2022, with no new infections detected for the following 16 days. Most patients had been vaccinated with SARS-CoV-2 inactivated vaccines. The disease profile associated with BA.1 infection, especially after vaccination with inactivated vaccines, is unclear. Whether BA.1 breakthrough infection after receiving inactivated vaccine could create a strong enough humoral immunity barrier against Omicron is not yet investigated.\n\nMethodsWe collected the clinical information and vaccination history of the 430 COVID-19 patients infected with Omicron BA.1. Re-positive cases and inflammation markers were monitored during the patients convalescence phase. Ordered multiclass logistic regression model was used to identify risk factors for COVID-19 disease severity. Authentic virus neutralization assays against SARS-CoV-2 wildtype, Beta and Omicron BA.1 were conducted to examine the plasma neutralizing titers induced after post-vaccination Omicron BA.1 infection, and were compared to a group of uninfected healthy individuals who were selected to have a matched vaccination profile.\n\nFindingsAmong the 430 patients, 316 (73.5%) were adults with a median age of 47 years, and 114 (26.5%) were under-age with a median age of 10 years. Female and male patients account for 55.6% and 44.4%, respectively. Most of the patients presented with mild (47.7%) to moderate diseases (50.2%), with only 2 severe cases (0.5%) and 7 (1.6%) asymptomatic infections. No death was recorded. 341 (79.3%) of the 430 patients received inactivated vaccines (54.3% BBIBP-CorV vs. 45.5% CoronaVac), 49 (11.4%) received adenovirus-vectored vaccines (Ad5-nCoV), 2 (0.5%) received recombinant protein subunit vaccines (ZF2001), and 38 (8.8%) received no vaccination. No vaccination is associated with a substantially higher ICU admission rate among Omicron BA.1 infected patients (2.0% for vaccinated patients vs. 23.7% for unvaccinated patients, P<0.001). Compared with adults, child patients presented with less severe illness (82.5% mild cases for children vs. 35.1% for adults, P<0.001), no ICU admission, fewer comorbidities (3.5% vs. 53.2%, P<0.001), and less chance of turning re-positive on nucleic acid tests (12.3% vs. 22.5%, P=0.019). For adult patients, compared with no prior vaccination, receiving 3 doses of inactivated vaccine was associated with significantly lower risk of severe disease (OR 0.227 [0.065-0.787], P=0.020), less ICU admission (OR 0.023 [0.002-0.214], P=0.001), lower re-positive rate on PCR (OR 0.240 [0.098-0.587], P=0.002), and shorter duration of hospitalization and recovery (OR 0.233 [0.091-0.596], P=0.002). At the beginning of the convalescence phase, patients who had received 3 doses of inactivated vaccine had substantially lower systemic immune-inflammation index (SII) and C-reactive protein than unvaccinated patients, while CD4+/CD8+ ratio, activated Treg cells and Th1/Th2 ratio were higher compared to their 2-dose counterparts, suggesting that receipt of 3 doses of inactivated vaccine could step up inflammation resolution after infection. Plasma neutralization titers against Omicron, Beta, and wildtype significantly increased after breakthrough infection with Omicron. Moderate symptoms were associated with higher plasma neutralization titers than mild symptoms. However, vaccination profiles prior to infection, whether 2 doses versus 3 doses or types of vaccines, had no significant effect on post-infection neutralization titer. Among recipients of 3 doses of CoronaVac, infection with Omicron BA.1 largely increased neutralization titers against Omicron BA.1 (8.7x), Beta (4.5x), and wildtype (2.2x), compared with uninfected healthy individuals who have a matched vaccination profile.\n\nInterpretationReceipt of 3-dose inactivated vaccines can substantially reduce the disease severity of Omicron BA.1 infection, with most vaccinated patients presenting with mild to moderate illness. Child patients present with less severe disease than adult patients after infection. Omicron BA.1 convalescents who had received inactivated vaccines showed significantly increased plasma neutralizing antibody titers against Omicron BA.1, Beta, and wildtype SARS-CoV-2 compared with vaccinated healthy individuals.\n\nFundingThis research is supported by Changping Laboratory (CPL-1233) and the Emergency Key Program of Guangzhou Laboratory (EKPG21-30-3), sponsored by the Ministry of Science and Technology of the Peoples Republic of China.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPrevious studies (many of which have not been peer-reviewed) have reported inconsistent findings regarding the effect of inactivated vaccines against the Omicron variant. On Mar 6, 2022, we searched PubMed with the query \"(SARS-CoV-2) AND ((Neutralisation) OR (Neutralisation)) AND ((Omicron) OR (BA.1)) AND (inactivated vaccine)\", without date or language restrictions. This search identified 18 articles, of which 13 were directly relevant.\n\nNotably, the participants in many of these studies have received only one or two doses of inactivated vaccine with heterologous booster vaccination; other studies have a limited number of participants receiving inactivated vaccines.\n\nAdded value of this studyTo date, this is the first study to report on the protective effect of inactivated vaccines against the severe disease caused by the Omicron variant. We examine and compare the disease profile of adults and children. Furthermore, we estimate the effect of post-vaccination omicron infection on plasma neutralization titers against Omicron and other SARS-COV-2 variants. Specifically, the disease profile of Omicron convalescents who had received two-dose primary series of inactivated vaccines with or without a booster dose prior to infection is compared with unvaccinated patients. We also analyzed the effect of infection on neutralizing activity by comparing vaccinated convalescents with vaccinated healthy individuals with matched vaccination profiles.\n\nImplications of all the available evidenceCompared with adults, child patients infected with Omicron tend to present with less severe disease and are less likely to turn re-positive on nucleic acid tests. Receipt of two-dose primary series or three doses of inactivated vaccine is a protective factor against severe disease, ICU admission, re-positive PCR and longer hospitalization. The protection afforded by a booster dose is stronger than two-dose primary series alone. Besides vaccination, infection with Omicron is also a key factor for elevated neutralizing antibody titers, enabling cross-neutralization against Omicron, wildtype (WT) and the Beta variant.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Hong Zheng M.D.", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Yunlong Cao", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100080, China" - }, - { - "author_name": "Xiaosu Chen M.D., Ph.D", - "author_inst": "Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Fengmei Wang M.D.", - "author_inst": "Tianjin Third Central Hospital, Institute of Hepatobiliary Disease, 83 Jintang Road, Hedong District, Tianjin 300170, China." - }, - { - "author_name": "Ye Hu M.D., Ph.D", - "author_inst": "Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100080, China" - }, - { - "author_name": "Yangyang Chai", - "author_inst": "Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100080, China" - }, - { - "author_name": "Yansong Shi", - "author_inst": "Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Yingmei Feng", - "author_inst": "Beijing Youan Hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Shuxun Liu", - "author_inst": "National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Medical University, Shanghai 200433, China" - }, - { - "author_name": "Yan Xie M.D.", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Xiaoliang Sunney Xie", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100080, China" - }, - { - "author_name": "Wentao Jiang", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin 300071, China" - }, - { - "author_name": "Zhongyang Shen M.D., Ph.D", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin 300071, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.08.22273513", "rel_title": "SARS-CoV-2 spike 340 and 337 mutations in Omicron variants are selected after Sotrovimab infusion in immunocompromised patients", @@ -304414,6 +303807,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.10.22273678", + "rel_title": "Dynamics of anti-Spike IgG antibody titer after the third BNT162b2 COVID-19 vaccination in the Japanese health care workers", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.10.22273678", + "rel_abs": "IntroductionMany countries are administering a third dose of some coronavirus disease 2019 (COVID-19) vaccines, but the evaluation of vaccine-induced immunity is insufficient. This study aimed to evaluate anti-spike immunoglobulin G (IgG) titers in the health care workers after the third BNT162b2 vaccination.\n\nMethodsDynamics of anti-spike IgG titers were assessed two months following the third BNT162b2 vaccination in 52 participants. All participants received the primary series of vaccination with BNT162b2 and received the third dose eight months after the second vaccination. Associations between anti-spike IgG titer, baseline characteristics, and adverse reactions were also evaluated.\n\nResultsThe geometric mean titer of anti-spike IgG one month after the third vaccination was 17400 AU/ml, which increased to approximately 30 times immediately before the third vaccination and approximately twice that one month after the second vaccination. In addition, participants with anti-spike IgG titers less than 10000 AU/ml after the second vaccination tended to have higher increases in ant-spike IgG titers before and after the third vaccination.\n\nThe decline rate of anti-spike IgG was significantly slower after the third vaccination as 35.7% than that after the second vaccination as 59.1%. The anti-spike IgG titer was significantly negatively associated with age (r = -0.31). Participants who had a headache at the vaccination showed significantly higher anti-spike IgG titer than those without a headache.\n\nConclusionsThe anti-spike IgG induced by primary immunization with BNT162b2 waned over time. The third dose of BNT162b2 substantially increased the anti-spike IgG with a slower decline rate.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hiroaki Ikezaki", + "author_inst": "Kyushu University Hospital" + }, + { + "author_name": "Hideyuki Nomura", + "author_inst": "Haradoi Hospital" + }, + { + "author_name": "Nobuyuki Shimono", + "author_inst": "Kyushu University Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.13.22273855", "rel_title": "Rapid displacement of SARS-CoV-2 variants within Japan correlates with cycle threshold values on routine RT-PCR testing", @@ -305273,37 +304693,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.04.14.22273759", - "rel_title": "Understanding community level influences on COVID-19 prevalence in England: New insights from comparison over time and space", - "rel_date": "2022-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273759", - "rel_abs": "Understanding and monitoring the major influences on SARS-CoV-2 prevalence is essential to inform policy making and devise appropriate packages of non-pharmaceutical interventions (NPIs). Through evaluating community level influences on the prevalence of SARS-CoV-2 infection and their spatiotemporal variations in England, this study aims to provide some insights into the most important risk parameters. We used spatial clusters developed in Jahanshahi and Jin, 2021 as geographical areas with distinct land use and travel patterns. We also segmented our data by time periods to control for changes in policies or development of the disease over the course of the pandemic. We then used multivariate linear regression to identify influences driving infections within the clusters and to compare the variations of those between the clusters. Our findings demonstrate the key roles that workplace and commuting modes have had on some of the sections of the working population after accounting for several interrelated influences including mobility and vaccination. We found communities of workers in care homes and warehouses and to a lesser extent textile and ready meal industries and those who rely more on public transport for commuting tend to carry a higher risk of infection across all residential area types and time periods.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chaitanya Joshi", - "author_inst": "Data Science Campus, Office for National Statistics, UK" - }, - { - "author_name": "Arif Ali", - "author_inst": "Data Science Campus, Office for National Statistics, UK" - }, - { - "author_name": "Li Chen", - "author_inst": "Data Science Campus, Office for National Statistics, UK" - }, - { - "author_name": "Kaveh Jahanshahi", - "author_inst": "Data Science Campus, Office for National Statistics, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.04.14.22272888", "rel_title": "Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia", @@ -305928,6 +305317,33 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2022.04.13.488264", + "rel_title": "Genomic surveillance unfolds the dynamics of SARS-CoV-2 transmission and divergence in Bangladesh over the past two years", + "rel_date": "2022-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.13.488264", + "rel_abs": "The highly pathogenic virus SARS-CoV-2 has shattered the healthcare system of the world causing the COVID-19 pandemic since first detected in Wuhan, China. Therefore, scrutinizing the genome structure and tracing the transmission of the virus has gained enormous interest in designing appropriate intervention strategies to control the pandemic. In this report, we examined 4622 sequences from Bangladesh and found that they belonged to thirty-five major PANGO lineages, while Delta alone accounted for 39%, and 78% were from just four primary lineages. Our research has also shown Dhaka to be the hub of viral transmission and observed the virus spreading back and forth across the country at different times by building a transmission network. The analysis resulted in 7659 unique mutations, with an average of 24.61 missense mutations per sequence. Moreover, our analysis of genetic diversity and mutation patterns revealed that eight genes were under negative selection pressure to purify deleterious mutations, while three genes were under positive selection pressure.\n\nImportanceWith 29,122 deaths, 1.95 million infections and a shattered healthcare system from SARS-CoV-2 in Bangladesh, the only way to avoid further complications is to break the transmission network of the virus. Therefore, it is vital to shedding light on the transmission, divergence, mutations, and emergence of new variants using genomic data analyses and surveillance. Here, we present the geographic and temporal distribution of different SARS-CoV-2 variants throughout Bangladesh over the past two years, and their current prevalence. Further, we have developed a transmission network of viral spreads, which in turn will help take intervention measures. Then we analyzed all the mutations that occurred and their effect on evolution as well as the currently present mutations that could trigger a new variant of concern. In short, together with an ongoing genomic surveillance program, these data will help to better understand SARS-CoV-2, its evolution, and pandemic characteristics in Bangladesh.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Tushar Ahmed Shishir", + "author_inst": "BRAC University" + }, + { + "author_name": "Taslimun Jannat", + "author_inst": "BRAC University" + }, + { + "author_name": "Iftekhar B Naser", + "author_inst": "BRAC University" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.04.11.22273719", "rel_title": "Pre-Pandemic COVID-19 in New York City: A descriptive analysis of COVID-19 illness prior to February 29, 2020", @@ -306938,65 +306354,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.04.04.22273376", - "rel_title": "From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand", - "rel_date": "2022-04-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273376", - "rel_abs": "New Zealands COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from elimination to suppression and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lauren Jelley", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand." - }, - { - "author_name": "Jordan Douglas", - "author_inst": "Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand." - }, - { - "author_name": "Xiaoyun Ren", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand." - }, - { - "author_name": "David Winter", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand." - }, - { - "author_name": "Andrea McNeill", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand." - }, - { - "author_name": "Sue Huang", - "author_inst": "Institute of Environmental Science and Research" - }, - { - "author_name": "Nigel French", - "author_inst": "Massey University" - }, - { - "author_name": "David Welch", - "author_inst": "University of Auckland" - }, - { - "author_name": "James Hadfield", - "author_inst": "Fred Hutchinson Cancer Research Centre, Seattle, Washington, USA." - }, - { - "author_name": "Joep de Ligt", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand." - }, - { - "author_name": "Jemma L Geoghegan", - "author_inst": "University of Otago" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.12.487379", "rel_title": "Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants", @@ -307969,6 +307326,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.10.22273663", + "rel_title": "The relation between COVID-19 vaccinations and public governance to improve preparedness of next pandemic impacts and crisis management: a global study", + "rel_date": "2022-04-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.10.22273663", + "rel_abs": "The goal of this study is to analyze the relationship between COVID-19 vaccinations and public governance performing a global analysis of more than 110 countries worldwide. Methodology applies the Independent Samples T-Test that compares the means of two independent groups (countries with high/low level of vaccinations) to determine whether there is statistical evidence that the associated population means of indicators of public governance are significantly different. Findings suggest that high levels of governance can support a better function of health systems in the rollout of vaccinations to cope with COVID-19 pandemic crisis. This study may assist long-run policy of governments to improve good governance and health systems of countries in order to reinforce the preparedness to face next pandemic threats and in general future crisis management in society.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mario Coccia", + "author_inst": "National Research Council of Italy" + }, + { + "author_name": "Igor Benati", + "author_inst": "IRCRES-CNR, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.04.05.22273373", "rel_title": "Should I stay or should I go? Observation post-vaccination during the COVID-19 pandemic and the law of unintended consequences", @@ -308533,57 +307913,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.04.11.487828", - "rel_title": "Key mutations on spike protein altering ACE2 receptor utilization and potentially expanding host range of emerging SARS-CoV-2 variants", - "rel_date": "2022-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487828", - "rel_abs": "Increasing evidence supports inter-species transmission of SARS-CoV-2 variants from human to domestic or wild animals during the ongoing COVID-19 pandemic, which is posing great challenges to epidemic control. Clarifying the host range of emerging SARS-CoV-2 variants will provide instructive information for the containment of viral spillover. The spike protein (S) of SARS-CoV-2 is the key determinant of receptor utilization, and therefore amino acid mutations on S will probably alter viral host range. Here, in order to evaluate the impact of S mutations, we constructed 20 Hela cell lines stably expressing ACE2 orthologs from different animals, and prepared 27 pseudotyped SARS-CoV-2 carrying different spike mutants, among which 20 bear single mutation and the other 7 were cloned from emerging SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.135), Lambda (B.1.429) and Mu (B.1.525). Using pseudoviral reporter assay, we identified that the substitutions of T478I and N501Y enabled the pseudovirus to utilize chicken ACE2, indicating potential infectivity to avian species. Furthermore, the S mutants of real SARS-CoV-2 variants comprising N501Y showed significantly acquired abilities to infect cells expressing mouse ACE2, indicating a critical role of N501Y in expanding SARS-CoV-2 host range. In addition, A262S and T478I significantly enhanced the utilization of various mammals ACE2. In summary, our results indicated that T478I and N501Y substitutions were two S mutations important for receptor adaption of SARS-CoV-2, potentially contributing to spillover of the virus to many other animal hosts. Therefore, more attention should be paid to SARS-CoV-2 variants with these two mutations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Qiong Wang", - "author_inst": "HNU: Hunan University" - }, - { - "author_name": "Sheng-Bao Ye", - "author_inst": "HNU: Hunan University" - }, - { - "author_name": "Zhi-Jian Zhou", - "author_inst": "HNU: Hunan University" - }, - { - "author_name": "Jin-Yan Li", - "author_inst": "HNU: Hunan University" - }, - { - "author_name": "Ji-Zhou Lv", - "author_inst": "Chinese Academy of Inspection and Quarantine" - }, - { - "author_name": "Bodan Hu", - "author_inst": "HKU: University of Hong Kong" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "HKU: University of Hong Kong" - }, - { - "author_name": "Ye Qiu", - "author_inst": "HNU: Hunan University" - }, - { - "author_name": "Xing-Yi Ge", - "author_inst": "Hunan University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.09.487739", "rel_title": "Disrupting ACE2 Dimerization Mitigates the Infection by SARS-COV-2", @@ -309244,6 +308573,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2022.04.07.22273581", + "rel_title": "Time series cross-correlation between home range and number of infected people during the medium term of COVID-19 Pandemic in a suburban city", + "rel_date": "2022-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273581", + "rel_abs": "Control of human mobility is among the most effective measures to prevent the spread of coronavirus disease 2019 (COVID-19). This study aims to clarify the correlation between home range and the number of people infected with SARS-CoV-2 during the medium-term of the COVID-19 pandemic in Ibaraki City. Home ranges are analyzed by the Minimum Convex Polygon method using mobile phone GPS location history data. We analyzed the time series cross-correlation between home range lengths and the number of infected people. Results reveal a slight positive correlation between home range and the number of infected people after one week during the medium-term of the COVID-19 pandemic. Regarding home range length, the cross-correlation coefficient is 0.4030 even at a lag level of six weeks, which has the most significant coefficient. Thus, a decrease in home range is only one of the indirect factors contributing toward a reduction in the number of infected people. This study makes a significant contribution to the literature by evaluating key public health challenges from the perspective of controliing the spread of the COVID-19 infectuion. Its findings has implications for policy makers, practitioners, and urban scientists seeking to promote urban sustainability.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Haruka KATO", + "author_inst": "Osaka Metropolitan University" + }, + { + "author_name": "Atsushi Takizawa", + "author_inst": "Osaka City University: Osaka Shiritsu Daigaku" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.07.22273555", "rel_title": "Longitudinal associations between physical activity and other health behaviours during the COVID-19 pandemic: A fixed effects analysis", @@ -310367,25 +309719,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.03.22273225", - "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemics in Mainland China", - "rel_date": "2022-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22273225", - "rel_abs": "BackgroundGlobally COVID-19 epidemics have caused tremendous disasters. China prevented effectively the spread of COVID-19 epidemics before 2022. Recently Omicron and Delta variants cause a surge in reported COVID-19 infections.\n\nMethodsUsing differential equations and real word data, this study modelings and simulates COVID-19 epidemic in mainland China, estimates transmission rates, recovery rates, and blocking rates to symptomatic and asymptomatic infections. The transmission rates and recovery rates of the foreign input COVID-19 infected individuals in mainland China have also been studied.\n\nResultsThe simulation results were in good agreement with the real word data. The recovery rates of the foreign input symptomatic and asymptomatic infected individuals are much higher than those of the mainland COVID-19 infected individuals. The blocking rates to symptomatic and asymptomatic mainland infections are lower than those of the previous epidemics in mainland China. The blocking rate implemented between March 24-31, 2022 may not prevent the rapid spreads of COVID-19 epidemics in mainland China. For the foreign input COVID-19 epidemics, the numbers of the current symptomatic individuals and the asymptomatic individuals charged in medical observations have decreased significantly after March 17 2022.\n\nConclusionsNeed to implement more strict prevention and control strategies to prevent the spread of the COVID-19 epidemics in mainland China. Keeping the present prevention and therapy measures to foreign input COVID-19 infections can rapidly reduce the number of foreign input infected individuals to a very low level.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lequan Min", - "author_inst": "University of Science and Technology Beijing" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.06.487394", "rel_title": "Prime-pull immunization of mice with a BcfA-adjuvanted vaccine elicits mucosal immunity and prevents SARS CoV-2 infection and pathology", @@ -311222,6 +310555,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.04.22273418", + "rel_title": "Interleukin-6 as a predictor of early weaning from invasive mechanical ventilation in patients with acute respiratory distress syndrome", + "rel_date": "2022-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273418", + "rel_abs": "BackgroundTherapeutic effects of steroids on acute respiratory distress syndrome (ARDS) requiring mechanical ventilation (MV) have been reported. However, predictive indicators of early weaning from MV post-treatment have not yet been defined, making treating established ARDS challenging. Interleukin (IL)-6 has been associated with the pathogenesis of ARDS.\n\nObjectiveOur aim was to clarify clinical utility of IL-6 level in ventilated patients with established ARDS.\n\nMethodsClinical, treatment, and outcome data were evaluated in 119 invasively ventilated patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-mediated ARDS. Plasma levels of IL-6 and C-reactive protein (CRP) were measured on days 1, 4, and 7 after intubation.\n\nResultsFifty-two patients were treated with dexamethasone (steroid group), while the remaining 67 patients were not (non-steroid group). Duration of MV use was significantly shorter in the steroid group compared to non-steroid group (11.5{+/-}0.6 vs. 16.1{+/-}1.0 days, P = 0.0005, respectively) along with significantly decreased levels of IL-6 and CRP. Even when restricted to the steroid group, among variables post-MV, IL-6 level on day 7 was most closely correlated with duration of MV use (Spearmans rank correlation coefficient [{rho}] = 0.73, P < 0.0001), followed by CRP level on day 7 and the percentage change in IL-6 or CRP levels between day 1 and day 7. Moreover, among these variables, IL-6 levels on day 7 showed the highest accuracy for withdrawal from MV within 11 days (AUC: 0.88), with optimal cutoff value of 20.6 pg/mL. Consistently, the rate of MV weaning increased significantly earlier in patients with low IL-6 ([≤] 20.6 pg/mL) than in those with high IL-6 (> 20.6 pg/mL) (log-rank test P < 0.0001).\n\nConclusionsIn invasively ventilated patients with established ARDS due to SARS-CoV-2, plasma IL-6 levels served as a predictor of early withdrawal from MV after dexamethasone administration.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "kazuya sakai", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + }, + { + "author_name": "Mototsugu Nishii", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + }, + { + "author_name": "Ryo Saji", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + }, + { + "author_name": "Reo Matsumura", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + }, + { + "author_name": "Fumihiro Ogawa", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + }, + { + "author_name": "Ichiro Takeuchi", + "author_inst": "Yokohama City University School of Medicine Graduate School of Medicine: Yokohama Shiritsu Daigaku Igakubu Daigakuin Igaku Kenkyuka" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2022.04.04.22273334", "rel_title": "Effect of Heat inactivation and bulk lysis on Real-Time Reverse Transcription PCR Detection of the SARS-COV-2: An Experimental Study", @@ -312169,33 +311541,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.05.487186", - "rel_title": "SARS-CoV-2 Omicron (BA.1 and BA.2) specific novel CD8+ and CD4+ T cell epitopes targeting spike protein.", - "rel_date": "2022-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.05.487186", - "rel_abs": "The Omicron (BA.1/B.1.1.529) variant of SARS-CoV-2 harbors an alarming 37 mutations on its spike protein, reducing the efficacy of current COVID-19 vaccines. This study identified CD8+ and CD4+ T cell epitopes from SARS-CoV-2 S protein mutants. To identify the highest quality CD8 and CD4 epitopes from the Omicron variant, we selected epitopes with a high binding affinity towards both MHC I and MHC II molecules and applied other clinical checkpoint predictors including immunogenicity, antigenicity, allergenicity, instability, and toxicity. Subsequently, we found eight Omicron (BA.1/B.1.1.529) specific CD8+ and eleven CD4+ T cell epitopes with a world population coverage of 76.16% and 97.46%, respectively. Additionally, we identified common epitopes across Omicron BA.1 and BA.2 lineages that target mutations critical to SARS-CoV-2 virulence. Further, we identified common epitopes across B.1.1.529 and other circulating SARS-CoV-2 variants, such as B.1.617.2 (Delta). We predicted CD8 epitopes binding affinity to murine MHC alleles to test the vaccine candidates in preclinical models. The CD8 epitopes were further validated using our previously developed software tool PCOptim. We then modeled the three-dimensional structures of our top CD8 epitopes to investigate the binding interaction between peptide-MHC and peptide-MHC-TCR complexes. Importantly, our identified epitopes are targeting the mutations on the RNA-binding domain and the fusion sites of S protein. This could potentially eliminate viral infections and form long-term immune responses compared to rather short-lived mRNA vaccines and maximize the efficacy of vaccine candidates against the current pandemic and potential future variants.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Simone Parn", - "author_inst": "Georgetown University" - }, - { - "author_name": "Kush Savsani", - "author_inst": "Virginia Commonwealth University" - }, - { - "author_name": "Sivanesan Dakshanamurthy", - "author_inst": "Georgetown University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.06.487325", "rel_title": "Delta-Omicron recombinant SARS-CoV-2 in a transplant patient treated with Sotrovimab", @@ -312980,6 +312325,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.04.05.487103", + "rel_title": "Evolution of Delta variant by non-Spike signature co-appearing mutations: trailblazer of COVID-19 disease outcome", + "rel_date": "2022-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.05.487103", + "rel_abs": "The high transmissibility and infectivity of a SARS-CoV-2 variant is usually ascribed to the Spike mutations, while emerging non-spike mutations might be a serious threat to the current Spike-recombinant vaccines. In addition to mutations in structural Spike glycoprotein, rapid accumulation of mutations across non-structural genes is leading to continuous virus evolution, altering its pathogenicity. We performed whole genome sequencing of SARS-CoV-2 positive samples collected from different clinical groups from eastern India, during the second pandemic wave (April-May, 2021). In addition to the several common spike mutations in Delta variant, two mutually explicit signature constellations of non-spike co-appearing mutations were identified, driving symptomatic and asymptomatic infections. We attempted to correlate these unique signatures of non-Spike co-appearing mutations to COVID-19 disease outcome. Results revealed that the Delta strains harboring a unique constellation of 9 non-spike co-appearing mutations could be the wheeler and dealer of symptomatic infection, even post vaccination. The strains predominantly driving asymptomatic infection possessed 7 non-spike co-appearing mutations, which were mutually exclusive in contrast to the set of mutations causing symptomatic disease. Phylodynamic analysis depicted high probability of emergence of these unique sub-clusters within India, with subsequent spread worldwide. Interestingly, some mutations of this signature were selected in Omicron and IHU variants, which suggest that gradual accumulation of such co-existing mutations may lead to emergence of more \"vaccine-evading variants\" in future. Hence, unfaltering genome sequencing and tracking of non-Spike mutations might be significant in formulation of any future vaccines against emerging SARS-CoV-2 variants that might evade the current vaccine-induced immunity.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anindita Banerjee", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Anup Mazumder", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Jayita Roy", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Agniva Majumdar", + "author_inst": "ICMR-NICED" + }, + { + "author_name": "Ananya Chatterjee", + "author_inst": "ICMR-NICED" + }, + { + "author_name": "Nidhan K Biswas", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Mamta Chawla-Sarkar", + "author_inst": "ICMR-NICED" + }, + { + "author_name": "Arindam Maitra", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Shanta Dutta", + "author_inst": "ICMR-NICED" + }, + { + "author_name": "Saumitra Das", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.04.05.22273167", "rel_title": "Low-dose IL-2 reduces IL-21+ T cells and induces a long-lived anti-inflammatory gene expression signature inversely modulated in COVID-19 patients", @@ -313959,29 +313359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.04.22273361", - "rel_title": "Long- and short-term effects of cross-immunity in epidemic dynamics", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273361", - "rel_abs": "The vertebrate immune system is capable of strong, focused adaptive responses that depend on T-cell specificity in recognizing antigenic sequences of a pathogen. Recognition tolerance and antigenic convergence cause cross-immune reactions that extend prompt, specific responses to rather similar pathogens. This suggests that reaching herd-immunity might be facilitated during successive epidemic outbreaks (e.g., SARS-CoV-2 waves with different variants). Qualitative studies play down this possibility because cross-immune protection is seldom sterilizing. We use minimal quantitative models to study how cross-immunity affects epidemic dynamics over short and long timescales. In the short scale, we investigate models of sterilizing and attenuating immunity, finding equivalences between both mechanisms--thus suggesting a key role of attenuating protection in achieving herd immunity. Our models render maps in epidemic-parameter space that discern threatening variants depending on acquired cross-immunity levels. We illustrate this application with SARS-CoV-2 data, including protection due to vaccination rates across countries. In the long-time scale, we model sterilizing cross-immunity between rolling pathogens to characterize statistical properties of successful strains. We find that sustained cross-immune protection alters the regions of epidemic-parameter space where large outbreaks happen. Our results suggest an optimistic revision concerning prospects for herd protection based on cross-immunity, including for the SARS-CoV-2 pandemics.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Iker Atienza-Diez", - "author_inst": "Spanish National Center for Biotechnology" - }, - { - "author_name": "Luis F Seoane", - "author_inst": "Spanish National Center for Biotechnology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.30.22273194", "rel_title": "Safety and Efficacy of Dupilumab for the Treatment of Hospitalized Patients with Moderate to Severe COVID 19: A Phase IIa Trial", @@ -314778,6 +314155,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.04.487067", + "rel_title": "Surface detection of SARS-CoV-2 by lateral flow LAMP", + "rel_date": "2022-04-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.04.487067", + "rel_abs": "Slowing the transmission of SARS-CoV-2 requires rapid and accurate diagnostic testing. Toward this end, loop-mediated isothermal amplification (LAMP), an isothermal genomic detection method, offers great promise but the readout tends to be difficult because it does not generate linear DNA products. Rapid antigen tests are coupled to lateral flow strips, with one (negative) or two (positive) bands providing simple rapid readout, but are less sensitive than genomic amplification methods. To address the need for a genomic amplification method that can be visualized on a lateral flow strip, we developed a novel strand-displacement probe. In this work we validate this pipeline for purified RNA, intact virus, and even virus deposited onto a surface. We demonstrate robust sensitivity (100 genomic copies) and and we demonstrate the utility of our assay as a surveillance system, with the capability to detect viral particles from surfaces, even after a week of complete dry-down. Our innovation couples the diagnostic advantages of a nucleic acid amplification test (NAAT) with the simplicity of lateral-flow readouts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Isabelle Dahl Acker", + "author_inst": "American University" + }, + { + "author_name": "Mark Joseph Ware", + "author_inst": "American University" + }, + { + "author_name": "John R. Bracht", + "author_inst": "American University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.03.31.22273257", "rel_title": "Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: international observational federated study based on electronic health records through the 4CE consortium ARDS after SARS-CoV-2 infection on young adult", @@ -315969,45 +315373,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.30.22273174", - "rel_title": "Dupilumab use is associated with protection from COVID-19 mortality: A retrospective analysis.", - "rel_date": "2022-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273174", - "rel_abs": "We previously found that type 2 immunity promotes COVID-19 pathogenesis in a mouse model. To test relevance to human disease we used electronic health record databases and determined that patients on dupilumab (anti-IL-4R monoclonal antibody that blocks IL-13 and IL-4 signaling) at the time of COVID-19 infection had lower mortality.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandra N Donlan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Indika Mallawaarachchi", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jennifer Sasson", - "author_inst": "University of Virginia" - }, - { - "author_name": "Robert Preissner", - "author_inst": "University of Medicine Berlin - Charite" - }, - { - "author_name": "Johanna Loomba", - "author_inst": "University of Virginia" - }, - { - "author_name": "William Petri Jr.", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.30.22273203", "rel_title": "COVID-19 vaccination coverage by company size and the effects of socioeconomic factors and workplace vaccination in Japan: a cohort study", @@ -316764,6 +316129,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.31.22273236", + "rel_title": "The impact of COVID-19 pandemic on influenza surveillance: a systematic review and meta-analysis", + "rel_date": "2022-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273236", + "rel_abs": "BackgroundInfluenza activity was reported to be below the seasonal levels during the COVID-19 pandemic globally. However, during the SARS-CoV-2 outbreak, the routine real-time surveillance of influenza like illness (ILI) and acute respiratory infection (ARI) was adversely affected due to the changes in priorities, economic constraints, repurposing of hospitals for COVID care and closure of outpatient services.\n\nMethodsA systematic review and meta-analysis were carried out to assess the pooled proportion of symptomatic cases tested for influenza virus before the current pandemic in 2019 and during the pandemic in 2020/21. An electronic search of PubMed/MEDLINE, Scopus and Google Scholar was carried out for the articles reporting the impact of the COVID-19 pandemic on Influenza surveillance among humans using search terms. The study was designed based on PRISMA guidelines and the meta-analysis was performed to synthesise the pooled proportion of patients sampled for influenza with 95% confidence interval (CI).\n\nResultsThe nine qualified studies from the WHO-European region, Canada, Japan, Germany, Italy, Spain, South Africa and the United States were pooled by random-effects meta-analysis. The overall pooled proportion of symptomatic cases sampled for influenza surveillance before and during the pandemic was 2.38% (95% CI 2.08%-2.67%) and 4.18% (95% CI 3.8%-4.52%) respectively. However, the pooled proportion of samples tested for influenza before the pandemic was 0.69% (95% CI 0.45-0.92%) and during the pandemic was 0.48% (95% CI 0.28-0.68%) when studies from Canada were excluded.\n\nConclusionThe meta-analysis concludes that globally there was a decline in influenza surveillance during the COVID-19 pandemic except in Canada.\n\nKey MessagesO_LIThe nine observational studies from Europe, Canada, Japan, South Africa and the United States were qualified for the meta-analysis\nC_LIO_LIA steep decline in the seasonal influenza activity in both northern and southern hemispheres was observed\nC_LIO_LIAlmost double the number of symptomatic cases were sampled as part of influenza surveillance during the current pandemic in Canada\nC_LIO_LIExcept in Canada, a decline in influenza surveillance globally during the COVID-19 pandemic was observed\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sasidharanpillai Sabeena", + "author_inst": "Self, Independent Researcher, Allure Residency, Lalitpur, Bagmati Province, Kathmandu, Nepal" + }, + { + "author_name": "N Ravishankar", + "author_inst": "Department of Biostatistics Vallabhbhai Patel Chest Institute University of Delhi New Delhi, Delhi 110007, India" + }, + { + "author_name": "Sudandiradas Robin", + "author_inst": "Manipal Institute of Virology Manipal Academy of Higher Education Karnataka, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.31.22273272", "rel_title": "Interpretation of non-responders to SARS-CoV-2 vaccines using WHO International Standard", @@ -317767,81 +317159,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.31.486561", - "rel_title": "Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike", - "rel_date": "2022-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.31.486561", - "rel_abs": "The SARS-CoV-2 spike protein is the target of neutralizing antibodies and the immunogen used in all currently approved vaccines. The global spread of the virus has resulted in emergence of lineages which are of concern for the effectiveness of immunotherapies and vaccines based on the early Wuhan isolate. Here we describe two SARS-CoV-2 isolates with large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis showed that the deletions result in complete reshaping of the antigenic surface of the NTD supersite. The remodeling of the NTD affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite for both spike variants. A unique escape mechanism with high antigenic impact observed in the {Delta}N135 variant was based on the loss of the Cys15-Cys136 disulfide due to the P9L-mediated shift of the signal peptide cleavage site and deletion of residues 136-144. Although the observed large loop and disulfide deletions are rare, similar modifications became independently established in several other lineages, highlighting the possibility of a general escape mechanism via the NTD supersite. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Xiaodi Yu", - "author_inst": "Janssen Pharmaceuticals" - }, - { - "author_name": "Jarek Juraszek", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Lucy Rutten", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Mark J. G. Bakkers", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Sven Blokland", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Niels J.F. van den Broek", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Annemiek Y.W. Verwilligen", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Pravien Abeywickrema", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Johan Vingerhoets", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Jean-Marc Neefs", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Shah A Mohamed Bakhash", - "author_inst": "University of Washington" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington" - }, - { - "author_name": "Alex Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Sujata Sharma", - "author_inst": "Janssen pharmaceuticals" - }, - { - "author_name": "Johannes P. M. Langedijk", - "author_inst": "Janssen pharmaceuticals" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.04.01.486695", "rel_title": "Omicron breakthrough infection drives cross-variant neutralization and memory B cell formation", @@ -318674,6 +317991,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2022.03.28.22273010", + "rel_title": "A 21L/BA.2-21K/BA.1 MixOmicron SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis", + "rel_date": "2022-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.28.22273010", + "rel_abs": "Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3 tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1,362 reads and mean prevalence of the majoritary nucleotide was 99.3{+/-}2.2% and 98.8{+/-}1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes were depleted or not of the 3 tip. This 3 terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philippe Colson", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Jeremy Delerce", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Elise Marion-Paris", + "author_inst": "Marseille University Hospitals" + }, + { + "author_name": "Jean-Christophe Lagier", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Marielle Bedotto", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Anthony LEVASSEUR", + "author_inst": "Aix-Marseille University" + }, + { + "author_name": "Pierre-Edouard Fournier", + "author_inst": "IHU Mediterranee Infection" + }, + { + "author_name": "Bernard LA SCOLA", + "author_inst": "Aix Marseille University" + }, + { + "author_name": "Didier Raoult", + "author_inst": "Aix-Marseille Universite IHU Mediterranee Infection" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.25.22272599", "rel_title": "Safety and immunogenicity of a reduced dose of the BNT162b2 mRNA COVID-19 vaccine (REDU-VAC): a single blind, randomized, non-inferiority trial", @@ -319897,53 +319265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.25.22272954", - "rel_title": "Psychosocial factors affecting COVID-19 vaccine uptake in the UK: a prospective cohort study (CoVAccS - wave 3)", - "rel_date": "2022-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272954", - "rel_abs": "BackgroundWe investigated factors associated with COVID-19 vaccine uptake, future vaccination intentions, and changes in beliefs and attitudes over time.\n\nMethodsProspective cohort study. 1500 participants completed an online survey in January 2021 (T1, start of vaccine rollout in the UK), of whom 1148 (response rate 76{middle dot}5%) completed another survey in October 2021 (T2, all UK adults offered two vaccine doses). Binary logistic regression analysis was used to investigate factors associated with subsequent vaccine uptake. Content analysis was used to investigate the main reasons behind future vaccine intentions (T2). Changes in beliefs and attitudes were investigated using analysis of variance.\n\nFindingsAt T2, 90{middle dot}0% (95% CI 88{middle dot}2%-91{middle dot}7%) of participants had received two doses of a COVID-19 vaccine, 2{middle dot}2% (95% CI 1{middle dot}3%-3{middle dot}0%) had received one dose, and 7{middle dot}4% (95% CI 5{middle dot}9%-8{middle dot}9%) had not been vaccinated. Uptake was associated with higher intention to be vaccinated at T1, greater perceived vaccination social norms, necessity of vaccination, and perceived safety of the vaccine. People who had initiated vaccination reported being likely to complete it, while those who had not yet received a vaccine reported being unlikely to be vaccinated in the future. At T2, participants perceived greater susceptibility to, but lower severity of, COVID-19 (p<0.001), than T1. Perceived safety and adequacy of vaccine information were higher (p<0.001).\n\nInterpretationTargeting modifiable beliefs about the safety and effectiveness of vaccination may increase uptake.\n\nFundingData collection was funded by a Keele University Faculty of Natural Sciences Research Development award and a Kings COVID Appeal Fund award.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID-19 vaccination intention was high at the start of the vaccine rollout in the UK. Research suggests that psychosocial factors are associated with vaccine uptake. However, most research on uptake of the COVID-19 vaccine has investigated factors associated with vaccination intention, and used a cross-sectional design.\n\nAdded value of this studyWe used a prospective cohort study (T1 conducted in January 2021, the start of the UK vaccine rollout; T2 conducted in October 2021, all UK adults offered two vaccine doses) to investigate factors associated with subsequent COVID-19 vaccination. Qualitative data on the main supporting reasons for future vaccination intentions in those partially or not vaccinated were analysed using content analysis. Changes in vaccine beliefs and attitudes (generally and COVID-19 specific) were also analysed.\n\nImplications of all the available evidenceIn our sample, more people reported having been vaccinated than had previously reported intending to be vaccinated. Vaccine uptake was strongly associated with previous vaccination intention, perceived social norms of vaccination, and greater perceived necessity and safety of vaccination. Those who had received at least one COVID-19 vaccine reported being likely to complete the schedule, whereas those who had not received a vaccine reported being unlikely to receive a vaccine.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Louise E. Smith", - "author_inst": "King's College London" - }, - { - "author_name": "Julius Sim", - "author_inst": "Keele University" - }, - { - "author_name": "Megan Cutts", - "author_inst": "Keele University" - }, - { - "author_name": "Hannah Dasch", - "author_inst": "King's College London" - }, - { - "author_name": "Richard Amlot", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Nick Sevdalis", - "author_inst": "King's College London" - }, - { - "author_name": "G James Rubin", - "author_inst": "King's College London" - }, - { - "author_name": "Susan Mary Sherman", - "author_inst": "Keele University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.30.22273165", "rel_title": "Effect of COVID-19 vaccination on menstrual periods in a prospectively recruited cohort", @@ -321344,6 +320665,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.28.22273027", + "rel_title": "Unravelling the link between sleep and mental health during the COVID-19 pandemic", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.28.22273027", + "rel_abs": "BackgroundThe emergence of COVID-19 brought unparalleled changes in peoples lifestyle, including sleep. We aimed to assess the bidirectional association between sleep quality and mental health and describe how sleep and mental health were affected in Sweden during the COVID-19 pandemic (between June 2020 and September 2021).\n\nMethodsData were obtained from the Omtanke2020 study. Participants who completed the baseline survey and 8 monthly follow-up surveys were included (N=9035). We described the distribution of sleep and mental health in the different Swedish regions using maps and over the study period with longitudinal graphs adjusting for sex, age, recruitment type (self-recruitment or invitation), and COVID-19 status. The inner relationships between mental health, sleep and covid infection were described through relative importance networks. Finally, we modelled how mental health affects sleep and vice versa using generalized estimating equations with different adjustments.\n\nResultsSeasonal and north-south regional variations were found in sleep and mental health outcomes at baseline and attenuated over time. The seasonal variation of sleep and mental health correlated moderately with the incidence rate of COVID-19 in the sample. Networks indicate that the relationship between COVID-19 incidence and mental health varies over time. We observed a bidirectional relationship between sleep quality and quantity at baseline and mental health at follow-up and vice versa.\n\nConclusionSleep quality and quantity at baseline was associated with adverse symptom trajectories of mental health at follow-up, and vice versa, during the COVID-19 pandemic. There is also a weak relationship between COVID-19 incidence, sleep, and mental health.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juan Gonzalez-Hijon", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna K K\u00e4hler", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Emma M Frans", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Unnur Anna Valdimarsd\u00f3ttir", + "author_inst": "University of Iceland" + }, + { + "author_name": "Patrick F Sullivan", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Fang Fang", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anik\u00f3 Lovik", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.29.22273151", "rel_title": "Substance use and associated factors among Adolescents during the Covid-19 pandemic in Eastern Ethiopia: A cross-sectional study", @@ -322651,57 +322015,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.27.485958", - "rel_title": "Genetically engineered MRI-trackable extracellular vesicles as SARS-CoV-2 mimetics for mapping ACE2 binding in vivo", - "rel_date": "2022-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.27.485958", - "rel_abs": "The elucidation of viral-receptor interactions and an understanding of virus-spreading mechanisms are of great importance, particularly in the era of pandemic. Indeed, advances in computational chemistry, synthetic biology, and protein engineering have allowed precise prediction and characterization of such interactions. Nevertheless, the hazards of the infectiousness of viruses, their rapid mutagenesis, and the need to study viral-receptor interactions in a complex in vivo setup, call for further developments. Here, we show the development of biocompatible genetically engineered extracellular vesicles (EVs) that display the receptor binding domain (RBD) of SARS-CoV-2 on their surface as coronavirus mimetics (EVsRBD). Loading EVsRBD with iron oxide nanoparticles makes them MRI-visible, and thus, allows mapping of the binding of RBD to ACE2 receptors non-invasively in live subjects. Importantly, the proposed mimetics can be easily modified to display the RBD of SARS-CoV-2mutants, namely Delta and Omicron, allowing rapid screening of newly raised variants of the virus. The proposed platform thus shows relevance and cruciality in the examination of quickly evolving pathogenic viruses in an adjustable, fast, and safe manner.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Andrea Galisova", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Jiri Zahradnik", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Hyla Allouche-Arnon", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Mattia I Morandi", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Paula Abou Karam", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Ori Avinoam", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Neta Regev-Rudzki", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Gideon Schreiber", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Amnon Bar-Shir", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.03.26.485903", "rel_title": "The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.", @@ -323754,6 +323067,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.26.22272984", + "rel_title": "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 variant transition in the Swedish population reveals higher viral quantity in BA.2 cases", + "rel_date": "2022-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.26.22272984", + "rel_abs": "Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious lineages dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sub-variant dominance in the Swedish population during January-March 2022. By analysis of 174,933 clinical nasopharyngeal swab samples using a custom variant-typing RT-PCR assay, we uncover nearly two-fold higher levels of viral RNA in cases with Omicron BA.2. Importantly, increased viral load in the upper pharynx upon BA.2 infection may provide part of the explanation why Omicron BA.2 is more transmissible and currently outcompetes the BA.1 variant across populations.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Antonio Lentini", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Antonio Pereira", + "author_inst": "ABC Labs" + }, + { + "author_name": "Ola Winqvist", + "author_inst": "ABC LAbs" + }, + { + "author_name": "Bj\u00f6rn Reinius", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.23.22272167", "rel_title": "Epidemiologic Assessment of Pediatric Inflammatory Bowel Disease Presentation in NYC During COVID-19", @@ -324885,37 +324229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.24.22272901", - "rel_title": "Impact of Vaccination, Prior Infection, and Therapy on Delta and Omicron Variants", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272901", - "rel_abs": "We studied 249,070 patients who were tested for SARS-CoV-2 in the Cleveland Clinic Health System between October 1, 2021 and January 31, 2022. We found that vaccination, especially with recent boosting, was more effective than prior infection and monoclonal antibody therapy against both the delta and omicron variants. Vaccination and prior infection were much less effective against infection with the omicron variant than with the delta variant, but the opposite was true of death after infection. Boosting greatly increased the effectiveness of the two mRNA vaccines against both infection and death, although its effects waned markedly after 6 months. In addition, monoclonal antibody therapy was notably less effective at preventing death from the omicron variant than from the delta variant. Finally, the relatively low mortality of the omicron variant was due to both the reduced lethality of this variant and the increased population immunity acquired from booster vaccination and previous infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xiaofeng Wang", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Joe Zein", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Xinge Ji", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Danyu Lin", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.25.22272946", "rel_title": "Understanding the role of mask-wearing during COVID-19 on the island of Ireland", @@ -325388,6 +324701,37 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.03.24.485649", + "rel_title": "B cell receptor repertoire analysis unveils dynamic antibody response and severity markers in COVID-19 patients", + "rel_date": "2022-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.24.485649", + "rel_abs": "Humoral and cell mediated immunity are critical against viral infections. The knowledge of composition, diversity, gene usage of the B cell repertoires helps in determining the immune response to SARS-CoV-2 infection. Examining B cell response provides insights on therapeutic antibodies, disease severity markers and aids in predicting vaccine response. We have analyzed public domain immunoglobulin sequencing data from PBMCs of SARS-CoV-2 infected individuals to gain a better understanding of B cell repertoire in patients. Public clonotypes showed increased usage of IGHV3, IGHV4, IGKV1, IGKV3, IGLV3 and IGLV2 family genes during the acute phase infection. Identical CDR3 sequences were identified for heavy (H), kappa (K) and lambda (L) chains across individuals, indicating the convergence of B cell selection during SARS-CoV-2 infection. While the immune repertoire dynamically changed over the course of convalescence, there were persistent clones across early and late timepoints. The diversity of antibody repertoire, measured by Shannon-Weiner diversity index for H and K chains, reduced during the acute phase of infection. In addition, the repertoire diversity was low in severe patients compared to patients with mild or moderate symptoms. Increased usage of IGHV4-59 gene was observed in COVID-19 patients with severe symptoms requiring ventilator support at 2 weeks and 3 weeks post symptom onset. IGHV4-59 is reported to have rheumatoid factor (RF) activity with high affinity for IgG and the elevated level of IGHV4-59 provides a potential mechanism for the increased autoimmune responses in severe patients. Correlation of the clinical features with the B cell receptor repertoire dynamics elucidated public antibody clonotypes and disease severity markers for COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Soumya Rao", + "author_inst": "Syngene International Limited" + }, + { + "author_name": "Kriti Srivastava", + "author_inst": "Syngene International Limited" + }, + { + "author_name": "Anupriya Verma", + "author_inst": "Syngene International Limited" + }, + { + "author_name": "Achintya Das", + "author_inst": "Syngene International Limited" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.21.485247", "rel_title": "Trivalent NDV-HXP-S vaccine protects against phylogenetically distant SARS-CoV-2 variants of concern in mice", @@ -326367,77 +325711,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.20.22272651", - "rel_title": "Dynamics of anti-SARS-CoV-2 seroconversion in individual patients and at the population level", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.20.22272651", - "rel_abs": "The immune response and specific antibody production in COVID-19 are among the key factors that determine both prognostics for individual patients and the global perspective for controlling the pandemics. So called \"dark figure\", that is, a part of population that has been infected but not registered by the health care system, make it difficult to estimate herd immunity and to predict pandemic trajectories.\n\nHere we present a follow up study of population screening for hidden herd immunity to SARS-CoV-2 in individuals who had never been positively diagnosed against SARS-CoV-2; the first screening was in May 2021, and the follow up in December 2021. We found that specific antibodies targeting SARS-CoV-2 detected in May as the \"dark figure\" cannot be considered important 7 months later due to their significant drop. On the other hand, among participants who at the first screening were negative for anti-SARS-CoV-2 IgG, and who have never been diagnosed for SARS-CoV-2 infection nor vaccinated, 26% were found positive for anti-SARS-CoV-2 IgG. This can be attributed to of the \"dark figure\" of the recent, fourth wave of the pandemic that occurred in Poland shortly before the study in December. Participants who were vaccinated between May and December demonstrated however higher levels of antibodies, than those who undergone mild or asymptomatic (thus unregistered) infection. Only 7% of these vaccinated participants demonstrated antibodies that resulted from infection (anti-NCP). The highest levels of protection were observed in the group that had been infected with SARS-CoV-2 before May 2021 and also fully vaccinated between May and December.\n\nThese observations demonstrate that the hidden fraction of herd immunity is considerable, however its potential to suppress the pandemics is limited, highlighting the key role of vaccinations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Alina Szewczyk-Dabrowska", - "author_inst": "Wroclaw Medical University, Department of Family Medicine, 1 Syrokomli St., 51-141 Wroclaw, Poland;; Regional Specialist Hospital in Wroclaw, Research and D" - }, - { - "author_name": "Wiktoria Budziar", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development, Kamienskiego 73a Wroclaw, Poland" - }, - { - "author_name": "Krzysztof Baniecki", - "author_inst": "Healthcare Centre in Boleslawiec, Jeleniogorska 4, Boleslawiec, Poland" - }, - { - "author_name": "Aleksandra Pikies", - "author_inst": "Healthcare Centre in Boleslawiec, Jeleniogorska 4, Boleslawiec, Poland" - }, - { - "author_name": "Marek Harhala", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamieskiego 73a, Wroclaw, Poland; Hirszfeld Institute of Immunology and Experimental " - }, - { - "author_name": "Natalia Jedruchniewicz", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland" - }, - { - "author_name": "Zuzanna Kazmierczak", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland; Hirszfeld Institute of Immunology and Experimenta" - }, - { - "author_name": "Katarzyna Gembara", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland; Hirszfeld Institute of Immunology and Experimenta" - }, - { - "author_name": "Tomasz Klimek", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland" - }, - { - "author_name": "Wojciech Witkiewicz", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland" - }, - { - "author_name": "Artur Nahorecki", - "author_inst": "Healthcare Centre in Boleslawiec, Jeleniogorska 4, Boleslawiec, Poland" - }, - { - "author_name": "Kamil Barczyk", - "author_inst": "Healthcare Centre in Boleslawiec, Jeleniogorska 4, Boleslawiec, Poland" - }, - { - "author_name": "Urszula Grata-Borkowska", - "author_inst": "Department of Family Medicine, Wroclaw Medical University, 1 Syrokomli St., 51-141 Wroclaw, Poland" - }, - { - "author_name": "Krystyna Dabrowska", - "author_inst": "Regional Specialist Hospital in Wroclaw, Research and Development Center, Kamienskiego 73a, Wroclaw, Poland; Hirszfeld Institute of Immunology and Experimental" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.21.22272480", "rel_title": "Altered microRNA expression in severe COVID-19: potential prognostic and pathophysiological role", @@ -327146,6 +326419,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.22.485413", + "rel_title": "A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues", + "rel_date": "2022-03-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.22.485413", + "rel_abs": "The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable prediction of RBD-hACE2 binding affinity changes upon amino acid substitutions can be valuable for public health surveillance and monitoring potential spillover and adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on protein sequence and structural features to predict experimental RBD-hACE2 binding affinities of 8,440 variants upon single and multiple amino acid substitutions in the RBD or ACE2. The model achieves a classification accuracy of 83.28% and a Pearson correlation coefficient of 0.85 between predicted and experimentally calculated binding affinities in five-fold cross-validation tests and predicts improved binding affinity for most circulating variants. We pro-actively used the CNN model to exhaustively screen for novel RBD variants with combinations of up to four single amino acid substitutions and suggested candidates with the highest improvements in RBD-ACE2 binding affinity for human and animal ACE2 receptors. We found that the binding affinity of RBD variants against animal ACE2s follows similar trends as those against human ACE2. White-tailed deer ACE2 binds to RBD almost as tightly as human ACE2 while cattle, pig, and chicken ACE2s bind weakly. The model allows testing whether adaptation of the virus for increased binding with other animals would cause concomitant increases in binding with hACE2 or decreased fitness due to adaptation to other hosts.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Chen Chen", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Veda Sheeresh Boorla", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Ratul Chowdhury", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Ruth H Nissly", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Abhinay Gontu", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Shubhada K Chothe", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Lindsey LaBella", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Padmaja Jakka", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Santhamani Ramasamy", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Kurt J Vandegrift", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Meera Surendran Nair", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Suresh V Kuchipudi", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Costas D Maranas", + "author_inst": "Pennsylvania State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.22.22272793", "rel_title": "People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses", @@ -328409,57 +327749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.22.22272769", - "rel_title": "Vaccine effectiveness of two and three doses of BNT162b2 and CoronaVac against COVID-19 in Hong Kong", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272769", - "rel_abs": "BackgroundHong Kong maintained extremely low circulation of SARS-CoV-2 until a major community epidemic of Omicron BA.2 starting in January 2022. Both mRNA BNT162b2 (BioNTech/Fosun Pharma) and inactivated CoronaVac (Sinovac) vaccines are widely available, however coverage has remained low in older adults. Vaccine effectiveness in this predominantly infection-naive population is unknown.\n\nMethodsWe used individual-level case data on mild/moderate, severe/fatal and fatal hospitalized COVID-19 from December 31, 2021 to March 8, 2022, along with census information and coverage data of BNT162b2 and CoronaVac. We used a negative binomial model, adjusting for age and calendar day to estimate vaccine effectiveness of one, two and three dose schedules of both vaccines, and relative effectiveness by number of doses and vaccine type.\n\nFindingsA total of 12.7 million vaccine doses were administered in Hong Kongs 7.3 million population, and we analyzed data from confirmed cases with mild/moderate (N=5,474), severe/fatal (N=5,294) and fatal (N=4,093) COVID-19. Two doses of either vaccine protected against severe disease and death, with higher effectiveness among adults [≥]60 years with BNT162b2 (VE: 88.2%, 95% confidence interval, CI: 84.4%, 91.1%) compared to CoronaVac (VE: 74.1%, 95% CI: 67.8%, 79.2%). Three doses of either vaccine offered very high levels of protection against severe outcomes (VE: 98.1%, 95% CI: 97.1%, 98.8%).\n\nInterpretationThird doses of either BNT162b2 or CoronaVac provide substantial additional protection against severe COVID-19 and should be prioritized, particularly in older adults who received CoronaVac primary schedules. Longer follow-up is needed to assess persistence of different vaccine platforms and schedules.\n\nFundingCOVID-19 Vaccines Evaluation Program, Chinese Center for Disease Control and Prevention", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Martina E. McMenamin", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joshua Nealon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yun Lin", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jessica Y. Wong", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Justin K. Cheung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Eric H. Y. Lau", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Peng Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gabriel M. Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Benjamin J. Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.22.22272745", "rel_title": "Effect of prior infection, vaccination, and hybrid immunity against symptomatic BA.1 and BA.2 Omicron infections and severe COVID-19 in Qatar", @@ -329288,6 +328577,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.19.22272419", + "rel_title": "Post- intravitreal injection endophthalmitis pattern during the COVID-19 pandemic with implementation of patient masking", + "rel_date": "2022-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.19.22272419", + "rel_abs": "PurposeTo evaluate the role of patient facial mask on the occurrence of post- intravitreal injection (IVI) endophthalmitis in a real word setting.\n\nDesignRetrospective cohort.\n\nParticipantsPatients receiving IVIs between 20 February 2019 and 20 February 2021; a 12-month period before the official beginning of COVID-19 epidemic in Iran and a 12-month period after that.\n\nInterventionIn the pre-COVID era patients underwent IVI without a facial mask while in the COVID era patients were treated with an untapped facial mask. Physicians and staff had facial mask in both periods. IVIs were administered in a dedicated operating room and no strict talk policy was followed.\n\nMain outcome measureThe rate of post-IVI endophthalmitis.\n\nResultsA total number of 53927 injections was performed during the study period: 34277 in pre-COVID and 19650 in COVID periods; with a 42.7 % decrease in the number of injections. The endophthalmitis occurred in 7 eyes (0.02%) in pre-COVID and 7 eyes (0.03%) in COVID era (p=0.40). In multivariate analysis, after adjustment for intercorrelations between eyes and multiple injections in one patient, there was no statistically significant association between wearing facial masks by the patients and risk of endophthalmitis (relative risk= 1.47, 95% confidence interval of 0.97-2.22; p=0.071).\n\nConclusionPatients facial masking is probably not associated with increased risk of post-injection endophthalmitis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Masoud Mirghorbani", + "author_inst": "Retina Service, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Fatemeh Bazvand", + "author_inst": "Retina Service, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Hamid Riazi Esfahani", + "author_inst": "Retina Service, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammadreza Mehrabi Bahar", + "author_inst": "Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mehdi Yaseri", + "author_inst": "Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Zarei", + "author_inst": "Retina Service, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "ophthalmology" + }, { "rel_doi": "10.1101/2022.03.20.22272677", "rel_title": "Acceptance of COVID-19 vaccine among healthcare workers in Katsina state, Northwest Nigeria", @@ -330459,41 +329787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.20.22272676", - "rel_title": "The outcome of Gynecologic Cancer Patients With The Covid-19 Infection: A Systematic Review And Meta-Analysis", - "rel_date": "2022-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.20.22272676", - "rel_abs": "ObjectiveCancer is a comorbidity that leads to progressive worsening of Covid-19 with increased mortality. This is a systematic review and meta-analysis to yield evidence of adverse outcomes of Covid-19 in gynecologic cancer.\n\nMethodsSearches through PubMed, Google Scholar, ScienceDirect, and medRxiv to find articles on the outcome of gynecologic cancer with Covid-19 (24 July 2021-19 February 2022). Newcastle-Ottawa Scale tool is used to evaluate the quality of included studies. Pooled odds ratio (OR), 95% confidence interval (CI), random-effects model were presented. This study was registered to PROSPERO (CRD42021256557).\n\nResultsWe accepted 51 studies (1991 gynecologic cancer with Covid-19). Covid-19 infection was lower in gynecologic cancer vs hematologic cancer (OR 0.71, CI 0.56-0.90, p 0.005). Severe Covid and death were lower in gynecologic cancer vs lung and hematologic cancer (OR 0.36, CI 0.16-0.80, p 0.01), (OR 0.52, CI 0.44-0.62, p <0.0001), (OR 0.26, CI 0.10-0.67 p 0.005), (OR 0.63, CI 0.47-0.83, p 0.001) respectively. Increased Covid death is seen in gynecologic cancer vs breast, non-covid cancer, and non-cancer covid (OR 1.50, CI 1.20-1.88, p 0.0004), (OR 11.83, CI 8.20-17.07, p <0.0001), (OR 2.98, CI 2.23-3.98, p <0.0001) respectively.\n\nConclusionGynecologic cancer has higher Covid-19 adverse outcomes compared to non-cancer, breast cancer, non-metastatic, and Covid-19 negative population. Gynecologic cancer has fewer Covid-19 adverse outcomes compared to other cancer types, lung cancer, and hematologic cancer. These findings may aid health policies and services during the ongoing global pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "I Gde Sastra Winata", - "author_inst": "Faculty of Medicine, Department of Obstetric and Gynecology, Udayana University, Denpasar, Bali, Indonesia." - }, - { - "author_name": "Januar Simatupang", - "author_inst": "Faculty of Medicine, Department of Obstetric and Gynecology, Christian University of Indonesia, Jakarta , Indonesia." - }, - { - "author_name": "Arie A Polim", - "author_inst": "Department of Obstetrics and Gynecology, School of Medicine and Health Sciences, Atmajaya Catholic University of Indonesia, Jakarta, Indonesia" - }, - { - "author_name": "Yakob Togar", - "author_inst": "Faculty of Medicine, Department of Obstetric and Gynecology, Christian University of Indonesia, Jakarta , Indonesia." - }, - { - "author_name": "Advenny Elisabeth Tondang", - "author_inst": "Faculty of Medicine, Department of Obstetric and Gynecology, Christian University of Indonesia, Jakarta , Indonesia." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2022.03.20.22272664", "rel_title": "An umbrella review and meta-analysis of the use of renin-angiotensin system drugs and COVID-19 outcomes: what do we know so far?", @@ -331278,6 +330571,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.20.485024", + "rel_title": "A Novel High-Throughput Single B-Cell Cloning Platform for Isolation and Characterization of High-Affinity and potent SARS-CoV-2 Neutralizing Antibodies", + "rel_date": "2022-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.20.485024", + "rel_abs": "Monoclonal antibodies (mAbs) that are specific to SARS-CoV-2 can be useful in diagnosing, preventing, and treating the coronavirus (COVID-19) illness. Strategies for the high-throughput and rapid isolation of these potent neutralizing antibodies are critical toward the development of therapeutically targeting COVID-19 as well as other infectious diseases. In the present study, a single B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing mAbs from patients blood samples. An RBD-specific antibody, SAR03, was discovered that showed high binding (ELISA and SPR) and neutralizing activity (competitive ELISA and pseudovirus-based reporter assay) against Sars-CoV-2. Mechanistic studies on human cells revealed that SAR03 competes with the ACE-2 receptor for binding with the RBD domain (S1 subunit) present in the spike protein of Sars-CoV-2. This study highlights the potential of the single B cell cloning method for the rapid and efficient screening of high-affinity and effective neutralizing antibodies for Sars-CoV-2 and other emerging infectious diseases.\n\nHighlightsO_LISingle B-cell cloning is a high-throughput and efficient method of generating high affinity neutralizing antibodies\nC_LIO_LISingle B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing monoclonal antibodies from patients blood samples.\nC_LIO_LIAn RBD-specific antibody, SAR03, was discovered that showed high binding and neutralizing activity against SARS-CoV-2.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Paritosh Parashar", + "author_inst": "Sarsuag Discovery Private Limited, Bengaluru, Karnataka 560100, India" + }, + { + "author_name": "Prabhakar B", + "author_inst": "Sarsuag Discovery Private Limited, Bengaluru, Karnataka 560100, India" + }, + { + "author_name": "Sonali Swain", + "author_inst": "Sarsuag Discovery Private Limited, Bengaluru, Karnataka 560100, India" + }, + { + "author_name": "Nisha Adhikari", + "author_inst": "Sarsuag Discovery Private Limited, Bengaluru, Karnataka 560100, India" + }, + { + "author_name": "Punit Aryan", + "author_inst": "Sarsuag Discovery Private Limited, Bengaluru, Karnataka 560100, India" + }, + { + "author_name": "Anupama Singh", + "author_inst": "Department of Biological Sciences and Bioengineering, IIT Kanpur, Kanpur, Uttar Pradesh 208016, India" + }, + { + "author_name": "Mohit Kwatra", + "author_inst": "Department of Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.18.484950", "rel_title": "Durable protection against SARS-CoV-2 Omicron induced by an adjuvanted subunit vaccine", @@ -332505,77 +331841,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.17.22272516", - "rel_title": "SARS-CoV-2 virus dynamics in recently infected people - data from a household transmission study", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272516", - "rel_abs": "We used daily real-time reverse-transcription polymerase chain reaction (rRT-PCR) results from 67 cases of SARS-CoV-2 infection in a household transmission study to examine the trajectory of cycle threshold (Ct) values, an inverse correlate of viral RNA concentration, from nasal specimens collected between April 2020 and May 2021. Ct values varied over the course of infection, across RT-PCR platforms, and by participant age. Specimens collected from children and adolescents showed higher Ct values and adults aged [≥]50 years showed lower Ct values than adults aged 18-49 years. Ct values were lower on days when participants reported experiencing symptoms.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Alexandra M. Mellis", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer K. Meece", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Natasha B. Halasa", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "James D. Chappell", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Huong Q McLean", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Carlos G Q Grijalva", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Kayla E Hanson", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Yuwei Zhu", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Ahra Kim", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jessica Deyoe", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Lynn C. Ivacic", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Carrie Reed", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Melissa A. Rolfes", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.16.22272508", "rel_title": "COVID-19 Disease Model with Reservoir of Infection : Cleaning Surfaces and Wearing Masks Strategies", @@ -333304,6 +332569,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.16.22272493", + "rel_title": "Outdoor long-range transmission of COVID-19 and patient zero", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272493", + "rel_abs": "Following the outdoor model of risk assessment developed in one of our previous studies, we demonstrate in the present work that long-range transport of infectious aerosols could initiate patient \"zero\" creation at distances downwind beyond one hundred kilometers. The very low probability of this outdoor transmission can be compensated by high numbers and densities of infected and susceptible people such as it occurs in large cities, respectively in the source and the target.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bertrand R. Rowe", + "author_inst": "Rowe Consulting" + }, + { + "author_name": "J. Brian A. Mitchell", + "author_inst": "MERL Consulting SAS" + }, + { + "author_name": "Andre Canosa", + "author_inst": "CNRS - Universite de Rennes 1" + }, + { + "author_name": "Roland Draxler", + "author_inst": "Meteozone Consulting" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.16.22272513", "rel_title": "Humoral and cellular immune responses to CoronaVac assessed up to one year after vaccination", @@ -334339,65 +333635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.16.22272465", - "rel_title": "No evidence for environmental transmission risk of SARS-CoV-2 in the UK's largest urban river system: London as a case study", - "rel_date": "2022-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272465", - "rel_abs": "The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated freshwaters is still poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. We investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over 8 months for SARS-CoV-2 RNA and infectious virus. Bivalves were sampled as sentinel species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. We found no evidence of SARS-CoV-2 RNA or infectious virus in UK samples, in contrast to RNA positive water and sediment samples from Serbia. Furthermore, we show that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for < 3 days, while RNA remained detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that infectivity should be embedded in future risk assessments of pathogen spillover.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Emma Ransome", - "author_inst": "Imperial College London" - }, - { - "author_name": "Faye Hobbs", - "author_inst": "Imperial College London" - }, - { - "author_name": "Scott Jones", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christopher Coleman", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Danielle Harris", - "author_inst": "Imperial College London" - }, - { - "author_name": "Guy Woodward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas Bell", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jahcub Trew", - "author_inst": "Imperial College London" - }, - { - "author_name": "Stoimir Kolarevi\u0107", - "author_inst": "University of Belgrade" - }, - { - "author_name": "Margareta Kra\u010dun-Kolarevi\u0107", - "author_inst": "University of Belgrade" - }, - { - "author_name": "Vincent Savolainen", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.15.22272438", "rel_title": "COVID-19 Vaccine Hesitancy among Marginalized Populations in the U.S. and Canada: Protocol for a Scoping Review", @@ -335102,6 +334339,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.14.22272130", + "rel_title": "Mid-term subclinical myocardial injury detection in patients recovered from COVID-19 according pulmonary lesion severity.", + "rel_date": "2022-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272130", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV 2) may cause damage of the cardiovascular system during the acute phase of infection. However, Recent studies described a mid and long-term subtle cardiac injuries after recovery from acute Coronavirus disease 19 (COVID-19).The aim of this study was to determine the relationship between the severity of chest computed tomography (CT) lesions and the persistence of subtle myocardial injuries at mid-term follow-up of patients recovered from COVID-19 infection.\n\nMethodsAll COVID-19 patients were enrolled prospectively in this study. Sensitive troponin T (hsTnT) and chest CT scan was performed in all patients at the acute phase of Covid-19 infection. At the mid-term follow up, conventional transthoracic echocardiograph and global longitudinal strain (GLS) of left and right ventricles (LV and RV) were determined and compared between patients with chest CT scan lesions less than 50% (Group 1) and those with severe chest CT scan greater or equal to 50% (Group 2).\n\nResultsThe mean age was 55 more or less than 14 years. Both LV GLS and RV GLS were significantly decreased in the group 2 (p=0.013 and p=0.011, respectively). LV GLS value more than -18% was noted in 43% of all the patients and RV GLS value more than -20% was observed in 48% of them. The group with severe chest CT scan lesions included more patients with reduced LV GLS and reduced RV GLS than the group with mild chest CT scan lesions (G1:29% vs. G2:57%, p=0.002) and (G1:36% vs. G2:60 %, p=0.009) respectively).\n\nConclusionPatients with severe chest CT scan lesions are more likely to develop subclinical myocardial damage. TTE could be recommended in patients recovering from COVID-19 to detect subtle LV and RV lesions.\n\nTrial registrationThe cohort of patients is a part of the research protocol (IORG 00093738 N{degrees}102/OMB 0990-0279) approved by the Hospital Ethics Committee.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "IKRAM CHAMTOURI", + "author_inst": "Cardiology B department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Rania Kaddoussi", + "author_inst": "Pneumology department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Hela Abroug", + "author_inst": "preventive medecine departement, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Mabrouk Abdelali", + "author_inst": "Fattouma Bourguiba University Hospital Department of Medical Imaging: Hopital Universitaire Fattouma Bourguiba Service d'Imagerie Medicale" + }, + { + "author_name": "Nesrine Fahem", + "author_inst": "Pneumology department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Taha Lassoued", + "author_inst": "Cardiology B department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Mariem Hafsa", + "author_inst": "HOPITAL KSAR HELAL et Hopital Moknine" + }, + { + "author_name": "Asma Ben Abdallah", + "author_inst": "Cardiology B department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Asma Achour", + "author_inst": "Fattouma Bourguiba University Hospital Department of Medical Imaging: Hopital Universitaire Fattouma Bourguiba Service d'Imagerie Medicale" + }, + { + "author_name": "Saoussen Chikh'Hmed", + "author_inst": "Pneumolgy department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Asma Migaou", + "author_inst": "pneumology department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "Walid Jomaa", + "author_inst": "cardiology B department Fattouma Bourguiba University Hospital" + }, + { + "author_name": "Asma Sriha", + "author_inst": "preventive medecine department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "khaldoun ben hamda", + "author_inst": "cardiology B department, Hopital Universitaire Fattouma Bourguiba a Monastir" + }, + { + "author_name": "faouzi maatouk", + "author_inst": "cardiology B department,Hopital Universitaire Fattouma Bourguiba a Monastir" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.03.15.484274", "rel_title": "Vascular dysregulation following SARS-CoV-2 infection involves integrin signaling through a VE-Cadherin mediated pathway", @@ -336121,41 +335433,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.15.22272192", - "rel_title": "Laboratory changes associated with medication non-adherence in patients with hypertension over six months of the COVID-19 pandemic", - "rel_date": "2022-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272192", - "rel_abs": "The coexistence of multiple diseases is common in the elderly and often accompanied by medication non-adherence. This study investigated the relationship between medication non- adherence and laboratory findings inpatients with hypertension and hypertensive comorbidities (i.e., diabetes and nephropathy) in southern Taiwan during 6 months of the coronavirus disease pandemic. This was a panel study and involved outpatients from three hospitals classified as regional hospitals or above. Questionnaireswere usedto collect information on patient demographics, diet, medication adherence, and laboratory data at the time of recruitment and 6 months after. A total of 140 patients with only hypertension and 98 patients with hypertension and comorbidities were recruited, and the changes inblood pressure andlaboratory data were assessed after 6 months. Analyses performed with generalized estimating equations showed that patients who had not forgotten to take medication had a higher estimated glomerular filtration rate. Moreover, patients who did not change their medication time arbitrarily had lower low- density lipoprotein levels. Furthermore, patients who did not stop or interrupt their medication arbitrarily had lower diastolic blood pressuresand low-density lipoprotein levels. Overall, patients with better medication adherence had better estimated glomerular filtration rates,lower low-density lipoprotein levels, and lower diastolic blood pressures.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shu-Mei Chang", - "author_inst": "Eda Hospital: E-Da Hospital" - }, - { - "author_name": "Yi-Chun Chen", - "author_inst": "ISU: I-Shou University" - }, - { - "author_name": "Chin-Feng Hsuan", - "author_inst": "Eda Hospital: E-Da Hospital" - }, - { - "author_name": "I-Cheng Lu", - "author_inst": "Eda Hospital: E-Da Hospital" - }, - { - "author_name": "Hung-Yi Chuang", - "author_inst": "Kaohsiung Medical University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.10.22271304", "rel_title": "ACE2 gene expression and inflammatory conditions in periodontal microenvironment of COVID-19 patients with and without diabetes evaluated by qPCR", @@ -336912,6 +336189,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.13.484191", + "rel_title": "Molecular docking between human TMPRSS2 and the serine protease Kunitz-type inhibitor rBmTI-A", + "rel_date": "2022-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.13.484191", + "rel_abs": "SARS-CoV-2 entrance into host cells is dependent of ACE2 receptor and viral protein S initiation by serine protease TMPRSS2. Cleavage of coronavirus protein S at the junctions Arg685/Ser686 and Arg815/Ser816 leads to the production of the S1/S2 and S2 fragments needed for the fusion of viral and cell membranes. Studying and identifying serine protease inhibitors is an important step towards the development of candidate drugs to prevent SARS-CoV-2 infection. It has already been stablished that camostat mesylate, a serine protease inhibitor, is capable of blocking TMPRSS2 activity and prevent SARS-CoV-2 entrance into host cells. In this work, the interaction between the two domains of Kunitz-type serine protease inhibitor rBmTI-A and TMPRSS2 was studied through molecular docking. rBmTI-A domain 2 (P1 site Leu84) had the best complex results with predicted binding affinity of -12 Kcal.mol-1 and predicted dissociation constant at 25{degrees}C of 1.6 nM. The results suggest that rBmTI-A is capable of binding TMPRSS2 cleavage site at the junction Arg815/Ser816 using essentially the same residues that camostat mesylate.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "L\u00edvia de Moraes Bomediano-Camillo", + "author_inst": "Centro de Ci\u00eancias Naturais e Humanas, Universidade Federal do ABC, S\u00e3o Bernardo do Campo, S\u00e3o Paulo, Brazil." + }, + { + "author_name": "Sergio Daishi Sasaki", + "author_inst": "Centro de Ci\u00eancias Naturais e Humanas, Universidade Federal do ABC, S\u00e3o Bernardo do Campo, S\u00e3o Paulo, Brazil." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.03.14.22272134", "rel_title": "Acidity of expiratory aerosols controls the infectivity of airborne influenza virus and SARS-CoV-2", @@ -337855,109 +337155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.11.22272269", - "rel_title": "Association of frailty, age, and biological sex with SARS-CoV-2 mRNA vaccine-induced immunity in older adults", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272269", - "rel_abs": "BackgroundMale sex and old age are risk factors for severe COVID-19, but the intersection of sex and aging on antibody responses to SARS-CoV-2 vaccines has not been characterized.\n\nMethodsPlasma samples were collected from older adults (75-98 years) before and after three doses of SARS-CoV-2 mRNA vaccination, and from younger adults (18-74 years) post-dose two, for comparison. Antibody binding to SARS-CoV-2 antigens (spike protein [S], S-receptor binding domain [S-RBD], and nucleocapsid [N]) and functional activity against S were measured against the vaccine virus and variants of concern (VOC).\n\nResultsVaccination induced greater antibody titers in older females than males, with both age and frailty associated with reduced antibody responses to vaccine antigens in males, but not females. ACE2 binding inhibition declined more than anti-S or anti-S-RBD IgG in the six months following the second dose (28-fold vs. 12- and 11-fold decreases in titer). The third dose restored functional antibody responses and eliminated disparities caused by sex, age, and frailty in older adults. Responses to the VOC were significantly reduced relative to the vaccine virus, with older males having lower titers to the VOC than females. Older adults had lower responses to the vaccine and VOC viruses than younger adults, with disparities being greater in males than females.\n\nConclusionOlder and frail males may be more vulnerable to breakthrough infections due to low antibody responses before receipt of a third vaccine dose. Promoting third dose coverage in older adults, especially males, is crucial to protecting this vulnerable population.\n\nBrief summarySARS-CoV-2 mRNA vaccination induces greater antibody response in older females than males, and age and frailty reduce responses in males only. These effects are eliminated by a third vaccine dose, highlighting the need for third dose coverage, especially in older males.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Janna R. Shapiro", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Han-Sol Park", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Tihitina Y. Aytenfisu", - "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Christopher Caputo", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "John S. Lee", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Trevor S. Johnston", - "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Huifen Li", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Pricila Hauk", - "author_inst": "Department of Chemical and Biomolecular Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA" - }, - { - "author_name": "Henning Jacobsen", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Yukang Li", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Engle Abrams", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Andrew J. Kocot", - "author_inst": "Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, US" - }, - { - "author_name": "Tianrui Yang", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Yushu Huang", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Steven M. Cramer", - "author_inst": "Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, US" - }, - { - "author_name": "Michael J. Betenbaugh", - "author_inst": "Department of Chemical and Biomolecular Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA" - }, - { - "author_name": "Amanda K. Debes", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Rosemary Morgan", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - }, - { - "author_name": "Aaron M. Milstone", - "author_inst": "Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Andrew H. Karaba", - "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Sean X. Leng", - "author_inst": "Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA." - }, - { - "author_name": "Sabra L. Klein", - "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.11.22272263", "rel_title": "Surveillance of COVID-19 cases associated with dental settings using routine health data from the East of Scotland with a description of efforts to break chains of transmission from October 2020 to December 2021.", @@ -338634,6 +337831,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2022.03.13.22272308", + "rel_title": "Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.13.22272308", + "rel_abs": "The SARS-CoV-2 Omicron (B.1.1.529) variant has two subvariants, BA.1 and BA.2, that are genetically quite divergent. We conducted a matched, test-negative, case-control study to estimate duration of protection of mRNA COVID-19 vaccines, after the second dose and after a third/booster dose, against BA.1 and BA.2 infections in Qatars population. BNT162b2 effectiveness against symptomatic BA.1 infection was highest at 46.6% (95% CI: 33.4-57.2%) in the first three months after the second dose, but then declined to [~]10% or below thereafter. Effectiveness rapidly rebounded to 59.9% (95% CI: 51.2-67.0%) in the first month after the booster dose, but then started to decline again. BNT162b2 effectiveness against symptomatic BA.2 infection was highest at 51.7% (95% CI: 43.2-58.9%) in the first three months after the second dose, but then declined to [~]10% or below thereafter. Effectiveness rapidly rebounded to 43.7% (95% CI: 36.5-50.0%) in the first month after the booster dose, but then declined again. Effectiveness against COVID-19 hospitalization and death was in the range of 70-80% any time after the second dose, and was greater than 90% after the booster dose. Similar patterns of protection were observed for the mRNA-1273 vaccine. mRNA vaccines provide only moderate and short-lived protection against symptomatic Omicron infections, with no discernable differences in protection against either the BA.1 or BA.2 subvariants. Vaccine protection against COVID-19 hospitalization and death is strong and durable after the second dose, but is more robust after a booster dose.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Sawsan AlMukdad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al-Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Maria K. Smatti", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohammad R. Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Zaina Al-Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al-Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul-Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al-Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al-Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al-Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.13.22272304", "rel_title": "Quantitative Trend Analysis of SARS-CoV-2 RNA in Municipal Wastewater Exemplified with Sewershed-Specific COVID-19 Clinical Case Counts", @@ -339833,57 +339141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.10.22272024", - "rel_title": "Prevalence and Predictors of Depression, Anxiety and Stress among Elderly in the aftermath of COVID-19: A Quantitative Study from Central India", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272024", - "rel_abs": "BackgroundElderly persons have been more prone to depression, anxiety and stress during COVID-19 pandemic. They need more care and support towards mental health during these difficult times.\n\nMethodologyThis was a cross-sectional and quantitative study conducted in the state of Madhya Pradesh, during the month of March 2021 to August 2021. Participants were recruited from a population aged more than 60 years, those who were able to read and write Hindi/English or having at least one family member; reporting to a tertiary care teaching hospital during the second wave of COVID-19 in India. Those who were confirmed COVID-19 cases & undergoing treatment, with diagnosed mental health disorders and who didnt give consent were excluded. A semi-structured questionnaire along with DASS-21 scale was completed by participants online.\n\nResultsOut of 690 subjects, 7.25% had mild and moderate depression, 0.58% had severe and extremely severe depression. Mild and moderate anxiety symptoms were reported by 9.56%, 2.46% reported severe and extremely severe anxiety. Mild and moderate stress was reported by 4.78%, while 0.42% were severely and extremely stressed. A positive statistical association was found between alcohol addiction and depression (p=0.028). The elderly subjects had a nap the day time were significantly less depressed during COVID-19 pandemic (p=0.033). It was found that older the subjects, more were they anxious during the pandemic (p=0.042). An association was found between alcohol addiction and stress (p=0.043).\n\nConclusionsDepressive symptoms in participants were positively correlated with alcohol addiction. Females reported higher level of stress. There is a felt need to formulate psychological interventions for elderly to improve their mental health and psychological resilience. We need to tackle and fight the stigma, fear and anxiety related to the COVID-19, which is greater than disease itself.\n\nKey messageO_ST_ABSWhat is already knownC_ST_ABSPsychological problems like anxiety, depressive symptoms, fearfulness, a state of uncertainty and stress are common in all age groups; furthermore older adults are more prone to develop mental health issues in wake of stressful situations.\n\nWhat this study adds toAbout one fourth of elderly developed anxiety, depression and stress during the COVID-19 pandemic.\n\nEffect on practice and policyThere is a need for proactive identification through screening of elderly for mental health issues following unprecedented stress like COVID-19 pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Varun Malhotra", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Danish Javed", - "author_inst": "All India Institute of Medical Sciences, Bhopal" - }, - { - "author_name": "Rajay Bharshankar", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Vijender Singh", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Namita Gautam", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Shweta Mishra", - "author_inst": "Department of AYUSH, All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Digpal Chundawat", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Anuradha Kushwah", - "author_inst": "All India Institute of Medical sciences, Bhopal" - }, - { - "author_name": "Gyanendra Singh", - "author_inst": "All India Institute of Medical sciences, Bhopal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.03.09.22272160", "rel_title": "Cross-sector Decision Landscape in Response to COVID-19: A Qualitative Analysis of North Carolina Decision-Makers", @@ -340800,6 +340057,49 @@ "type": "confirmatory results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.03.08.483451", + "rel_title": "Reorganization of F-actin nanostructures is required for the late phases of SARS-CoV-2 replication in pulmonary cells.", + "rel_date": "2022-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.08.483451", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is worldwide the main cause of the COVID-19 pandemic. After infection of human pulmonary cells, intracellular viral replication take place in different cellular compartments resulting in the destruction of the host cells and causing severe respiratory diseases. Although cellular trafficking of SARS-CoV-2 have been explored, little is known about the role of the cytoskeleton during viral replication in pulmonary cells. Here we show that SARS-CoV-2 infection induces dramatic changes of F-actin nanostructures overtime. Ring-like actin nanostructures are surrounding viral intracellular organelles, suggesting a functional interplay between F-actin and viral M clusters during particle assembly. Filopodia-like structures loaded with viruses to neighbour cells suggest these structures as mechanism for cell-to-cell virus transmission. Strikingly, gene expression profile analysis and PKN inhibitor treatments of infected pulmonary cells reveal a major role of alpha-actinins superfamily proteins in SARS-CoV-2 replication. Overall, our results highlight cell actors required for SARS-CoV2 replication that are promises for antiviral targets.\n\nTeaserImpairing regulation of actin filaments inhibits SARS-CoV-2 particle production in human pulmonary cells.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jitendriya Swain", + "author_inst": "CNRS UMR9004 IRIM" + }, + { + "author_name": "Peggy Merida", + "author_inst": "CNRS UMR9004 IRIM" + }, + { + "author_name": "Karla Rubio", + "author_inst": "University of Lorraine" + }, + { + "author_name": "David Bracquemond", + "author_inst": "CNRS" + }, + { + "author_name": "Israel Aguilar-Ordo\u00f1ez", + "author_inst": "Instituto Nacional de Medicina Gen\u00e9mica (INMEGEN)" + }, + { + "author_name": "Stefan Guenther", + "author_inst": "Max-Planck Institute for Heart and Lung Research" + }, + { + "author_name": "Delphine Muriaux", + "author_inst": "CNRS UMR9004 IRIM - Institute of Research in Infectiology Montpellier" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.07.22272055", "rel_title": "Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring", @@ -341979,273 +341279,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.08.22271905", - "rel_title": "Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22271905", - "rel_abs": "BackgroundSARS-CoV-2 vaccination of persons aged 12 years and older has reduced disease burden in the United States. The COVID-19 Scenario Modeling Hub convened multiple modeling teams in September 2021 to project the impact of expanding vaccine administration to children 5-11 years old on anticipated COVID-19 burden and resilience against variant strains.\n\nMethodsNine modeling teams contributed state- and national-level projections for weekly counts of cases, hospitalizations, and deaths in the United States for the period September 12, 2021 to March 12, 2022. Four scenarios covered all combinations of: 1) presence vs. absence of vaccination of children ages 5-11 years starting on November 1, 2021; and 2) continued dominance of the Delta variant vs. emergence of a hypothetical more transmissible variant on November 15, 2021. Individual team projections were combined using linear pooling. The effect of childhood vaccination on overall and age-specific outcomes was estimated by meta-analysis approaches.\n\nFindingsAbsent a new variant, COVID-19 cases, hospitalizations, and deaths among all ages were projected to decrease nationally through mid-March 2022. Under a set of specific assumptions, models projected that vaccination of children 5-11 years old was associated with reductions in all-age cumulative cases (7.2%, mean incidence ratio [IR] 0.928, 95% confidence interval [CI] 0.880-0.977), hospitalizations (8.7%, mean IR 0.913, 95% CI 0.834-0.992), and deaths (9.2%, mean IR 0.908, 95% CI 0.797-1.020) compared with scenarios where children were not vaccinated. This projected effect of vaccinating children 5-11 years old increased in the presence of a more transmissible variant, assuming no change in vaccine effectiveness by variant. Larger relative reductions in cumulative cases, hospitalizations, and deaths were observed for children than for the entire U.S. population. Substantial state-level variation was projected in epidemic trajectories, vaccine benefits, and variant impacts.\n\nConclusionsResults from this multi-model aggregation study suggest that, under a specific set of scenario assumptions, expanding vaccination to children 5-11 years old would provide measurable direct benefits to this age group and indirect benefits to the all-age U.S. population, including resilience to more transmissible variants.", - "rel_num_authors": 63, - "rel_authors": [ - { - "author_name": "Rebecca K. Borchering", - "author_inst": "The Pennsylvania State University, University Park, Pennsylvania" - }, - { - "author_name": "Luke C. Mullany", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Emily Howerton", - "author_inst": "The Pennsylvania State University, University Park, Pennsylvania" - }, - { - "author_name": "Matteo Chinazzi", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Claire P. Smith", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Michelle Qin", - "author_inst": "Harvard University, Cambridge, Massachusetts" - }, - { - "author_name": "Nicholas G. Reich", - "author_inst": "University of Massachusetts Amherst, Amherst, Massachusetts" - }, - { - "author_name": "Lucie Contamin", - "author_inst": "University of Pittsburgh, Pittsburgh, Pennsylvania" - }, - { - "author_name": "John Levander", - "author_inst": "University of Pittsburgh, Pittsburgh, Pennsylvania" - }, - { - "author_name": "Jessica Kerr", - "author_inst": "University of Pittsburgh, Pittsburgh, Pennsylvania" - }, - { - "author_name": "J Espino", - "author_inst": "University of Pittsburgh, Pittsburgh, Pennsylvania" - }, - { - "author_name": "Harry Hochheiser", - "author_inst": "University of Pittsburgh, Pittsburgh, Pennsylvania" - }, - { - "author_name": "Kaitlin Rainwater-Lovett", - "author_inst": "Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Matt Kinsey", - "author_inst": "Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Kate Tallaksen", - "author_inst": "Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Shelby Wilson", - "author_inst": "Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Lauren Shin", - "author_inst": "Johns Hopkins University Applied Physics Laboratories, Laurel, Maryland" - }, - { - "author_name": "Joseph C. Lemaitre", - "author_inst": "\u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne, Lausanne, Switzerland" - }, - { - "author_name": "Juan Dent Hulse", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Joshua Kaminsky", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Elizabeth C. Lee", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Javier Perez-Saez", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Jessica T. Davis", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Kunpeng Mu", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Xinyue Xiong", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Ana Pastore y Piontti", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Northeastern University, Boston, Massachusetts" - }, - { - "author_name": "Ajitesh Srivastava", - "author_inst": "University of Southern California, Los Angeles, California" - }, - { - "author_name": "Przemyslaw Porebski", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Srinivasan Venkatramanan", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Aniruddha Adiga", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Bryan Lewis", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Brian Klahn", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Joseph Outten", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Benjamin Hurt", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Jiangzhuo Chen", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Henning Mortveit", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Amanda Wilson", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Madhav Marathe", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Stefan Hoops", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Parantapa Bhattacharya", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Dustin Machi", - "author_inst": "University of Virginia, Charlottesville, Virginia" - }, - { - "author_name": "Shi Chen", - "author_inst": "University of North Carolina at Charlotte, Charlotte, North Carolina" - }, - { - "author_name": "Rajib Paul", - "author_inst": "University of North Carolina at Charlotte, Charlotte, North Carolina" - }, - { - "author_name": "Daniel Janies", - "author_inst": "University of North Carolina at Charlotte, Charlotte, North Carolina" - }, - { - "author_name": "Jean-Claude Thill", - "author_inst": "University of North Carolina at Charlotte, Charlotte, North Carolina" - }, - { - "author_name": "Marta Galanti", - "author_inst": "Columbia University" - }, - { - "author_name": "Teresa K. Yamana", - "author_inst": "Columbia University" - }, - { - "author_name": "Sen Pei", - "author_inst": "Columbia University" - }, - { - "author_name": "Jeffrey Shaman", - "author_inst": "Columbia University" - }, - { - "author_name": "Guido Espa\u00f1a", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Sean Cavany", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Sean Moore", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Alex Perkins", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Jessica M. Healy", - "author_inst": "CDC COVID-19 Response Team" - }, - { - "author_name": "Rachel B. Slayton", - "author_inst": "CDC COVID-19 Response Team" - }, - { - "author_name": "Michael A. Johansson", - "author_inst": "CDC COVID-19 Response Team" - }, - { - "author_name": "Matthew Biggerstaff", - "author_inst": "CDC COVID-19 Response Team" - }, - { - "author_name": "Katriona Shea", - "author_inst": "The Pennsylvania State University, University Park, Pennsylvania" - }, - { - "author_name": "Shaun Truelove", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland" - }, - { - "author_name": "Michael C. Runge", - "author_inst": "U.S. Geological Survey Eastern Ecological Science Center, Laurel, Maryland" - }, - { - "author_name": "C\u00e9cile Viboud", - "author_inst": "Fogarty International Center, National Institutes of Health, Bethesda, Maryland" - }, - { - "author_name": "Justin Lessler", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.08.22272111", "rel_title": "Risk Perceptions and Private Protective Behaviors: Evidence from COVID-19 Pandemic", @@ -343054,6 +342087,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.09.483600", + "rel_title": "DiSCERN - Deep Single Cell Expression ReconstructioN for improved cell clustering and cell subtype and state detection", + "rel_date": "2022-03-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.09.483600", + "rel_abs": "Single cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering and cell type identification. Here we present DISCERN, a novel deep generative network that reconstructs missing single cell gene expression using a reference dataset. DISCERN outperforms competing algorithms in expression inference resulting in greatly improved cell clustering, cell type and activity detection, and insights into the cellular regulation of disease. We used DISCERN to detect two unseen COVID-19-associated T cell types, cytotoxic CD4+ and CD8+ Tc2 T helper cells, with a potential role in adverse disease outcome. We utilized T cell fraction information of patient blood to classify mild or severe COVID-19 with an AUROC of 81% that can serve as a biomarker of disease stage. DISCERN can be easily integrated into existing single cell sequencing workflows and readily adapted to enhance various other biomedical data types.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Fabian Hausmann", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Can Ergen", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Robin Khatri", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Mohamed Marouf", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Sonja H\u00e4nzelmann", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Nicola Gagliani", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Samuel Huber", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Pierre Machart", + "author_inst": "Center for Molecular Neurobiology Hamburg" + }, + { + "author_name": "Stefan Bonn", + "author_inst": "Center for Molecular Neurobiology Hamburg" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.03.07.22272036", "rel_title": "Diagnostic accuracy of age-adjusted D-dimer for pulmonary embolism among Emergency Department patients with suspected SARS-COV-2: A Canadian COVID-19 Emergency Department Rapid Response Network study", @@ -344101,81 +343185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.07.22271219", - "rel_title": "DIAGNOSTIC ACCURACY OF NON-INVASIVE DETECTION OF SARS-COV-2 INFECTION BY CANINE OLFACTION", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.07.22271219", - "rel_abs": "BACKGROUNDThroughout the COVID-19 pandemic, testing individuals remains a key action. One approach to rapid testing is to consider the olfactory capacities of trained detection dogs.\n\nMETHODSProspective cohort study in two community COVID-19 screening centers. Two nasopharyngeal swabs (NPS), one saliva and one sweat samples were simultaneously collected. The dog handlers (and the dogs...) were blinded with regards to the Covid status. The diagnostic accuracy of non-invasive detection of SARS-CoV-2 infection by canine olfaction was assessed as compared to nasopharyngeal RT-PCR as the reference standard, saliva RT-PCR and nasopharyngeal antigen testing.\n\nRESULTS335 ambulatory adults (143 symptomatic and 192 asymptomatic) were included. Overall, 109/335 participants tested positive on nasopharyngeal RT-PCR either in symptomatic (78/143) or in asymptomatic participants (31/192). The overall sensitivity of canine detection was 97% (95% CI, 92 to 99) and even reached 100% (95% CI, 89 to 100) in asymptomatic individuals compared to NPS RT-PCR. The specificity was 91% (95% CI, 72 to 91), reaching 94% (95% CI, 90 to 97) for asymptomatic individuals. The sensitivity of canine detection was higher than that of nasopharyngeal antigen testing (97% CI: 91 to 99 versus 84% CI: 74 to 90, p=0.006), but the specificity was lower (90% CI: 84 to 95 versus 97% CI: 93 to 99, p=0.016).\n\nCONCLUSIONSNon-invasive detection of SARS-CoV-2 infection by canine olfaction could be one alternative to NPS RT-PCR when it is necessary to obtain a result very quickly according to the same indications as antigenic tests in the context of mass screening.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Dominique GRANDJEAN", - "author_inst": "Ecole Nationale Veterinaire d'Alfort" - }, - { - "author_name": "Caroline Elie", - "author_inst": "hopital necker aphp" - }, - { - "author_name": "Capucine Gallet", - "author_inst": "ecole nationale veterinaire d'alfort" - }, - { - "author_name": "Clothilde Julien", - "author_inst": "ecole nationale veterinaire d'alfort" - }, - { - "author_name": "Vinciane Roger", - "author_inst": "ecole nationale veterinaire d'alfort" - }, - { - "author_name": "loic Desquilbet", - "author_inst": "ecole nationale veterinaire d'alfort" - }, - { - "author_name": "Guillaume Alvergnat", - "author_inst": "ministry of interior UAE" - }, - { - "author_name": "Severine Delarue", - "author_inst": "Hopital Saint Louis APHP" - }, - { - "author_name": "Audrey Gabassi", - "author_inst": "Hopital Saint Louis APHP" - }, - { - "author_name": "Marine Minier", - "author_inst": "Hoiptal Saint Louis APHP" - }, - { - "author_name": "Laure Choupeaux", - "author_inst": "Hopital Necker APHP" - }, - { - "author_name": "Soleine Kerneis", - "author_inst": "Hopital Bichat APHP" - }, - { - "author_name": "Constance Delaugere", - "author_inst": "Hopital Saint Louis APHP" - }, - { - "author_name": "Jerome Le Goff", - "author_inst": "Hopital Saint Louis APHP" - }, - { - "author_name": "Jean Marc Treluyer", - "author_inst": "Hopital Necker APHP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.05.22271959", "rel_title": "13 cis retinoic acid improved the outcomes of COVID-19 patients. A randomized clinical trial", @@ -344976,6 +343985,141 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.04.479488", + "rel_title": "Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease", + "rel_date": "2022-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.04.479488", + "rel_abs": "Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against coronaviruses that cause severe disease, for anticipating novel pandemic-causing viruses, and to respond more effectively to SARS-CoV-2 variants. The emergence of the Omicron variant of SARS-CoV-2 has illustrated the limitations of solely targeting the receptor binding domain (RBD) of the envelope Spike (S)-protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors that target a conserved S2 region in the fusion machinery on betacoronavirus spikes. Select bnAbs show broad in vivo protection against all three pathogenic betacoronaviruses, SARS-CoV-1, SARS-CoV-2 and MERS-CoV, that have spilled over into humans in the past 20 years to cause severe disease. The bnAbs provide new opportunities for antibody-based interventions and key insights for developing pan-betacoronavirus vaccines.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Panpan Zhou", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ge Song", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Wan-ting He", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Nathan Beutler", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Longping V. Tse", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "David R. Martinez", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Alexandra Schafer", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Fabio Anzanello", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Peter Yong", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Linghang Peng", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Katharina Dueker", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Rami Musharrafieh", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Sean Callaghan", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Meng Yuan", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Hejun Liu", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Oliver Limbo", + "author_inst": "IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Mara Parren", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Elijah Garcia", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Stephen A. Rawlings", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Davey M. Smith", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "David Nemazee", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Joseph G. Jardine", + "author_inst": "IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Yana Safonova", + "author_inst": "Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA" + }, + { + "author_name": "Thomas Rogers", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Lisa E. Gralinski", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Dennis R. Burton", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.05.483092", "rel_title": "mRNA-based vaccine candidate COReNAPCIN(R) induces robust humoral and cellular immunity in mice and non-human primates", @@ -345871,61 +345015,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.03.05.22271084", - "rel_title": "Changing dynamics of SARS-CoV2 B.1.617.2 (Delta variant) outbreak in the United Kingdom: Shifting of SARS-CoV2 infections from younger to elderly populations with increasing hospitalizations and mortality among elderly.", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.05.22271084", - "rel_abs": "BackgroundTo assess the comprehensive dynamics of outcomes during the SARS-CoV2 B.1.617.2 (Delta variant) compared to the Alpha variant outbreak in the United Kingdom.\n\nMethodsIn this observational study of the cases reported by Public Health England for confirmed (sequencing and genotyping), SARS-CoV2 cases Delta variant (n=592,692) and Alpha variant (n=150,934) were used. Outcomes were analyzed by age groups and compared with all reported weekly cases in the UK.\n\nResultsThe Delta variant surge is associated with a significantly lower case fatality rate (0.43% vs 1.07; RR 0.39; 95% CI 0.37-0.42; P<0.0001); lower odds of hospitalization (2.1% vs 3.0%; RR 0.70; 95% CI 0.68-0.73; P<0.0001) than the Alpha variant. During the Delta variant surge there were significant increased cases (11.3% to 21.1%, RR 1.87; 95% CI 1.84-1.89; P<0.0001), hospitalizations (40.2% to 56.5%; RR 1.40, 95% CI 1.3-1.46; P<0.0001) among confirmed Delta variant cases in the [≥]50 years age group during the August 3-September 12, 2021 period compared to earlier reported cases. There was also a significant increase in total weekly COVID-19 deaths noted among [≥]70 years old age group (71.4% to 75.1%; RR 1.05; 95% CI 1.01-1.08; P=0.0028) during August 6-October 8, 2021 compared to June 4-July 30, 2021 period.\n\nConclusionsThe Delta variant surge is associated with significantly lower mortality and hospitalizations than the Alpha variant. As the Delta variant surge progressed, [≥]50 years old had a significant increased percentage of cases, hospitalizations and a significant increased COVID-19 deaths occurred among [≥]70 years old age group.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Venkata Rami Reddy Emani", - "author_inst": "Central Valley Cardiovascular Associates, Inc" - }, - { - "author_name": "Abirath Surender Nakka", - "author_inst": "Stockton Primary Care" - }, - { - "author_name": "Kartik Kumar Goswami", - "author_inst": "San Joaquin Critical Care Medial Group" - }, - { - "author_name": "Shaila Reddy Emani", - "author_inst": "Central Valley Cardiovascular Associates, Inc" - }, - { - "author_name": "Kailash Reddy Maddula", - "author_inst": "Central Valley Cardiovascular Associates, Inc" - }, - { - "author_name": "Nikhila Komati Reddy", - "author_inst": "Stockton Primary Care" - }, - { - "author_name": "Nidhi Komati Reddy", - "author_inst": "Stockton Primary Care" - }, - { - "author_name": "Dheeraj Nandanoor", - "author_inst": "Synergy Med" - }, - { - "author_name": "Sanjeev Goswami", - "author_inst": "San Joaquin Critical Care Medial Group" - }, - { - "author_name": "Raghunath Reddy", - "author_inst": "Stockton Primary Care" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.06.22271974", "rel_title": "Competitive fitness of emerging SARS-CoV-2 variants is linked to their Distinctiveness relative to preceding lineages from that region", @@ -346494,6 +345583,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.03.22271601", + "rel_title": "Immunogenicity and reactogenicity against the SARS-CoV-2 variants following heterologous primary series involving CoronaVac and ChAdOx1 and BNT162b2 plus heterologous BNT162b2 booster vaccination: An open-label randomized study in healthy Thai adults.", + "rel_date": "2022-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271601", + "rel_abs": "We evaluated the immunogenicity and reactogenicity of heterologous COVID-19 primary series vaccination schedules. Participants were randomized to one of seven groups that received two-dose homologous BNT162b2 or heterologous combinations of CoronaVac, ChAdOx1 and BNT162b2, with 4 weeks interval. Of 210 participants, median age was 38 (19-60) years, 51% were female. The groups that received BNT162b2 as second dose induced the highest virus-specific IgG response against the ancestral strain [BNT162b2: geometric mean concentration (GMC) 2133-2249, 95%CI 1558 to 3055; ChAdOx1: 851-1201, 95%CI 649 to 1522; CoronaVac: 137-225, 95%CI 103-286 BAU/mL], neutralising antibodies (NAb) against Beta and Delta, and interferon gamma response. All groups induced low to negligible NAb against Omicron. A BNT162b2 booster (3rd dose) following heterologous CoronaVac and ChAdOx1 regimens induced >140-fold increase in NAb titres against Omicron. Our findings indicate that heterologous regimens using BNT162b2 as the second dose may be considered an alternative schedule to maximize immune response.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Suvimol Niyomnaitham", + "author_inst": "Faculty of Medicine, Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Zheng Quan Toh", + "author_inst": "Murdoch Children Research Institute" + }, + { + "author_name": "Patimaporn Wongprompitak", + "author_inst": "Faculty of Medicine, Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Laddawan Jansarikit", + "author_inst": "Faculty of Medicine, Siriraj Hospital, Mahidol University" + }, + { + "author_name": "Kanjana Srisutthisamphan", + "author_inst": "National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science Development Agency (NSTDA)" + }, + { + "author_name": "Sompong Sapsutthipas", + "author_inst": "Department of Medical Sciences, Institute of Biological Products" + }, + { + "author_name": "Yuparat Jantraphakorn", + "author_inst": "National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science Development Agency (NSTDA)" + }, + { + "author_name": "Natthakarn Mingngamsup", + "author_inst": "Department of Medical Sciences, Institute of Biological Products" + }, + { + "author_name": "Paul Licciardi", + "author_inst": "Murdoch Children Research Institute" + }, + { + "author_name": "Kulkanya Chokephaibulkit", + "author_inst": "Faculty of Medicine, Siriraj Hospital, Mahidol University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.03.22271159", "rel_title": "Spike mutations of the SARS-CoV-2 Omicron: more likely to occur in the epitopes", @@ -347625,33 +346769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.02.22271767", - "rel_title": "Estimating relative generation times and relative reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta in Denmark", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271767", - "rel_abs": "The Omicron variant is the most transmissible variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) we had so far. The BA.1 and BA.2 sublineages of Omicron are circulating in Europe and it is urgent to evaluate the transmissibility of these sub-lineages. Using a mathematical model describing trajectories of variant frequencies that assumes a constant ratio in generation times and a constant ratio in effective reproduction numbers among variants, trajectories of variant frequencies in Denmark from November 22, 2021 to February 26, 2022 were analyzed. We found that the generation times of Omicron BA.1 and BA.2 are 0.60 (95%CI: 0.59-0.62) and 0.51 (95%CI: 0.50-0.52) of the length of that of Delta, respectively. We also found that the effective reproduction number of Omicron BA.1 is 1.99 (95% CI: 1.98-2.02) times and that of Omicron BA.2 is 2.51 (95% CI: 2.48- 2.55) times larger than the effective reproduction number of Delta. The generation times of Omicron BA.2 is 0.85 (95% CI:0.84-0.86) the length of that of BA.1 and that the effective reproduction number of Omicron BA.2 is 1.26 (95% CI:1.25-1.26) times larger than that of Omicron BA.1. These estimates on the ratio of generation times and the ratio of effective reproduction numbers has epidemiologically important implications. The duration of quarantine for people who contacted with an Omicron BA.1 and BA.2 patient can be reduced to 60% and 51% of that for Delta, respectively. The control measures against Omicron BA.1 and BA.2 need to reduce contacts between infectious and susceptible people respectively by 50% (95% CI: 49-50%) and 60% (95% CI: 60-61%) compared to that against Delta to achieve the same effect on their control.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kimihito Ito", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Chayada Piantham", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Hiroshi Nishiura", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.02.22271656", "rel_title": "Analyzing county-wide trends in Tennessee Covid-19 rates, Median Household Income, and Presence of Hospital", @@ -348312,6 +347429,57 @@ "type": "confirmatory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.03.482731", + "rel_title": "The interaction of calcium ions with specific residues in the SARS-CoV fusion peptide and the regulation of viral infectivity", + "rel_date": "2022-03-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.03.482731", + "rel_abs": "The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca+2 binding which promote membrane insertion. We first mutated the negatively charged residues in the SARS CoV-1 FP to assay their role in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants reduced syncytia formation and pseudoparticle transduction. Interestingly, the D812A mutation led to increased pseudoparticle transduction, indicating the Ca2+ effect depends on binding at specific FP sites. To interpret mechanistically these results and learn how specific modes of FP-Ca2+ binding modulate membrane insertion, we performed molecular dynamics simulations. Preferred residue pairs for Ca2+ binding were identified (E801/D802; E801/D830; D812/E821) which promote FP membrane insertion. In contrast, binding to residues E821/D825 inhibited FP membrane insertion, which is also supported by our biological assays. Our findings show that Ca2+ binding to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion, whereas binding to the E801/D802 and D821/D825 pairs is detrimental. These conclusions provide an improved and nuanced mechanistic understanding of calcium binding modes to FP residues and their dynamic effects on host cell entry.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Juliana Carten", + "author_inst": "Cornell University" + }, + { + "author_name": "George Khelashvili", + "author_inst": "Weill Medical College of Cornell University" + }, + { + "author_name": "Miya Kristine Bidon", + "author_inst": "Cornell University" + }, + { + "author_name": "Marco Straus", + "author_inst": "Cornell University" + }, + { + "author_name": "Tiffany Tang", + "author_inst": "Cornell University" + }, + { + "author_name": "Javier A. Jaimes", + "author_inst": "Cornell University" + }, + { + "author_name": "Harel Weinstein", + "author_inst": "Weill Cornell Medical College of Cornell University" + }, + { + "author_name": "Gary Whittaker", + "author_inst": "Cornell Univ" + }, + { + "author_name": "Susan Daniel", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.03.482819", "rel_title": "Zinc pyrithione is a potent inhibitor of PLPro and cathepsin L enzymes with ex vivo inhibition of SARS-CoV-2 entry and replication", @@ -349651,69 +348819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.02.28.22271674", - "rel_title": "Assessment of Potential Risk Factors for COVID-19 among Health Care Workers in a Health Care Setting in Delhi, India -A Cohort Study", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271674", - "rel_abs": "IntroductionHealth care workers (HCW) are among the most vulnerable for contracting the COVID-19 infection. Understanding the extent of human-to-human transmission of the COVID-19 infection among HCW is critical in management of this infection and for policy making. We did this study to observe seropositivity and estimate new infection by seroconversion among HCW and predict the risk factors for infection.\n\nMethodsA cohort study was conducted at a tertiary dedicated COVID-19 hospital in New Delhi during first and second wave of the COVID-19 pandemic. All HCW working in the hospital during the study period who come in contact with the patients, were our study population. The data was collected by a detailed face to face interview along with serological assessment for anti-COVID-19 antibodies at baseline and endline, and assessment of daily symptoms. Prediction of potential risk factors for seroprevalence and seroconversion was done by logistic regression keeping the significance at p<0.05.\n\nResultsA total of 192 HCW were recruited in this study, out of which, 119 (61.97%) at baseline and 108 (77.7%) at endline were seropositive for COVID-19. About two-third (63.5%) had close contact, 5.2% had exposure during aerosol procedures, 30.2% had exposure with a patients body fluid while majority (85.4%) had exposure to contact surface around the patient. Almost all were wearing PPE and following IPC measures during their recent contact with a COVID-19 patient. Seroconversion was observed among 36.7% of HCWs while 64.0% had a serial rise in titer of antibodies during the follow-up period. Association of seropositivity was observed negatively with doctors [OR:0.353, CI:0.176-0.710], COVID-19 symptoms [OR:0.210, CI:0.054-0.820], comorbidities [OR:0.139, CI: 0.029 - 0.674], and recent Infection Prevention Control (IPC) training [OR:0.250, CI:0.072 - 0.864], while positively associated with partially [OR:3.303, CI: 1.256-8.685], as well as fully vaccination for COVID-19 [OR:2.428, CI:1.118-5.271]. Seroconversion was positively associated with doctor as profession [OR: 13.04, CI: 3.39 - 50.25] and with partially [OR: 4.35, CI: 1.070 - 17.647], as well as fully vaccinated for COVID-19 [OR: 6.08, CI: 1.729 - 21.40]. No significant association was observed between adherence to any of the IPC measures and PPE (personal protective equipment) adopted by the HCW during the recent contact with COVID-19 patients and seroconversion.\n\nConclusionA high seropositivity and seroconversion could be either due to exposure to COVID-19 patients or concurrent immunization against COVID-19 disease. In this study the strongest association of seropositivity and seroconversion was observed with recent vaccination. IPC measures were practiced by almost all the HCW in these settings, and thus were not found to be affecting seroconversion. Further study using anti N antibodies serology, which are positive following vaccination may help us to find out the reason for the seropositivity and seroconversion in HCW.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Mridu Dudeja", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Aqsa Shaikh", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Farzana Islam", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Yasir Alvi", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Mohammad Ahmad", - "author_inst": "World Health Organisation Country Office for India" - }, - { - "author_name": "Varun Kashyap", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Vishal Singh", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Anisur Rahman", - "author_inst": "World Health Organisation Country Office for India" - }, - { - "author_name": "Meely Panda", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Neetu Shree", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Shyamasree Nandy", - "author_inst": "Hamdard Institute of Medical Science and Research" - }, - { - "author_name": "Vineet Jain", - "author_inst": "Hamdard Institute of Medical Science and Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.01.22271685", "rel_title": "Patients with CLL have similar high risk of death upon the omicron variant of COVID-19 as previously during the pandemic.", @@ -350438,6 +349543,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2022.02.18.22271039", + "rel_title": "Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and signs of neurodegeneration: a prospective cross-sectional study", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22271039", + "rel_abs": "ImportanceGrowing evidence suggests that coronavirus disease 2019 (COVID-19) is associated with neurological sequelae. However, the underlying pathophysiological mechanisms resulting in central nervous system (CNS) derogation remain unclear.\n\nObjectiveTo identify severity-dependent immune mechanisms in the cerebrospinal fluid (CSF) and plasma of COVID-19 patients and their association with brain imaging alterations.\n\nDesignProspective cross-sectional cohort study.\n\nSettingThis study was performed from August 2020 to April 2021. Participants were enrolled in the outpatient clinics, hospital wards and intensive care units (ICU) of two clinical sites in Basel and Zurich, Switzerland.\n\nParticipantsAge >18 years and a positive SARS-CoV-2 test result were inclusion criteria. Potentially matching individuals were identified (n=310), of which 269 declined to participate and 1 did not match inclusion criteria. Paired CSF and plasma samples, as well as brain images, were acquired. The COVID-19 cohort (n=40; mean [SD] age, 54 [20] years; 17 women (42%)) was prospectively assorted by neurological symptom severity (classes I, II and III). Age/sex-matched inflammatory (n=25) and healthy (n=25) CSF and plasma control samples were obtained. For volumetric brain analysis, a healthy age/sex-matched control cohort (n=36) was established.\n\nExposuresLumbar puncture, blood sampling and cranial MRI and/or CT.\n\nMain outcomes and measuresProteomics, standard parameters and antibody profiling of paired CSF and plasma samples in COVID-19 patients and controls. Brain imaging and gray matter volumetric analysis in association with biomarker profiles. Follow-up after 10-months.\n\nResultsCOVID-19 patients displayed a plasma cytokine storm but a non-inflammatory CSF profile. Class III patients displayed signs of blood-brain barrier (BBB) impairment and a polyclonal B cell response targeting self- and non-self antigens. Decreased regional brain volumes were present in COVID-19 patients and associated with specific CSF and plasma parameters.\n\nConclusion and relevanceNeuro-COVID class III patients had a strong, peripheral immune response resulting in (1) BBB impairment (2) ingress of (auto-)antibodies, (3) microglia activation and neuronal damage signatures. Our data point towards several potentially actionable targets that may be addressed to prevent COVID-19-related neurological sequelae.\n\nTrial registrationThe trial (NCT04472013) was registered on clinicaltrials.gov.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSDoes a severity-dependent pattern of immune mechanisms exist in the cerebrospinal fluid (CSF) and plasma of COVID-19 patients and are these associated with clinical and brain imaging findings?\n\nFindingsNeuro-COVID patients display a robust class III-specific peripheral immune response resulting in (1) blood-brain barrier (BBB) impairment, (2) ingress of (auto-)antibodies, (3) microglia activation and neuronal damage signatures. Integration of MRIs, brain volumetry and proteomics identified biomarkers associated with regional brain volume loss in severe Neuro-COVID.\n\nMeaningWe provide a multidimensional framework of mechanisms associated with severe Neuro-COVID and present possible targets to prevent COVID-19-related neurological sequelae.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Manina Maja Etter", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Tomas Martins", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Laila Kulsvehagen", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Elisabeth Poessnecker", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Wandrille Duchemin", + "author_inst": "University of Basel" + }, + { + "author_name": "Sabrina Hogan", + "author_inst": "University of Basel" + }, + { + "author_name": "Gretel Sanabria Diaz", + "author_inst": "University of Basel" + }, + { + "author_name": "Jannis Mueller", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Alessio Chiappini", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Jonathan Rychen", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Noemi Eberhard", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Lester Melie-Garcia", + "author_inst": "Lausanne University Hospital (CHUV)" + }, + { + "author_name": "Emanuela Keller", + "author_inst": "University Hospital" + }, + { + "author_name": "Ilijas Jelcic", + "author_inst": "University Hospital Zurich" + }, + { + "author_name": "Martin Siegemund", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Hans Pargger", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Jens Kuhle", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Johanna Oechtering", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Caroline Eich", + "author_inst": "University of Basel" + }, + { + "author_name": "Alexandar Tzankov", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Matthias Matter", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Oezguer Yaldizli", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Johanna Lieb", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Marios Nikos Psychogios", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Caroline Berkemeier", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Karoline Leuzinger", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Hans Hirsch", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Cristina Granziera", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Anne-Katrin Proebstel", + "author_inst": "University Hospital Basel" + }, + { + "author_name": "Gregor Hutter", + "author_inst": "University of Basel and University Hospital Basel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.02.28.22270969", "rel_title": "Development and validation of a quantitative instrument for measuring temporal and social disorientation in the Covid-19 crisis", @@ -351521,257 +350761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.27.22271399", - "rel_title": "The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization", - "rel_date": "2022-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.27.22271399", - "rel_abs": "BackgroundIn October 2020, the National Cancer Institute (NCI) Serological Sciences Network (SeroNet) was established to study the immune response to COVID-19, and \"to develop, validate, improve, and implement serological testing and associated technologies.\" SeroNet is comprised of 25 participating research institutions partnering with the Frederick National Laboratory for Cancer Research (FNLCR) and the SeroNet Coordinating Center. Since its inception, SeroNet has supported collaborative development and sharing of COVID-19 serological assay procedures and has set forth plans for assay harmonization.\n\nMethodsTo facilitate collaboration and procedure sharing, a detailed survey was sent to collate comprehensive assay details and performance metrics on COVID-19 serological assays within SeroNet. In addition, FNLCR established a protocol to calibrate SeroNet serological assays to reference standards, such as the U.S. SARS-CoV-2 serology standard reference material and First WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin (20/136), to facilitate harmonization of assay reporting units and cross-comparison of study data.\n\nResultsSeroNet institutions reported development of a total of 27 ELISA methods, 13 multiplex assays, 9 neutralization assays, and use of 12 different commercial serological methods. FNLCR developed a standardized protocol for SeroNet institutions to calibrate these diverse serological assays to reference standards.\n\nConclusionsSeroNet institutions have established a diverse array of COVID-19 serological assays to study the immune response to SARS-CoV-2 virus and vaccines. Calibration of SeroNet serological assays to harmonize results reporting will facilitate future pooled data analyses and study cross-comparisons.", - "rel_num_authors": 59, - "rel_authors": [ - { - "author_name": "Amy B. Karger", - "author_inst": "University of Minnesota" - }, - { - "author_name": "James D. Brien", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Jayne M. Christen", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Santosh Dhakal", - "author_inst": "The Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Troy J. Kemp", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Sabra L. Klein", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Ligia A. Pinto", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Lakshmanane Premkumar", - "author_inst": "University of North Carolina School of Medicine" - }, - { - "author_name": "John D. Roback", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Raquel A. Binder", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Karl William Boehme", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Suresh Boppana", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "James M. Crawford", - "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" - }, - { - "author_name": "John L Daiss", - "author_inst": "MicroB-plex, Inc." - }, - { - "author_name": "Alan P. Dupuis II", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Ana M Espino", - "author_inst": "University of Puerto Rico Medical Sciences Campus" - }, - { - "author_name": "Adolfo Firpo-Betancourt", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Catherine Forconi", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "J. Craig Forrest", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Roxie C. Girardin", - "author_inst": "NYSDOH" - }, - { - "author_name": "Douglas A. Granger", - "author_inst": "Salimetrics, LLC" - }, - { - "author_name": "Steve W. Granger", - "author_inst": "Salimetrics, LLC" - }, - { - "author_name": "Natalie S. Haddad", - "author_inst": "Emory University" - }, - { - "author_name": "Christopher D Heaney", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Danielle T. Hunt", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Christopher L. King", - "author_inst": "Case Western Reserve School of Medicine" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kate Kruczynski", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Joshua LaBaer", - "author_inst": "Arizona State University Biodesign Institute" - }, - { - "author_name": "F. Eun-Hyung Lee", - "author_inst": "Emory University" - }, - { - "author_name": "William T. Lee", - "author_inst": "Wadsworth Center/New York State Department of Health" - }, - { - "author_name": "Shan-Lu Liu", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Gerard Lozanski", - "author_inst": "The Ohio State University Medical Center" - }, - { - "author_name": "Todd Lucas", - "author_inst": "Michigan State University" - }, - { - "author_name": "Damodara Rao Mendu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ann M. Moormann", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Vel Murugan", - "author_inst": "Arizone State University Biodesign Institute" - }, - { - "author_name": "Nkemakonam C. Okoye", - "author_inst": "Donald and Barbara Zucker School of Medicine at Hofstra/Northwell" - }, - { - "author_name": "Petraleigh Pantoja", - "author_inst": "University of Puerto Rico-Medical Sciences Campus" - }, - { - "author_name": "Anne F. Payne", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Jin Park", - "author_inst": "Arizona State University Biodesign Institute" - }, - { - "author_name": "Swetha Pinninti", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Amelia K Pinto", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Nora Pisanic", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Ji Qiu", - "author_inst": "Arizona State University Biodesign Institute" - }, - { - "author_name": "Carlos A Sariol", - "author_inst": "University of Puerto Rico" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lusheng Song", - "author_inst": "Arizona State University Biodesign Institute" - }, - { - "author_name": "Tara L. Steffen", - "author_inst": "Saint Louis University" - }, - { - "author_name": "E. Taylor Stone", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Linda M. Styer", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Stefani N. Thomas", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Bharat Thyagarajan", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jennifer L Yates", - "author_inst": "Wadsworth Center / New York State Department of Health" - }, - { - "author_name": "Kimia Sobhani", - "author_inst": "Cedars-Sinai Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.26.22271509", "rel_title": "Effect of booster vaccination against Delta and Omicron variants in Iceland", @@ -352312,6 +351301,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.28.22271624", + "rel_title": "A compartmental Mathematical model of COVID-19 intervention scenarios for Mumbai", + "rel_date": "2022-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271624", + "rel_abs": "A new mathematical method with an outstanding potential to predict the incidence of COVID-19 diseases has been proposed. The model proposed is an improvement to the SEIR model. In order to improve the basic understanding of disease spread and outcomes, four compartments included presymptomatic, asymptomatic, quarantine hospitalized and hospitalized. We have studied COVID-19 cases in the city of Mumbai. We first gather clinical details and fit it on death cases using the Lavenberg-Marquardt model to approximate the various parameters. The model uses logistic regression to calculate the basic reproduction number over time and the case fatality rate based on the age-category scenario of the city of Mumbai. Two types of case fatality rate are calculated by the model: one is CFR daily, and the other is total CFR. The total case fatality rate is 4.2, which is almost the same as the actual scenario. The proposed model predicts the approximate time when the disease is at its worst and the approximate time when death cases barely arise and determines how many hospital beds in the peak days of infection would be expected. The proposed model outperforms the classic ARX, SARIMAX and the ARIMA model. And It also outperforms the deep learning models LSTM and Seq2Seq model. To validate results, RMSE, MAPE and R squared matrices are used and are represented using Taylor diagrams graphically.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Avaneesh Singh", + "author_inst": "Indian Institute of Information Technology Design and Manufacturing Jabalpur" + }, + { + "author_name": "Manish Kumar Bajpai", + "author_inst": "Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.28.22271615", "rel_title": "Cross-cultural adaptation and validation of the COVID Stress Scales in Greek", @@ -353463,77 +352475,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2022.02.28.22271571", - "rel_title": "Discriminatory ability of gas chromatography-ion mobility spectrometry to identify patients hospitalised with COVID-19 and predict prognosis", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271571", - "rel_abs": "BackgroundTests that can diagnose COVID-19 rapidly and predict prognosis would be significantly beneficial. We studied the ability of breath analysis using gas chromatography-ion mobility spectrometry (GC-IMS) for diagnosis of COVID-19 and as a predictor for subsequent requirement for Continuous Positive Airway Pressure (CPAP).\n\nMethodsWe undertook a single centre prospective observational study in patients with COVID-19, other respiratory tract infections and healthy controls. Participants provided one breath sample for GC-IMS analysis. We used cross validation analysis to create models that were then tested against the original cohort data. Further multivariable analysis was undertaken to adjust for differences between the comparator groups.\n\nResultsBetween 01/02/2021 and 24/05/2021 we recruited 113 participants, of whom 72 (64%) had COVID-19, 20 (18%) had another respiratory tract infection and 21 (19%) were healthy controls. Differentiation between patients with COVID-19 and healthy controls, and patients with COVID-19 and those with other respiratory tract infections, was achieved with high accuracy. Identification of patients with subsequent requirement for CPAP was completed with moderate accuracy and was not independently associated on multivariable analysis.\n\nConclusionsWe have shown that GC-IMS has a high capability to distinguish between acute COVID-19 infection and other disease states. Breath analysis shows promise as a predictor of subsequent requirement for CPAP in hospitalised patients with COVID-19. This platform has considerable benefits due to the test being rapid, non-invasive and not requiring specialist laboratory processing.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Joshua Nazareth", - "author_inst": "University of Leicester" - }, - { - "author_name": "Daniel Pan", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jee Whang Kim", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jack Leach", - "author_inst": "University of Leicester" - }, - { - "author_name": "James G Brosnan", - "author_inst": "University of Leicester" - }, - { - "author_name": "Adam Ahmed", - "author_inst": "University of Leicester" - }, - { - "author_name": "Emma Brodrick", - "author_inst": "IMSPEX Diagnostics Ltd" - }, - { - "author_name": "Alfian Wicaksono", - "author_inst": "University of Warwick" - }, - { - "author_name": "Emma Daulton", - "author_inst": "University of Warwick" - }, - { - "author_name": "Caroline Williams", - "author_inst": "University of Leicester" - }, - { - "author_name": "Pranabashis Haldar", - "author_inst": "University of Leicester" - }, - { - "author_name": "James Covington", - "author_inst": "University of Warwick" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - }, - { - "author_name": "Amandip Sahota", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.19.22271227", "rel_title": "Assessment of indoor biological air quality at a mass gathering event in an unimproved exhibition facility during the COVID-19 pandemic using a novel air sampling technology.", @@ -354262,6 +353203,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.26.22271545", + "rel_title": "SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study", + "rel_date": "2022-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271545", + "rel_abs": "ObjectivesHealthcare workers (HCWs) are at higher risk of contracting coronavirus disease-19 (COVID-19) than the general population. This study assessed the roles of various exposures and personal protective equipment (PPE) use on that risk for HCWs working in primary care, long-term-care facilities (LTCFs) or hospitals.\n\nMethodsWe conducted a matched case-control (1:1) study (10 April-9 July 2021). Cases (HCWs with confirmed COVID-19) and controls (HCWs without any COVID-19-positive test or symptoms) recruited by email were invited to complete an online questionnaire on their exposures and PPE use. Questions covered the 10 days preceding symptom onset for cases (or testing if asymptomatic) or inclusion for controls.\n\nResultsA total of 4152 matched cases and controls were included. The multivariable conditional logistic regression analysis retained exposure to an infected person outside work (adjusted odds ratio, 19.9 [95% confidence intervaI, 12.4-31.9]), an infected colleague (2.26 [1.53-3.33]) or COVID-19 patients (2.37 [1.66-3.40]), as independent predictors of COVID-19 in HCWs, while partial or complete immunization was protective. Eye protection (0.57 [0.37-0.87]) and wearing a gown (0.58 [0.34-0.97]) during COVID-19 patient care were protective, while wearing an apron slightly increased the risk of infection (1.47 [1.00-2.18]). N95-respirator protection was comparable to that of surgical masks. Results were consistent across healthcare-facility categories.\n\nConclusionsHCWs were more likely to get COVID-19 in their personal sphere than during occupational activities. Our results suggest that eye protection for HCWs during patient care should be actively promoted.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Martin Belan", + "author_inst": "Universite de Paris, INSERM, IAME, Paris, France" + }, + { + "author_name": "Tiffany Charmet", + "author_inst": "Institut Pasteur, Universite de Paris, Emerging Diseases Epidemiology Unit, Paris, France" + }, + { + "author_name": "Laura Schaeffer", + "author_inst": "Institut Pasteur, Universite de Paris, Emerging Diseases Epidemiology Unit, Paris, France" + }, + { + "author_name": "Sarah Tubiana", + "author_inst": "Universite de Paris, INSERM, IAME, Paris, France ; Centre d'Investigation Clinique, Inserm CIC 1425, Paris, France" + }, + { + "author_name": "Xavier Duval", + "author_inst": "Universite de Paris, INSERM, IAME, Paris, France ; Centre d'Investigation Clinique, Inserm CIC 1425,Paris, France" + }, + { + "author_name": "Jean-Christophe Lucet", + "author_inst": "Universite de Paris, INSERM, IAME, Paris, France ; Equipe de Prevention du Risque Infectieux (EPRI), AP-HP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Arnaud Fontanet", + "author_inst": "Institut Pasteur, Universite de Paris, Emerging Diseases Epidemiology Unit, Paris, France ; Conservatoire National des Arts et Metiers, Unite PACRI, Paris, Fran" + }, + { + "author_name": "Gabriel Birgand", + "author_inst": "Centre d Appui la Prevention des Infections Associees aux Soins des Pays de la Loire, Nantes, France ; NIHR Health Protection Research Unit in Healthcare Assoc" + }, + { + "author_name": "Solen Kerneis", + "author_inst": "Universite de Paris, INSERM, IAME, Paris, France ; Equipe de Prevention du Risque Infectieux (EPRI), AP-HP, Hopital Bichat, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.26.22271097", "rel_title": "Factors associated with the decay of anti-SARS-CoV-2 neutralizing antibodies among recipients of an adenoviral vector-based AZD1222 and a whole-virion inactivated (BBV152) vaccine in Chennai, India: a cross-sectional cohort study", @@ -355149,65 +354141,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.25.481978", - "rel_title": "Transcriptomic landscapes of SARS-CoV-2-infected and bystander lung cells reveal a selective upregulation of NF-\u03baB-dependent coding and non-coding proviral transcripts", - "rel_date": "2022-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481978", - "rel_abs": "Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of SARS-CoV-2 infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and lncRNAs, including transcripts coding for antiviral factors, such as interferons (IFN). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-{kappa}B pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-{kappa}B pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Anvita Bhargava", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ugo Szachnowski", - "author_inst": "Institut Curie" - }, - { - "author_name": "Maxime Chazal", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Dominika Foretek", - "author_inst": "Insitut Curie" - }, - { - "author_name": "Sophie-Marie Aicher", - "author_inst": "Insitut Pasteur" - }, - { - "author_name": "Juliana Pipoli da Fonseca", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Patricia Jeannin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Guillaume Beauclair", - "author_inst": "Universit\u00e9 Paris-Saclay" - }, - { - "author_name": "Marc Monot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Antonin Morillon", - "author_inst": "CNRS-institut Curie" - }, - { - "author_name": "Nolwenn Jouvenet", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.25.481957", "rel_title": "A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F", @@ -355880,6 +354813,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.02.23.22271433", + "rel_title": "Effectiveness of the third dose of BNT162b2 vaccine on neutralizing Omicron variant in the Japanese population", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271433", + "rel_abs": "IntroductionThe vaccine against SARS-CoV-2 provides humoral immunity to fight COVID-19; however, the acquired immunity gradually declines. Booster vaccination restores reduced humoral immunity; however, its effect on newly emerging variants, such as the Omicron variant, is a concern. As the waves of COVID-19 cases and vaccine programs differ between countries, it is necessary to know the domestic effect of the booster.\n\nMethodsSerum samples were obtained from healthcare workers (20-69 years old) in the Pfizer BNT162b2 vaccine program at the Toyama University Hospital 6 months after the second dose (6mA2D, n = 648) and 2 weeks after the third dose (2wA3D, n = 565). The anti-SARS-CoV-2 antibody level was measured, and neutralization against the wild-type and variants (Delta and Omicron) was evaluated using pseudotyped viruses. Data on booster-related events were collected using questionnaires.\n\nResultsThe median anti-SARS-CoV-2 antibody was >30.9-fold elevated after the booster (6mA2D, 710.0 U/mL [interquartile range (IQR): 443.0-1068.0 U/mL]; 2wA3D, 21927 U/mL [IQR: 15321.0->25000.0 U/mL]). Median neutralizing activity using 100-fold sera against wild-type-, Delta-, and Omicron-derived variants was elevated from 84.6%, 36.2%, and 31.2% at 6mA2D to >99.9%, 99.1%, and 94.6% at 2wA3D, respectively. The anti-SARS-CoV-2 antibody levels were significantly elevated in individuals with fever [≥]37.5 {degrees}C, general fatigue, and myalgia, local swelling, and local hardness.\n\nConclusionThe booster effect, especially against the Omicron variant, was observed in the Japanese population. These findings contribute to the precise understanding of the efficacy and side effects of the booster and the promotion of vaccine campaigns.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hitoshi Kawasuji", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yoshitomo Morinaga", + "author_inst": "University of Toyama" + }, + { + "author_name": "Hideki Tani", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Yumiko Saga", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Makito Kaneda", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yushi Murai", + "author_inst": "University of Toyama" + }, + { + "author_name": "Akitoshi Ueno", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yuki Miyajima", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yasutaka Fukui", + "author_inst": "University of Toyama" + }, + { + "author_name": "Kentaro Nagaoka", + "author_inst": "University of Toyama" + }, + { + "author_name": "Chikako Ono", + "author_inst": "Osaka University" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Hideki Niimi", + "author_inst": "University of Toyama" + }, + { + "author_name": "Yoshihiro Yamamoto", + "author_inst": "University of Toyama" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.21.22271310", "rel_title": "Psychosocial factors associated with mental health and quality of life during the COVID-19 pandemic among low-income urban dwellers in Peninsular Malaysia", @@ -356967,65 +355971,6 @@ "type": "contradictory results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.22.481491", - "rel_title": "Molnupiravir (MK-4482) is efficacious against Omicron and other SARS-CoV-2 variants in the Syrian hamster COVID-19 model", - "rel_date": "2022-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.22.481491", - "rel_abs": "The recent emergence of the SARS-CoV-2 Omicron variant of concern (VOC) containing a heavily mutated spike protein capable of escaping preexisting immunity, identifies a continued need for interventional measures. Molnupiravir (MK-4482), an orally administered nucleoside analog, has demonstrated efficacy against earlier SARS-CoV-2 lineages and was recently approved for SARS-CoV-2 infections in high-risk adults. Here we assessed the efficacy of MK-4482 against the earlier Alpha, Beta and Delta VOCs and Omicron in the Syrian hamster COVID-19 model. Omicron replication and associated lung disease in vehicle treated hamsters was reduced compared to the earlier VOCs. MK-4482 treatment inhibited virus replication in the lungs of Alpha, Beta and Delta VOC infected hamsters. Importantly, MK-4482 profoundly inhibited virus replication in the upper and lower respiratory tract of hamsters infected with the Omicron VOC. Consistent with its mutagenic mechanism, MK-4482 treatment had a more pronounced inhibitory effect on infectious virus titers compared to viral RNA genome load. Histopathologic analysis showed that MK-4482 treatment caused a concomitant reduction in the level of lung disease and viral antigen load in infected hamsters across all VOCs examined. Together, our data indicate the potential of MK-4482 as an effective antiviral against known SARS-CoV-2 VOCs, especially Omicron, and likely future SARS-CoV-2 variants.\n\nOne Sentence SummaryMK-4482 inhibits replication of multiple SARS-CoV-2 variants of concern, including Omicron, in the Syrian hamster COVID-19 model", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kyle Rosenke", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Atsushi Okumura", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Matthew C Lewis", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Kimberly Meade-White", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "W. Forrest Bohler", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Amanda Griffin", - "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Rebecca Rosenke", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Carl Shaia", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Michael Jarvis", - "author_inst": "University of Plymouth" - }, - { - "author_name": "Heinz Feldmann", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.21.22271309", "rel_title": "Association of Workload and Practice of Respectful Maternity Care Among the Healthcare Providers, Before and During the COVID-19 Pandemic in South Western Nepal: A Cross-Sectional Study", @@ -357650,6 +356595,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.22.480950", + "rel_title": "A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding", + "rel_date": "2022-02-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.22.480950", + "rel_abs": "T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. This approach identifies binders missed by computational prediction, highlighting the potential for systemic computational errors given even state-of-the-art training data, and underlines design considerations for epitope identification experiments. This platform serves as a framework for examining relationships between viral conservation and MHC binding, and can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of this approach for determining high-confidence peptide-MHC binding.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Brooke D Huisman", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Zheng Dai", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "David K. Gifford", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Michael E Birnbaum", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.23.481620", "rel_title": "Pre-clinical testing of two serologically distinct chimpanzee-origin adenovirus vectors expressing spike of SARS-CoV-2", @@ -358529,93 +357505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.22.22271041", - "rel_title": "Scottish COVID CAncer iMmunity Prevalence (SCCAMP) - a longitudinal study of patients with cancer receiving active anti-cancer treatment during the COVID-19 pandemic", - "rel_date": "2022-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22271041", - "rel_abs": "BackgroundCancer and systemic anti-cancer treatment (SACT) have been identified as possible risk factors for infection and related severe illness associated with SARS-CoV-2 virus as a consequence of immune suppression. The Scottish COVID CAncer iMmunity Prevalence (SCCAMP) study aims to characterise the incidence and outcomes of SARS-Cov-2 infection in patients undergoing active anti-cancer treatment during the COVID-19 pandemic and their antibody response following vaccination.\n\nPatients and MethodsEligible patients were those attending secondary care for active anti-cancer treatment for a solid tumour. Blood samples were taken for total SARS-CoV-2 antibody assay (Siemens) at baseline and after 1.5, 3, 6 and 12 months. Data on COVID-19 infection, vaccination, cancer type, treatment and outcome was obtained from routine electronic health records.\n\nResultsThe study recruited 766 eligible participants between 28th May 2020 and 31st October 2021. The median age was 62.7 years, and 66.5% were female. Most received cytotoxic chemotherapy (79%), with the remaining 14% receiving immunotherapy and 7% receiving another form of anti-cancer therapy (radiotherapy, other systemic anti-cancer treatment). 48 (6.3%) tested positive for SARS-CoV-2 by PCR during the study period. The overall infection rate matched that of the age-matched local general population until May 2021, after which population levels appeared higher. Antibody testing detected additional evidence of infection prior to vaccination, taking the total number to 58 (7.6%). There was no significant difference in SARS-CoV-2 PCR positive test rates based on type of anti-cancer treatment. Mortality proportion was similar between those who died within 90 days of a positive SARS-CoV-2 PCR and those with no positive PCR (10.4% vs 10.6%). Death from all causes was lowest among vaccinated patients, and of the patients who had a positive SARS-CoV-2 PCR at any time, all of those who died during the study period were unvaccinated. Multivariate analysis correcting for age, gender, socioeconomic status, comorbidities and number of previous medications revealed that vaccination was associated with a significantly lower infection rate regardless of treatment with chemotherapy or immunotherapy with hazard ratios of 0.307 (95% CI 0.144-0.6548) or 0.314 (95% CI 0.041-2.367) in vaccinated patients respectively. Where antibody data was available, 96.3% of patients successfully raised SARS-CoV-2 antibodies at a time point after vaccination. This was unaffected by treatment type.\n\nConclusionSCCAMP provides real-world evidence that patients with cancer undergoing SACT have a high antibody response and protection from SARS-CoV-2 infection following COVID-19 vaccination.\n\nHighlights- The SCCAMP dataset represents the largest longitudinal study of patients with cancer undergoing anti-cancer treatment during the COVID-19 pandemic\n- Rates of infection in the cancer cohort mirrored those of the local age adjusted population\n- Vaccination was effective in patients with cancer undergoing active treatment in terms of antibody response and SARS-CoV-2 PCR rates\n- Treatment type did not impact the rate of SARS-CoV-2 antibody response", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Karin Purshouse", - "author_inst": "University of Edinburgh/Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "John P Thomson", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Mah\u00e9va Vallet", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Lorna Alexander", - "author_inst": "Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "Isaac Bonisteel", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Maree Brennan", - "author_inst": "Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "David Cameron", - "author_inst": "University of Edinburgh/Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "Jonine Figueroa", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Elizabeth Furrie", - "author_inst": "Department of Immunology, Ninewells Hospital and Dundee Medical School" - }, - { - "author_name": "Pamela Haig", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Mattea Heck", - "author_inst": "The University of Edinburgh Medical School" - }, - { - "author_name": "Hugh McCaughan", - "author_inst": "Clinical Infection Research Group, Regional Infectious Diseases Unit" - }, - { - "author_name": "Paul D Mitchell", - "author_inst": "The University of Edinburgh" - }, - { - "author_name": "Heather McVicars", - "author_inst": "Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "Lorraine Primrose", - "author_inst": "Edinburgh Cancer Centre, NHS Lothian" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Clinical Infection Research Group, Regional Infectious Diseases Unit" - }, - { - "author_name": "Natalie Wilson", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Peter S Hall", - "author_inst": "University of Edinburgh/Edinburgh Cancer Centre, NHS Lothian" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2022.02.22.22271342", "rel_title": "Impact of BNT162b2 mRNA Vaccination on the Development of Short and Long-term Vaccine-Related Adverse Events in Inflammatory Bowel Disease: A Multi-Center Prospective Study", @@ -359248,6 +358137,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.02.20.22270449", + "rel_title": "Quantifying the effect of isolation and negative certification on COVID-19 transmission", + "rel_date": "2022-02-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.20.22270449", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIsolation of close contact people and negative test certification are used to manage the spread of new coronavirus infections worldwide. These effectively prevent the spread of infection in advance, but they can lead to a decline in socio-economic activity. Thus, the present study quantified the extent to which isolation and negative test certification respectively reduce the risk of infection. To this end, a discrete-time SEIR model was used as the infectious disease model, and equations for calculating the conditional probability of non-infection status given negative test results on two different days were derived. Then the respective non-infection probabilities with two negative PCR test results, and with one negative PCR test result and one antigen test result, were quantified. By substituting initial parameters of the SEIR model into these probabilities, the present study revealed the following: (1) isolating close contact individuals can reduce by 80% the risk of infection during the first five days, but five more days are needed to reduce the risk 10% more, and seven more days to reduce the risk 20% more; and (2) if an individual with a negative PCR test result has a negative antigen test result the next day, then his or her infection probability is between 0.6% and 0.7%. Our results show that five-day isolation has a proportionally greater effect on risk reduction, compared to longer isolation; and thus, if an isolation period of longer than five days is contemplated, both the risk reduction and the negative effects from such increased isolation should be considered. Regarding negative test certification, our results provide those in managerial positions, who must decide whether to accept the risk and hold mass-gathering events, with quantitative information that may be useful in their decision-making.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jun-ichi Takeshita", + "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" + }, + { + "author_name": "Michio Murakami", + "author_inst": "Osaka University" + }, + { + "author_name": "Masashi Kamo", + "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" + }, + { + "author_name": "Wataru Naito", + "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" + }, + { + "author_name": "Tetsuo Yasutaka", + "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" + }, + { + "author_name": "Seiya Imoto", + "author_inst": "The University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.21.22270793", "rel_title": "Examining disparities relating to service reach and patient engagement with COVID-19 remote home monitoring services in England: a mixed methods rapid evaluation", @@ -360502,49 +359430,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.21.22271306", - "rel_title": "Tackling the first COVID-19 wave at the Cape Town Hospital of Hope: Why was it such a positive experience for staff?", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271306", - "rel_abs": "BackgroundIn contrast to alarming reports of exhaustion and burnout amongst healthcare workers in the first wave of the COVID-19 pandemic, we noticed surprisingly positive staff experiences of working in a COVID-19 field hospital in South Africa. The 862-bed Hospital of Hope was established at the Cape Town International Convention Centre specifically to cope with the effects of the first wave of the COVID-19 pandemic in Cape Town.\n\nMethodsWe aimed to systematically describe and assess the effects on staff and the local health system. A cross-sectional descriptive study design was employed using mixed methods including record reviews and interviews with key informants.\n\nResultsQuantitative results confirmed high job satisfaction and low staff infection rates. The emerging themes from the qualitative data are grouped around a \"bulls eye\" of the common purpose of person-centredness, from both patient and staff perspectives, and include staff safety and support, rapid communication, continuous learning and adaptability, underpinned by excellent teamwork. The explanations for the positive feedback included good disaster planning, adequate resources, and an extraordinary responsiveness to the need.\n\nConclusionsThe Hospital of Hope staff experience produced significant learnings for the design and management of routine health services outside of a disaster situation. The adaptability and responsiveness of the facility and its staff was largely a product of the unprecedented nature of the pandemic, but such approaches could benefit routine health services enormously, as individual hospitals and health facilities realize their place in a system that is more than the sum of its parts.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Steve Reid", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Mitan Nana", - "author_inst": "University of Cape Town Faculty of Health Sciences" - }, - { - "author_name": "Theo Abrahams", - "author_inst": "Western Cape Department of Health" - }, - { - "author_name": "Klaus Von Pressentin", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Ronit Okun", - "author_inst": "Western Cape Department of Health" - }, - { - "author_name": "Tasleem Ras", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Nadia Hussey", - "author_inst": "Western Cape Department of Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.18.22271191", "rel_title": "Childhood Trauma Exposure Increases Long COVID Risk", @@ -361365,6 +360250,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.15.22271018", + "rel_title": "COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine", + "rel_date": "2022-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.15.22271018", + "rel_abs": "BackgroundCharacterizing the experience and impact of the COVID-19 pandemic among various populations remains challenging due to the limitations inherent in common data sources such as the electronic health record (EHR) or convenience sample surveys.\n\nObjectiveTo describe testing behaviors, symptoms, impact, vaccination status and case ascertainment during the COVID-19 pandemic using integrated data sources.\n\nMethodsIn summer 2020 and 2021, we surveyed participants enrolled in the Biobank at the Colorado Center for Personalized Medicine (CCPM, N = 180,599) about their experience with COVID-19. Prevalence of testing, symptoms, and the impacts of COVID-19 on employment, family life, and physical and mental health were calculated overall and by demographic categories. Using the Electronic Health Record (EHR), we compared COVID-19 case ascertainment and characteristics in the EHR versus the survey.\n\nResultsOf the 25,063 survey respondents (13.9%), 42.5% had been tested for COVID-19 and of those, 12.8% tested positive. Nearly half of those tested had symptoms and/or had been exposed to someone who was infected. Young adults (18-29 years) and Hispanics were more likely to have positive tests compared to older adults and persons of other racial/ethnic groups. Mental health (54.6%) and family life (48.8%) were most negatively affected by the pandemic and more so among younger groups and women; negative impacts on employment were more commonly reported among Black respondents. After integration with EHR data up to the time of the survey completion, 4.0% of survey respondents (n=1,006) had discordant COVID-19 case status between the EHR and the survey. Using all longitudinal EHR and survey data, we identified 11,472 COVID-positive cases among Biobank participants (6.4%). In comparison to COVID-19 cases identified through the survey, EHR-identified cases were younger and more likely to be Hispanic.\n\nConclusionsIntegrated data assets such as the Biobank at the CCPM are key resources for population health monitoring in response to public health emergencies, such as the COVID-19 pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Randi K Johnson", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Katie M Marker", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "David Mayer", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Jonathan Shortt", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "David Kao", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Kathleen C Barnes", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + }, + { + "author_name": "Jan T Lowery", + "author_inst": "Colorado Center for Personalized Medicine" + }, + { + "author_name": "Christopher R Gignoux", + "author_inst": "Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.19.22270722", "rel_title": "Insights on Telemedicine Use by Physiatrists Before, During, and Beyond the COVID-19 Pandemic", @@ -362568,121 +361500,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.18.22270995", - "rel_title": "Host and microbiome features of secondary infections in lethal covid-19", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22270995", - "rel_abs": "Secondary infections contribute significantly to covid-19 mortality but host and microbial factors driving this sequel remain poorly understood. We performed an autopsy study of 20 covid-19 cases and 14 controls from the first pandemic wave. Autopsies combined with microbial cultivation and deep RNA sequencing (RNAseq) allowed us to define major organ pathologies and specify secondary infections. Lethal covid-19 segregated into two main death causes separating cases with either dominant diffuse alveolar damage (DAD) or secondary infections of lungs. Lung microbiome changes were profound in covid-19 showing a reduced biodiversity and increased presence of prototypical bacterial and fungal pathogens in cases with secondary infections. Deep RNAseq of lung tissues distinctly mirrored death causes and cellular deconvolution stratified DAD cases into subgroups with different cellular compositions. Myeloid cells, including macrophages, and complement C1q activation were found to be strong stratifying factors suggesting a pathophysiological link possibly leading to tolerance in DAD subgroups. Moreover, several signs of immune-impairment were evident in covid-19 lungs including strong induction of inhibitory immune-checkpoints. Thus, our study highlights profound alterations of the local immunity in covid-19, wherein immune-impairment leads to reduced antimicrobial defense favoring the development of secondary infections on top of SARS-CoV-2 infection.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Martin Zacharias", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Karl Kashofer", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Philipp Wurm", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Peter Regitnig", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Moritz Schuette", - "author_inst": "Alacris Theranostics GmbH, Max-Planck-Strasse 3, D-12489 Berlin, Germany" - }, - { - "author_name": "Margit Neger", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Sandra Ehmann", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Leigh M. Marsh", - "author_inst": "Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstrasse 6/VI, A-8010 Graz, Austria" - }, - { - "author_name": "Grazyna Kwapiszewska", - "author_inst": "Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstrasse 6/VI, A-8010 Graz, Austria" - }, - { - "author_name": "Martina Loibner", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Anna Birnhuber", - "author_inst": "Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstrasse 6/VI, A-8010 Graz, Austria" - }, - { - "author_name": "Eva Leitner", - "author_inst": "Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austr" - }, - { - "author_name": "Andrea Thueringer", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Elke Winter", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Stefan Sauer", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Marion J. Pollheimer", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Fotini R. Vagena", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Carolin Lackner", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Barbara Jelusic", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Lesley Ogilvie", - "author_inst": "Alacris Theranostics GmbH, Max-Planck-Strasse 3, D-12489 Berlin, Germany" - }, - { - "author_name": "Marija Durdevic", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Bernd Timmermann", - "author_inst": "Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany" - }, - { - "author_name": "Hans Lehrach", - "author_inst": "Alacris Theranostics GmbH, Max-Planck-Strasse 3, D-12489 Berlin, Germany" - }, - { - "author_name": "Kurt Zatloukal", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - }, - { - "author_name": "Gregor Gorkiewicz", - "author_inst": "Diagnostic and Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2022.02.17.22270679", "rel_title": "Evolutionary Trajectories of SARS-CoV-2 Alpha and Delta Variants in White-Tailed Deer in Pennsylvania", @@ -363391,6 +362208,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.17.480940", + "rel_title": "Preparing for the next COVID: Deep Reinforcement Learning trained Artificial Intelligence discovery of multi-modal immunomodulatory control of systemic inflammation in the absence of effective anti-microbials", + "rel_date": "2022-02-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.17.480940", + "rel_abs": "BackgroundDespite a great deal of interest in the application of artificial intelligence (AI) to sepsis/critical illness, most current approaches are limited in their potential impact: prediction models do not (and cannot) address the lack of effective therapeutics and current approaches to enhancing the treatment of sepsis focus on optimizing the application of existing interventions, and thus cannot address the development of new treatment options/modalities. The inability to test new therapeutic applications was highlighted by the generally unsatisfactory results from drug repurposing efforts in COVID-19.\n\nHypothesisAddressing this challenge requires the application of simulation-based, model-free deep reinforcement learning (DRL) in a fashion akin to training the game-playing AIs. We have previously demonstrated the potential of this method in the context of bacterial sepsis in which the microbial infection is responsive to antibiotic therapy. The current work addresses the control problem of multi-modal, adaptive immunomodulation in the circumstance where there is no effective anti-pathogen therapy (e.g., in a novel viral pandemic or in the face of resistant microbes).\n\nMethodsThis is a proof-of-concept study that determines the controllability of sepsis without the ability to pharmacologically suppress the pathogen. We use as a surrogate system a previously validated agent-based model, the Innate Immune Response Agent-based Model (IIRABM), for control discovery using DRL. The DRL algorithm trains an AI on simulations of infection where both the control and observation spaces are limited to operating upon the defined immune mediators included in the IIRABM (a total of 11). Policies were learned using the Deep Deterministic Policy Gradient approach, with the objective function being a return to baseline system health.\n\nResultsDRL trained an AI policy that improved system mortality from 85% to 10.4%. Control actions affected every one of the 11 targetable cytokines and could be divided into those with static/unchanging controls and those with variable/adaptive controls. Adaptive controls primarily targeted 3 different aspects of the immune response: 2nd order pro-inflammation governing TH1/TH2 balance, primary anti-inflammation, and inflammatory cell proliferation.\n\nDiscussionThe current treatment of sepsis is hampered by limitations in therapeutic options able to affect the biology of sepsis. This is heightened in circumstances where no effective antimicrobials exist, as was the case for COVID-19. Current AI methods are intrinsically unable to address this problem; doing so requires training AIs in contexts that fully represent the counterfactual space of potential treatments. The synthetic data needed for this task is only possible through the use of high-resolution, mechanism-based simulations. Finally, being able to treat sepsis will require a reorientation as to the sensing and actuating requirements needed to develop these simulations and bring them to the bedside.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Dale Larie", + "author_inst": "University of Vermont Larner College of Medicine" + }, + { + "author_name": "Gary An", + "author_inst": "University of Vermont" + }, + { + "author_name": "Chase Cockrell", + "author_inst": "University of Vermont" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.18.480872", "rel_title": "SARS-CoV-2 has not emerged in roe, red or fallow deer in Germany or Austria during the COVID 19 pandemic", @@ -364466,57 +363310,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.02.17.22270551", - "rel_title": "Natural Trajectory of Recovery of COVID-19 Associated Olfactory Loss", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22270551", - "rel_abs": "ImportancePrevalence of post-viral olfactory loss has increased dramatically due to the frequency and severity of olfactory dysfunction associated with infection by the SARS-CoV-2 virus.\n\nObjectiveTo determine the trajectory of COVID-19 olfactory loss over a six-month period. A key secondary objective is to assess predictive factors associated with the recovery of olfaction.\n\nDesignLongitudinal repeated-measures study that enrolled from May 5, 2020 to February 2, 2021, with the last date of data collection on June 15, 2021.\n\nSettingBarnes-Jewish HealthCare/Washington University School of Medicine facilities (Saint Louis, Missouri, USA).\n\nParticipantsIndividuals who tested positive for SARS-CoV-2 by real-time polymerase chain reaction on nasopharyngeal swab and indicated olfactory loss on COVID-19 screening questionnaire. Individuals were excluded if they had previously diagnosed history of olfactory loss, neurodegenerative disorders, less than 18 years of age, admitted to hospital service, unable to read, write, and understand English, or lacked computer or internet access.\n\nInterventions/ExposuresWatch and wait for spontaneous recovery.\n\nMain Outcome(s) and Measure(s)Participants completed olfactory assessments every 30 days for six months. Each assessment consisted of the University of Pennsylvania Smell Identification Test (UPSIT), an objective \"scratch-and-sniff\" test, and Clinical Global Impressions (CGI), a subjective Likert rating scale.\n\nResultsThe mean age was 41 years old (SD = 16). 39 (80%) were female and 42 (86%) white. At baseline assessment of objective olfaction, 18 (36%) participants had anosmia or severe hyposmia. Subjective, complete recovery at six months was 81% (95% CI 74% to 88%). Likelihood of recovery was associated with age less than 50 years (aHR = 8.1 (95% CI 1.1 to 64.1)) and mild olfactory loss at baseline (UPSIT = 30-33 for males and 31-34 for females) (aHR 6.2 (95% CI 1.2 to 33.0)).\n\nConclusions and RelevanceThe trajectory of olfactory recovery among adults with COVID-19 olfactory loss illustrated rapid recovery within 2-3 weeks of infection, and by six months 81% had recovered based on self-report. Age less than 50 years old and mild severity of olfactory loss at baseline were associated with increased likelihood of recovery of olfaction. These findings can be used to inform shared decision-making with patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Amish Khan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jake J. Lee", - "author_inst": "Washington university School of Medicine" - }, - { - "author_name": "Thuelfaqar Rammaha", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Shruti Gupta", - "author_inst": "Medical College of Georgia - Augusta University" - }, - { - "author_name": "Harrison Smith", - "author_inst": "New York Medical College, Valhalla, NY" - }, - { - "author_name": "Thomas Kannampallil", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Nyssa Farrell", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Dorina Kallogjeri", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jay Francis Piccirillo", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.16.22270842", "rel_title": "The SARS-CoV2 envelope is distinct from host membranes, exposes pro-coagulant lipids, and can be inactivated in vivo by surfactant-containing oral rinses.", @@ -365325,6 +364118,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.15.480603", + "rel_title": "A possible way to relate the effects of SARS-CoV-2 induced changes in transferrin to severe COVID-19 associated diseases", + "rel_date": "2022-02-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.15.480603", + "rel_abs": "The potentially life-threatening Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is responsible for the coronavirus pandemic in 2019 (COVID-19). The transferrin as an essential component of iron-metabolism was suggested to be a link between iron transport associated diseases and COVID-19 infection.\n\nThe effect of SARS-CoV-2 on human whole blood was studied by differential scanning calorimetry. The analysis and deconvolution of the thermal transition curves showed that the Tm of transferrin related second peak decreased by 5.16 {degrees}C (6.4%) in the presence of SARS-CoV-2 virus. The ratio of the under-curve area of the two main peaks was greatly affected while the total enthalpy of the heat denaturation was nearly unchanged in the presence of the virus.\n\nBased on the results it is possible to conclude that SARS-CoV-2 through binding to transferrin can influence its Fe3+ uptake by inducing thermodynamic changes. Transferrin may stay in iron-free apo-conformational state, which probably depends on the SARS-CoV-2 concentration.\n\nSARS-CoV-2 might induce disturbance in the erythropoiesis due to the free iron overload generated iron toxicity. As a late consequence iron toxicity related hepatocellular carcinoma can even develop.\n\nOur work can support the basic role of transferrin in COVID-19 related severe diseases.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elek Telek", + "author_inst": "Department of Biophysics, Medical School, University of Pecs, H-7624, Pecs, Szigeti str. 12, Hungary" + }, + { + "author_name": "Zoltan Ujfalusi", + "author_inst": "Department of Biophysics, Medical School, University of Pecs, H-7624, Pecs, Szigeti str. 12, Hungary" + }, + { + "author_name": "Gabor Kemenesi", + "author_inst": "National Laboratory of Virology, University of Pecs, H-7624, Pecs, Ifjusag str. 20, Hungary" + }, + { + "author_name": "Brigitta Zana", + "author_inst": "National Laboratory of Virology, University of Pecs, H-7624, Pecs, Ifjusag str. 20, Hungary" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "National Laboratory of Virology, University of Pecs, H-7624, Pecs, Ifjusag str. 20, Hungary" + }, + { + "author_name": "Andras Lukacs", + "author_inst": "Department of Biophysics, Medical School, University of Pecs, H-7624, Pecs, Szigeti str. 12, Hungary" + }, + { + "author_name": "Gabor Hild", + "author_inst": "Department of Biophysics, Medical School, University of Pecs, H-7624, Pecs, Szigeti str. 12, Hungary, Department of Medical Imaging, Clinical Centre, University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.02.15.480585", "rel_title": "Mathematical model of a cytokine storm", @@ -366308,37 +365144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.02.14.22268832", - "rel_title": "Users' Reactions on Announced Vaccines against COVID-19 Before Marketing in France: Analysis of Twitter posts", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22268832", - "rel_abs": "BackgroundWithin a few months, the COVID-19 pandemic has spread to many countries and has been a real challenge for health systems all around the world. This unprecedented crisis has led to a surge of online discussions about potential cures for the disease. Among them, vaccines have been at the heart of the debates, and have faced lack of confidence before marketing in France.\n\nObjectiveThis study aims to identify and investigate the opinion of French Twitter users on the announced vaccines against COVID-19 through sentiment analysis.\n\nMethodsThis study was conducted in two phases. First, we filtered a collection of tweets related to COVID-19 from February to August 2020 with a set of keywords associated with vaccine mistrust using word embeddings. Second, we performed sentiment analysis using deep learning to identify the characteristics of vaccine mistrust. The model was trained on a hand labeled subset of 4,548 tweets.\n\nResultsA set of 69 relevant keywords were identified as the semantic concept of the word \"vaccin\" (vaccine in French) and focus mainly on conspiracies, pharmaceutical companies, and alternative treatments. Those keywords enabled to extract nearly 350k tweets in French. The sentiment analysis model achieved a 0.75 accuracy. The model then predicted 16% of positive tweets, 41% of negative tweets and 43% of neutral tweets. This allowed to explore the semantic concepts of positive and negative tweets and to plot the trends of each sentiment. The main negative rhetoric identified from users tweets was that vaccines are perceived as having a political purpose, and that COVID-19 is a commercial argument for the pharmaceutical companies.\n\nConclusionsTwitter might be a useful tool to investigate the arguments of vaccine mistrust as it unveils a political criticism contrasting with the usual concerns on adverse drug reactions. As the opposition rhetoric is more consistent and more widely spread than the positive rhetoric, we believe that this research provides effective tools to help health authorities better characterize the risk of vaccine mistrust.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alexandre Dupuy-Zini", - "author_inst": "Sorbonne Universit\u00e9, Universit\u00e9 Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique M\u00e9dicale et d'Ing\u00e9nierie des connaissances en e-Sant\u00e9, LIMICS, Paris, Fr" - }, - { - "author_name": "Bissan Audeh", - "author_inst": "Sorbonne Universit\u00e9, Universit\u00e9 Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique M\u00e9dicale et d'Ing\u00e9nierie des connaissances en e-Sant\u00e9, LIMICS, Paris, Fr" - }, - { - "author_name": "Amandine Gagneux-Brunon", - "author_inst": "Centre International de Recherche en Infectiologie, Team GIMAP, Univ Lyon, Universit\u00e9 Jean Monnet, Universit\u00e9 Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530" - }, - { - "author_name": "Cedric Bousquet", - "author_inst": "Sorbonne Universit\u00e9, Universit\u00e9 Sorbonne Paris Nord, INSERM, Laboratoire d'Informatique M\u00e9dicale et d'Ing\u00e9nierie des connaissances en e-Sant\u00e9, LIMICS, Paris, Fr" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.02.11.22270775", "rel_title": "Favipiravir, lopinavir-ritonavir or combination therapy (FLARE): a randomised, double blind, 2x2 factorial placebo-controlled trial of early antiviral therapy in COVID-19", @@ -367303,6 +366108,181 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.14.480353", + "rel_title": "The BNT162b2 mRNA SARS-CoV-2 vaccine induces transient afucosylatedIgG1 in naive but not antigen-experienced vaccinees", + "rel_date": "2022-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.14.480353", + "rel_abs": "The onset of severe SARS-CoV-2 infection is characterized by the presence of afucosylated IgG1 responses against the viral spike (S) protein, which can trigger exacerbated inflammatory responses. Here, we studied IgG glycosylation after BNT162b2 SARS-CoV-2 mRNA vaccination to explore whether vaccine-induced S protein expression on host cells also generates afucosylated IgG1 responses. SARS-CoV-2 naive individuals initially showed a transient afucosylated anti-S IgG1 response after the first dose, albeit to a lower extent than severely ill COVID-19 patients. In contrast, previously infected, antigen-experienced individuals had low afucosylation levels, which slightly increased after immunization. Afucosylation levels after the first dose correlated with low fucosyltransferase 8 (FUT8) expression levels in a defined plasma cell subset. Remarkably, IgG afucosylation levels after primary vaccination correlated significantly with IgG levels after the second dose. Further studies are needed to assess efficacy, inflammatory potential, and protective capacity of afucosylated IgG responses.\n\nOne sentence summaryA transient afucosylated IgG response to the BNT162b2 mRNA vaccine was observed in naive but not in antigen-experienced individuals, which predicted antibody titers upon the second dose.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Julie Van Coillie", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Tamas Pongracz", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Johann Rahmoeller", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Hung-Jen Chen", + "author_inst": "Department of Medical Biochemistry, Amsterdam UMC" + }, + { + "author_name": "Chiara E. Geyer", + "author_inst": "Center for Experimental and Molecular Medicine, Amsterdam Infection & Immunity Institute" + }, + { + "author_name": "Lonneke A. van Vught", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Jana S. Buhre", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Tonci Sustic", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Thijs L.J. van Osch", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Maurice Steenhuis", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Willianne Hoepel", + "author_inst": "Department of Rheumatology and Clinical Immunology, Amsterdam UMC" + }, + { + "author_name": "Wenjun Wang", + "author_inst": "Center for Proteomics and Metabolomics, Leiden University Medical Center" + }, + { + "author_name": "Anne Lixenfeld", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Jan Nouta", + "author_inst": "Center for Proteomics and Metabolomics, Leiden University Medical Center" + }, + { + "author_name": "Sofie Keijzer", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Federica Linty", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Remco Visser", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Mads Delbo Larsen", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Emily L. Martin", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Inga Kuensting", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Selina Lehrian", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Vera von Kopylow", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Carsten Kern", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Hanna Lunding", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Menno P.J. de Winther", + "author_inst": "Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands" + }, + { + "author_name": "Niels van Mourik", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Theo Rispens", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Tobias Graf", + "author_inst": "Medical Department 3, University Medical Center of Schleswig-Holstein" + }, + { + "author_name": "Marleen A. Slim", + "author_inst": "Center for Experimental and Molecular Medicine, Amsterdam UMC" + }, + { + "author_name": "Rene P. Minnaar", + "author_inst": "Amsterdam UMC Biobank" + }, + { + "author_name": "Marije K. Bomers", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Jonne J. Sikkens", + "author_inst": "Amsterdam AMC" + }, + { + "author_name": "Alexander P. J. Vlaar", + "author_inst": "Department of Intensive Care, Amsterdam University Medical Centers" + }, + { + "author_name": "Ellen C. van der Schoot", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Jeroen den Dunnen", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Marc Ehlers", + "author_inst": "Laboratories of Immunology and Antibody Glycan Analysis, Institute of Nutritional Medicine, University of Luebeck and University Medical Center of Schleswig-Hol" + }, + { + "author_name": "Manfred Wuhrer", + "author_inst": "Center for Proteomics and Metabolomics, Leiden University Medical Center" + }, + { + "author_name": "Gestur Vidarsson", + "author_inst": "Sanquin Research" + }, + { + "author_name": "- Fatebenefratelli-Sacco Infectious Diseases Physicians group", + "author_inst": "-" + }, + { + "author_name": "- UMC COVID-19 S3/HCW study group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.10.22270607", "rel_title": "Prior SARS-CoV2 infection in vaccinated solid organ transplant recipients induces potent neutralization responses against variants, including Omicron", @@ -368386,69 +367366,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2022.02.15.22270974", - "rel_title": "A randomized clinical trial of a booster dose with low versus standard dose of AZD1222 in adult after 2 doses of inactivated vaccines", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.15.22270974", - "rel_abs": "BackgroundImmunogenicity of inactivated SARS-CoV-2 vaccine has waning antibody over time. With the emergence of the SARS-CoV-2 delta variant, which requires higher neutralizing antibody to prevent infection, a booster dose is needed.\n\nObjectiveTo evaluate immunogenicity and reactogenicity of standard- versus low-dose ChAdOx1 nCoV-19 vaccine booster after CoronaVac in healthy adults.\n\nMethodsA double-blinded, randomized, controlled trial of adult, aged 18-59 years, with completion of 2-dose CoronaVac at 21-28 days apart for more than 2 months was conducted. Participants were randomized to receive AZD1222 (Oxford/AstraZeneca) intramuscularly; standard dose (SD, 5x1010 viral particles) or low dose (LD, 2.5x1010 viral particles). Surrogate virus neutralization test (sVNT) against wild type and delta variant, and anti-spike-receptor-binding-domain IgG (anti-S-RBD IgG) were compared as geometric mean ratio (GMR) at day 14 and 90 between LD and SD arms.\n\nResultsFrom July-August 2021, 422 adults with median age of 44 (IQR 36-51) years were enrolled. The median interval from CoronaVac to AZD1222 booster was 77 (IQR 64-95) days. At baseline, geometric means (GMs) of sVNT against delta variant and anti-S-RBD IgG were 18.1%inhibition (95%CI 16.4-20.0) and 111.5 (105.1-118.3) BAU/ml. GMs of sVNT against delta variant and anti-S-RBD IgG in SD were 95.6%inhibition (95%CI 94.3-97.0) and 1975.1 (1841.7-2118.2) BAU/ml at day 14, and 89.4%inhibition (86.4-92.4) and 938.6 (859.9-1024.4) BAU/ml at day 90, respectively. GMRs of sVNT against delta variant and anti-S-RBD IgG in LD compared to SD were 1.00 (95%CI 0.98-1.02) and 0.84 (0.76-0.93) at day 14, and 0.98 (0.94-1.03) and 0.89 (0.79-1.00) at day 90, respectively. LD recipients had significantly lower rate of fever (6.8%vs25.0%) and myalgia (51.9%vs70.7%) compared to SD.\n\nConclusionHalf-dose AZD1222 booster after 2-dose inactivated SARS-CoV-2 vaccination had non-inferior immunogenicity, yet lower systemic reactogenicity. Fractional low-dose AZD1222 booster should be considered especially in resource-constrained settings.\n\nHighlights- Low dose AZD1222 could boost comparable immunity to standard dose in healthy adult who completed 2 doses of inactivated SARS-CoV-2 vaccines.\n- Less reactogenicity occurred in low-dose AZD1222 booster than standard-dose recipients.\n\n\nThai Clinical Trials Registry (thaiclinicaltrials.org): TCTR20210722003", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sira Nanthapisal", - "author_inst": "Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand" - }, - { - "author_name": "Thanyawee Puthanakit", - "author_inst": "Center of Excellence in Pediatric Infectious Diseases and Vaccines, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" - }, - { - "author_name": "Peera Jaru-Ampornpan", - "author_inst": "Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC)" - }, - { - "author_name": "Rapisa Nantanee", - "author_inst": "Pediatric Allergy and Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn Univer" - }, - { - "author_name": "Pimpayao Sodsai", - "author_inst": "Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" - }, - { - "author_name": "Orawan Himananto", - "author_inst": "Monoclonal Antibody Production and Application Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC)" - }, - { - "author_name": "Jiratchaya Sophonphan", - "author_inst": "The HIV Netherlands Australia Thailand Research Collaboration (HIV-NAT), The Thai Red Cross AIDS Research Centre, Bangkok, Thailand" - }, - { - "author_name": "Pintip Suchartlikitwong", - "author_inst": "Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" - }, - { - "author_name": "Narin Hiransuthikul", - "author_inst": "Department of Preventive and Social Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" - }, - { - "author_name": "Pornpimon Angkasekwinai", - "author_inst": "Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand" - }, - { - "author_name": "Auchara Tangsathapornpong", - "author_inst": "Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand" - }, - { - "author_name": "Nattiya Hirankarn", - "author_inst": "Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.14.22270965", "rel_title": "Experiences of the physicians in the largest COVID-19 dedicated hospital of Bangladesh about COVID-19 and its aftermath", @@ -369281,6 +368198,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.13.22270898", + "rel_title": "Risk of severe COVID-19 in patients with inflammatory rheumatic diseases treated with immunosuppressive therapy in Scotland", + "rel_date": "2022-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.13.22270898", + "rel_abs": "ObjectivesTo investigate the association of severe COVID-19 in those with inflammatory rheumatic diseases (IRD) treated with immunosuppressive drugs.\n\nMethodsA list of 4633 patients on biologics and targeted synthetic (ts) DMARDs in March 2020 was linked to a case-control study that includes all cases of COVID-19 in Scotland.\n\nResultsBy 22 November 2021 433 of the 4633 patients treated with biologics and tsDMARDs had been diagnosed with COVID-19, of whom 58 had been hospitalised. With all those in the population not on DMARDs as reference category, the rate ratio for hospitalised COVID-19 associated with DMARD treatment was 2.14 (95% CI 2.02 to 2.26) in those on conventional synthetic (cs) DMARDs, 2.01 (95% CI 1.38 to 2.91) in those on TNF inhibitors as the only biologic agent, and 3.83 (95% CI 2.65 to 5.56) in those on other biologic agents. Among those on csDMARDs, rate ratios for hospitalised COVID-19 were lowest at 1.66 (95% CI 1.51 to 1.82) in those on methotrexate and highest at 5.4 (95% CI 4.4 to 6.7) in those on glucocorticoids at average dose >10 mg/day prednisolone equivalent.\n\nConclusionThe risk of hospitalised COVID-19 is elevated in IRD patients treated with immunosuppressive drugs. Of these drugs, methotrexate, hydroxychloroquine, and TNF inhibitors carry the lowest risk, JAK inhibitors and B-cell depleting agents a higher risk and prednisolone the highest risk. A larger study is needed to estimate reliably the risks associated with each class of biologic agent.\n\nKey messagesO_LIRisk of hospitalised COVID-19 is about twofold higher in IRD patients treated with immunosuppressive therapies - csDMARDS or biologics - than in the general population.\nC_LIO_LIRisk is lowest in those treated with methotrexate, hydroxychoroquine and TNF inhibitors. Of the other biologic drugs, treatment with B cell depleters and JAK inhibitors is associated with higher risk but the numbers are too small for risk associated with each drug class to be estimated reliably.\nC_LIO_LIThe risk of severe COVID-19 with glucocorticoids at a dose greater than 10 mg/day prednisolone equivalent is higher than that of any other drug class studied.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Paul M McKeigue", + "author_inst": "Usher Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG" + }, + { + "author_name": "Duncan Porter", + "author_inst": "Gartnavel General Hospital, 1053 Gt Western Rd, Glasgow G12 0YN" + }, + { + "author_name": "Rosemary J Hollick", + "author_inst": "Aberdeen Centre for Arthritis and Musculoskeletal Health (Epidemiology Group), School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberd" + }, + { + "author_name": "Stuart J Ralston", + "author_inst": "Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh E" + }, + { + "author_name": "David A McAllister", + "author_inst": "Institute of Health and Wellbeing, University of Glasgow, 1 Lilybank Gardens, Glasgow G12 8RZ" + }, + { + "author_name": "Helen M Colhoun", + "author_inst": "Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh E" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2022.02.10.22270804", "rel_title": "FOLIC ACID AND METHOTREXATE USE AND THEIR ASSOCIATION WITH COVID-19 DIAGNOSIS AND MORTALITY: AN ANALYSIS FROM THE UK BIOBANK", @@ -370520,57 +369476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270836", - "rel_title": "Persistence, prevalence, and polymorphism of sequelae after COVID-19 in young adults", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270836", - "rel_abs": "BackgroundCOVID-19 sequelae are poorly defined with an ambiguous pathophysiology. Persistent sequelae could have global, public health and societal ramifications. We aimed to describe sequelae presenting more than six months after COVID-19 in non-hospitalized young adults.\n\nMethodsA prospective, longitudinal cohort study followed-up on young Swiss Armed Forces (SAF) personnel. The comprehensive test battery was administered during a single full day of testing at the University of Zurich. It quantified the impact of SARS-CoV-2 infection on cardiovascular, pulmonary, neurological, renal, ophthalmological, male reproductive, psychological, and general health in addition to laboratory parameters.\n\nResultsWe included 501 participants (5.6% females) with a median age of 21 years (range 19-29). Cases of previous COVID -19 (>6 months (mean 10 months) since diagnosis, n=177) were compared with never infected controls (n=248). We also included more recent COVID-19 cases ([≤]6 months, n=19) and asymptomatically infected individuals (n=49). We found a significant trend towards metabolic disorders, higher Body Mass Index (BMI) (p=0.03), lower aerobic threshold (p=0.007), higher blood cholesterol (p<0.001) and low-density lipoprotein LDL levels (p<0.001) in participants> 6 months post Covid-19 when compared to controls. There were no significant differences in psychosocial questionnaire scores, ophthalmological outcomes, sperm quality or motility between controls and those infected more than 6 months previously with SARS-CoV-2.\n\nConclusionsYoung, previously healthy, individuals largely recover from mild infection and the multi-system impact of the infection is less that seen in older or hospitalized patients. These results may be extrapolated to health-care workers and other young workforce adults. However, the constellation of higher body mass index, dyslipidemia and lower physical endurance 6 months post COVID-19 is suggestive of a higher risk of developing metabolic disorders and possible cardiovascular complications. These findings will guide investigation and follow-up management.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jeremy Werner Deuel", - "author_inst": "University of Zurich" - }, - { - "author_name": "Elisa Lauria", - "author_inst": "University of Zurich" - }, - { - "author_name": "Thibault Lovey", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sandrine Zweifel", - "author_inst": "University Hospital Zurich" - }, - { - "author_name": "Mara Isabella Meier", - "author_inst": "University Hospital Zurich" - }, - { - "author_name": "Roland Zust", - "author_inst": "Spiez Laboratory" - }, - { - "author_name": "Nejla Gultekin", - "author_inst": "Swiss Armed Forces" - }, - { - "author_name": "Andreas Stettbacher", - "author_inst": "Swiss Armed Forces" - }, - { - "author_name": "Patricia Schlagenhauf", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.11.22270841", "rel_title": "Underdispersion in the reported Covid-19 case and death numbers may suggest data manipulations", @@ -371295,6 +370200,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.10.480009", + "rel_title": "Binding Interactions between RBD of Spike-Protein and Human ACE2 in Omicron variant", + "rel_date": "2022-02-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.10.480009", + "rel_abs": "Emergence of new SARS-CoV-2 Omicron VOC (OV) has exacerbated the COVID-19 pandemic due to a large number of mutations in the spike-protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strain. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly due predominantly to strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.\n\nTOC GRAPHICS\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/480009v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (102K):\norg.highwire.dtl.DTLVardef@88f654org.highwire.dtl.DTLVardef@1e42d14org.highwire.dtl.DTLVardef@14b7d04org.highwire.dtl.DTLVardef@fca7d0_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bahaa Jawad", + "author_inst": "University of Missouri-Kansas City" + }, + { + "author_name": "Puja Adhikari", + "author_inst": "University of Missouri-Kansas City" + }, + { + "author_name": "Rudolf Podgornik", + "author_inst": "University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Wai-Yim Ching", + "author_inst": "University of Missouri-Kansas City" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.02.11.480063", "rel_title": "Molecular Dynamics Simulations Studies On The Effects Of Mutations On The Binding Affinities Between SARS-CoV-2 Spike RBD And Human ACE2", @@ -372145,41 +371081,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.02.09.479781", - "rel_title": "Engineering Defensin \u03b1-helix to produce high-affinity SARS-CoV-2 Spike protein binding ligands.", - "rel_date": "2022-02-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479781", - "rel_abs": "The binding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein to the Angiotensin-Converting Enzyme 2 (ACE2) receptor expressed on the host cells is a critical initial step for viral infection. This interaction is blocked through competitive inhibition by soluble ACE2 protein. Therefore, developing high-affinity and cost-effective ACE2 peptidomimetic ligands that disrupt this protein-protein interaction is a promising strategy for viral diagnostics and therapy. We employed human and plant defensins, a class of small and highly stable proteins, and engineered the amino acid residues on its conformationally constrained alpha-helices to mimic the critical residues on the ACE2 helix 1 that interacts with the Spike-protein. The engineered proteins were soluble and purified to homogeneity with high yield from a bacterial expression system. The proteins demonstrated exceptional thermostability, high-affinity binding to the Spike protein with dissociation constants in the low nanomolar range, and were used in a diagnostic assay that detected SARS-CoV-2 neutralizing antibodies. This work addresses the challenge of developing helical peptidomimetics by demonstrating that defensins provide promising scaffolds to engineer alpha-helices in a constrained form for designing high-affinity ligands.\n\nBroad audience statementThe engineered proteins developed in this study are cost-effective and highly stable reagents for SARS-CoV-2 detection. These features may allow large-scale and cost-effective production of diagnostic tests to assist COVID-19 diagnostic and prevention.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Leonardo Antonio Fernandes", - "author_inst": "Universidade do Estado de Santa Catarina" - }, - { - "author_name": "Anderson Albino Gomes", - "author_inst": "Universidade do Estado de Santa Catarina" - }, - { - "author_name": "Maria de Lourdes Borba Magalhaes", - "author_inst": "Universidade do Estado de Santa Catarina" - }, - { - "author_name": "Partha Ray", - "author_inst": "University of California" - }, - { - "author_name": "Gustavo Felippe da Silva", - "author_inst": "Universidade do Estado de Santa Catarina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.02.09.479786", "rel_title": "Predicting Epitope Candidates for SARS-CoV-2", @@ -373084,6 +371985,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.08.22270668", + "rel_title": "Community vaccination can shorten the COVID-19 isolation period: an individual-based modeling approach", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270668", + "rel_abs": "BackgroundIsolation of infected individuals and quarantine of their contacts are usually employed to mitigate the transmission of SARS-CoV-2. While 14-day isolation of infected individuals could effectively reduce the risk of subsequence transmission, it also significantly impacts the patients financial, psychological, and emotional well-being. It is, therefore, vital to investigate how the isolation duration could be shortened when effective vaccines are available and in what circumstances we can live with COVID-19 without isolation and quarantine.\n\nMethodsAn individual-based modeling approach was employed to estimate the likelihood of secondary infections and the likelihood of an outbreak following the isolation of an index case for a range of isolation periods. Our individual-based model integrates the viral loads and infectiousness profiles of vaccinated and unvaccinated infected individuals. The effects of waning vaccine-induced immunity against Delta and Omicron variant transmission were also investigated.\n\nResultsIn the baseline scenario in which all individuals are unvaccinated, and no nonpharmaceutical interventions are employed, there is a chance of about 3% that an unvaccinated index case will make at least one secondary infection after being isolated for 14 days, and a sustained chain of transmission can occur with a chance of less than 1%. We found that at the outbreak risk equivalent to that of 14-day isolation in the baseline scenario, the isolation duration can be shortened to 7.33 days (95% CI 6.68-7.98) if 75% of people in the community are fully vaccinated during the last three months. In the best-case scenario in which all individuals in the community are fully vaccinated, isolation of infected individuals may no longer be necessary. However, to keep the outbreak risk low, a booster vaccination may be necessary three months after full vaccination. Finally, our simulations showed that the reduced vaccine effectiveness against transmission of the Omicron variant does not much affect the risk of an outbreak if the vaccine effectiveness against infection is maintained at a high level via booster vaccination.\n\nConclusionsThe isolation duration of a vaccine breakthrough infector could be safely shortened if a majority of people in the community are immune to SARS-CoV-2 infection. A booster vaccination may be necessary three months after full vaccination to keep the outbreak risk low.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chayanin Sararat", + "author_inst": "Biophysics Group, Department of Physics, Faculty of Science, Mahidol University" + }, + { + "author_name": "Jidchanok Wangkanai", + "author_inst": "Biophysics Group, Department of Physics, Faculty of Science, Mahidol University" + }, + { + "author_name": "Chaiwat Wilasang", + "author_inst": "Biophysics Group, Department of Physics, Faculty of Science, Mahidol University" + }, + { + "author_name": "Tanakorn Chantanasaro", + "author_inst": "Biophysics Group, Department of Physics, Faculty of Science, Mahidol University" + }, + { + "author_name": "Charin Modchang", + "author_inst": "Biophysics Group, Department of Physics, Faculty of Science, Mahidol University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.08.22270657", "rel_title": "COPD and social distancing in the UK", @@ -374111,105 +373047,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.02.09.479669", - "rel_title": "Auto-Immunoproteomics Analysis of COVID-19 ICU Patients Revealed Increased Levels of Autoantibodies Related to Male Reproductive System", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479669", - "rel_abs": "The role of autoantibodies in coronavirus disease (COVID-19) complications is not yet fully understood. The current investigation screened two independent cohorts of 97 COVID-19 patients (Discovery (Disc) cohort from Qatar (n = 49) and Replication (Rep) cohort from New York (n = 48)) utilizing high-throughput KoRectly Expressed (KREX) immunome protein-array technology. Autoantibody responses to 57 proteins were significantly altered in the COVID-19 Disc cohort compared to healthy controls (P [≤] 0.05). The Rep cohort had altered autoantibody responses against 26 proteins compared to non-COVID-19 ICU patients that served as controls. Both cohorts showed substantial similarities (r2 = 0.73) and exhibited higher autoantibodies responses to numerous transcription factors, immunomodulatory proteins, and human disease markers. Analysis of the combined cohorts revealed elevated autoantibody responses against SPANXN4, STK25, ATF4, PRKD2, and CHMP3 proteins in COVID-19 patients. KREX analysis of the specific IgG autoantibody responses indicates that the targeted host proteins are supposedly increased in COVID-19 patients. The autoantigen-autoantibody response was cross-validated for SPANXN4 and STK25 proteins using Uniprot BLASTP and sequence alignment tools. SPANXN4 is essential for spermiogenesis and male fertility, which may predict a potential role for this protein in COVID-19 associated male reproductive tract complications and warrants further research.\n\nSignificance StatementCoronavirus disease (COVID-19), caused by the SARS-CoV-2 virus, has emerged as a global pandemic with a high morbidity rate and multiorgan complications. It is observed that the host immune system contributes to the varied responses to COVID-19 pathogenesis. Autoantibodies, immune system proteins that mistakenly target the bodys own tissue, may underlie some of this variation. We screened total IgG autoantibody responses against 1,318 human proteins in two COVID-19 patient cohorts. We observed several novel markers in COVID-19 patients that are associated with male fertility, such as sperm protein SPANXN4, STK25, and the apoptotic factor ATF4. Particularly, elevated levels of autoantibodies against the testicular tissue-specific protein SPANXN4 offer significant evidence of anticipating the protein role in COVID-19 associated male reproductive complications.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Frank Schmidt", - "author_inst": "Proteomics Core, Weill Cornell Medicine - Qatar, Doha, Qatar" - }, - { - "author_name": "Houari B Abdesselem", - "author_inst": "Qatar Biomedical Research Institute" - }, - { - "author_name": "Karsten Suhre", - "author_inst": "Weill Cornell Medicine - Qatar" - }, - { - "author_name": "muhammad umar Sohail", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Maryam Al-Nesf", - "author_inst": "Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar" - }, - { - "author_name": "Ilham Bensmail", - "author_inst": "Qatar Biomedical Research Institute" - }, - { - "author_name": "Fathima Mashod", - "author_inst": "Proteomics Core, Weill Cornell Medicine - Qatar, Doha, Qatar." - }, - { - "author_name": "Hina Sarwath", - "author_inst": "Weill Cornell Medicine - Qatar" - }, - { - "author_name": "Jorg Bernhardt", - "author_inst": "University of Greifswald" - }, - { - "author_name": "Ti-Myen Tan", - "author_inst": "Sengenics Corporation" - }, - { - "author_name": "Priscilla E Morris", - "author_inst": "Sengenics Corporation" - }, - { - "author_name": "Edward J Schenck", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "David Price", - "author_inst": "Department of Medicine, New York Presbyterian Hospital, Weill Cornell Medical Center, Weill Cornell Medicine, New York, NY, USA." - }, - { - "author_name": "Nishant Vaikath", - "author_inst": "Qatar Biomedical Research Institute" - }, - { - "author_name": "Vidya Mohamed-Ali", - "author_inst": "Anti-Doping Laboratory Qatar" - }, - { - "author_name": "Mohammed Al-Maadheedh", - "author_inst": "Anti-Doping Laboratory Qatar" - }, - { - "author_name": "Abdelilah Arredouani", - "author_inst": "Diabetes Research Center, QBRI, HBKU, Qatar Foundation, Doha, Qatar" - }, - { - "author_name": "Julie V Decock", - "author_inst": "Qatar Biomedical Research Institute" - }, - { - "author_name": "Jonathan Blackburn", - "author_inst": "Institute of Infectious Disease and Molecular Medicine" - }, - { - "author_name": "Augustine M. K. Choi", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Omar M.A. El-Agnaf", - "author_inst": "Qatar Biomedical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.08.479664", "rel_title": "SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export", @@ -375262,6 +374099,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.06.22270346", + "rel_title": "Changes in the number of public health nurses employed in local governments in Japan during the Covid-19 pandemic: A cross-sectional study", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.06.22270346", + "rel_abs": "ObjectivesThis study aims to clarify the recruitment of public health nurses in local governments in Japan during the Covid-19 pandemic.\n\nStudy designA cross-sectional study.\n\nMethodsA cross-sectional study of 150 local governments that have public health centers in Japan was conducted. The survey period was November to December 2021. The survey items were the number of full-time and part-time public health nurses (PHNs), the number of PHNs who resigned or retired from the job, and the number of PHN recruitment examinations for each year from 2017 to 2021. For all variables, the mean, standard deviation, maximum, and minimum values for each type of municipality and year were calculated, and a one-way analysis of variance was performed.\n\nResultsThe recovery rate was 54.0% (81/150). Although a statistically significant difference was not recorded in the change in employment status of PHNs from 2019 to 2020, during the year that COVID-19 infection began in Japan, the number of full-time PHNs increased by only 2.6 at the maximum, while the number of part-time PHNs was 5.2{+/-}8.3 to 10.8{+/-}9.6 (p = 0.61) for prefectures, from 13.6{+/-}13.1 to 21.5{+/-}34.8 (p = 0.23) for city, and from 16.8{+/-}26.8 to 52.3{+/-}132.5 (p = 0.70) for ward.\n\nConclusionsThis study reveals that support for the increased workload due to COVID-19 is heavily dependent on part-time PHNs. Drastic change to the ideal way of the original countermeasure to Covid-19 in Japan or the supply of stronger human support to the public health center might be desired.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kazuya Taira", + "author_inst": "Department of Human Health Sciences, Graduate School of Medicine, Kyoto University" + }, + { + "author_name": "Rikuya Hosokawa", + "author_inst": "Department of Human Health Sciences, Graduate School of Medicine, Kyoto University" + }, + { + "author_name": "Misa Shiomi", + "author_inst": "Department of Human Health Sciences, Graduate School of Medicine, Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2022.02.07.22269889", "rel_title": "Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2", @@ -376357,57 +375221,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.07.22270617", - "rel_title": "Genetic immune response and antibody repertoire of heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270617", - "rel_abs": "Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than two doses of BNT162b2 or ChAdOx1. Yet, the molecular transcriptome, the germline allelic variants of immunoglobulin loci and anti-Omicron antibody levels induced by the heterologous vaccination have not been formally investigated. Moreover, there is a paucity of COVID vaccine studies including diverse genetic populations. Here, we show a robust molecular immune transcriptome and antibody repertoire in 51 office workers from the Republic of Korea after a heterologous ChAdOx1-BNT162b2 vaccination or a homologous ChAdOx1-ChAdOx1 vaccination. Anti-spike-specific IgG antibody levels in the heterologous group increased from 14,000 U/ml to 142,000 AU/ml within eight days after the BNT162b2 vaccination. In contrast, antibody levels in the homologous group increased two-fold after the second ChAdOx1 dose. Antibody titers against the Omicron spike protein as compared to the ancestral strain were reduced to a lesser extent in the heterologous group. RNA-seq conducted on immune cells demonstrated a stronger activation of interferon-induced genetic programs in the heterologous cohort. An increase of specific IGHV clonal transcripts encoding neutralizing antibodies was preferentially detected in the heterologous cohort. Enrichment of B cell and CD4+ T cell responses were observed following both heterologous and homologous vaccination using scRNA-seq, but clonally expanded memory B cells were relatively stronger in the ChAdOx1-BNT162b2 cohort. In summary, a heterologous vaccination with ChAdOx1 followed by BNT162b2 provides an innate and adaptive immune response exceeding that seen in homologous ChAdOx1 vaccinations but equivalent to that seen in homologous BNT162b2 vaccination.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hye Kyung Lee", - "author_inst": "National Institute of Diabetes, Digestive and Kidney Diseases" - }, - { - "author_name": "Jinyoung Go", - "author_inst": "Department of Biochemistry and Molecular Biology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea." - }, - { - "author_name": "Heungsup Sung", - "author_inst": "Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea." - }, - { - "author_name": "Seong Who Kim", - "author_inst": "Department of Biochemistry and Molecular Biology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea." - }, - { - "author_name": "Mary Walter", - "author_inst": "Clinical Core, National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA." - }, - { - "author_name": "Ludwig Knabl", - "author_inst": "TyrolPath, Zams, Austria" - }, - { - "author_name": "Priscilla A. Furth", - "author_inst": "Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA" - }, - { - "author_name": "Lothar Hennighausen", - "author_inst": "National Institute of Diabetes, Digestive and Kidney Diseases" - }, - { - "author_name": "Jin Won Huh", - "author_inst": "Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea." - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.07.22270020", "rel_title": "Post-marketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12-39 years in Italy: a multi-database, self-controlled case series study", @@ -377240,6 +376053,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.07.22270332", + "rel_title": "Evaluating Fomite Risk of Brown Paper Bags Storing Personal Protective Equipment Exposed to SARS-CoV-2: A Quasi-Experimental Study", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270332", + "rel_abs": "IntroductionLiterature is lacking on the safety of storing contaminated PPE in paper bags for reuse, potentially increasing exposure to frontline healthcare workers (HCW) and patients.\n\nObjectivesTo evaluate the effectiveness of paper bags as a barrier for fomite transmission of SARS-CoV-2 by storing limited reusable face masks, respirators, and face shields.\n\nMethodsThis quasi-experimental study evaluated the presence of SARS-CoV-2 on the interior and exterior surfaces of paper bags containing PPE that had aerosolized exposures in clinical and simulated settings. Between May and October 2020, 30 unique PPE items were collected from critical and intermediate care COVID-19 units at two urban hospitals. Exposed PPE, worn by either an infected patient or HCW during a SARS-CoV-2 aerosolizing event, were placed into an unused brown paper bag. Samples were tested at 30-minute and 12-hour intervals.\n\nResultsA total of 177 swabs were processed from 30 PPE samples. We found a (12/177 total) 6.8% positivity rate among all samples across both collection sites. Highest positivity rates were associated with ventilator disconnection (1/6 samples, 16.7% positivity) and exposure to respiratory droplets from coughing (2/24 samples, 8.3% positivity), compared to exposure to high-flow nasal cannula (8/129 samples, 6.2% positivity) or tracheostomy surgery (1/18 samples, 5.6% positivity). Positivity rates differed between hospital units. Total positivity rates were similar between 30-minute (6.7%) and 12-hour (6.9%) sample testing time intervals. Control samples exposed to inactivated SARS-CoV-2 droplets had higher total viral counts than samples exposed to nebulized aerosols.\n\nConclusionsData suggests paper bags are not a significant fomite risk for SARS-CoV-2 transmission. However, controls demonstrated a risk with droplet exposure. Data can inform guidelines for storing and re-using PPE in situations of limited supplies during future pandemics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kyirsty Unger", + "author_inst": "Oregon Health and Science University, Providence St. Joseph" + }, + { + "author_name": "Leslie Dietz", + "author_inst": "University of Oregon" + }, + { + "author_name": "Patrick F Horve", + "author_inst": "University of Oregon" + }, + { + "author_name": "Amber Lin", + "author_inst": "Oregon Health and Science University" + }, + { + "author_name": "Kevin G Van Den Wymelenberg", + "author_inst": "University of Oregon" + }, + { + "author_name": "Bory Kea", + "author_inst": "Oregon Health and Science University" + }, + { + "author_name": "Erin Kinney", + "author_inst": "Oregon Health and Science University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.02.07.22270629", "rel_title": "Evaluation of a Rapid and Accessible RT-qPCR Approach for SARS-CoV-2 Variant of Concern Identification", @@ -378471,69 +377327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.02.07.22270579", - "rel_title": "The use of social media platforms by migrant and ethnic minority populations during the COVID-19 pandemic: a systematic review", - "rel_date": "2022-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270579", - "rel_abs": "ObjectiveTo determine the extent and nature of social media use in migrant and ethnic minority communities for COVID-19 information, and implications for preventative health measures including vaccination intent and uptake.\n\nDesignA systematic review of published and grey literature following the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) guidelines\n\nEligibility Criteria for study selectionGlobal research reporting the use of social media by migrants and/or ethnic minority groups in relation to COVID-19.\n\nData extractionWe extracted data on key outcomes, study design, country, population under study, and sample size.\n\nResults1849 unique records were screened, and 21 data sources included in our analysis involving migrant and ethnic minority populations in the UK, US, China, Jordan, Qatar, and Turkey. We found evidence of consistent use of a range of social media platforms for COVID-19 information in some migrant and ethnic minority populations (including WeChat, Facebook, WhatsApp, Instagram, Twitter, YouTube), which may stem from difficulty in accessing COVID-19 information in their native languages or from trusted sources. There were positive and negative associations with social media use reported, with some evidence suggesting circulating misinformation and social media use may be associated with lower participation in preventative health measures, including vaccine intent and uptake, findings of which are likely relevant to multiple population groups.\n\nConclusionsSocial media platforms are an important source of information about COVID-19 for some migrant and ethnic minority populations. Urgent actions and further research are now needed to better understand the use of social media platforms for accessing health information by different population groups - particularly groups who are marginalised from health systems - effective approaches to tackling circulating misinformation, and to seize on opportunities to make better use of social media platforms to support public health communication and improve vaccine uptake.\n\nRegistrationThis study has been registered with PROSPERO (CRD42021259190).", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Lucy P Goldsmith", - "author_inst": "St George's, University of London" - }, - { - "author_name": "May Rowland-Pomp", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Kristin Hanson", - "author_inst": "Kingston University London" - }, - { - "author_name": "Anna Deal", - "author_inst": "St George's, UOL" - }, - { - "author_name": "Alison F Crawshaw", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Sally E Hayward", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Felicity Knights", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Jessica Carter", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Ayesha Ahmad", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Mohammad Razai", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Tushna Vandrevala", - "author_inst": "St George's, University of London" - }, - { - "author_name": "Sally Hargreaves", - "author_inst": "St George's, University of London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.02.05.22270416", "rel_title": "Characteristics and preparedness for COVID-19 outbreaks of Australian residential aged care facilities: A cross-sectional survey", @@ -379518,6 +378311,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.05.22270453", + "rel_title": "Estimating the risk reduction of isolation on COVID-19 non-household transmission and severe/critical illness in non-immune individuals: September to November 2021", + "rel_date": "2022-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270453", + "rel_abs": "In the fall 2021, immunity mandates/passports for COVID-19 started to be discussed and implemented globally. In addition to increasing vaccination levels, these interventions isolate non-immune individuals from various settings to reduce non-household transmission and severe/critical illness. This is based on the hypothesis that the non-immune are at high absolute risk of these outcomes. However, these absolute risks were not quantified in the literature such that the absolute risk reductions of isolation on these outcomes remain unknown. This study estimated these absolute risks from September to November 2021 prior to the emergence of Omicron (B.1.1.529) using known data on the risk of infection, transmission in non-household settings, and age-stratified severe/critical illness in non-immune individuals for the Delta (B.1.617.2) variant, focusing on the European Union, United Kingdom, United States, Canada, Australia, and Israel. This allowed us to quantify the absolute risk reductions of isolation on (1) non-household transmission from the non-immune and (2) severe/critical illness amongst the non-immune in these regions during this period. We observed that on any given day the absolute risk reductions of isolation were typically small for transmission in most types of non-household settings and severe/critical illness in most age-groups, especially those aged <40. During a wave or sustained higher infection risks, the risk reductions were modest only for transmission in intimate social gatherings and severe/critical illness in adults aged [≥]50-60. The limitations of this study and the implications for the expected benefits of isolating non-immune individuals on reducing these outcomes are discussed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aaron Prosser", + "author_inst": "McMaster University" + }, + { + "author_name": "Bartosz Helfer", + "author_inst": "University of Wroclaw" + }, + { + "author_name": "David L Streiner", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.06.22270550", "rel_title": "SARS-CoV-2 mRNA vaccination fails to elicit humoral and cellular immune responses in multiple sclerosis patients receiving fingolimod", @@ -380821,45 +379641,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.31.22270192", - "rel_title": "Modinterv COVID-19: An online platform to monitor the evolution of epidemic curves", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270192", - "rel_abs": "We present the software ModInterv as an informatics tool to monitor, in an automated and user-friendly manner, the evolution and trend of COVID-19 epidemic curves, both for cases and deaths. The ModInterv software uses parametric generalized growth models, together with LOWESS regression analysis, to fit epidemic curves with multiple waves of infections for countries around the world as well as for states and cities in Brazil and the USA. The software automatically accesses publicly available COVID-19 databases maintained by the Johns Hopkins University (for countries as well as states and cities in the USA) and the Federal University of Vicosa (for states and cities in Brazil). The richness of the implemented models lies in the possibility of quantitatively and reliably detecting the distinct acceleration regimes of the disease. We describe the backend structure of software as well as its practical use. The software helps the user not only to understand the current stage of the epidemic in a chosen location but also to make short term predictions as to how the curves may evolve. The app is freely available on the internet (http://fisica.ufpr.br/modinterv), thus making a sophisticated mathematical analysis of epidemic data readily accessible to any interested user.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Arthur A. Brum", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Giovani L. Vasconcelos", - "author_inst": "Universidade Federal do Paran\u00e1" - }, - { - "author_name": "Gerson C. Duarte-Filho", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Raydonal Ospina", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Francisco A. G. Almeida", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Ant\u00f4nio M. S. Mac\u00eado", - "author_inst": "Universidade Federal de Pernambuco" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.04.22270087", "rel_title": "ARTIFICIAL INTELLIGENCE TOOLS FOR EFFECTIVE MONITORING OF POPULATION AT DISTANCE DURING COVID-19 PANDEMIC. RESULTS FROM AN ITALIAN PILOT FEASIBILITY STUDY (RICOVAI-19 STUDY).", @@ -381560,6 +380341,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.01.22270253", + "rel_title": "Safety and Immunogenicity of An Egg-Based Inactivated Newcastle Disease Virus Vaccine Expressing SARS-CoV-2 Spike: Interim Results of a Randomized, Placebo-Controlled, Phase 1/2 Trial in Vietnam", + "rel_date": "2022-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270253", + "rel_abs": "Production of affordable coronavirus disease 2019 (COVID-19) vaccines in low- and middle-income countries is needed. NDV-HXP-S is an inactivated egg-based Newcastle disease virus (NDV) vaccine expressing the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Wuhan-Hu-1. The spike protein was stabilized and incorporated into NDV virions by removing the polybasic furin cleavage site, introducing the transmembrane domain and cytoplasmic tail of the fusion protein of NDV, and introducing six prolines for stabilization in the prefusion state. Vaccine production and clinical development was initiated in Vietnam, Thailand, and Brazil. Here the interim results from the first stage of the randomized, dose-escalation, observer-blind, placebo-controlled, phase 1/2 trial conducted at the Hanoi Medical University (Vietnam) are presented. Healthy adults aged 18-59 years, non-pregnant, and with self-reported negative history for SARS-CoV-2 infection were eligible. Participants were randomized to receive one of five treatments by intramuscular injection twice, 28 days apart: 1 g +/-CpG1018 (a toll-like receptor 9 agonist), 3 g alone, 10 g alone, or placebo. Participants and personnel assessing outcomes were masked to treatment. The primary outcomes were solicited adverse events (AEs) during 7 days and subject-reported AEs during 28 days after each vaccination. Investigators further reviewed subject-reported AEs. Secondary outcomes were immunogenicity measures (anti-spike immunoglobulin G [IgG] and pseudotyped virus neutralization). This interim analysis assessed safety 56 days after first vaccination (day 57) in treatment-exposed individuals and immunogenicity through 14 days after second vaccination (day 43) per protocol. Between March 15 and April 23, 2021, 224 individuals were screened and 120 were enrolled (25 per group for active vaccination and 20 for placebo). All subjects received two doses. The most common solicited AEs among those receiving active vaccine or placebo were all predominantly mild and included injection site pain or tenderness (<58%), fatigue or malaise (<22%), headache (<21%), and myalgia (<14%). No higher proportion of the solicited AEs were observed for any group of active vaccine. The proportion reporting vaccine-related AEs during the 28 days after either vaccination ranged from 4% to 8% among vaccine groups and was 5% in controls. No vaccine-related serious adverse event occurred. The immune response in the 10 g formulation group was highest, followed by 1 g +CpG1018, 3 g, and 1 g formulations. Fourteen days after the second vaccination, the geometric mean concentrations (GMC) of 50% neutralizing antibody against the homologous Wuhan-Hu-1 pseudovirus ranged from 56.07 IU/mL (1 g, 95% CI 37.01, 84.94) to 246.19 IU/mL (10 g, 95% CI 151.97, 398.82), with 84% to 96% of vaccine groups attaining a [≥] 4-fold increase over baseline. This was compared to a panel of human convalescent sera (N=29, 72.93 95% CI 33.00-161.14). Live virus neutralization to the B.1.617.2 (Delta) variant of concern was reduced but in line with observations for vaccines currently in use. Since the adjuvant has shown modest benefit, GMC ratio of 2.56 (95% CI, 1.4 - 4.6) for 1 g +/-CpG1018, a decision was made not to continue studying it with this vaccine. NDV-HXP-S had an acceptable safety profile and potent immunogenicity. The 3 g dose was advanced to phase 2 along with a 6 g dose. The 10 g dose was not selected for evaluation in phase 2 due to potential impact on manufacturing capacity. ClinicalTrials.gov NCT04830800.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Anh Duc Dang", + "author_inst": "National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hai Ba Trung District, Hanoi, Vietnam" + }, + { + "author_name": "Thiem Dinh Vu", + "author_inst": "National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hai Ba Trung District, Hanoi, Vietnam" + }, + { + "author_name": "Ha Hai Vu", + "author_inst": "National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hai Ba Trung District, Hanoi, Vietnam" + }, + { + "author_name": "Van Thanh Ta", + "author_inst": "Hanoi Medical University, 1 Ton That Tung Street, Dong Da District, Hanoi, Vietnam" + }, + { + "author_name": "Anh Thi Van Pham", + "author_inst": "Hanoi Medical University, 1 Ton That Tung Street, Dong Da District, Hanoi, Vietnam" + }, + { + "author_name": "Mai Thi Ngoc Dang", + "author_inst": "Hanoi Medical University, 1 Ton That Tung Street, Dong Da District, Hanoi, Vietnam" + }, + { + "author_name": "Be Van Le", + "author_inst": "Institute of Vaccines and Medical Biologicals, 9 Pasteur, Xuong Huan, Nha Trang city, Khanh Hoa, Vietnam" + }, + { + "author_name": "Thai Huu Duong", + "author_inst": "Institute of Vaccines and Medical Biologicals, 9 Pasteur, Xuong Huan, Nha Trang city, Khanh Hoa, Vietnam" + }, + { + "author_name": "Duoc Van Nguyen", + "author_inst": "Institute of Vaccines and Medical Biologicals, 9 Pasteur, Xuong Huan, Nha Trang city, Khanh Hoa, Vietnam" + }, + { + "author_name": "Saranath Lawpoolsri", + "author_inst": "Center of Excellence for Biomedical and Public Health Informatics (BIOPHICS), Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchath" + }, + { + "author_name": "Pailinrut Chinwangso", + "author_inst": "Center of Excellence for Biomedical and Public Health Informatics (BIOPHICS), Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchath" + }, + { + "author_name": "Jason S McLellan", + "author_inst": "College of Natural Sciences, The University of Texas at Austin, 120 Inner Campus Dr Stop G2500, Austin, TX 78712, USA" + }, + { + "author_name": "Ching-Lin Hsieh", + "author_inst": "College of Natural Sciences, The University of Texas at Austin, 120 Inner Campus Dr Stop G2500, Austin, TX 78712, USA" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Peter Palese", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Weina Sun", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Jose L Martinez", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Irene Gonzalez-Dominguez", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Stefan Slamanig", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Juan Manuel Carreno", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Johnstone Tcheou", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Ariel Raskin", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA" + }, + { + "author_name": "Huong Minh Vu", + "author_inst": "WHO Vietnam Country Office, 304 Kim Ma Street, Ba Dinh District, Hanoi, Vietnam" + }, + { + "author_name": "Thang Cong Tran", + "author_inst": "PATH Vietnam, 1101, 11th Floor, Hanoi Towers, 49 Hai Ba Trung Street, Hoan Kiem District, Hanoi, Vietnam" + }, + { + "author_name": "Huong Mai Nguyen", + "author_inst": "PATH Vietnam, 1101, 11th Floor, Hanoi Towers, 49 Hai Ba Trung Street, Hoan Kiem District, Hanoi, Vietnam" + }, + { + "author_name": "Laina D Mercer", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Rama Raghunandan", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Manjari Lal", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Jessica A White", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Richard Hjorth", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Bruce L Innis", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + }, + { + "author_name": "Rami Scharf", + "author_inst": "PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.03.478930", "rel_title": "Comprehensive analysis of next-generation sequencing data in COVID-19 and its secondary complications", @@ -382815,41 +381743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.03.22270357", - "rel_title": "Transparency and reporting characteristics of COVID-19 randomized controlled trials.", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270357", - "rel_abs": "Randomized controlled trials (RCTs) are essential to support clinical decision making. We assessed the transparency, completeness and consistency of reporting of 244 reports (120 peer-reviewed journal publications; 124 preprints) of RCTs assessing pharmacological interventions for the treatment of COVID-19 published the first 17 months of the pandemic (up to May 31, 2021). Transparency was poor. Only 55% of trials were prospectively registered; 39% made their full protocols available and 29% provided access to their statistical analysis plan. Only 6% completely reported the most important information. Primary outcome(s) reported in trial registries and published reports were inconsistent in 47% of trials. Of the 124 RCTs published as preprint, 76 were secondarily published in a peer-reviewed journal. There was no major improvement after the peer-review process.\n\nLack of transparency, completeness and consistency of reporting is an important barrier to trust, interpretation and synthesis in COVID-19 clinical trials.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Philipp Kapp", - "author_inst": "Cochrane France" - }, - { - "author_name": "Laura Esmail", - "author_inst": "Cochrane France" - }, - { - "author_name": "Lina Ghosn", - "author_inst": "Cochrane France" - }, - { - "author_name": "Philippe Ravaud", - "author_inst": "Cochrane France" - }, - { - "author_name": "Isabelle Boutron", - "author_inst": "Cochrane France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.03.22269712", "rel_title": "Comparative evaluation of oral lesions: Tale - the Covid 19 Tells", @@ -383654,6 +382547,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.02.478719", + "rel_title": "COVID-19 infection enhances susceptibility to oxidative-stress induced parkinsonism", + "rel_date": "2022-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.02.478719", + "rel_abs": "BackgroundViral induction of neurological syndromes has been a concern since parkinsonian-like features were observed in patients diagnosed with encephalitis lethargica subsequent to the 1918 influenza pandemic. Given the similarities in the systemic responses following SARS-CoV-2 infection with those observed after pandemic influenza, there is a question if a similar syndrome of post-encephalic parkinsonism could follow COVID-19 infection.\n\nObjectivesTo determine if prior infection with SARS-CoV-2 increased sensitivity to a mitochondrial toxin known to induce parkinsonism.\n\nMethodshACE2 mice were infected with SARS-CoV-2 to induce mild to moderate disease. After 31 days recovery, mice were administered a non-lesion inducing dose of the parkinsonian toxin MPTP. Subsequent neuroinflammation and SNpc dopaminergic neuron loss was determined and compared to SARS-CoV-2 or MPTP alone.\n\nResultshACE2 mice infected with SARS-CoV-2 or MPTP showed no SNpc DA neuron loss following MPTP. In mice infected and recovered from SARS-CoV-2 infection, MPTP induced a 23% or 19% greater loss of SNpc dopaminergic neurons than SARS-CoV-2 or MPTP, respectively (p{square}<{square}0.05).\n\nExamination of microglial activation showed a significant increase in the number of activated microglia in the SARS-CoV-2 + MPTP group compared to SARS-CoV-2 or MPTP alone.\n\nConclusionsOur observations have important implications for long-term public health, given the number of people that have survived SARS-CoV-2 infection as well as for future public policy regarding infection mitigation. However, it will be critical to determine if other agents known to increase risk of PD also have synergistic effects with SARS-CoV-2 and if are abrogated by vaccination.\n\nFundingThis work was supported by grant from the State of North Carolina (PS, JE, DOR, RJS) and R21 NS122280 (RJS).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Richard Jay Smeyne", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Jeffery Eells", + "author_inst": "East Carolina University" + }, + { + "author_name": "Debotri Chatterjee", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Matthew Byrne", + "author_inst": "Thomas Jefferson University" + }, + { + "author_name": "Shaw M Akula", + "author_inst": "East Carolina University" + }, + { + "author_name": "Srinivas Sriramula", + "author_inst": "East Carolina University" + }, + { + "author_name": "Peter Schmidt", + "author_inst": "New York University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.02.02.478671", "rel_title": "Development and optimisation of a high-throughput screening assay for in vitro anti-SARS-CoV-2 activity: evaluation of 5676 phase 1 passed structures", @@ -384733,61 +383669,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.31.22270200", - "rel_title": "Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants", - "rel_date": "2022-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270200", - "rel_abs": "IntroductionInformation on vaccine effectiveness and viral loads in a context of novel variants of concern (VOC) emergence is of key importance to inform public health policies. This study aimed to estimate a measure of comparative vaccine effectiveness between Omicron (BA.1) and Delta (B.1.617.2 and sub-lineages) VOC according to vaccination exposure (primary or booster) and time since primary vaccination and to compare cycle threshold (Ct) values between Omicron and Delta VOC infections according to the vaccination status as an indirect measure of viral load.\n\nMethodsWe developed a case-case study using data on RT-PCR SARS-CoV-2 positive cases notified in Portugal during weeks 49-51 2021. The odds of vaccination in Omicron cases were compared to Delta using logistic regression adjusted for age group, sex, region and week of diagnosis and laboratory of origin. RT-PCR Ct values were compared by vaccination status and variant using linear regression model.\n\nResultsHigher odds of vaccination were observed in cases infected by Omicron (BA.1) VOC compared to Delta (B.1.617.2) VOC cases for both complete primary vaccination (OR=2.1; CI 95% :1.8 to 2.4) and booster dose (OR= 5.2; CI 95%: 3.1 to 8.8), indicating vaccine effectiveness reduction against Omicron. No differences in distribution of Ct-values between these two VOC were observed for any vaccination exposure categories.\n\nConclusionConsistent lower VE was observed against Omicron infection. Complete primary vaccination may not be protective against SARS-CoV-2 infection in regions where Omicron variant is dominant, but a massive rollout of booster vaccination campaign can contribute to reduce SARS-CoV-2 incidence in the population.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Irina Kislaya", - "author_inst": "National Institute of Health Doutor Ricardo Jorge" - }, - { - "author_name": "ANDRE PERALTA SANTOS", - "author_inst": "Dire\u00e7\u00e3o Geral da Sa\u00fade" - }, - { - "author_name": "Vitor Borges", - "author_inst": "National Institute of Health Doutor Ricardo Jorge" - }, - { - "author_name": "Lu\u00eds Vieira", - "author_inst": "National Institute of Health Doutor Ricardo Jorge" - }, - { - "author_name": "Carlos Sousa", - "author_inst": "Unilabs" - }, - { - "author_name": "Bibiana Ferreira", - "author_inst": "Algarve Biomedical Center Research Institute" - }, - { - "author_name": "Ana Pelerito", - "author_inst": "Portuguese Red Cross Laboratory" - }, - { - "author_name": "Jo\u00e3o Paulo Gomes", - "author_inst": "National Institute of Health Doutor Ricardo Jorge" - }, - { - "author_name": "Pedro Pinto Leite", - "author_inst": "Dire\u00e7\u00e3o Geral da Sa\u00fade" - }, - { - "author_name": "Baltazar Nunes", - "author_inst": "National Institute of Health Doutor Ricardo Jorge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.02.22270295", "rel_title": "Real-life performance of a COVID-19 rapid antigen detection test targeting the SARS-CoV-2 nucleoprotein for diagnosis of COVID-19 due to the Omicron variant", @@ -385592,6 +384473,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2022.01.31.22270178", + "rel_title": "SARS-CoV-2 antibody seroprevalence in cancer patients on systemic antineoplastic treatment in the first wave of the COVID-19 pandemic in Portugal", + "rel_date": "2022-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270178", + "rel_abs": "At the time of the first wave of the COVID-19 pandemic cancer patients were considered to be at high risk of serious illness and had a higher exposure risk since they needed frequent and non- deferrable hospital visits. Serologic tests were not routinely used and seroprevalence in this population was unknown.\n\nA single-center cross-sectional study was developed to determine the seroprevalence of anti- SARS-CoV-2 antibodies (Abs) in cancer patients undergoing systemic antineoplastic treatment. One hundred patients were consecutively recruited in a two-week period (6th to 20th May, 2020) and serum samples were tested for the presence of IgM and IgG Abs directed against both spike and nucleocapsid SARS-CoV-2 proteins in two distinct timepoints (at recruitment and four to eight weeks later). IgG positive results were subject to confirmation, in the same serum sample, using two distinct assays.\n\nAt the time of the first study visit, no patient had a previously confirmed diagnosis of COVID-19, one reported previous contact with a COVID-19 patient and all had a baseline SARS-CoV-2 negative RT-PCR. Two patients tested positive for SARS-CoV-2 IgG in the first study visit, which was not confirmed in either of the two confirmatory assays. Seventy-two patients were tested at the second study visit, all with negative IgG test. IgM was persistently positive at both study visits in one patient and was positive in another patient at the second study visit, both with negative RT-PCR and serum IgG. No patient tested RT-PCR positive within the study timeframe.\n\nNo evidence of prior or acute SARS-CoV-2 infection was documented in this cohort of cancer patients undergoing systemic treatment and no additional exposure risk was documented compared to general population seroprevalence studies. The study was inconclusive regarding the role of SARS-CoV-2 serology in cancer patients in the early phase of the pandemic. This study did show that, with adherence to recommended preventive measures, it was safe to maintain systemic cancer therapy.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Gon\u00e7alo Fernandes", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Paulo Paix\u00e3o", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Laura Brum", + "author_inst": "Synlab Portugal" + }, + { + "author_name": "Teresa Padr\u00e3o", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Jorge Correia", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Joana Albuquerque", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Catarina Pulido", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "M\u00f3nica Nave", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Teresa Tim\u00f3teo", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "T\u00e2nia Rodrigues", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Filipe Costa", + "author_inst": "Hospital da Luz Lisboa" + }, + { + "author_name": "Jos\u00e9 L. Passos-Coelho", + "author_inst": "Hospital da Luz Lisboa" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2022.02.01.22270250", "rel_title": "Humoral response, associated symptoms and profile of patients infected by SARS-CoV-2 with taste or smell disorders in the SAPRIS multicohort study.", @@ -386499,65 +385443,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.31.478497", - "rel_title": "Human Cardiac Organoids to Model COVID-19 Cytokine Storm Induced Cardiac Injuries", - "rel_date": "2022-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478497", - "rel_abs": "Acute cardiac injuries occur in 20-25% of hospitalized COVID-19 patients. Despite urgent needs, there is a lack of 3D organotypic models of COVID-19 hearts for mechanistic studies and drug testing. Herein, we demonstrate that human cardiac organoids (hCOs) are a viable platform to model the cardiac injuries caused by COVID-19 hyperinflammation. As IL-1{beta}is an upstream cytokine and a core COVID-19 signature cytokine, it was used to stimulate hCOs to induce the release of a milieu of proinflammatory cytokines that mirror the profile of COVID-19 cytokine storm. The IL-1 {beta} treated hCOs recapitulated transcriptomic, structural, and functional signatures of COVID-19 hearts. The comparison of IL-1{beta} treated hCOs with cardiac tissue from COVID-19 autopsies illustrated the critical roles of hyper-inflammation in COVID-19 cardiac insults and indicated the cardioprotective effects of endothelium. The IL-1{beta} treated hCOs also provide a viable model to assess the efficacy and potential side effects of immunomodulatory drugs, as well as the reversibility of COVID-19 cardiac injuries at baseline and simulated exercise conditions.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Dimitrios C Arhontoulis", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Charles Kerr", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Dylan Richards", - "author_inst": "Clemson University" - }, - { - "author_name": "Kelsey Tjen", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Nathaniel Hyams", - "author_inst": "Clemson University" - }, - { - "author_name": "Jefferey A Jones", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Kristine Deleon-Pennell", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Donald R Menick", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Diana Lindner", - "author_inst": "University Heart and Vascular Center Hamburg" - }, - { - "author_name": "Dirk Westermann", - "author_inst": "University Heart and Vascular Center Hamburg" - }, - { - "author_name": "Ying Mei", - "author_inst": "Clemson University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.01.31.478460", "rel_title": "A Genetically Encoded BRET-based SARS-CoV-2 Mpro Protease Activity Sensor", @@ -387246,6 +386131,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.01.22270232", + "rel_title": "Protection by 4th dose of BNT162b2 against Omicron in Israel", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270232", + "rel_abs": "BACKGROUNDOn January 2, 2022, Israel began administering a fourth dose of BNT162b2 vaccine (Pfizer-BioNTech) to people aged over 60 years and at-risk populations, who had received a third dose of vaccine at least 4 months earlier. The effect of the fourth dose on confirmed coronavirus 2019 disease (Covid-19) and severe illness are still unclear.\n\nMETHODSWe extracted data for the Omicron-dominated period January 15 through January 27, 2022, from the Israeli Ministry of Health database regarding 1,138,681 persons aged over 60 years and eligible for the fourth dose. We compared the rate of confirmed Covid-19 and severe illness between those who had received a fourth dose at least 12 days earlier, those who had received only three doses, and those 3 to 7 days after receiving the fourth dose. We used Poisson regression after adjusting for possible confounding factors.\n\nRESULTSThe rate of confirmed infection was lower in people 12 or more days after their fourth dose than among those who received only three doses and those 3 to 7 days after vaccination by factors of 2.0 (95% confidence interval [CI], 2.0 to 2.1) and 1.9 (95% CI, 1.8 to 2.0), respectively. The rate of severe illness was lower by factors of 4.3 (95% CI, 2.4 to 7.6) and 4.0 (95% CI, 2.2 to 7.5).\n\nCONCLUSIONSRates of confirmed Covid-19 and severe illness were lower following a fourth dose compared to only three doses.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yinon M. Bar-On", + "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Yair Goldberg", + "author_inst": "Technion - Israel Institute of Technology, Israel" + }, + { + "author_name": "Micha Mandel", + "author_inst": "The Hebrew University of Jerusalem, Israel" + }, + { + "author_name": "Omri Bodenheimer", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Ofra Amir", + "author_inst": "Technion - Israel Institute of Technology, Israel" + }, + { + "author_name": "Laurence Freedman", + "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" + }, + { + "author_name": "Sharon Alroy-Preis", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Nachman Ash", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Amit Huppert", + "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" + }, + { + "author_name": "Ron Milo", + "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.31.22268856", "rel_title": "COVID-19 contact tracing during first delta wave, Lebanon, 2021", @@ -388529,41 +387469,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.29.22270032", - "rel_title": "Assessment of Out of Pocket Expenditure and associated factors for availing COVID-19 vaccination by the beneficiaries in Bengaluru: South India", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270032", - "rel_abs": "BackgroundGovernment of India has introduced COVID 19 vaccination in Jan 2021. There are no studies on out of pocket expenditure in COVID-19 vaccination in India, hence this study was undertaken to estimate the out of pocket expenditure for availing COVID 19 vaccine, to assess the factors associated with out of pocket expenditure for COVID vaccination and adverse events following immunisation.\n\nMethodsThis is a cross-sectional study conducted during Sep 2021-Dec 2021 of a medical college. A total of 438 study subjects above 18 years fulfilling inclusion and exclusion criteria were studied using probability proportional to population size. Data was collected using interview method by pre-tested semi structured proforma and analysed using descriptive & inferential statistics.\n\nResultsThe mean direct cost in Government vaccination centre was 3.24{+/-} 6.74 INR, indirect cost 809.10{+/-}1076.35 INR, total cost was 812.34 {+/-}1079.49 INR.The mean direct cost in private vaccination centre was 1446.9{+/-}1845.65 INR, indirect cost 1140{+/-}1398 INR and total cost was 2586.90{+/-}2241.54 INR.\n\nThe mean total cost was OOPE for COVID 19 vaccination was 852.80 {+/-}1128.512 INR, out of which direct cost was only 36.17({+/-}359.20). The higher mean OOPE was found in loss of wages 670.02 INR. The factors associated with higher out of pocket expenditure was type of vaccine (P=0.031, OR=2.141, 95% CI=1.07-4.24) occupation of the study subject (P=0.000, OR=2.043, 95% CI= 1.37-3.03), reported stress following vaccination (P= 0.018, OR=1.72, 95%CI=1.098-2.703), adverse event within 48hrs (P=0.006, OR=2.125, 95% CI= 1.248-3.62), received any medication for adverse event (P=0.041, OR= 1.721, 95% CI= 1.022-2.84)\n\nConclusionMajority of the study subjects utilized public facility. The higher mean out of pocket expenditure was for indirect cost loss of wages. This study shows that type of vaccine, occupation of the study subject and adverse event within 48 hrs, had 2 times higher out of pocket expenditure compared to other factors. Among the AEFI, fever was the most common, followed by pain at the injection site and myalgia.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sunil Kumar Dodderi", - "author_inst": "Dept of Community Medicine,Akash Institute of Medical Sciences and Research Centre, Bangalore" - }, - { - "author_name": "Lakshmi H", - "author_inst": "Dept of Community Medicine, Akash Institute of Medical Sciences and Research Centre, Bangalore" - }, - { - "author_name": "Srividya J", - "author_inst": "Dept of Community Medicine, Akash Institute of Medical Sciences and Research Centre, Bangalore" - }, - { - "author_name": "Manjula S", - "author_inst": "Dept of Community Medicine, Akash Institute of Medical Sciences and Research Centre, Bangalore" - }, - { - "author_name": "Swathi R S", - "author_inst": "Akash Institute of Medical Sciences and Research Centre, Bangalore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.30.22269992", "rel_title": "\"Populist Attitude and Conspiracist beliefs contribution to the overconfidence about the risk of Covid-19: implications for Preventive Health Behaviors\"", @@ -389144,6 +388049,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.01.26.477819", + "rel_title": "Analysis of receptors responsible for the dysfunction of the human immune system by different viral infections", + "rel_date": "2022-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.26.477819", + "rel_abs": "There are difficulties in creating direct anti-viral drugs for all viruses, including new, suddenly arising infections, such as COVID-19. Therefore, pathogenetic therapy is often used to treat severe viral infections. Despite significant distinctions in the etiopathogenesis of viral diseases, they are often associated with the substantial dysfunction of the immune system. To identify shared mechanisms of immune dysfunction during infection by nine different viruses (cytomegalovirus, Ebstein-Barr virus, human T-cell leukemia virus type 1, Hepatitis B and C viruses, human immunodeficiency virus, Dengue virus, SARS-CoV, and SARS-CoV-2), we applied analysis of corresponding transcription profiles from peripheral blood mononuclear cells (PBMC). As a result, we revealed common pathways, cellular processes, and master regulators for studied viral infections. We found that all nine viral infections cause immune activation, exhaustion, cell proliferation disruption, and increased susceptibility to apoptosis. An application of network analysis allowed us to identify receptors of PBMC that are the proteins at the top of signaling pathways, which may be responsible for the observed transcription changes. The identified relationships between some of them and virus-induced immune disfunction are new, with little or no information in the literature, e.g., receptors for autocrine motility factor, insulin, prolactin, angiotensin II, and immunoglobulin epsilon.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sergey M Ivanov", + "author_inst": "Institute of biomedical chemistry" + }, + { + "author_name": "Olga A Tarasova", + "author_inst": "Institute of Biomedical Chemistry" + }, + { + "author_name": "Vladimir V Poroikov", + "author_inst": "Institute of biomedical chemistry" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.29.478316", "rel_title": "Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies", @@ -390231,69 +389163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.21268247", - "rel_title": "Serum Neutralizing Activity of mRNA-1273 Against the SARS-CoV-2 B.1.1.529 (Omicron) Variant: A Preliminary Report", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.21268247", - "rel_abs": "The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant has led to growing concerns of increased transmissibility and escape of both natural and vaccine-induced immunity. In this analysis, sera from adult participants in a phase 2 clinical study (NCT04405076) were tested for neutralizing activity against B.1.1.529 after a 2-dose (100 {micro}g) mRNA-1273 primary vaccination series and after a 50-{micro}g mRNA-1273 booster dose. Results from this preliminary analysis show that 1 month after completing the primary series, mRNA-1273-elicited serum neutralization of B.1.1.529 was below the lower limit of quantification; however, neutralization was observed at 2 weeks after the mRNA-1273 booster dose, although at a reduced level relative to wild-type SARS-CoV-2 (D614G) and lower than that observed against D614G at 1 month after the primary series.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Diana Lee", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Laura E. Avena", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Daniela Montes Berrueta", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Angela Choi", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Judy Oestreicher", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "William Hillebrand", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "HongHong Zhou", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Rolando Pajon", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.28.22270005", "rel_title": "Development and External Validation of a Mixed-Effects Deep Learning Model to Diagnose COVID-19 from CT Imaging", @@ -391042,6 +389911,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.28.22269986", + "rel_title": "Neutralizing Activities against the Omicron Variant after a Heterologous Booster in Healthy Adults Receiving Two Doses of CoronaVac Vaccination", + "rel_date": "2022-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22269986", + "rel_abs": "BackgroundThe use of an inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine (CoronaVac) against SARS-CoV-2 is implemented worldwide. However, waning immunity and breakthrough infections have been observed. Therefore, we hypothesized that the heterologous booster might improve the protection against the delta and omicron variants.\n\nMethodsA total of 224 individuals who completed the two-dose CoronaVac for six months were included. We studied reactogenicity and immunogenicity following a heterologous booster with the inactivated vaccine (BBIBP), the viral vector vaccine (AZD1222), and the mRNA vaccine (both BNT162B2 and mRNA-1273). We also determined immunogenicity at 3- and 6-months boosting intervals.\n\nResultsThe solicited adverse events (AEs) were mild to moderate and well-tolerated. Total RBD immunoglobulin (Ig), anti-RBD IgG, focus reduction neutralization test (FRNT50) against delta and omicron variants, and T cell response were highest in the mRNA-1273 group followed by the BNT162b2, AZD1222 and BBIBP groups, respectively. We also witnessed a higher total Ig anti-RBD in the long-interval than in the short-interval groups.\n\nConclusionsAll four booster vaccines significantly increased binding and NAbs in individuals immunized with two doses of CoronaVac. The present evidence may benefit vaccine strategies development to thwart variants of concern, including the omicron variant.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Thaneeya Duangchinda", + "author_inst": "Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development" + }, + { + "author_name": "Warangkana Chantima", + "author_inst": "Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand" + }, + { + "author_name": "Pattarakul Pakchotanon", + "author_inst": "Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK, Chinese Academy of Medical Science(CAMS) Oxford " + }, + { + "author_name": "Sittisak Honsawek", + "author_inst": "Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, B" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand Royal Society of Thailand (FRS(T)), Sanam Suea" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.28.22270009", "rel_title": "Comparative effectiveness of COVID-19 vaccination against death and severe disease in an ongoing nationwide mass vaccination campaign", @@ -392025,33 +390985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.27.22269947", - "rel_title": "COVID-19 vaccine attitude and its predictors among people living with chronic health conditions in Ibadan, Nigeria", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269947", - "rel_abs": "AbstractsO_ST_ABSBackgroundC_ST_ABSGlobally COVID-19 has caused death among millions of people and new cases continue to be reported daily, including in Nigeria. With the efforts of the Nigerian government to ensure everyone gets vaccinated, the vaccination attitude and its predictors among persons with chronic health conditions remains unclear. The study was therefore conducted to assess vaccination attitude and determine its associated factors among people living with chronic health conditions.\n\nMethodsA descriptive cross-sectional study was conducted among 423 patients attending the medical outpatient clinic of University College Hospital, Ibadan, Oyo State, Nigeria; before COVID-19 vaccination commencement. Data were collected on socio-demographic and COVID-19 related characteristics, via Open Data Kit (ODK) software. The Vaccine Attitude Examination (Vax) Scale including its four subscales was adopted to assess attitude towards COVID-19 vaccine uptake. The main outcome was vaccine attitude status defined as positive if a VAX sum score was above the median value; otherwise, non-positive. Data were analysed using Chi-square and multivariate logistic regression analyses at 5% significance level.\n\nResultsHypertension (27.4%), diabetes mellitus (22.0%) and heart conditions/diseases (19.6%) were the top three conditions being managed by the participants. The overall proportion of patients with a positive attitude towards the uptake of COVID-19 vaccination was 46.6%; while 29.6% trusted the vaccine benefit, 46.6% were not worried about the aftermath effect of the vaccine and 11.1% were not concerned about the vaccine commercial profiteering. Factors associated with overall vaccine attitude were level of education, income, knowledge of COVID-19, living room arrangement, and confidence in government (p<0.05). The main influential factor on general vaccine positive attitude and the four subscales was confidence in the government.\n\nConclusionLess than half of people living with a chronic medical condition had a positive attitude towards the COVID vaccine. The attitudes are mediated strongly by confidence in the government and several sociodemographic and COVID related characteristics. A lot still needs to be done to achieve the prescribed herd immunity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lucia Yetunde Ojewale", - "author_inst": "University of Ibadan" - }, - { - "author_name": "Rotimi Felix Afolabi", - "author_inst": "College of Medicine, University of Ibadan" - }, - { - "author_name": "Adesola Ogunniyi", - "author_inst": "College of Medicine, University of Ibadan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.24.22269745", "rel_title": "Cardiovascular, respiratory and functional effects of tele-supervised home-based exercise training in individuals recovering from COVID-19 hospitalization: A randomized clinical trial", @@ -392864,6 +391797,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.01.26.22269910", + "rel_title": "Fifteen Days in December: Capture and Analysis of Omicron-Related Travel Restrictions", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269910", + "rel_abs": "Following the identification of the Omicron variant of the SARS-CoV-2 virus in late November 2021, governments worldwide took actions intended to minimize the impact of the new variant within their borders. Despite guidance from the World Health Organization advising a risk-based approach, many rapidly implemented stringent policies focused on travel restrictions. In this paper, we capture 221 national-level travel policies issued during the three weeks following publicization of the Omicron variant. We characterize policies based upon whether they target travelers from specific countries or focus more broadly on enhanced screening, and explore differences in approaches at the regional level. We find that initial reactions almost universally focused on entry bans and flight suspensions from Southern Africa, and that policies continued to target travel from these countries even after community transmission of the Omicron variant was detected elsewhere in the world. While layered testing and quarantine requirements were implemented by some countries later in this three-week period, these enhanced screening policies were rarely the first response. The timing and conditionality of quarantine and testing requirements were not coordinated between countries or regions, creating logistical complications and burdening travelers with costs. Overall, response measures were rarely tied to specific criteria or adapted to match the unique epidemiology of the new variant.\n\nSummary boxO_LIDuring the initial three-week period following the discovery of the SARS-CoV-2 Omicron variant, nations rushed to implement travel restrictions - often at odds with guidance from the World Health Organization.\nC_LIO_LIBy sourcing and cataloging initial national-level travel restrictions worldwide, we demonstrate how the distribution of entry bans, flight suspensions, quarantine measures, vaccination requirements, and testing protocols evolved in response to emerging information during a period of uncertainty.\nC_LIO_LICountries that issued entry bans almost universally targeted the same Southern African countries and continued to do so even after widespread community transmission of the Omicron variant was reported elsewhere in the world.\nC_LIO_LILayers of testing and quarantine requirements were added later during the observation period but were rarely the initial response, with the exception of restrictions issued by countries in Africa, where leading with enhanced screening measures was more common.\nC_LIO_LIAnalysis of the disconnect between travel restrictions and transmission patterns that followed emergence of the Omicron variant provides a basis to inform evidence-based control measures for future virus mitigation efforts.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jordan Schermerhorn", + "author_inst": "Georgetown University" + }, + { + "author_name": "Alaina Case", + "author_inst": "Talus Analytics" + }, + { + "author_name": "Ellie Graeden", + "author_inst": "Talus Analytics" + }, + { + "author_name": "Justin Kerr", + "author_inst": "Talus Analytics" + }, + { + "author_name": "Mackenzie Moore", + "author_inst": "Georgetown University" + }, + { + "author_name": "Siobhan Robinson-Marshall", + "author_inst": "Georgetown University" + }, + { + "author_name": "Trae Wallace", + "author_inst": "Talus Analytics" + }, + { + "author_name": "Emily Woodrow", + "author_inst": "Georgetown University" + }, + { + "author_name": "Rebecca Katz", + "author_inst": "Georgetown University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.01.26.22269819", "rel_title": "Comparison of total and neutralizing SARS-CoV-2 spike antibodies against omicron and other variants in paired samples after two or three doses of mRNA vaccine", @@ -394139,81 +393123,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.27.22269944", - "rel_title": "Persistently reduced humoral and cellular immune response following third SARS-CoV-2 mRNA vaccination in anti-CD20-treated multiple sclerosis patients", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269944", - "rel_abs": "ObjectiveTo examine humoral and cellular response in multiple sclerosis patients on anti-CD20 therapy after third BNT162b2 mRNA SARS-CoV-2 vaccination.\n\nMethodsA prospective longitudinal study design from first throughout third vaccination in Danish and American MS centers. All participants were treated with ocrelizumab. Antibody (Ab) levels were assessed before and after third vaccination using SARS-CoV-2 IgG II Quant assay (Abbott Laboratories). B- and T-lymphocytes enumeration was done with BD Multitest6-color TBNK reagent. Spike-specific T-cell responses were measured through PBMC stimulation with spike peptide pools (JPT Peptide Technologies).\n\nResultsWe found that 14.0%, 37.7%, and 33.3% were seropositive after first, second and third vaccination. The median Ab-levels were 74.2 BAU/mL (range: 8.5-2427), 43.7 BAU/ml (range: 7.8-366.1) and 31.3 BAU/mL (range: 7.9-507.0) after first, second and third vaccination, respectively. No difference was found in levels after second and third vaccination (p=0.1475). Seropositivity dropped to 25.0% of participants before the third vaccination, a relative reduction of 33.3% (p=0.0020). No difference was found between frequencies of spike reactive CD4+ and CD8+ T-cells after second (0.65 {+/-} 0.08% and 0.95 {+/-} 0.20%, respectively) and third vaccination (0.99 {+/-} 0.22% and 1.3 {+/-} 0.34%), respectively.\n\nConclusionIn this longitudinal cohort we found no significant increased humoral or cellular response with administration of a third SARS-CoV-2 mRNA vaccination. These findings suggest the need for clinical strategies to include allowance of B cell reconstitution before repeat vaccination and/or provision of pre-exposure prophylactic monoclonal antibodies.\n\nKey PointsO_ST_ABSWhat is already known on this topicC_ST_ABSStudies have described decreased humoral response and sustained T-cell reactivity after standard two-dose SARS-CoV-2 mRNA vaccination during anti-CD20 therapy in multiple sclerosis participants.\n\nWhat this study addsPersistently decreased humoral, but stable cellular reactivity following a third SARS-CoV-2 mRNA vaccination.\n\nHow this study might affect research, practice or policyThe findings suggest the need for clinical strategies to include allowance of B cell reconstitution before repeat vaccination and/or provision of pre-exposure prophylactic monoclonal antibodies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Hamza Mahmood Bajwa", - "author_inst": "University Hospital of Southern Denmark, Department of Neurology, Esbjerg, DK" - }, - { - "author_name": "Frederik Novak", - "author_inst": "University Hospital of Southern Denmark, Department of Neurology, Esbjerg, DK" - }, - { - "author_name": "Anna Christine Nilsson", - "author_inst": "Odense University Hospital, Department of Clinical Immunology, Odense, DK" - }, - { - "author_name": "Christian Nielsen", - "author_inst": "Odense University Hospital, Department of Clinical Immunology, Odense, DK" - }, - { - "author_name": "Dorte K. Holm", - "author_inst": "Odense University Hospital, Department of Clinical Immunology, Odense, DK" - }, - { - "author_name": "Kamilla Oestergaard", - "author_inst": "Nordsjaellands Hospital, Department of Neurology, Hillerod, DK" - }, - { - "author_name": "Agnes Hauschultz Witt", - "author_inst": "Hospitalsenhed Midt, Department of Neurology, Viborg, DK" - }, - { - "author_name": "Keld-Erik Byg", - "author_inst": "Odense Universitetshospital, Department of Rheumatology, Odense, DK" - }, - { - "author_name": "Isik S. Johansen", - "author_inst": "Odense University Hospital, Department of Infectious Diseases, Odense, DK" - }, - { - "author_name": "Kristen Mittl", - "author_inst": "University California San Francisco, Department of Neurology, San Francisco, USA" - }, - { - "author_name": "William Rowles", - "author_inst": "University California San Francisco, Department of Neurology, San Francisco, USA" - }, - { - "author_name": "Scott Zamvil", - "author_inst": "University California San Francisco, Department of Neurology, San Francisco, USA" - }, - { - "author_name": "Riley Bove", - "author_inst": "Multiple Sclerosis Center at UCSF, Department of Neurology, San Francisco, CA, USA" - }, - { - "author_name": "Joseph J. Sabatino", - "author_inst": "University California San Francisco, Department of Neurology, San Francisco, USA" - }, - { - "author_name": "Tobias Sejbaek", - "author_inst": "University Hospital of Southern Denmark, Department of Neurology, Esbjerg, DK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.01.27.22269961", "rel_title": "A Micronized Electrostatic Precipitator Respirator Effectively Removes Ambient SARS-CoV-2 Bioaerosols", @@ -394974,6 +393883,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.25.477757", + "rel_title": "Defining the Substrate Envelope of SARS-CoV-2 Main Protease to Predict and Avoid Drug Resistance", + "rel_date": "2022-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477757", + "rel_abs": "Coronaviruses, as exemplified by SARS-CoV-2, can evolve and spread rapidly to cause severe disease morbidity and mortality. Direct acting antivirals (DAAs) are highly effective in decreasing disease burden especially when they target essential viral enzymes, such as proteases and polymerases, as demonstrated in HIV-1 and HCV and most recently SARS-CoV-2. Optimization of these DAAs through iterative structure-based drug design has been shown to be critical. Particularly, the evolutionarily conserved molecular mechanisms underlying viral replication can be leveraged to develop robust antivirals against rapidly evolving viral targets. The main protease (Mpro) of SARS-CoV-2, which is evolutionarily constrained to recognize and cleave 11 specific sites to promote viral maturation, exemplifies one such target. In this study we define the substrate envelope of Mpro by determining the molecular basis of substrate recognition, through nine high-resolution cocrystal structures of SARS-CoV-2 Mpro with the viral cleavage sites. These structures enable identification of evolutionarily vulnerable sites beyond the substrate envelope that may be susceptible to drug resistance and compromise binding of the newly developed Mpro inhibitors.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ala M Shaqra", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Sarah Zvornicanin", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Qiu Yu Huang", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Gordon J Lockbaum", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Mark Knapp", + "author_inst": "Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA" + }, + { + "author_name": "Laura Tandeske", + "author_inst": "Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA" + }, + { + "author_name": "David T Barkan", + "author_inst": "Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA" + }, + { + "author_name": "Julia Flynn", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Daniel NA Bolon", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Stephanie Moquin", + "author_inst": "Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA" + }, + { + "author_name": "Dustin Dovala", + "author_inst": "Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA" + }, + { + "author_name": "Ne\u015fe Kurt Yilmaz", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + }, + { + "author_name": "Celia A Schiffer", + "author_inst": "Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.01.24.477545", "rel_title": "Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19", @@ -396089,37 +395065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.25.22269822", - "rel_title": "Long term effectiveness of inactivated vaccine BBIBP-CorV (Vero Cells) against COVID-19 associated severe and critical hospitalization in Morocco", - "rel_date": "2022-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269822", - "rel_abs": "INTRODUCTIONWe provide national estimates of the real-world Vaccine effectiveness (VE) based on nationally available surveillance data. The study aimed to estimate the effectiveness of the inactivated Covid-19 vaccine BBIBP-CorV (Vero Cells) Sinopharm vaccine currently deployed in Morocco to reduce the risk of hospitalization from a severe infection of SARS- CoV-2 virus within 9 months after vaccination.\n\nMETHODSWe conducted a test-negative, case-control study among a population aged 18 years or older who were tested by rt-PCR for SARS-CoV-2 infection from February to October 2021 in Morocco. From the national laboratory COVID-19 database; we identified cases who were rt-PCR positive amongst severe and critical COVID-19 cases and controls who had a negative rt-PCR test for SARS-CoV-2. From the national vaccination register (NVR); individuals vaccinated with COVID-19 Vaccine (Vero Cell) and those unvaccinated were identified and included in the study. The linkage between databases was conducted for the study of Vaccination status based on the timing of the vaccine receipt relative to the SARS-CoV-2 rt-PCR test date. For each person, who tested positive for SARS-CoV-2, we identified a propensity score-matched control participant who was tested negative. We estimated vaccine effectiveness using conditional logistic regression.\n\nRESULTSAmong 12884 persons who tested positive and 12885 propensity score-matched control participants, the median age was 62 years, 47.2% of whom were female. As a function of time after vaccination of second dose vaccination, vaccine effectiveness during the first month was 88% (95% CI, 84-91), 87% (95% CI: 83-90) during the second and third month, 75% (95% CI: 67-80) during the fourth month, 61% (95% CI: 54-67) during the fifth month, and 64% (95% CI: 59-69) beyond the sixth month. VE remained high and stable during the first three months in the two-age subgroup. In the fourth month, the VE in the older population aged 60 years and above (64%) was reduced by 20 points compared to VE in the younger population (84%).\n\nCONCLUSIONA Sinopharm vaccine is highly protective against serious SARS-CoV-2 infection under real-world conditions. Protection remained high and stable during the first three months following the second dose and decreases slightly beyond the fourth month especially beyond 60 years.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jihane Belayachi", - "author_inst": "Mohammed V University in Rabat" - }, - { - "author_name": "Majdouline Obtel", - "author_inst": "Mohamed V University in Rabat, Morocco" - }, - { - "author_name": "Rachid Razine", - "author_inst": "Mohamed V University in Rabat, Morocco" - }, - { - "author_name": "Redouane Abouqal", - "author_inst": "Mohamed V University in Rabat, Morocco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.17.22269242", "rel_title": "Efficacy and Safety of a Plant-Based Virus-Like Particle Vaccine for COVID-19 Adjuvanted with AS03", @@ -397164,6 +396109,189 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.25.477789", + "rel_title": "Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine", + "rel_date": "2022-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477789", + "rel_abs": "The widespread SARS-CoV-2 in humans results in the continuous emergence of new variants. Recently emerged Omicron variant with multiple spike mutations sharply increases the risk of breakthrough infection or reinfection, highlighting the urgent need for new vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x), which showed high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine comprised of STFK and STFK1628x elicited high titers of broad-spectrum antibodies to neutralize all 14 circulating SARS-CoV-2 variants, including Omicron; and fully protected vaccinees from intranasal SARS-CoV-2 challenges of either the ancestral strain or immune-evasive Beta variant. Strikingly, the vaccination of hamsters with the bivalent vaccine completely blocked the within-cage virus transmission to unvaccinated sentinels, for either the ancestral SARS-CoV-2 or Beta variant. Thus, our study provides new insights and antigen candidates for developing next-generation COVID-19 vaccines.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Yangtao Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shaojuan Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yali Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Lunzhi Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qingbing Zheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Min Wei", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yang Shi", + "author_inst": "Xiamen University" + }, + { + "author_name": "Zikang Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jian Ma", + "author_inst": "Xiamen University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Meifeng Nie", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jin Xiao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Zehong Huang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Peiwen Chen", + "author_inst": "The University of Hong Kong, Shantou University" + }, + { + "author_name": "Huilin Guo", + "author_inst": "Xiamen University" + }, + { + "author_name": "Miaolin Lan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jingjing Xu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Wangheng Hou", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yunda Hong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Dabing Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hui Sun", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hualong Xiong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ming Zhou", + "author_inst": "Xiamen University" + }, + { + "author_name": "Che Liu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Wenjie Guo", + "author_inst": "Xiamen University" + }, + { + "author_name": "Huiyu Guo", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jiahua Gao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Zhixiong Li", + "author_inst": "Fujian Maternity and Child Health Hospital" + }, + { + "author_name": "Haitao Zhang", + "author_inst": "Fujian Maternity and Child Health Hospital" + }, + { + "author_name": "Xinrui Wang", + "author_inst": "Fujian Maternity and Child Health Hospital" + }, + { + "author_name": "Shaowei Li", + "author_inst": "Xiamen University" + }, + { + "author_name": "Tong Cheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qinjian Zhao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yixin Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ting Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Tianying Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hua Cao", + "author_inst": "Fujian Maternity and Child Health Hospital" + }, + { + "author_name": "Huachen Zhu", + "author_inst": "The University of Hong Kong, Shantou University" + }, + { + "author_name": "Quan Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yi Guan", + "author_inst": "The University of Hong Kong, Shantou University" + }, + { + "author_name": "NingShao Xia", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.24.477505", "rel_title": "Biodistribution and Environmental Safety of a Live-attenuated YF17D-vectored SARS-CoV-2 Vaccine Candidate", @@ -398107,41 +397235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.22.477323", - "rel_title": "Harringtonine has the effects of double blocking SARS-CoV-2 membrane fusion", - "rel_date": "2022-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.22.477323", - "rel_abs": "Fusion with host cell membrane is the main mechanism of infection of SARS-CoV-2. Here, we propose a new strategy to double block SARS-CoV-2 membrane fusion by using Harringtonine (HT), a small-molecule antagonist. By using cell membrane chromatography (CMC), we found that HT specifically targeted the SARS-CoV-2 S protein and host cell TMPRSS2, and then confirmed that HT can inhibit pseudotyped virus membrane fusion. Furthermore, HT successfully blocked SARS-CoV-2 infection, especially in the delta and Omicron mutant. Since HT is a small-molecule antagonist, it is minimally affected by the continuous variation of SARS-CoV-2. Our findings show that HT is a potential small-molecule antagonist with a new mechanism of action against SARS-CoV-2 infection, and thus HT mainly targets the S protein, and thus, greatly reduces the damage of the S proteins autotoxicity to the organ system, has promising advantages in the clinical treatment of COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shaohong Chen", - "author_inst": "1.State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China 2.University of Ch" - }, - { - "author_name": "Qiang Ding", - "author_inst": "School of Medicine, Tsinghua University, Beijing, China" - }, - { - "author_name": "Xinghai Zhang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Yan Wu", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - }, - { - "author_name": "Huajun Zhang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.01.24.22269741", "rel_title": "The Choice of Response Alternatives in COVID-19 Social Science Surveys", @@ -398694,6 +397787,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.01.24.477633", + "rel_title": "Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern", + "rel_date": "2022-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.24.477633", + "rel_abs": "The 2019 coronavirus disease (COVID-19) pandemic has had devastating impacts on our global health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has now overtaken the Delta variant and become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q493K/R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our result could help explain the Omicron variants prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.\n\nTOC GRAPHIC\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC=\"FIGDIR/small/477633v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (47K):\norg.highwire.dtl.DTLVardef@1997fcborg.highwire.dtl.DTLVardef@951e96org.highwire.dtl.DTLVardef@b3956org.highwire.dtl.DTLVardef@e15ef9_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Seonghan Kim", + "author_inst": "Lehigh University" + }, + { + "author_name": "Yi Liu", + "author_inst": "Lehigh University" + }, + { + "author_name": "Matthew Ziarnik", + "author_inst": "Lehigh University" + }, + { + "author_name": "Yiwei Cao", + "author_inst": "Lehigh University" + }, + { + "author_name": "X. Frank Zhang", + "author_inst": "Lehigh University" + }, + { + "author_name": "Wonpil Im", + "author_inst": "Lehigh University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.01.22.22269660", "rel_title": "Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons", @@ -399913,41 +399045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.24.22269775", - "rel_title": "Massive covidization of research citations and the citation elite", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269775", - "rel_abs": "Massive scientific productivity accompanied the COVID-19 pandemic. We evaluated the citation impact of COVID-19 publications relative to all scientific work published in 2020-2021 and assessed the impact on scientist citation profiles. Using Scopus data until August 1, 2021, COVID-19 items accounted for 4% of papers published, 20% of citations received to papers published in 2020-2021 and >30% of citations received in 36 of the 174 disciplines of science (up to 79.3% in General and Internal Medicine). Across science, 98 of the 100 most-cited papers published in 2020-2021 were related to COVID-19. 110 scientists received >=10,000 citations for COVID-19 work, but none received >=10,000 citations for non-COVID-19 work published in 2020-2021. For many scientists, citations to their COVID-19 work already accounted for more than half of their total career citation count. Overall, these data show a strong covidization of research citations across science with major impact on shaping the citation elite.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "John Ioannidis", - "author_inst": "Stanford University" - }, - { - "author_name": "Eran Bendavid", - "author_inst": "Stanford University" - }, - { - "author_name": "Maia Salholz-Hillel", - "author_inst": "Berlin Institute of Health" - }, - { - "author_name": "Kevin W Boyack", - "author_inst": "SciTech Strategies" - }, - { - "author_name": "Jeroen Baas", - "author_inst": "Elsevier" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.18.22269433", "rel_title": "Risk factors for developing symptomatic COVID-19 in older residents of nursing homes: A hypothesis-generating observational study", @@ -400544,6 +399641,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.24.22269757", + "rel_title": "Modelling preventive measures and their effect on generation times in emerging epidemics", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269757", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWWe present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a homogeneously mixing community. The model is based on an infectivity process, which we define through stochastic contact and infectiousness processes, so that each individual has an independent infectivity profile. In particular, we monitor variations of the reproduction number and of the distribution of generation times. We show that some interventions, i.e. uniform reduction and vaccination, affect the former while leaving the latter unchanged, whereas other interventions, i.e. isolation, screening and contact tracing, affect both quantities. We provide a theoretical analysis of the variation of these quantities, and we show that, in practice, the variation of the generation time distribution can be significant and that it can cause biases in the estimation of basic reproduction numbers. The framework, because of its general nature, captures the properties of many infectious diseases, but particular emphasis is on COVID-19, for which numerical results are provided.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Martina Favero", + "author_inst": "Stockholm University" + }, + { + "author_name": "Gianpaolo Scalia Tomba", + "author_inst": "University of Rome Tor Vergata" + }, + { + "author_name": "Tom Britton", + "author_inst": "Stockholm University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.23.22269718", "rel_title": "Values and preferences of the general population in Indonesia in relation to COVID-19 self-testing: A cross-sectional survey", @@ -401615,49 +400739,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.21.22269664", - "rel_title": "Waning of Vaccine-Conferred Protection against SARS-CoV-2 Infection: Matched Case-Control Test-Negative Design Study in Two High-Risk Populations", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269664", - "rel_abs": "To distinguish waning of vaccine responses from differential variant protection, we performed a test-negative case-control analysis during a Delta variant-dominant period in Californias prisons. We found that infection odds increased each 28-day period post-vaccination, reaching 3.4-fold (residents) to 4.7-fold (staff) increased odds of infection after 180 days.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jeremy D Goldhaber-Fiebert", - "author_inst": "Stanford University" - }, - { - "author_name": "Lea Prince", - "author_inst": "Stanford University" - }, - { - "author_name": "Elizabeth T Chin", - "author_inst": "Stanford University" - }, - { - "author_name": "David Leidner", - "author_inst": "California Department of Corrections and Rehabilitation" - }, - { - "author_name": "David M Studdert", - "author_inst": "Stanford University" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.21.22269671", "rel_title": "Impact of COVID-19 symptoms on social aspects of life of female long haulers: A qualitative study", @@ -402430,6 +401511,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.22.22269689", + "rel_title": "ESTIMATING THE EFFECT OF VACCINATION ON THE CASE-FATALITY RATE FOR COVID-19", + "rel_date": "2022-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269689", + "rel_abs": "ObjectiveTo evaluate the benefits of vaccination on the case fatality rate (CFR) for COVID-19 infections.\n\nDesignMultivariate modeling of data from electronic medical records\n\nSetting130 medical centers of the United States Department of Veterans Affairs\n\nParticipants339,772 patients with COVID-19 confirmed by nucleic acid amplification testing as of September 30, 2021\n\nMethodsThe primary outcome was death within 60 days of the diagnosis. Patients were considered vaccinated if they had completed a full series >= 14 days prior to diagnosis. Cases presenting in July - September of 2021 were considered to have the delta variant. Logistic regression was used to derive adjusted odds ratios (OR) for vaccination and infection with delta versus earlier variants. Models were adjusted for demographic traits, standard comorbidity indices, selected clinical terms, and 3 novel parameters representing all prior diagnoses, all prior vital signs/ baseline laboratory tests, and current outpatient treatment. Patients with a delta infection were divided into 8 cohorts based upon the time from vaccination to diagnosis (in 4-week blocks). A common model was used to estimate the odds of death associated with vaccination for each cohort relative that of all unvaccinated patients.\n\nResults9.1% of subjects had been fully vaccinated, and 21.5% were presumed to have the delta variant. 18,120 patients (5.33%) died within 60 days of their diagnoses. The adjusted OR for delta infection was 1.87 +/- 0.05 which corresponds to a relative risk of 1.78. The overall adjusted OR for prior vaccination was 0.280 +/- 0.011 corresponding to a relative risk of 0.291. The study of vaccine cohorts with a delta infection showed that the raw CFR rose steadily after 10-14 weeks. However, the OR for vaccination remained stable for 10-34 weeks.\n\nConclusionsOur study confirms that delta is substantially more lethal than earlier variants and that vaccination is an effective means of preventing COVID death. After adjusting for major selection biases, we found no evidence that the benefits of vaccination on CFR declined over 34 weeks.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Glen H Murata", + "author_inst": "New Mexico VA Health Care System" + }, + { + "author_name": "Allison E Murata", + "author_inst": "VA Cooperative Studies Program - Clinical Research Pharmacy Coordinating Center" + }, + { + "author_name": "Douglas J Perkins", + "author_inst": "University of New Mexico School of Medicine" + }, + { + "author_name": "Heather M Campbell", + "author_inst": "VA Cooperative Studies Program - Clinical Research Pharmacy Coordinating Center" + }, + { + "author_name": "Jenny T Mao", + "author_inst": "New Mexico VA Health Care System" + }, + { + "author_name": "Brent Wagner", + "author_inst": "New Mexico VA Health Care System" + }, + { + "author_name": "Benjamin H Mcmahon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Curt H Hagedorn", + "author_inst": "New Mexico VA Health Care System" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.18.22269217", "rel_title": "Shorter serial intervals in SARS-CoV-2 cases with Omicron variant compared to Delta variant in the Netherlands, 13 - 19 December 2021", @@ -403713,25 +402841,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.19.22269576", - "rel_title": "Joinpoint Regression to Determine the Impact of COVID-19 on Mortality in Europe: A Longitudinal Analysis From 2000 to 2020 in 27 Countries", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269576", - "rel_abs": "The novel coronavirus disease 2019 (COVID-19) represented the most extensive health emergency in human history. However, to date, there is still a lot of uncertainty about the exact death toll the pandemic has claimed. In particular, the number of official deaths could be vastly underestimated. Despite this, many conspirationists speculate that COVID-19 is not a dangerous disease. Therefore, in this manuscript, we use joinpoint regression analysis to estimate the impact of COVID-19 in 27 European countries by comparing annual mortality trends from 2000 to 2020. Furthermore, we provide accessible evidence even for a non-expert audience. Siegel (A1) and Holm-Bonferroni (A2) approaches were employed to assess the significance of the results separately. In conclusion, these results estimate that COVID-19 increased the overall mortality in Europe by 10% (A1: P < .001, A2: Adjusted P = .001). In 16 out of 27 countries (59.3%), the excess mortality ranged from 7.4% to 18.5% (A1: P < .003, A2: Adjusted P < .040). Comparison of the excess mortalities distribution to the null counterfactual showed that the mortality increase was highly significant across Europe (Adjusted P < .001).", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Alessandro Rovetta", - "author_inst": "R&C Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.19.22269572", "rel_title": "Monitoring SARS-CoV-2 genome evolution in a localized population", @@ -404452,6 +403561,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.18.22268965", + "rel_title": "Safety Profile of Sinopharm COVID-19 Vaccine and Breakthrough Infections in Pakistan", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22268965", + "rel_abs": "BackgroundTo determine the safety profile of Sinopharm COVID-19 vaccine and identify breakthrough infections.\n\nMethodThe study design was analytical cross sectional. An online questionnaire was filled by 1033 respondentsbetween 16th and 22nd April 2021. Adults who had received both doses of Sinopharm COVID-19 vaccine more than a week ago or only a single dose with serious side effect were included in the study. The frequency and severity of vaccination related side effects were assessed and breakthrough infection identified.\n\nResultsThe mean age of participants was 36.7 {+/-} 12.91(18 - 92) years. Ninety one percent of participants (n=946) were health care professionals. One fifth (n=225/1033, 21.8%) had suffered from COVID-19 infection prior to vaccination, confirmed using the nasal RT-PCR test. None of the participants reported serious (grade III) or life threatening (grade IV) adverse reactions after either of the two doses. The most common side effects after the first dose were pain at injection site (20.3%), fatigue (20.3%), headache (13.9%), myalgia (12.5%) and fever (9.3%) whereas after the second dose were fatigue (16.8%), pain at injection site (15.8%), myalgia (14%) and fever (6.7%). The side effects were more common in participants who had previous history of COVID-19 infection. Of 225 previously infected participants, 97(43.1%) (p value=0.020) and 90 (40%) (p value=0.001) participants had side effects after 1st and 2nd dose respectively. 16 participants (1.55%) developed PCR positive COVID-19 infection two weeks after the second dose while 3(0.29%) participants had a re-infection. There was one case of probable severe COVID-19 infection, 2 weeks after the second dose and recovered completely with treatment.\n\nConclusionOur study shows that Sinopharm COVID-19 vaccine is generally safe with no serious side effects. The side effects were however, more common in inviduals who already had COVID-19 infection. The COVID-19 breakthrough infection and reinfection could occur after the vaccination.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Wajiha Rizwan", + "author_inst": "Pediatric Medicine Department The Childrens Hospital and Institute of Child Health Lahore" + }, + { + "author_name": "Ahmad Uzair Qureshi", + "author_inst": "King Edward Medical University, Lahore" + }, + { + "author_name": "Muhammad Nasir Rana", + "author_inst": "The Childrens Hospital and Institute of Child Health, Lahore" + }, + { + "author_name": "Mubeen Nazar Duggal", + "author_inst": "The Childrens Hospital and Institute of Child Health, Lahore" + }, + { + "author_name": "Muhammad Sohaib", + "author_inst": "The Childrens Hospital and Institute of Child Health, Lahore" + }, + { + "author_name": "Masood Sadiq", + "author_inst": "The Childrens Hospital and Institute of Child Health, Lahore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.18.22269445", "rel_title": "SARS-CoV-2 surveillance (09/2020 - 03/2021) in elementary schools and daycare facilities in Bavaria", @@ -405435,33 +404583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2022.01.19.22269395", - "rel_title": "Temporal trends in legionellosis national notification data and the effect of COVID-19, Switzerland, 2000- 2020", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269395", - "rel_abs": "The notification rate of legionellosis in Switzerland and other European countries has markedly increased over the last 20 years. Here, we investigated the Swiss notification data on legionellosis from 2000-2020 in regards of overall time trend, content and data quality. We further explored the impact of the COVID-19 pandemic on the reported case numbers using an interrupted time series approach. Between 2000 and 2020, 5,980 cases were included in our analysis. The annual crude notification rate for legionellosis cases increased from 1.1/100,000 population (CI: 0.9 - 1.4) in 2000 to 5.6/100,000 population (CI: 5.1 - 6.1) in 2020. In recent years, the summer peaks have been more pronounced and some shifted earlier in the year. The highest notification rate was recorded in 2018 with 6.7/100,000 population (CI: 6.2 - 7.3). The hospitalisation rate for notified cases remained high across all study years (89.9%), while the case fatality rate slightly decreased (from 7.7% to 3.6%). COVID-19 containment measures, such as travel restrictions and/or related behavioural changes, are associated with a temporary decline in cases of 35%. Overall, the quality of the notification data was good. Clinical data were more susceptible to interferences than data from laboratory reporting, which could be observed most clearly in the decline of clinical reports by 4.3 percentage points in 2020. As the case classification for Legionnaires disease includes pneumonia symptoms, this decline could lead to an underestimation of Legionnaires disease cases, yet the continuous reporting though the diagnostic laboratories suggested a robust surveillance system for legionellosis in Switzerland.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fabienne Beatrice Fischer", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland" - }, - { - "author_name": "Daniel M\u00e4usezahl", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland" - }, - { - "author_name": "Monica N. Wymann", - "author_inst": "Federal Office of Public Health, Berne, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.18.22269200", "rel_title": "Infection and transmission risks in schools and contribution to the COVID-19 pandemic in Germany - a retrospective observational study using nation-wide and regional health and education agency notification data", @@ -406190,6 +405311,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.13.22268997", + "rel_title": "Detection and upsurge of SARS-CoV-2 Omicron variant in Islamabad Pakistan", + "rel_date": "2022-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22268997", + "rel_abs": "The SARS-CoV-2 omicron variant was first detected in South Africa in November, 2021 and has rapidly spread to more than 90 countries. The emergence of Omicron variant demands for enhanced genomic surveillance to track the mutation profile and spread of virus. In the current study, we have sequenced 15 whole-genome sequences of SARS-CoV-2 Omicron variant from Islamabad region of Pakistan. Among the 15 isolates, 66% were from Islamabad whereas 33% of cases had international travel history of United Kingdom, Maldives, South Africa, and Oman. The detection of Omicron in local community and in travelers highlights the need for rigorous screening at national level and at entry points in order to contain the spread of variant.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Massab Umair Dr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Aamer Ikram Prof.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Zaira Rehman Dr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Syed Adnan Haider Mr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Nazish Badar Ms.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhammad Ammar Mr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Qasim Ali Mr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Abdul Aahad Mr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Rana Suleman Mr.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Ayesha Khalid Ms.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Amna Tariq Ms.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Zunera Jamal Ms.", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhammad Salman Dr.", + "author_inst": "National Institute of Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.19.476998", "rel_title": "Discovery of a SARS-CoV-2 Broadly-Acting Neutralizing Antibody with Activity against Omicron and Omicron + R346K Variants", @@ -407381,117 +406569,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.01.19.22269521", - "rel_title": "Loss of Y in leukocytes as a risk factor for critical COVID-19 in men", - "rel_date": "2022-01-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269521", - "rel_abs": "COVID-19 shows an unexplained, strong male bias for severity and mortality. Loss of Y (LOY) in myeloid cells is a risk factor candidate in COVID-19 because of associations with many age-related diseases and its effect on transcription of immune genes. We report the highest levels of LOY in cells that are crucial for the development of severe COVID-19 phenotype, such as low-density neutrophils, granulocytes, and monocytes reaching 46%, 32%, and 29%, respectively, from men with critical COVID-19 (n=139). LOY in sorted subpopulations of leukocytes correlated with increased thrombocyte count, thromboembolic events, invasive mechanical ventilation and a history of vessel disease. In recovered patients, LOY decreased in whole blood and peripheral blood mononuclear cells. Moreover, sc-RNA-seq analysis of CD14+ monocytes from 30 COVID-19 males and 34 controls revealed pervasive transcriptional downregulation in LOY-cells, notably affecting HLA class I and II genes important for antigen presentation. The data support a link between LOY and emergency myelopoiesis as well as the role of LOY in modulation of COVID-19 severity. Our results might also be relevant for other viral infections showing similar male bias.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Bozena Bruhn-Olszewska", - "author_inst": "Uppsala University" - }, - { - "author_name": "Hanna Davies", - "author_inst": "Uppsala University" - }, - { - "author_name": "Daniil Sarkisyan", - "author_inst": "Uppsala University" - }, - { - "author_name": "Ulana Juhas", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Edyta Rychlicka-Buniowska", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Magdalena Wojcik", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Monika Horbacz", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Marcin Jakalski", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Pawel Olszewski", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Jakub O. Westholm", - "author_inst": "Stockholm University" - }, - { - "author_name": "Agata Smialowska", - "author_inst": "Stockholm University" - }, - { - "author_name": "Karol Wierzba", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Asa Torinsson Naluai", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Niklas Jern", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Lars-Magnus Andersson", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Josef Jarhult", - "author_inst": "Uppsala University" - }, - { - "author_name": "Natalia Filipowicz", - "author_inst": "Medical University of Gdansk" - }, - { - "author_name": "Eva Tiensuu Janson", - "author_inst": "Uppsala University" - }, - { - "author_name": "Sten Rubertsson", - "author_inst": "Uppsala University" - }, - { - "author_name": "Miklos Lipcsey", - "author_inst": "Uppsala University" - }, - { - "author_name": "Magnus Gisslen", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Michael Hultstrom", - "author_inst": "Uppsala University" - }, - { - "author_name": "Robert Frithiof", - "author_inst": "Uppsala Universitet" - }, - { - "author_name": "Jan P Dumanski", - "author_inst": "Uppsala Universitet" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.01.15.22269335", "rel_title": "Retention of Neutralizing response against SARS-CoV-2 Omicron variant in Sputnik V vaccinated individuals", @@ -408439,6 +407516,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.21266111", + "rel_title": "SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients.", + "rel_date": "2022-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.21266111", + "rel_abs": "Patients with COVID-19 may develop abnormal inflammatory response and lymphopenia, followed in some cases by delayed-onset syndromes, often long-lasting after the initial SARS-CoV-2 infection. As viral infections may activate human endogenous retroviral elements (HERV), we studied the effect of SARS-CoV-2 on HERV-W and HERV-K envelope (ENV) expression, known to be involved in immunological and neurological pathogenesis of human diseases. Our results have showed that the exposure to SARS-CoV-2 virus activates early HERV-W and K transcription but only HERV-W ENV protein expression, in an infection- and ACE2-independent way within peripheral blood mononuclear cell cultures from one-third of healthy donors. Moreover, HERV-W ENV protein was significantly increased in serum and plasma of COVID-19 patients, correlating with its expression in CD3+ lymphocytes and with disease severity. Finally, HERV-W ENV was found expressed in post-mortem tissues of lungs, heart, brain olfactory bulb and nasal mucosa from acute COVID-19 patients in cell-types relevant for COVID-19-associated pathogenesis within affected organs, but different from those expressing of SARS-CoV-2 antigens. Altogether, the present study revealed that SARS-CoV-2 can induce HERV-W ENV expression in cells from individuals with symptomatic and severe COVID-19. Our data suggest that HERV-W ENV is likely to be involved in pathogenic features underlying symptoms of acute and post-acute COVID. It highlights the importance to further understand patients genetic susceptibility to HERV-W activation and the relevance of this pathogenic element as a prognostic marker and a therapeutic target in COVID-19 associated syndromes.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/21266111v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (68K):\norg.highwire.dtl.DTLVardef@1be71a1org.highwire.dtl.DTLVardef@1621b8org.highwire.dtl.DTLVardef@fff085org.highwire.dtl.DTLVardef@107cb0c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Benjamin Charvet", + "author_inst": "GeNeuro Innovation, Lyon, France." + }, + { + "author_name": "Joanna Brunel", + "author_inst": "GeNeuro Innovation, Lyon, France" + }, + { + "author_name": "Justine Pierquin", + "author_inst": "GeNeuro Innovation, Lyon, France" + }, + { + "author_name": "Mathieu Iampietro", + "author_inst": "CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, Universite de Lyon, Universite Claude Bernard Lyon 1, Ecole Normale Superieure" + }, + { + "author_name": "Didier Decimo", + "author_inst": "CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, Universite de Lyon, Universite Claude Bernard Lyon 1, Ecole Normale Superieure" + }, + { + "author_name": "Nelly Queruel", + "author_inst": "GeNeuro Innovation, Lyon, France" + }, + { + "author_name": "Alexandre Lucas", + "author_inst": "We-Met platform, I2MC/Inserm/Universite Paul Sabatier UMR1297, Toulouse, France" + }, + { + "author_name": "Maria del Mar Encabo-Berzosa", + "author_inst": "Biobanco del Sistema de Salud de Aragon, Instituto Aragones de Ciencias de la Salud (IACS), Zaragoza, Spain" + }, + { + "author_name": "Izaskun Arenaz", + "author_inst": "Biobanco del Sistema de Salud de Aragon, Instituto Aragones de Ciencias de la Salud (IACS), Zaragoza, Spain" + }, + { + "author_name": "Tania Perez Marmolejo", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico." + }, + { + "author_name": "Francina Valezka Bolanos Morales", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Arturo Ivan Gonzalez Gonzalez", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Armando Castorena Maldonado", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Cesar Luna Rivero", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Cyrille Mathieu", + "author_inst": "CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, Universite de Lyon, Universite Claude Bernard Lyon 1, Ecole Normale Superieure" + }, + { + "author_name": "Patrick Kury", + "author_inst": "Department of Neurology, Medical Faculty, Heinrich-Heine-University, Dusseldorf, Germany" + }, + { + "author_name": "Jose Flores-Rivera", + "author_inst": "Department of Neurology, National Institute of Neurology and Neurosurgery, Mexico City, Mexico" + }, + { + "author_name": "Santiago Avila Rios", + "author_inst": "Centro de Investigacion en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Gonzalo Salgado Montes de Oca", + "author_inst": "Centro de Investigacion en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico Ciudad, Mexico" + }, + { + "author_name": "Jon Schoorlemmer", + "author_inst": "ARAID Foundation; Instituto Aragones de Ciencias de la Salud (IACS); Grupo B46_20R de la DGA and GIIS-028 del IISA; all Zaragoza, Spain" + }, + { + "author_name": "Branka Horvat", + "author_inst": "CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, Universite de Lyon, Universite Claude Bernard Lyon 1, Ecole Normale Superieure" + }, + { + "author_name": "Herve JF Perron", + "author_inst": "Geneuro-Innovation ; GeNeuro, Plan les Ouates, Geneva, Switzerland" + } + ], + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.17.22269249", "rel_title": "Non-Communicable Diseases Risk Factors and the Risk of COVID-19 Infection among University Employees in Indonesia", @@ -409282,85 +408462,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.17.22269081", - "rel_title": "Real-world monitoring of BNT162b2 vaccine-induced SARS-CoV-2 B and T cell immunity in naive healthcare workers: a prospective single center study", - "rel_date": "2022-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269081", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing COVID-19 pandemic. To prevent the massive COVID-19 burden, several vaccination campaigns were initiated. We performed a single center observational trial to evaluate adaptive immunity in naive healthcare workers upon BNT162b2 vaccination.\n\nMethodsSerological analysis was performed through conventional immunoassays. Antibody functionality was analyzed via in vitro neutralization assays. Circulating receptor-binding domain (RBD) specific B cells were assessed via flowcytometry. The induction of SARS-CoV-2 specific T cells was investigated through interferon-{gamma} release assay combined with flowcytometric profiling of activated CD4 and CD8 T cells.\n\nResultsThree months after vaccination, all but one of the subjects (N = 31) displayed vaccine-induced neutralizing antibodies. In 10 out of 31 subjects, circulating RBD specific B cells were found of which the rate showed moderate correlation to serological parameters. Specific interferon-{gamma} release was present in all subjects and correlated with the significant upregulation of CD69 on CD4+ and CD8+ T cells and CD40L on CD4+ T cells. Interestingly, no relation was found between B and T cell parameters. In addition, one symptomatic breakthrough infection with the SARS-CoV-2 alpha variant of concern was reported.\n\nConclusionThree months post vaccination, both humoral and cellular immune responses are detectable in all but one participant. No correlation was found between the magnitude of both B and T cell responses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Bas Calcoen", - "author_inst": "Laboratory for Thrombosis Research, KU Leuven campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Kim Callebaut", - "author_inst": "AZ Groeninge Hospital, Department of Laboratory Medicine, Kortrijk, Belgium" - }, - { - "author_name": "Aline Vandenbulcke", - "author_inst": "Laboratory for Thrombosis Research, KU Leuven campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Nico Callewaert", - "author_inst": "AZ Groeninge Hospital, Department of Laboratory Medicine, Kortrijk, Belgium" - }, - { - "author_name": "Xavier Bossuyt", - "author_inst": "Department of Microbiology, Immunology and Transplantation, KU Leuven and Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium" - }, - { - "author_name": "Johan Van Weyenbergh", - "author_inst": "Laboratory for Clinical and Epidemiological Virology, KU Leuven Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Piet Maes", - "author_inst": "Laboratory for Clinical and Epidemiological Virology, KU Leuven Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Maya Imbrechts", - "author_inst": "PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Thomas Vercruysse", - "author_inst": "Laboratory of Virology and Chemotherapy KU Leuven Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Hendrik Jan Thibaut", - "author_inst": "Laboratory of Virology and Chemotherapy KU Leuven Rega Institute, Leuven, Belgium" - }, - { - "author_name": "Dorinja Zapf", - "author_inst": "Institut fur experimentelle Immunologie, EUROIMMUN Medizinische Labordiagnostika AG , Lubeck, Germany" - }, - { - "author_name": "Kersten Dieckmann", - "author_inst": "Institut fur experimentelle Immunologie, EUROIMMUN Medizinische Labordiagnostika AG , Lubeck, Germany" - }, - { - "author_name": "Karen Vanhoorelbeke", - "author_inst": "Laboratory for Thrombosis Research, KU Leuven campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Nick Geukens", - "author_inst": "PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Simon De Meyer", - "author_inst": "Laboratory for Thrombosis Research, KU Leuven campus Kulak Kortrijk, Kortrijk, Belgium" - }, - { - "author_name": "Wim Maes", - "author_inst": "PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.16.22269146", "rel_title": "Development and validation of the Symptom Burden Questionnaire\u2122 for Long COVID: a Rasch analysis", @@ -409981,6 +409082,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.16.22269161", + "rel_title": "Forecast of omicron wave time evolution", + "rel_date": "2022-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269161", + "rel_abs": "Adopting an early doubling time of three days for the rate of new infections with the omicron mutant the temporal evolution of the omicron wave in different countries is predicted. The predictions are based on the susceptible-infectious-recovered/removed (SIR) epidemic compartment model with a constant stationary ratio k = (t)/a(t) between the infection (a(t)) and recovery ((t)) rate. The fixed early doubling time then uniquely relates the initial infection rate a0 to the ratio k, which therefore determines the full temporal evolution of the omicron waves. For each country three scenarios (optimistic, pessimistic, intermediate) are considered and the resulting pandemic parameters are calculated. These include the total number of infected persons, the maximum rate of new infections, the peak time and the maximum 7-day incidence per 100000 persons. Among the considered European countries Denmark has the smallest omicron peak time and the recently observed saturation of the 7-day incidence value at 2478 is in excellent agreement with the prediction in the optimistic scenario. For Germany we predict peak times of the omicron wave ranging from 32 to 38 and 45 days after the start of the omicron wave in the optimistic, intermediate and pessimistic scenario, respectively, with corresponding maximum SDI values of 7090, 13263 and 28911, respectively. Adopting Jan 1st, 2022 as the starting date our predictions implies that the maximum of the omicron wave is reached between Feb 1 and Feb 15, 2022. Rather similar values are predicted for Switzerland. Due to an order of magnitude smaller omicron hospitalization rate, due to the high percentage of vaccinated and boostered population, the German health system can cope with maximum omicron SDI value of 2800 which is about a factor 2.5 smaller than the maximum omicron SDI value 7090 in the optimistic case. By either reducing the duration of intensive care during this period of maximum, and/or by making use of the nonuniform spread of the omicron wave across Germany, it seems that the German health system can barely cope with the omicron wave avoiding triage decisions. The reduced omicron hospitalization rate also causes significantly smaller mortality rates compared to the earlier mutants in Germany. In the optimistic scenario one obtains for the total number of fatalities 7445 and for the maximum death rate 418 per day which are about one order of magnitude smaller than the beta fatality rate and total number.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Reinhard Schlickeiser", + "author_inst": "Institut fur Theoretische Physik, Lehrstuhl IV: Weltraum- und Astrophysik, Ruhr-Universitat Bochum, D-44780 Bochum, Germany" + }, + { + "author_name": "Martin Kroger", + "author_inst": "ETH Zurich, Zurich, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.01.15.22269356", "rel_title": "Distinct Vaccine Efficacy Rates Among Health Care Workers During a COVID-19 Outbreak in Jordan", @@ -410868,69 +409992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.14.22269182", - "rel_title": "Immunosuppression impaired the immunogenicity of inactivated SARS-CoV-2 vaccine in non-dialysis kidney disease patients", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269182", - "rel_abs": "Patients with chronic kidney disease (CKD) are at higher risk for coronavirus disease 2019 (COVID-19)-related morbidity and mortality. However, a significant portion of CKD patients showed hesitation toward vaccination in telephone survey of our center. Yet no serial data available on humoral response in patients with CKD, especially those on immunosuppression. We conducted a pilot, prospective study to survey the safety and humoral response to inactivated SARS-CoV-2 vaccine in CKD patients receiving a 2-dose immunization of inactivated SARS-CoV-2 vaccine. We found the neutralizing antibody titers in CKD patients was significantly lower than that in healthy controls, hypertension patients, and diabetes patients. Notably, immunosuppressive medication rather than eGFR levels or disease types showed effect on the reduction of immunogenicity. Interestingly, a third dose significantly boosted neutralizing antibody in CKD patients while immunosuppressants impeded the boosting effects. In conclude, our data demonstrates that CKD patients, even for those on immunosuppression treatment, can benefit from a third vaccination boost by improving their humoral immunity.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yuemiao Zhang", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Xingzi Liu", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Miaomiao Lin", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Jincan Zan", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Yitong Hu", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Xiangqiu Wang", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Wenqi Wu", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Taicheng Zhou", - "author_inst": "Center Lab and Liver Disease Research Center, the Affiliated Hospital of Yunnan University, Kunming, Yunnan 650091, China" - }, - { - "author_name": "Hong Zhang", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Jicheng Lv", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Li Yang", - "author_inst": "Peking University First Hospital" - }, - { - "author_name": "Zijie Zhang", - "author_inst": "State Key Laboratory for Conservation and Utilization of Bio-resource and School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2022.01.13.22269244", "rel_title": "Prognostic Value of Serum/Plasma Neurofilament Light Chain for COVID-19 Associated Mortality", @@ -411799,6 +410860,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.12.22269192", + "rel_title": "Imprinted SARS-CoV-2-specific memory lymphocytes define hybrid immunity", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269192", + "rel_abs": "Immune memory is tailored by cues that lymphocytes perceive during priming. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic created a situation in which nascent memory could be tracked through additional antigen exposures. Both SARS-CoV-2 infection and vaccination induce multifaceted, functional immune memory, but together they engender improved protection from disease, termed \"hybrid immunity\". We therefore investigated how vaccine-induced memory is shaped by previous infection. We found that following vaccination, previously infected individuals generated more SARS-CoV-2 RBD-specific memory B cells and variant-neutralizing antibodies and a distinct population of IFN-{gamma} and IL-10-expressing memory SARS-CoV-2 spike-specific CD4+ T cells than previously naive individuals. While additional vaccination could increase humoral memory, it did not recapitulate the distinct CD4+ T cell cytokine profile in previously naive individuals. Thus, imprinted features of SARS-CoV-2-specific memory lymphocytes define hybrid immunity.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Lauren B. Rodda", + "author_inst": "Department of Immunology, University of Washington School of Medicine, Seattle, WA USA, 98109." + }, + { + "author_name": "Peter A. Morawski", + "author_inst": "Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA USA, 98101." + }, + { + "author_name": "Kurt B. Pruner", + "author_inst": "Department of Immunology, University of Washington School of Medicine, Seattle, WA USA, 98109." + }, + { + "author_name": "Mitchell L. Fahning", + "author_inst": "Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA USA, 98101." + }, + { + "author_name": "Christian A. Howard", + "author_inst": "Department of Immunology, University of Washington School of Medicine, Seattle, WA USA, 98109." + }, + { + "author_name": "Nicholas Franko", + "author_inst": "Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, USA, 98109." + }, + { + "author_name": "Jennifer Logue", + "author_inst": "Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, USA, 98109." + }, + { + "author_name": "Julie Eggenberger", + "author_inst": "Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA, 98109." + }, + { + "author_name": "Caleb Stokes", + "author_inst": "Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA, 98109." + }, + { + "author_name": "Inah Golez", + "author_inst": "Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA, 98109." + }, + { + "author_name": "Malika Hale", + "author_inst": "Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA" + }, + { + "author_name": "Michael Gale Jr.", + "author_inst": "Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA, 98109." + }, + { + "author_name": "Helen Y Chu", + "author_inst": "Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, USA, 98109." + }, + { + "author_name": "Daniel J. Campbell", + "author_inst": "Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, USA, 98109." + }, + { + "author_name": "Marion Pepper", + "author_inst": "Department of Immunology, University of Washington School of Medicine, Seattle, WA USA, 98109." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.12.22269193", "rel_title": "Application of the Logistic Model to the COVID-19 Pandemic in South Africa and the United States: Correlations and Predictions", @@ -413118,45 +412254,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.10.22268985", - "rel_title": "An ensemble prediction model for COVID-19 mortality risk", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.10.22268985", - "rel_abs": "BackgroundIts critical to identify COVID-19 patients with a higher death risk at early stage to give them better hospitalization or intensive care. However, thus far, none of the machine learning models has been shown to be successful in an independent cohort. We aim to develop a machine learning model which could accurately predict death risk of COVID-19 patients at an early stage in other independent cohorts.\n\nMethodsWe used a cohort containing 4711 patients whose clinical features associated with patient physiological conditions or lab test data associated with inflammation, hepatorenal function, cardiovascular function and so on to identify key features. To do so, we first developed a novel data preprocessing approach to clean up clinical features and then developed an ensemble machine learning method to identify key features.\n\nResultsFinally, we identified 14 key clinical features whose combination reached a good predictive performance of AUC 0.907. Most importantly, we successfully validated these key features in a large independent cohort containing 15,790 patients.\n\nConclusionsOur study shows that 14 key features are robust and useful in predicting the risk of death in patients confirmed SARS-CoV-2 infection at an early stage, and potentially useful in clinical settings to help in making clinical decisions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jie Li", - "author_inst": "Harbin Institute of technology" - }, - { - "author_name": "Xin Li", - "author_inst": "Harbin Institute of Technology" - }, - { - "author_name": "John Hutchinson", - "author_inst": "University of Calgary" - }, - { - "author_name": "Mohammad Asad", - "author_inst": "University of Calgary" - }, - { - "author_name": "Yadong Wang", - "author_inst": "Harbin Institute of Technology" - }, - { - "author_name": "Edwin Wang", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2022.01.12.22269133", "rel_title": "Humoral and T-cell immune response after three doses of mRNA SARS-CoV-2 vaccines in fragile patients: the Italian VAX4FRAIL study", @@ -414049,6 +413146,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.11.22269101", + "rel_title": "Racial/ethnic disparities in exposure to COVID-19, susceptibility to COVID-19 and access to health care - findings from a U.S. national cohort", + "rel_date": "2022-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269101", + "rel_abs": "We examined the influence of racial/ethnic differences in socioeconomic position on COVID-19 seroconversion and hospitalization within a community-based prospective cohort enrolled in March 2020 and followed through October 2021 (N=6740). The ability to social distance as a measure of exposure to COVID-19, susceptibility to COVID-19 complications, and access to healthcare varied by race/ethnicity with non-white participants having more exposure risk and more difficulty with healthcare access than white participants. Participants with more (versus less) exposure had greater odds of seroconversion (aOR:1.64, 95% Confidence Interval [CI] 1.18-2.29). Participants with more susceptibility and more barriers to healthcare had greater odds of hospitalization (respective aOR:2.36; 1.90-2.96 and 2.31; 1.69-2.68). Race/ethnicity positively modified the association between susceptibility and hospitalization (aORnon-White:2.79, 2.06-3.78). Findings may explain the disproportionate burden of COVID-19 infections and complications among Hispanic and non-Hispanic Black persons. Primary and secondary prevention efforts should address disparities in exposure, COVID-19 vaccination, and treatment.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "McKaylee Robertson", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Meghana Shamsunder", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Ellen Brazier", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Mekhala Mantravadi", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Madhura S Rane", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Drew A Westmoreland", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Angela Parcesepe", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rebecca Zimba", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Andrew R Maroko", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Sarah Kulkarni", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Christian Grov", + "author_inst": "CUNY ISPH" + }, + { + "author_name": "Denis Nash", + "author_inst": "CUNY Graduate School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.10.475752", "rel_title": "A novel structure-based approach for identification of vertebrate susceptibility to SARS-CoV-2: implications for future surveillance programmes", @@ -415112,65 +414272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.07.22268803", - "rel_title": "General anxiety and depression are associated with the physical activity and social interaction levels: Study in Argentinean university students during the COVID-19 outbreak", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268803", - "rel_abs": "BackgroundDue to the coronavirus disease 2019 (COVID-19), the planet is going through a historical time of exceptional concern and uncertainty, which impacts peoples mental health. Here, we explored the levels of depression and Generalized Anxiety Disorder (GAD) and their relation with the degree of physical activity and social interaction during the pandemic.\n\nMethodsWe performed a structured survey containing the PHQ-9 and GAD-7 tests to evaluate depressive symptoms and GAD levels. We also asked about weekly physical activity and the level of social interaction. We surveyed two groups of University students in the Buenos Aires Metropolitan Area: an internal group from the Instituto Tecnologico de Buenos Aires (ITBA), and an external group of students from multiple universities. The survey was conducted in late October/early-November 2020, after a peak of contagions. Some of the participants were surveyed again in January 2021, during academic holidays and after a valley of contagion, for longitudinal analysis\n\nResultsOur data show that men and women of both groups exhibited a significant positive linear correlation between depression and GAD levels. Moreover, low levels of depression and anxiety were associated with performing physical activity for more than two days a week and to longer periods of social interaction. Finally, the second survey revealed a decrease of the symptoms.\n\nConclusionsOur results suggest that performing regular physical activity and avoiding long periods of social isolation gave benefits to mental health. We suggest that public policies could consider protecting these behaviors under health and safety standards.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alejo Barbuzza", - "author_inst": "Universidad de Buenos Aires" - }, - { - "author_name": "Pedro Benedetti", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Celina Goyeneche", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Victoria Reppucci", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Franco Moscato", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Daniela Ramirez Butavand", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Cynthia Katche", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Jorge Horacio Medina", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Diego Moncada", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Haydee Viola", - "author_inst": "Instituto Tecnologico de Buenos Aires" - }, - { - "author_name": "Fabricio Ballarini", - "author_inst": "Instituto Tecnologico de Buenos Aires" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.01.09.22268984", "rel_title": "Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis", @@ -415959,6 +415060,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2022.01.11.22268736", + "rel_title": "COVID-19 vaccination breakthrough infections in a real-world setting: Using community reporters to evaluate vaccine effectiveness", + "rel_date": "2022-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22268736", + "rel_abs": "BackgroundCOVID-19 has highlighted the need for new methods of pharmacovigilance. Here we use community volunteers to obtain systematic information on vaccine effectiveness and the nature and severity of breakthrough infections.\n\nMethodsBetween December 15, 2020 to September 16, 2021, 10,412 unpaid community-based participants reported the following information to an on-line registry: COVID-19 test results, vaccination (Pfizer, Moderna, or Johnson & Johnson), COVID-19 symptoms and perceived severity using a 4-point scale. COVID-19 infections were described for those who were 1) fully vaccinated, 2) partially vaccinated (received first of two dose vaccines or were <14 days post-final dose), or 3) unvaccinated.\n\nResultsOf 8,554 who were vaccinated, COVID-19 infections were reported by 74 (1.0%) of those who were fully vaccinated and 198 (2.3%) of those who were partially vaccinated. Among the 74 participants who reported a breakthrough infection after full vaccination, the median time to reported positive test result was 104.5 days (Interquartile range: 77-135 days), with no difference among vaccine manufactures. One quarter (25.7%) of breakthrough infections in the fully vaccinated cases were asymptomatic. More than 97% of fully vaccinated participants reported no moderate/severe symptoms compared to 89.3% of the unvaccinated cases; and only 1.4% of fully vaccinated participants reported experiencing at least 3 moderate to severe symptoms compared to 7.8% in the unvaccinated.\n\nConclusionPerson-generated health data, also referred to as patient-reported outcomes, is a useful resource for quantifying breakthrough infections and their severity, showing here that fully vaccinated participants report no or very mild COVID-19 symptoms.\n\nTrial registrationClinicaltrials.gov NCT04368065, EU PAS Register EUPAS36240", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Matthew W Reynolds", + "author_inst": "IQVIA Real-World Solutions" + }, + { + "author_name": "Yiqiong Xie", + "author_inst": "IQVIA Real-World Solutions" + }, + { + "author_name": "Kendall B Knuth", + "author_inst": "IQVIA Real-World Solutions" + }, + { + "author_name": "Christina D Mack", + "author_inst": "IQVIA Real-World Solutions" + }, + { + "author_name": "Emma Brinkley", + "author_inst": "IQVIA Real-World Solutions" + }, + { + "author_name": "Stephen Toovey", + "author_inst": "Pegasus Research" + }, + { + "author_name": "Nancy A Dreyer", + "author_inst": "IQVIA Real-World Solutions" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.11.22269065", "rel_title": "The incidence and mortality of COVID-19 related TB infection in Sub-Saharan Africa: A systematic review and meta-analysis", @@ -417018,125 +416162,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.07.22268914", - "rel_title": "Egg-derived anti-SARS-CoV-2 immunoglobulin Y (IgY) with broad variant activity as intranasal prophylaxis against COVID-19: preclinical studies and randomized controlled phase 1 clinical trial", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268914", - "rel_abs": "COVID-19 emergency use authorizations and approvals for vaccines were achieved in record time. However, there remains a need to develop additional safe, effective, easy-to-produce, and inexpensive prevention to reduce the risk of acquiring SARS-CoV-2 infection. This need is due to difficulties in vaccine manufacturing and distribution, vaccine hesitancy, and, critically, the increased prevalence of SARS-CoV-2 variants with greater contagiousness or reduced sensitivity to immunity. Antibodies from eggs of hens (immunoglobulin Y; IgY) that were administered receptor-binding domain (RBD) of the SARS-CoV-2 spike protein were developed as nasal drops to capture the virus on the nasal mucosa. Although initially raised against the 2019 novel coronavirus index strain (2019- nCoV), these anti-SARS-CoV-2 RBD IgY surprisingly had indistinguishable enzyme-linked immunosorbent assay binding against variants of concern that have emerged, including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). This is distinct for sera from immunized or convalescent patients. Culture neutralization titers against available Alpha, Beta, and Delta were also indistinguishable from the index SARS-CoV-2 strain. Efforts to develop these IgY for clinical use demonstrated that the intranasal anti-SARS-CoV-2 RBD IgY preparation showed no binding (cross-reactivity) to a variety of human tissues and had an excellent safety profile in rats following 28-day intranasal delivery of the formulated IgY. A double-blind, randomized, placebo- controlled phase 1 study evaluating single-ascending and multiple doses of anti-SARS-CoV-2 RBD IgY administered intranasally for 14 days in 48 healthy adults also demonstrated an excellent safety and tolerability profile, and no evidence of systemic absorption. As these antiviral IgY have broad selectivity against many variants of concern, are fast to produce, and are a low-cost product, their use as prophylaxis to reduce SARS-CoV-2 viral transmission warrants further evaluation. (ClinicalTrials.gov: NCT04567810, https://www.clinicaltrials.gov/ct2/show/NCT04567810)", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Lyn Frumkin", - "author_inst": "Stanford" - }, - { - "author_name": "Michaela Lucas", - "author_inst": "University of Western Australia" - }, - { - "author_name": "Curt Scribner", - "author_inst": "Independent Regulatory Consultant" - }, - { - "author_name": "Nastassja Ortega-Heinly", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Jayden Rogers", - "author_inst": "Linear Clinical Research Ltd" - }, - { - "author_name": "Gang Yin", - "author_inst": "Sutro Biopharma Inc" - }, - { - "author_name": "Trevor J Hallam", - "author_inst": "Sutro Biopharma Inc" - }, - { - "author_name": "Alice Yam", - "author_inst": "Sutro Biopharma Inc" - }, - { - "author_name": "Kristin Bedard", - "author_inst": "Sutro Biopharma Inc" - }, - { - "author_name": "Rebecca Begley", - "author_inst": "Stanford University" - }, - { - "author_name": "Courtney A Cohen", - "author_inst": "United States Army Medical Research Institute of Medical Research of Infectious Diseases" - }, - { - "author_name": "Catherine V Badger", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Shawn A Abbasi", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "John M Dye", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Brian McMillan", - "author_inst": "Bravado Pharmaceuticals" - }, - { - "author_name": "Michael Wallach", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Traci L Bricker", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Astha Joshi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Adrianus C. M. Boon", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Suman Pokhrel", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Benjamin R Kraemer", - "author_inst": "Stanford University" - }, - { - "author_name": "Lucia Lee", - "author_inst": "Stanford University" - }, - { - "author_name": "Stephen Kargotich", - "author_inst": "Stanford University" - }, - { - "author_name": "Mahima Agogiya", - "author_inst": "Stanford University" - }, - { - "author_name": "Tom St. John", - "author_inst": "Independent Scientist" - }, - { - "author_name": "Daria Mochly-Rosen", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.08.22268920", "rel_title": "Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England", @@ -417841,6 +416866,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.09.22268991", + "rel_title": "COVID-19 impact on Socio-economic and Health Interventions: A Gaps and Peaks analysis using Clustering Approach", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268991", + "rel_abs": "A quantifiable model to describe the peaks and gaps during the several waves of COVID-19 is generated and applied to the progression of 120 countries. The number of waves encountered and how many more to be encountered is a question which is currently explored by all the scientific communities. In the same quest, an attempt has been made to quantitatively model the peaks and the gaps within them which have been encountered by 120 most affected countries from February 2020 - December 2021. These 120 countries were ranked based on the number of confirmed cases and deaths recorded during this period. This study further cluster these countries based on socio-economic and health interventions to find an association with three dependent features of COVID-19 i.e. number of confirmed cases, deaths and death-infectivity rate. The findings in this study suggests that, every wave had multiple peaks within them and as the number of peaks increased, predicting their growth rate or decline rate turns to be extremely difficult. However, considering the clusters which share the common features even with diverse countries, there is some possibility to predict what might be coming next. This study involves exhaustive analysis of reliable data which are available in open access and marks an important aspect to the COVID-19 research communities.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hridoy Jyoti Mahanta", + "author_inst": "CSIR North East Institute of Science and Technology" + }, + { + "author_name": "G Narahari Sastry", + "author_inst": "CSIR North East Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.10.21268254", "rel_title": "SARS-CoV-2 risk taxation model and validation based on large scale Dutch test-events", @@ -418975,89 +418023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.04.22268715", - "rel_title": "The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Black Queen rule", - "rel_date": "2022-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268715", - "rel_abs": "The nature and dynamics of mutations associated with the emergence, spread and vanishing of SARS-CoV-2 variants causing successive waves are complex1-5. We determined the kinetics of the most common French variant (\"Marseille-4\") for 10 months since its onset in July 20205. Here, we analysed and classified into subvariants and lineages 7,453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1{+/-}1.4 months, during which 4.1{+/-}2.6 mutations accumulated. Growth rate was 0.079{+/-}0.045, varying from 0.010 to 0.173. All the lineages exhibited a \"gamma\" distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in several mink lineages and in the alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Philippe Colson", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "philippe Gautret", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Jeremy Delerce", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Herve Chaudet", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Pierre Pontarotti", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Patrick Forterre", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Raphael Tola", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Marielle Bedotto", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Lea Delorme", - "author_inst": "Aix-Marseille university" - }, - { - "author_name": "Anthony LEVASSEUR", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Jean-Christophe Lagier", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Matthieu Million", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Nouara Yahi", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Jacques Fantini", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Bernard La Scola", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Pierre-Edouard Fournier", - "author_inst": "IHU Mediterranee Infection" - }, - { - "author_name": "Didier Raoult", - "author_inst": "Aix Marseille Universite IHU Mediterranee Infection" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.07.22268869", "rel_title": "BNT162b2 post-exposure-prophylaxis against COVID-19", @@ -419854,6 +418819,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.06.475303", + "rel_title": "Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape", + "rel_date": "2022-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.06.475303", + "rel_abs": "The rapid spread of SARS-CoV-2 variants poses a constant threat of escape from monoclonal antibody and vaccine countermeasures. Mutations in the ACE2 receptor binding site on the surface S protein have been shown to disrupt antibody binding and prevent viral neutralization. Here, we use a directed evolution-based approach to engineer three neutralizing antibodies for enhanced binding to S protein. The engineered antibodies showed increased in vitro functional activity in terms of neutralization potency and/or breadth of neutralization against viral variants. Deep mutational scanning revealed that higher binding affinity reduced the total number of viral escape mutations. Studies in the Syrian hamster model showed two examples where the affinity matured antibody provided superior protection compared to the parental antibody. These data suggest that monoclonal antibodies for anti-viral indications could benefit from in vitro affinity maturation to reduce viral escape pathways and appropriate affinity maturation in vaccine immunization could help resist viral variation.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Fangzhu Zhao", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Celina Keating", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Gabriel Ozorowski", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Namir Shaabani", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Irene M. Francino-Urdaniz", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Shawn Barman", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Oliver Limbo", + "author_inst": "IAVI" + }, + { + "author_name": "Alison Burns", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Panpan Zhou", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Michael Ricciardi", + "author_inst": "GWU" + }, + { + "author_name": "Jordan Woehl", + "author_inst": "IAVI" + }, + { + "author_name": "Quoc Tran", + "author_inst": "IAVI" + }, + { + "author_name": "Hannah L Turner", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Linghang Peng", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Deli Huang", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "David Nemazee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Devin Sok", + "author_inst": "IAVI" + }, + { + "author_name": "John R Teijaro", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Timothy A Whitehead", + "author_inst": "University of Colorado, Boulder" + }, + { + "author_name": "Andrew B Ward", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Dennis Burton", + "author_inst": "Scripps Institute" + }, + { + "author_name": "Joseph G Jardine", + "author_inst": "IAVI" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.01.07.22268906", "rel_title": "Inpatient COVID-19 Mortality Rates: What are the predictors?", @@ -420801,65 +419873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.05.22268648", - "rel_title": "Durability of Protection against COVID-19 Breakthrough Infections and Severe Disease by Vaccines in the United States", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268648", - "rel_abs": "BackgroundIntrinsic durability of immune responses elicited by COVID-19 vaccines will drive vaccine effectiveness long-term across settings and may differ by vaccine type. We aimed here to determine durability of protection of three COVID-19 vaccines BNT162b2, mRNA-1273 and Ad26.COV2.S following primary vaccination against breakthrough infections, hospitalisations, and intensive care unit (ICU) admissions in the United States (US).\n\nMethodsUsing national claims and laboratory data covering 168 million lives, we conducted a matched case-control study with fully vaccinated individuals between January 1 and September 7, 2021. Odds ratios (OR) for developing outcomes in months two through six following primary vaccination were estimated relative to the first month after primary vaccination for each vaccine separately. Results compare each vaccine to itself and are not directly comparative. Odds ratios were translated into vaccine effectiveness (VE) using assumptions about event rates in an unvaccinated cohort.\n\nFindingsRelative to its baseline, stable protection was observed for the single-shot Ad26.COV2.S against infections and severe disease. Relative to their baseline protection waned overtime against infections for BNT162b2 and mRNA-1273 and against hospitalisations for BNT162b2. No waning of baseline protection was observed at any time for ICU admissions for all three vaccines. Calculated baseline VE was consistent with the published literature.\n\nInterpretationWhile the starting protection level provided by the primary series may differ by vaccine type and mechanism of action, this study demonstrated by comparing each vaccine to its own baseline protection that the three vaccines in three separate populations may have different durability profiles. Further investigation is required to fully characterize the durability profile of the three vaccines. Moreover, as the COVID-19 pandemic continues, and as more countries and populations implement a standard of care consisting of three doses of the mRNA vaccines or two doses of Ad26.COV2.S, further investigation is critical to understand the level of protection and the durability of response over longer periods, novel variants and in response to homologous and heterologous boosting.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Amanda Zheutlin", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Miles Ott", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Ran Sun", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Natalia Zemlianskaia Zemlianskaia", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Meagan Rubel", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Jennifer Hayden", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Breno Neri", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Tripthi Kamath", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Najat Khan", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Sebastian Schneeweiss", - "author_inst": "Division of Pharmacoepidemiology Department of Medicine Brigham and Womens Hospital and Harvard Medical School" - }, - { - "author_name": "Khaled Sarsour", - "author_inst": "Janssen Research and Development" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.03.22268663", "rel_title": "The Governance of Pandemics in Primary Health Care: The Governance Strategies Adopted by Health Facility Governing Committees in Times of COVID Pandemic in Tanzania", @@ -421563,6 +420576,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.01.21268271", + "rel_title": "Safety and immunogenicity of anti-SARS CoV-2 conjugate vaccine SOBERANA 02 in a two-dose or three-dose heterologous scheme in adults: Phase IIb Clinical Trial", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.01.21268271", + "rel_abs": "BackgroundWe report results of immunogenicity, safety and reactogenicity of SOBERANA 02 in a two-dose or three-dose heterologous scheme in adults in a phase IIb clinical trial.\n\nMethodThis phase IIb trial was designed as parallel, multicentre, adaptive, double blind, randomized and placebo-controlled. Subjects (N=810) aged 19-80 years were randomized to receive two doses of the recombinant SARS CoV-2 receptor binding domain (RBD) conjugated to tetanus toxoid (SOBERANA 02) and a third dose of dimeric RBD (SOBERANA Plus) 28 days apart; two production batches of active ingredient of SOBERANA 02 were evaluated. Primary outcome was the percentage of seroconverted subjects with [≥]4-fold the anti-RBD IgG concentration. Secondary outcomes were safety, reactogenicity and neutralizing antibodies.\n\nResultsSeroconversion rate in vaccinees was respectively 76.3 and 96.8% after two or three doses, compared with 7.3% in placebo group. Anti-RBD IgG increased significantly after first and second dose of SOBERANA 02 respect to placebo group; and the third dose with SOBERANA Plus boosts the response compared to the second dose. Neutralizing IgG antibodies were detected against D614G and VOCs , {beta} and {delta}. Specific and functional antibodies were detected at least until 7-8 months after the third dose. The frequency of serious adverse events (AEs) associated with vaccination was very low (0.1%); with only one serious AE consistent with vaccination. Local pain was the most frequent AE.\n\nConclusionsTwo doses of SOBERANA 02 were well tolerated, safe an immunogenic in adults aged 19-80 years old. The heterologous combination with a third dose of SOBERANA Plus increased neutralizing antibodies, detectable 7-8 months after finishing the vaccination schedule.\n\nTrial registryhttps://rpcec.sld.cu/trials/RPCEC00000347", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Maria Eugenia-Toledo-Romani", + "author_inst": "Pedro Kouri Tropical Medicine Institute, Av Novia del Mediodia, Kv 6 1/2, La Lisa, Habana, 11400, Cuba Havana" + }, + { + "author_name": "Mayra Garcia-Carmenate", + "author_inst": "19 de Abril Polyclinic. Tulipan Street between Panorama y Oeste, Nuevo Vedado, Plaza de la Revolucion, La Habana 10400, Cuba." + }, + { + "author_name": "Leslyhana Verdecia-Sanchez", + "author_inst": "Clinic #1. 21 St. and 190, La Lisa. Habana, Cuba" + }, + { + "author_name": "Suzel Perez-Rodriguez", + "author_inst": "19 de Abril Polyclinic. Tulipan Street between Panorama y Oeste, Nuevo Vedado, Plaza de la Revolucion, La Habana 10400, Cuba." + }, + { + "author_name": "Meybis Rodriguez-Gonzalez", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Carmen Valenzuela-Silva", + "author_inst": "Cybernetics, Mathematics and Physics Institute. 15th Street #55, Vedado, Plaza de la Revolucion, La Habana 10400, Cuba." + }, + { + "author_name": "Beatriz Paredes-Moreno", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Belinda Sanchez-Ramirez", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Raul Gonzalez-Mugica", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Tays Hernandez-Garcia", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Ivette Orosa-Vazquez", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Marianniz Diaz-Hernandez", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Maria T Perez-Guevara", + "author_inst": "National Civil Defense Research Laboratory. San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Juliet Enriquez-Puertas", + "author_inst": "National Civil Defense Research Laboratory. San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Enrique Noa-Romero", + "author_inst": "National Civil Defense Research Laboratory. San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Ariel Palenzuela-Diaz", + "author_inst": "Centre for Immunoassays. 134 St and 25, Cubanacan, Playa, La Habana, 11600 Cuba" + }, + { + "author_name": "Gerardo Baro-Roman", + "author_inst": "Centre for Immunoassays. 134 St and 25, Cubanacan, Playa, La Habana, 11600 Cuba" + }, + { + "author_name": "Ivis Mendoza-Hernandez", + "author_inst": "National Clinical Trials Coordinating Center. 5th Ave and 62, Miramar, Playa, Havana, Cuba." + }, + { + "author_name": "Yaima Munoz", + "author_inst": "National Clinical Trials Coordinating Center. 5th Ave and 62, Miramar, Playa, Havana, Cuba." + }, + { + "author_name": "Yanet Gomez-Maceo", + "author_inst": "Clinic #1. 21 St. and 190, La Lisa. Habana, Cuba" + }, + { + "author_name": "Bertha L Santos Vega", + "author_inst": "19 de Abril Polyclinic. Tulipan Street between Panorama y Oeste, Nuevo Vedado, Plaza de la Revolucion, La Habana 10400, Cuba." + }, + { + "author_name": "Sonsire Fernandez-Castillo", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Yanet Climent-Ruiz", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Laura M Rodriguez-Noda", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Darielys Santana-Mederos", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Yanelda Garcia-Vega", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Guang Wu-Chen", + "author_inst": "Chengdu Olisynn Biotech. Co. Ltd., and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Peoples Re" + }, + { + "author_name": "Delaram Doroud", + "author_inst": "Pasteur Institute of Iran. No. 69, Pasteur Ave, Tehran 1316943551, Islamic Republic of Iran" + }, + { + "author_name": "Alireza Biglari", + "author_inst": "Pasteur Institute of Iran. No. 69, Pasteur Ave, Tehran 1316943551, Islamic Republic of Iran" + }, + { + "author_name": "Tammy Boggiano-Ayo", + "author_inst": "Centre of Molecular Immunology. 15th Ave. and 216 Street, Siboney, Playa, Havana, Cuba." + }, + { + "author_name": "Yury Valdes-Balbin", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Dagmar Garcia-Rivera", + "author_inst": "Finlay Vaccine Institute. 21st Ave. No. 19810 between 198 and 200 Streets, Atabey, Playa, Havana, Cuba" + }, + { + "author_name": "Vicente Verez-Bencomo", + "author_inst": "Finlay Vaccine Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.04.21268275", "rel_title": "Daily Lactobacillus Probiotic versus Placebo in COVID-19-Exposed Household Contacts (PROTECT-EHC): A Randomized Clinical Trial", @@ -422462,37 +421622,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.01.04.474958", - "rel_title": "Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants", - "rel_date": "2022-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.474958", - "rel_abs": "A highly efficient and robust multiple scales in silico protocol, consisting of atomistic constant charge Molecular Dynamics (MD), constant-charge coarse-grain (CG) MD and constant-pH CG Monte Carlo (MC), has been used to study the binding affinities, the free energy of complexation of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 (originally derived from SARS-CoV-1 patients almost two decades ago) and 11 SARS-CoV-2 variants including the wild type. CR3022 binds strongly to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, but chooses a different site rather than the receptor-binding motif (RBM) of RBD, allowing its combined use with other mAbs against new emerging virus variants. Totally 235,000 mAbs structures were generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be clearly best against all virus variants, and surprisingly, all 10 candidates and the native CR3022 did exhibit a higher affinity for the Omicron variant with its highest number of mutations (15) of them all considered in this study. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Clearly, mAbs carrying a lower net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy towards designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Andrei Neamtu", - "author_inst": "University of Medicine and Pharmacy of Iasi" - }, - { - "author_name": "Francesca Mocci", - "author_inst": "University of Cagliari" - }, - { - "author_name": "Aatto Laaksonen", - "author_inst": "Stockholm University" - }, - { - "author_name": "Fernando Luis Barroso da Silva", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.01.04.475015", "rel_title": "SARS-CoV-2 Infection of Microglia Elicits Pro-inflammatory Activation and Apoptotic Cell Death", @@ -423161,6 +422290,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.01.04.22268771", + "rel_title": "Detection of fecal coliforms and SARS-CoV-2 RNA in sewage and recreational waters in the Ecuadorian Coast: a call for improving water quality regulation", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268771", + "rel_abs": "Wastewater surveillance represents an alternative approach for the diagnosis and early detection of infectious agents of public health importance. This study aimed to evaluate SARS-CoV-2 and other quality markers in oxidation lagoons, estuarine areas and seawater at Guayas and Santa Elena in Ecuador. Sample collections were conducted twice at 42 coastal sites and 2 oxidation lagoons during dry and rainy seasons (2020-2021). Physico-chemical and microbiological parameters were evaluated to determine organic pollution. Quantitative reverse transcription PCR was conducted to detect SARS-CoV-2. Results showed high levels of Escherichia coli and low dissolved oxygen concentrations. SARS-CoV-2 was detected in sea-waters and estuaries with salinity levels between 34.2-36.4 PSU and 28.8 {degrees}C-31.3 {degrees}C. High amounts of fecal coliforms were detected and correlated with the SARS-CoV-2 shedding. We recommend to decentralized autonomous governments in developing countries such as Ecuador to implement corrective actions and establish medium-term mechanisms to minimize a potential contamination route.\n\nHIGHLIGHTSO_LISARS-CoV-2 RNA was detected in estuaries, bays and the wastewater treatment systems in Playas and Santa Elena.\nC_LIO_LIHigh levels of fecal coliforms were detected along shorelines.\nC_LIO_LIWater quality parameters revealed a negative impact on the beaches studied associated with human activities.\nC_LI", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Maritza Cardenas", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Ambiente Sociedad & Empresa Research Group. University of Guayaquil, Faculty of Che" + }, + { + "author_name": "Leandro Patinoa", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Ambiente Sociedad & Empresa Research Group. Direccion Tecnica de Investigacion, Des" + }, + { + "author_name": "Beatriz Pernia", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Instituto de Investigaciones de Recursos Naturales, Facultad de Ciencias Naturales, " + }, + { + "author_name": "Roberto Erazo", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Ambiente Sociedad & Empresa Research Group." + }, + { + "author_name": "Carlos Munoz", + "author_inst": "Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Magaly Valencia-Avellan", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Direccion Tecnica de Investigacion, Desarrollo e Innovacion, Instituto Nacional de I" + }, + { + "author_name": "Mariana Lozada", + "author_inst": "Laboratorio de Microbiologia Ambiental, Instituto de Biologia de Organismos Marinos, CONICET." + }, + { + "author_name": "Mary Regato-Arrata", + "author_inst": "Centro de Referencia Nacional de Virus Exantematicos, Gastroentericos y transmitidos por vectores. Instituto Nacional de Investigacion en Salud Publica." + }, + { + "author_name": "Miguel Barrera", + "author_inst": "Ambiente Sociedad & Empresa Research Group. University of Guayaquil, Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria Universidad " + }, + { + "author_name": "Segundo Aquino", + "author_inst": "Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Stalyn Moyanoc", + "author_inst": "Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Stefania Fuentes", + "author_inst": "Ambiente Sociedad & Empresa Research Group. Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Javier Duque", + "author_inst": "Red Interinstitucional para el Estudio de Ecosistemas Acuaticos de Ecuador. Ambiente Sociedad & Empresa Research Group. Faculty of Chemical Engineering, Univer" + }, + { + "author_name": "Luis Velazquez-Araque", + "author_inst": "Ambiente Sociedad & Empresa Research Group. Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Bertha Carpio", + "author_inst": "Direccion de Medio Ambiente-Gobierno Autonomo Descentralizado Provincial de Santa Elena." + }, + { + "author_name": "Carlos Mendez-Roman", + "author_inst": "Area Nacional de Recreacion Playas Villamil, Ministerio del Ambiente y Agua, Playas." + }, + { + "author_name": "Carlos Calle", + "author_inst": "Ambiente Sociedad & Empresa Research Group. University of Guayaquil." + }, + { + "author_name": "Guillermo Cardenas", + "author_inst": "Ambiente Sociedad & Empresa Research Group. University of Guayaquil." + }, + { + "author_name": "David Guizado-Herrera", + "author_inst": "Faculty of Chemical Engineering, University of Guayaquil, Cdla. Universitaria, Universidad de Guayaquil." + }, + { + "author_name": "Clara Lucia Tello", + "author_inst": "Direccion Tecnica de Investigacion, Desarrollo e Innovacion, Instituto Nacional de Investigacion en Salud Publica." + }, + { + "author_name": "Veronica Bravo-Basantes", + "author_inst": "LAB CESTTA, Via a Daule km 1,5. Parque California 2, bodega C 36." + }, + { + "author_name": "Josue Zambranod", + "author_inst": "Direccion Tecnica de Investigacion, Desarrollo e Innovacion, Instituto Nacional de Investigacion en Salud Publica." + }, + { + "author_name": "Jhannelle D Francis", + "author_inst": "University of Manitoba." + }, + { + "author_name": "Miguel Uyaguari", + "author_inst": "University of Manitoba." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.04.21268586", "rel_title": "T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all prior infected and vaccinated individuals", @@ -424244,45 +423484,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.01.03.474773", - "rel_title": "Reduced interferon antagonism but similar drug sensitivity in Omicron variant compared to Delta variant SARS-CoV-2 isolates", - "rel_date": "2022-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.03.474773", - "rel_abs": "The SARS-CoV-2 Omicron variant is currently causing a large number of infections in many countries. A number of antiviral agents are approved or in clinical testing for the treatment of COVID-19. Despite the high number of mutations in the Omicron variant, we here show that Omicron isolates display similar sensitivity to eight of the most important anti-SARS-CoV-2 drugs and drug candidates (including remdesivir, molnupiravir, and PF-07321332, the active compound in paxlovid), which is of timely relevance for the treatment of the increasing number of Omicron patients. Most importantly, we also found that the Omicron variant displays a reduced capability of antagonising the host cell interferon response. This provides a potential mechanistic explanation for the clinically observed reduced pathogenicity of Omicron variant viruses compared to Delta variant viruses.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Denisa Bojkova", - "author_inst": "Institute of Medical Virology" - }, - { - "author_name": "Marek Widera", - "author_inst": "University Hospital, Goethe University Frankfurt am Main" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Mark N Wass", - "author_inst": "University of Kent" - }, - { - "author_name": "Martin Michaelis", - "author_inst": "University of Kent" - }, - { - "author_name": "Jindrich N Cinatl Jr.", - "author_inst": "Klinikum der Goethe-Universitaet" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.04.474908", "rel_title": "Maternal cytokine response after SARS-CoV-2 infection during pregnancy", @@ -425099,6 +424300,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.02.474028", + "rel_title": "A dual-receptor mechanism between integrins and ACE2 widens SARS-CoV-2 tissue tropism", + "rel_date": "2022-01-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.02.474028", + "rel_abs": "In addition to the ACE2 receptor, SARS-CoV-2 binds to integrins to gain host cell entry and trigger pro-inflammatory integrin-mediated signalling cascades. Integrins, therefore, are likely candidates for a dual-receptor mechanism with ACE2 to explain the increased infectivity seen in SARS-CoV-2 models. As integrins are primarily expressed in vasculature and persistent vasculopathy is seen in COVID-19, examining the role of endothelial integrin involvement is crucial in uncovering the pathophysiology of SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Danielle Nader", + "author_inst": "RCSI University of Medicine and Health Sciences" + }, + { + "author_name": "Timothy E Gressett", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Md Lokman Hossen", + "author_inst": "Florida International University" + }, + { + "author_name": "Prem P Chapagain", + "author_inst": "Florida International University" + }, + { + "author_name": "Steven W. Kerrigan", + "author_inst": "RCSI University of Medicine and Health Sciences" + }, + { + "author_name": "Gregory Bix", + "author_inst": "Tulane University" + } + ], + "version": "1", + "license": "cc_no", + "type": "contradictory results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.12.31.474593", "rel_title": "Cell culture model system utilizing engineered A549 cells to express high levels of ACE2 and TMPRSS2 for investigating SARS-CoV-2 infection and antivirals", @@ -426254,77 +425494,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.02.474743", - "rel_title": "Reduced Pathogenicity of the SARS-CoV-2 Omicron Variant in Hamsters", - "rel_date": "2022-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.02.474743", - "rel_abs": "The SARS-CoV-2 Omicron (B.1.1.529) variant has proven highly transmissible and has outcompeted the Delta variant in many regions of the world1. Early reports have also suggested that Omicron may result in less severe clinical disease in humans. Here we show that Omicron is less pathogenic than prior SARS-CoV-2 variants in Syrian golden hamsters. Infection of hamsters with the SARS-CoV-2 WA1/2020, Alpha, Beta, or Delta strains led to 4-10% weight loss by day 4 and 10-17% weight loss by day 6, as expected2,3. In contrast, infection of hamsters with two different Omicron challenge stocks did not result in any detectable weight loss, even at high challenge doses. Omicron infection still led to substantial viral replication in both the upper and lower respiratory tracts and pulmonary pathology, but with a trend towards higher viral loads in nasal turbinates and lower viral loads in lung parenchyma compared with WA1/2020 infection. These data suggest that the SARS-CoV-2 Omicron variant may result in more robust upper respiratory tract infection but less severe lower respiratory tract clinical disease compared with prior SARS-CoV-2 variants.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Katherine McMahan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Victoria Giffin", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Lisa Tostanoski", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Benjamin Chung", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Mazuba Siamatu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Mehul Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Peter Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Cesar Piedra-Mora", - "author_inst": "Tufts University" - }, - { - "author_name": "Amanda Martinot", - "author_inst": "Tufts University" - }, - { - "author_name": "Swagata Kar", - "author_inst": "Bioqual" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Dan H. Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.30.474610", "rel_title": "Robust expansion of phylogeny for fast-growing genome sequence data", @@ -427041,6 +426210,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.30.21268558", + "rel_title": "Point-of-care lung ultrasound predicts severe disease and death due to COVID-19: a prospective cohort study.", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268558", + "rel_abs": "ObjectiveThe clinical utility of point-of-care lung ultrasound (LUS) for disease severity triage of hospitalized patients with COVID-19 is unclear.\n\nDesignProspective cohort study\n\nSettingA large tertiary care center in Maryland, USA between April 2020 to September 2021.\n\nPatientsHospitalized adults ([≥]18 years of age) with positive SARS-CoV-2 RT-PCR results.\n\nInterventionsNone.\n\nMeasurements and Main ResultsAll patients were scanned using a standardized protocol including 12 lung zones and followed to determine clinical outcomes until hospital discharge and vital status at 28-days. Ultrasounds were independently reviewed for lung and pleural line artifacts and abnormalities, and the mean Lung Ultrasound Score (ranging from 0 to 3) across lung zones (mLUSS) was determined. The primary outcome was time to ICU-level care, defined as high flow oxygen, noninvasive, or mechanical ventilation, within 28-days of the initial ultrasound. Cox proportional hazards regression models adjusted for age and sex were fit for mLUSS and each ultrasound covariate. A total of 264 participants were enrolled in the study; the median age was 59 years and 114 (43.2) % of participants were female. The median mLUSS was 1 (interquartile range: 0.5 to 1.3). Following enrollment, 29 (11.0%) participants went on to require ICU-level care and 14 (5.3%) subsequently died by 28 days. Each increase in mLUSS at enrollment was associated with disease progression to ICU-level care (aHR = 3.63; 95% CI: 1.23 to 10.65) and 28-day mortality (aHR = 4.50; 95% CI: 1.52 to 13.31). Pleural line abnormalities were independently associated with disease progression to ICU-level care (aHR = 18.86; CI: 1.57 to 226.09).\n\nConclusionsParticipants with a mLUSS [≥]1 or pleural line changes on LUS had an increased likelihood of subsequent requirement of high flow oxygen or greater. LUS is a promising tool for assessing risk of COVID-19 progression at the bedside.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Paul W Blair", + "author_inst": "The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD; Division of Infectious Diseases, Johns Hopkins University School of Medi" + }, + { + "author_name": "Trishul Siddharthan", + "author_inst": "Division of Pulmonary and Critical Care Medicine, University of Miami, Miami, FL; Division of Pulmonary and Critical Care Medicine, Johns Hopkins University Sch" + }, + { + "author_name": "Gigi Liu", + "author_inst": "Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Jiawei Bai", + "author_inst": "Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD" + }, + { + "author_name": "Joshua East", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Phabiola Herrera", + "author_inst": "Division of Pulmonary and Critical Care Medicine, University of Miami, Miami, FL" + }, + { + "author_name": "Lalaine Anova", + "author_inst": "The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD" + }, + { + "author_name": "Varun Mahadevan", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Shakir Hossen", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Stefanie Seo", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Olamide Sonuga", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Joshua Lawrence", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Jillian Peters", + "author_inst": "Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Andrea Cox", + "author_inst": "Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD" + }, + { + "author_name": "Katherine Fenstermacher", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Sophia Shea", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Richard E. Rothman", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Bhakti Hansoti", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Lauren Sauer", + "author_inst": "Department of Emergency Medicine, Johns Hopkins University, Baltimore MD" + }, + { + "author_name": "Ciprian Crainiceanu", + "author_inst": "Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD" + }, + { + "author_name": "Danielle V. Clark", + "author_inst": "The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.30.21268509", "rel_title": "Viral cultures, PCR Cycle threshold values and viral load estimation for COVID-19 infectious potential assessment in transplant patients: systematic review - Protocol Version 29 December 2021", @@ -428308,73 +427580,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.30.21268538", - "rel_title": "Protective effect of BNT162b2 vaccination on aerobic capacity following mild to moderate SARS-CoV-2 infection: a cross sectional study, Israel, March-December 2021", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268538", - "rel_abs": "We compared 23 unvaccinated to 15 vaccinated patients previously infected with SARS-CoV-2 in terms of their aerobic capacity measured by a cardio pulmonary exercise test (CPET). Compared with unvaccinated individuals, those vaccinated had a higher heart rate, higher VO2. Our results suggest objective limitations to exercise capacity in the months following acute COVID19 illness, mitigated by vaccination", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yair Blumberg", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Ziv Medical Centre" - }, - { - "author_name": "Michael Edelstein", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Ziv Medical Centre" - }, - { - "author_name": "Kamal Abu Jabal", - "author_inst": "Azrieli Faculty of Medicine Bar-Ilan University; Ziv Medical Centre" - }, - { - "author_name": "Ron Golan", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Yuval Perets", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University" - }, - { - "author_name": "Musa Saad", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Tatyana Levinas", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Ziv Medical Centre" - }, - { - "author_name": "Saleem Dabbah", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Zeev Israeli", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Ziv Medical Centre" - }, - { - "author_name": "Salah Yacoubi", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Alaa Abu Raya", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Anat Amital", - "author_inst": "Ziv Medical Centre" - }, - { - "author_name": "Majdi Halabi", - "author_inst": "Azrieli Faculty of Medicine, Bar-Ilan University; Ziv Medical Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.31.21268583", "rel_title": "From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021)", @@ -429203,6 +428408,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.12.29.21268501", + "rel_title": "A cohort study of the effect of SARS-CoV-2 point of care rapid RT-PCR at the Emergency Department on targeted admission", + "rel_date": "2021-12-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268501", + "rel_abs": "(ii)BackgroundTo prevent nosocomial transmission of SARS-CoV-2, infection control measures are implemented for patients with symptoms compatible with COVID-19 until reliable test results are available. This delay targeted admission to the most appropriate ward based on the medical condition. SARS-CoV-2 rapid antigen detection (RAD) tests and point of care (POC) rapid RT-PCR were introduced at emergency departments (EDs) in late 2020, but the consequence on targeted admission is unknown.\n\nObjectivesTo assess the effect of RAD tests and POC rapid RT-PCR (VitaPCR, Credo Diagnostics, Singapore) on targeted admission.\n\nMethodsPatients presenting at the ED of a referral hospital (N = 2,940) between 13-Nov-2020 and 12-Jan-2021 were included. The study period was delimited by introduction of RAD tests and VitaPCR. Participant data was collected retrospectively, and outcome variables were length-of-stay (LoS), intrahospital transfers and targeted admission to COVID-19 ward.\n\nResultsRAD tests reduced ED LoS for participants with positive tests or that were not tested. Negative VitaPCR results reduced mean hospital LoS by 1.5 (95%CI: 0.3-2.7) days and admissions to COVID-19 wards from 34.5 (95%CI: 28.9-40.5) to 14.7 (95%CI: 11.1-19.1) per 100 admissions. Introduction of VitaPCR reduced transfers between hospital wards in the first 5 days from 50.0 (95%CI: 45.0-55.0) to 34.0 (95%CI: 30.3-37.9) per 100 admissions.\n\nConclusionRAD tests enabled rapid detection of SARS-CoV-2 infection which had pronounced effects on LoS at the ED. VitaPCR added the possibility of exclusion of the infection which increased targeted admissions, reduced intrahospital transfers and lead to shorter stay at the hospital.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Susanne E Mortazavi", + "author_inst": "Lund University, Skane University Hospital, Department of Laboratory Medicine, Division of Clinical Chemistry and Pharmacology, Lund, Sweden" + }, + { + "author_name": "Malin Inghammar", + "author_inst": "Lund University, Skane University Hospital, Department of Clinical Sciences Lund, Section for Infection Medicine, Lund, Sweden" + }, + { + "author_name": "Claus Christansen", + "author_inst": "Clinical Microbiology, Laboratory medicine Skane, Region Skane" + }, + { + "author_name": "Anne-Katrine Pesola", + "author_inst": "Clinical Microbiology, Laboratory medicine Skane, Region Skane" + }, + { + "author_name": "Mikael Stenkilsson", + "author_inst": "Department of Emergency and Internal Medicine, Skane University Hospital, Lund, Sweden" + }, + { + "author_name": "Magnus Paulsson", + "author_inst": "Lund University, Skane University Hospital, Department of Clinical Sciences Lund, Section for Infection Medicine, Lund, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.28.21268491", "rel_title": "Neutralization of ancestral SARS-CoV-2 and variants Alpha, Beta, Gamma, Delta, Zeta and Omicron by mRNA vaccination and infection-derived immunity through homologous and heterologous variants", @@ -430382,53 +429626,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.30.474516", - "rel_title": "Viral population genomics reveals host and infectivity impact on SARS-CoV-2 adaptive landscape", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474516", - "rel_abs": "Public health surveillance, drug treatment development, and optimization of immunological interventions all depend on understanding pathogen adaptation, which differ for specific pathogens. SARS-CoV-2 is an exceptionally successful human pathogen, yet complete understanding of the forces driving its evolution is lacking. Here, we leveraged almost four million SARS-CoV-2 sequences originating mostly from non-vaccinated naive patients to investigate the impact of functional constraints and natural immune pressures on the sequence diversity of the SARS-CoV-2 genome. Overall, we showed that the SARS-CoV-2 genome is under strong and intensifying levels of purifying selection with a minority of sites under diversifying pressure. With a particular focus on the spike protein, we showed that sites under selection were critical for protein stability and virus fitness related to increased infectivity and/or reduced neutralization by convalescent sera. We investigated the genetic diversity of SARS-CoV-2 B and T cell epitopes and determined that the currently known T cell epitope sequences were highly conserved. Outside of the spike protein, we observed that mutations under selection in variants of concern can be associated to beneficial outcomes for the virus. Altogether, the results yielded a comprehensive map of all sites under selection across the entirety of SARS-CoV-2 genome, highlighting targets for future studies to better understand the virus spread, evolution and success.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kaitlyn Gayvert", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Richard Copin", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Sheldon McKay", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Ian Setliff", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Wei Keat Lim", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Alina Baum", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Christos A Kyratsous", - "author_inst": "Regeneron Pharmaceuticals, Inc." - }, - { - "author_name": "Gurinder S Atwal", - "author_inst": "Regeneron Pharmaceuticals, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.12.29.474469", "rel_title": "Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020", @@ -431201,6 +430398,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.27.21268429", + "rel_title": "Detection of the omicron variant in international travellers and their family contacts in India", + "rel_date": "2021-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268429", + "rel_abs": "HighlightsWith the emergence of the Variant of Concern, omicron (B.1.1.529), India has enhanced genomic surveillance in international travellers. The omicron variant was detected in 59 cases from different States; 40 from Maharashtra, 17 from Rajasthan and one each from Gujrat and Tamil Nadu. The positive cases and their contacts were asymptomatic and genomic surveillance could identify two clusters, one from Maharashtra and another from Rajasthan.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Varsha A Potdar", + "author_inst": "ICMR-NIV, Pune" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Kavita lole", + "author_inst": "ICMR-NIV, Pune" + }, + { + "author_name": "Sarah Cherian", + "author_inst": "ICMR-NIV, Pune" + }, + { + "author_name": "Jayanti Shastri", + "author_inst": "Kasturba Hospital Mumbai" + }, + { + "author_name": "Bharati Malhotra", + "author_inst": "SMS hospital Jaipur" + }, + { + "author_name": "sumit Dutt Bhardwaj", + "author_inst": "ICMR-NIV, Pune" + }, + { + "author_name": "Alpana Razdan", + "author_inst": "genestrings, Delhi" + }, + { + "author_name": "Manohar Lal Choudhary", + "author_inst": "ICMR-NIV, Pune" + }, + { + "author_name": "Nivedita Gupta", + "author_inst": "ICMR Delhi" + }, + { + "author_name": "Priya Abraham", + "author_inst": "ICMR-NIV, Pune" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.25.21268211", "rel_title": "Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection", @@ -432484,61 +431740,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.28.21268451", - "rel_title": "SARS-CoV-2 seroprevalence in Delhi, India: September October 2021: a population based seroepidemiological study", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268451", - "rel_abs": "BackgroundWe conducted a repeat serosurvey in Delhi, India to estimate the seroprevalence of SARS-CoV-2 in the general population and compare the antibody prevalence in the vaccinated and non-vaccinated groups.\n\nMethodsThis cross-sectional study was conducted from September 24 to October 14 2021 in 280 wards of Delhi among 27811 participants selected through a multistage sampling technique with housing settlement based stratification. The SARS-CoV-2 immunoglobulin (IgG) antibodies were screened with the VITROS(R) (Ortho Clinical Diagnostics, Raritan, NJ, USA) assay (90% sensitivity, 100% specificity).\n\nResultsA total of 24895 (89.5%) samples were seropositive. The crude seroprevalence was 87.99% (95% CI 89.1, 89.8), weighted for age and sex was 88% (95% CI 87.6, 88.4), and after adjustment of assay performance was estimated as 97.5% (95% CI 97.0, 98.0). The weighted seroprevalence in the 11 districts ranged from 84.9% (South-West district) to 90.8% (East district) Females in all the age-groups (<18, 18-49 and [≥]50) had significantly higher odds of seropositivity (p<0.001). On adjusted analysis, the odds of seroconversion in the participants vaccinated with at-least one dose of either Covid-19 vaccine (Covishield/Covaxin) was more than four times compared to the unvaccinated (aRR 4.2 (3.8, 4.6)). The seroprevalence was also comparable among the complete and partially vaccinated subgroups for both vaccines (Table 4). Most (86.8%) seropositive individuals had a SARS-CoV-2 signal/cut-off [≥]4.0 except in children\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1482d5forg.highwire.dtl.DTLVardef@19ab8a1org.highwire.dtl.DTLVardef@cf675dorg.highwire.dtl.DTLVardef@8b427aorg.highwire.dtl.DTLVardef@b96a54_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 4.C_FLOATNO O_TABLECAPTIONVaccination status and seroprevalence of antibodies to SARS-CoV-2, Delhi, September-October 2021*\n\nC_TABLECAPTION C_TBL ConclusionsWe observed IgG antibodies against SARS-CoV-2 in most of the general population of Delhi with likely higher antibody titres in the vaccinated compared to the unvaccinated groups.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Pragya Sharma", - "author_inst": "Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Saurav Basu", - "author_inst": "Maulana Azad Medical College, New Delhi and Indian Institute of Public Health-Delhi" - }, - { - "author_name": "Suruchi Mishra", - "author_inst": "Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Ekta Gupta", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Reshu Aggarwal", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "PRATIBHA RAMCHANDRA KALE", - "author_inst": "Institute of liver and biliary sciences" - }, - { - "author_name": "Nutan Mundeja", - "author_inst": "Directorate General Health Services, Government of NCT, Delhi" - }, - { - "author_name": "B S Charan", - "author_inst": "Directorate General Health Services, Government of NCT, Delhi" - }, - { - "author_name": "Gautam Kumar Singh", - "author_inst": "Directorate General Health Services, Government of NCT, Delhi" - }, - { - "author_name": "Mongjam Meghachandra Singh", - "author_inst": "Maulana Azad Medical College, New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.27.21268462", "rel_title": "Evolution of COVID-19 Health Disparities in Arizona", @@ -433363,6 +432564,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.12.27.21268464", + "rel_title": "Control Strategies for the Third wave of COVID-19 infection in India: A Mathematical Model Incorporating Vaccine Effectiveness", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268464", + "rel_abs": "The waning effectiveness of the COVID-19 vaccines and the emergence of a new variant Omicron has given rise to the possibility of another outbreak of the infection in India. COVID-19 has caused more than 34 million reported cases and 475 thousand deaths in India so far, and it has affected the country at the root level, socially as well as economically. After going through different control measures, mass vaccination has been achieved to a large extent for the highly populous country, and currently under progress. India has already been hit by a massive second wave of infection in April-June, 2021 mainly due to the delta variant, and might see a third wave in the near future that needs to be controlled with effective control strategies. In this paper, we present a compartmental epidemiological model with vaccinations incorporating the dose-dependent effectiveness. We study a possible sudden outbreak of SARS-CoV2 variants in the future, and bring out the associated predictions for various vaccination rates and point out optimum control measures. Our results show that for transmission rate 30% higher than the current rate due to emergence of new variant or relaxation of social distancing conditions, daily new cases can peak to 250k in March 2022, taking the second dose effectiveness dropping to 50% in the future. Combination of vaccination and controlled lockdown or social distancing is the key to tackling the current situation and for the coming few months. Our simulation results show that social distancing measures show better control over the disease spread than the higher vaccination rates.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Namitha A Sivadas", + "author_inst": "Vellore Institute of Technology" + }, + { + "author_name": "Ashutosh Mahajan", + "author_inst": "Vellore Institute of Technology" + }, + { + "author_name": "Pooja Panda", + "author_inst": "Vellore Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.27.21268463", "rel_title": "Real-time Estimation of Global CFR Ascribed to COVID-19 Confirmed Cases Applying Machine Learning Technique", @@ -434630,85 +433858,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.27.474251", - "rel_title": "Mapping the allosteric effects that define functional activity of SARS-CoV-2 specific antibodies", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474251", - "rel_abs": "Previous studies on the structural relationship between human antibodies and SARS-CoV-2 have focused on generating static snapshots of antibody complexes with the Spike trimer. However, antibody-antigen interactions are dynamic, with significant binding-induced allosteric effects on conformations of antibody and its target antigen. In this study, we employ hydrogen-deuterium exchange mass spectrometry, in vitro assays, and molecular dynamics simulations to investigate the allosteric perturbations linked to binding events between a group of human antibodies with differential functional activities, and the Spike trimer from SARS-CoV-2. Our investigations have revealed key dynamic features that define weakly or moderately neutralizing antibodies versus those with strong neutralizing activity. These results provide mechanistic insights into the functional modes of human antibodies against COVID-19, and provide a rationale for effective antiviral strategies.\n\nTeaserDifferent neutralizing antibodies induce site-specific allosteric effects across SARS-CoV-2 Spike protein", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nikhil Kumar Tulsian", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Palur Venkata Raghuvamsi", - "author_inst": "National University of Singapore - Kent Ridge Campus: National University of Singapore" - }, - { - "author_name": "Xinlei Qian", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Gu Yue", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Bhuvaneshwari D/O Shunmuganathan", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Firdaus Samsudin", - "author_inst": "Bioinformatics Institute, A*STAR" - }, - { - "author_name": "Yee Hwa Wong", - "author_inst": "NTU" - }, - { - "author_name": "Lin Jianqing", - "author_inst": "National Technological University, Singapore" - }, - { - "author_name": "Kiren Purushotorman", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Mary Kozma McQueen", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Bei Wang", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "Julien Lescar", - "author_inst": "Nanyang Technological University" - }, - { - "author_name": "Cheng-I Wang", - "author_inst": "Singapore Immunology Network, A*STAR, Singapore" - }, - { - "author_name": "Ganesh Anand", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Peter J Bond", - "author_inst": "A*STAR Bioinformatics Institute, Singapore" - }, - { - "author_name": "Paul A MacAry", - "author_inst": "Life Sciences Institute, National University of Singapore" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.12.27.474315", "rel_title": "Peptide-based epitope design on non-structural proteins of SARS-CoV-2", @@ -435605,6 +434754,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.12.21.21268075", + "rel_title": "Assessing Immunity by Quantitative Measurement of SARS-CoV-2 IgG Antibodies in Fingerstick Samples", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268075", + "rel_abs": "COVID-19 has affected billions of people around the world directly or indirectly. The response to the pandemic has focused on preventing the spread of the disease and improving treatment options. Diagnostic technologies have played a key role in this response since the beginning of the pandemic. As vaccines and other treatments have been developed and deployed, interest in understanding and measuring the individual level of immune protection has increased. Historically, use of antibody titers to measure systemic immunity has been constrained by an incomplete understanding of the relationship between antibodies and immunity, the lack of international standards for antibody concentration to enable cross-study comparisons, and insufficient clinical data to allow for the development of robust antibody-immunity models.\n\nHowever, these constraints have recently shifted. With a deeper understanding of antibodies, the promulgation of WHO antibody standards, and the development of immunity models using datasets from multiple COVID-19 vaccine trials, certain types of quantitative antibody tests may now provide a way to monitor individual or community immunity against COVID-19. Specifically, tests that quantitate the concentration of anti-RBD IgG -antibodies that target the receptor binding domain of the S1 spike protein component of the SARS-CoV-2 virus - show promise as a useful and scalable measure of the COVID-19 immunity of both individuals and communities. However, to fulfill this promise, a rapid and easy-to-administer test is needed.\n\nTo address this important clinical need, Brevitest deployed its point-of-care-capable technology platform that can run a rapid (<15 minute), quantitative antibody test with a sample of 10 l of whole blood from a fingerstick. The test we validated on this platform measures the concentration of anti-RBD IgG in Binding Antibody Units per milliliter (BAU/mL) per WHO Reference Standard NIBSC 20/136.\n\nIn this paper, we present studies used to characterize the Brevitest anti-RBD IgG assay and evaluate its clinical performance, lower limits of measurement, precision, linearity, interference, and cross-reactivity. The results demonstrate the ability of this assay to measure a patients anti-RBD IgG concentration. This information, together with models developed from recent COVID-19 vaccine clinical trials, can provide a means of assessing the current level of immune protection of an individual or community against COVID-19 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Javier T. Garza", + "author_inst": "Brevitest Technologies, Inc." + }, + { + "author_name": "Jacob Quick", + "author_inst": "Brevitest Technologies, Inc." + }, + { + "author_name": "Dev Chatterjee", + "author_inst": "Brevitest Technologies, Inc." + }, + { + "author_name": "Robert Patrick Garr", + "author_inst": "Brevitest Technologies, Inc." + }, + { + "author_name": "Atul Varadhachary", + "author_inst": "Brevitest Technologies, Inc." + }, + { + "author_name": "Leo Linbeck III", + "author_inst": "Brevitest Technologies, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.25.474152", "rel_title": "A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 delta variant", @@ -437204,165 +436392,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.23.21268177", - "rel_title": "Breakthrough SARS-CoV-2 infections after COVID-19 mRNA vaccination in MS patients on disease modifying therapies", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268177", - "rel_abs": "BackgroundPatients with Multiple Sclerosis (pwMS) treated with anti-CD20 or fingolimod showed a reduced humoral response to mRNA-based SARS-CoV-2 vaccines, while the degree of such responses is unimpaired and similar in pwMS treated with other disease modifying therapies (DMTs), or untreated. However, the nature of the SARS-CoV-2 vaccine-induced immune response is based also on cellular immunity and there is emerging evidence that anti-SARS-CoV-2 specific CD4 and CD8 T cell responses can be detected after vaccination also in patients with low antibody levels. In this study we aimed to monitor the risk of breakthrough SARS-CoV-2 infection and to identify correlates of reduced protection in frail vaccinated pwMS on different DMTs.\n\nMethodsWe designed a long term clinical follow-up of the CovaXiMS (Covid-19 vaccine in Multiple Sclerosis), a prospective multicenter cohort study enrolling pwMS scheduled for SARS-CoV-2 vaccination with mRNA vaccines and tested for SARS-CoV-2 antibodies before and after the second vaccine dose. These patients were followed with periodic phone calls up to a mean time of 6 months, and all the SARS-CoV-2 breakthrough infections were registered. The impact of DMTs on cumulative incidence of breakthrough Covid-19 cases was presented by Kaplan-Meier curves. A multivariable logistic model was run to assess factors associated to a higher risk of breakthrough infections.\n\nFindings1705 pwMS (81.6% BNT162b2 and 18.4% mRNA-1273) had a full vaccination cycle (2 vaccine doses, 21/28 days apart). Of them, 1509 (88.5%) had blood assessment 4 weeks after the second vaccine dose. During follow-up, 23 breakthrough Covid-19 infections (cumulative incidence: 1.5%, SE=0.3%) were detected after a mean of 108 days after the second dose (range, 18-230). Of them, 9 were on ocrelizumab, one on rituximab, 4 on fingolimod, 6 on dimethyl-fumarate, one on teriflunomide, and 2 were untreated. Just two cases (a woman on ocrelizumab and a man on teriflunomide) required hospitalization. The probability to be infected was associated only with SARS-CoV-2 antibody levels measured after 4 weeks from the second vaccine dose (HR=0.63, p=0.007); an antibody level of 660 U/mL was calculated as the cutoff for higher risk of infection.\n\nInterpretationOur data show that the risk of breakthrough SARS-CoV-2 infections is mainly associated with reduced levels of the virus-specific humoral immune response.\n\nFundingFISM [2021/Special-Multi/001]; the Italian Ministry of Health grant Progetto Z844A 5x1000. Italian Ministry of Health: Ricerca Corrente to IRCCS Ospedale Policlinico San Martino.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Maria Pia Sormani", - "author_inst": "Department of Health Sciences, Section of Biostatistics, University of Genova, ItalyIRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Irene Schiavetti", - "author_inst": "Department of Health Sciences, Section of Biostatistics, University of Genova, Italy" - }, - { - "author_name": "Matilde Inglese", - "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, ItalyDepartment of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI) an" - }, - { - "author_name": "Luca Carmisciano", - "author_inst": "Department of Health Sciences, Section of Biostatistics, University of Genova, Italy" - }, - { - "author_name": "Alice Laroni", - "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, ItalyDepartment of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI) an" - }, - { - "author_name": "Caterina Lapucci", - "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, ItalyDepartment of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI) an" - }, - { - "author_name": "Valeria Visconti", - "author_inst": "Laboratory Medicine, IRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Carlo Serrati", - "author_inst": "Department of Neurology, Imperia Hospital, Imperia, Italy" - }, - { - "author_name": "Ilaria Gandoglia", - "author_inst": "Neurology Unit, Galliera Hospital" - }, - { - "author_name": "Tiziana Tassinari", - "author_inst": "S.C. Neurologia - Ospedale Santa Corona Pietra Ligure (Sv)" - }, - { - "author_name": "Germana Perego", - "author_inst": "SC Neurologia ASL 4 Chiavarese" - }, - { - "author_name": "Giampaolo Brichetto", - "author_inst": "AISM Rehabilitation Center, Genoa, Italy" - }, - { - "author_name": "Paola Gazzola", - "author_inst": "Centro Sclerosi Multipla S.C. Neurologia Asl 3 Genovese" - }, - { - "author_name": "Antonio Mannironi", - "author_inst": "Department of Neurology, SantAndrea Hospital, La Spezia, Italy" - }, - { - "author_name": "Maria Laura Stromillo", - "author_inst": "Clinica Neurologica e Malattie Neurometaboliche, Universita degli Studi di Siena" - }, - { - "author_name": "Cinzia Cordioli", - "author_inst": "Centro Sclerosi Multipla ASST Spedali Civili di Brescia" - }, - { - "author_name": "Doriana Landi", - "author_inst": "Multiple Sclerosis Clinical and Research Unit, Department of Systems Medicine, Tor Vergata University and Hospital, Rome, Italy" - }, - { - "author_name": "Marinella Clerico", - "author_inst": "Dipartimento di Scienze Cliniche e Biologiche, Universita di Torino Universita di Torino" - }, - { - "author_name": "Elisabetta Signoriello", - "author_inst": "Centro Sclerosi Multipla, II Clinica Neurologica, Universita della Campania Luigi Vanvitelli" - }, - { - "author_name": "Jessica Frau", - "author_inst": "Centro Sclerosi Multipla Ospedale Binaghi Cagliari - ATS Sardegna, Universita di Cagliari" - }, - { - "author_name": "Maria Teresa Ferr\u00f2", - "author_inst": "Neuroimmunology, Center for Multiple Sclerosis, Cerobrovascular Department, Neurological Unit, ASST Crema" - }, - { - "author_name": "Alessia Di Sapio", - "author_inst": "Department of Neurology, Regina Montis Regalis Hospital, Mondovi, Italy" - }, - { - "author_name": "Livia Pasquali", - "author_inst": "Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Italy" - }, - { - "author_name": "Monica Ulivelli", - "author_inst": "Department of Medicine, Surgery and Neuroscience, University of Siena" - }, - { - "author_name": "Fabiana Marinelli", - "author_inst": "Multiple Sclerosis Center, Fabrizio Spaziani Hospital, via Armando Fabi, Frosinone Italy" - }, - { - "author_name": "Marcello Manzino", - "author_inst": "Neurologia, Ospedale San Paolo, Savona, Italy" - }, - { - "author_name": "Graziella Callari", - "author_inst": "UOC Neurologia e Centro SM Fondazione Istituto G. Giglio, Cefalu" - }, - { - "author_name": "Rosa Iodice", - "author_inst": "Clinica Neurologica, DSNRO Universita Federico II di Napoli" - }, - { - "author_name": "Giuseppe Liberatore", - "author_inst": "Neuromuscular and Neuroimmunology Service, IRCCS Humanitas Research Hospital, Rozzano, Italy" - }, - { - "author_name": "Francesca Caleri", - "author_inst": "MS Center, Department of Neurology, F. Tappeiner Hospital Meran (BZ), Italy" - }, - { - "author_name": "Anna Maria Repice", - "author_inst": "Department of Neurology 2, Careggi University Hospital, Florence, Italy" - }, - { - "author_name": "Susanna Cordera", - "author_inst": "Department of Neurology, Ospedale Regionale, Aosta, Italy" - }, - { - "author_name": "Mario Alberto Battaglia", - "author_inst": "Research Department, Italian Multiple Sclerosis Foundation, Genoa, ItalyDepartment of Life Sciences, University of Siena, Italy" - }, - { - "author_name": "Marco Salvetti", - "author_inst": "Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Italy IRCC" - }, - { - "author_name": "Diego Franciotta", - "author_inst": "Autoimmunology Laboratory, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Antonio Uccelli", - "author_inst": "IRCCS Ospedale Policlinico San Martino, Genova, ItalyDepartment of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI) an" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.12.22.21268127", "rel_title": "Humoral and cellular immune responses to SARS CoV-2 vaccination in Persons with Multiple Sclerosis and NMOSD patients receiving immunomodulatory treatments", @@ -437991,6 +437020,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.20.21267877", + "rel_title": "Immunosequencing and epitope mapping reveal substantial preservation of the T cell immune response to Omicron generated by SARS-CoV-2 vaccines", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21267877", + "rel_abs": "The Omicron SARS-CoV-2 variant contains 34 mutations in the spike gene likely impacting protective efficacy from vaccines. We evaluated the potential impact of these mutations on the cellular immune response. Combining epitope mapping to SARS-CoV-2 vaccines that we have determined from past experiments along with T cell receptor (TCR) repertoire sequencing from thousands of vaccinated or naturally infected individuals, we estimate the abrogation of the cellular immune response in Omicron. Although 20% of CD4+ T cell epitopes are potentially affected, the loss of immunity mediated by CD4+ T cells is estimated to be slightly above 30% as some of the affected epitopes are relatively more immunogenic. For CD8+ T cells, we estimate a loss of approximately 20%. These reductions in T cell immunity are substantially larger than observed in other widely distributed variants. Combined with the expected substantial loss of neutralization from antibodies, the overall protection provided by SARS-CoV-2 vaccines could be impacted adversely. From analysis of prior variants, the efficacy of vaccines against symptomatic infection has been largely maintained and is strongly correlated with the T cell response but not as strongly with the neutralizing antibody response. We expect the remaining 70% to 80% of on-target T cells induced by SARS-CoV-2 vaccination to reduce morbidity and mortality from infection with Omicron.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Damon H. May", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Benjamin E. R. Rubin", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Sudeb C. Dalai", + "author_inst": "Adaptive Biotechnologies and Stanford University School of Medicine" + }, + { + "author_name": "Krishna Patel", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Shahin Shafiani", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Rebecca Elyanow", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Matthew T. Noakes", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Thomas M. Snyder", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Harlan S. Robins", + "author_inst": "Adaptive Biotechnologies" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21268130", "rel_title": "High Rate of Asymptomatic Carriage Associated with Variant Strain Omicron", @@ -439130,65 +438210,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.23.21268315", - "rel_title": "Genomic diversification of long polynucleotide fragments is a signature of emerging SARS-CoV-2 variants of concern", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268315", - "rel_abs": "Highly transmissible or immuno-evasive SARS-CoV-2 variants have intermittently emerged and outcompeted previously circulating strains, resulting in repeated COVID-19 surges, reinfections, and breakthrough infections in vaccinated individuals. With over 5 million SARS-CoV-2 genomes sequenced globally over the last 2 years, there is unprecedented data to decipher how competitive viral evolution results in the emergence of fitter SARS-CoV-2 variants. Much attention has been directed to studying how specific mutations in the Spike protein impact its binding to the ACE2 receptor or viral neutralization by antibodies, but there is limited knowledge of a genomic signature that is shared primarily by the sequential dominant variants. Here we introduce a methodology to quantify the genome-wide distinctiveness of polynucleotide fragments of various lengths (3-to 240-mers) that constitute SARS-CoV-2 sequences (freely available at https://academia.nferx.com/GENI). Compared to standard phylogenetic distance metrics and overall mutational load, the quantification of distinctive 9-mer polynucleotides provides a higher resolution of separation between VOCs (Reference = 89, IQR: 65-108; Alpha = 166, IQR: 150-182; Beta 130, IQR: 113-147; Gamma = 165, IQR: 152-180; Delta = 234, IQR: 216-253; and Omicron = 294, IQR: 287-315). Omicrons exceptionally high genomic distinctiveness may confer a competitive advantage over both prior VOCs (including Delta) and the recently emerged and highly mutated B.1.640.2 (IHU) lineage. Expanding on this analysis, evaluation of genomic distinctiveness weighted by intra-lineage 9-mer conservation for 1,363 lineages annotated in GISAID highlights that genomic distinctiveness has increased over time (R2=0.37) and that VOCs score significantly higher than contemporary non-VOC lineages, with Omicron among the most distinctive lineages observed till date. This study demonstrates the value of characterizing new SARS-CoV-2 variants by their genome-wide polynucleotide distinctiveness and emphasizes the need to go beyond a narrow set of mutations at known functionally or antigenically salient sites on the Spike protein. The consistently higher distinctiveness of each emerging VOC compared to prior VOCs suggests that real-time monitoring of genomic distinctiveness would aid in more rapid assessment of viral fitness.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Karthik Murugadoss", - "author_inst": "nference" - }, - { - "author_name": "Michiel JM Niesen", - "author_inst": "nference" - }, - { - "author_name": "Bharathwaj Raghunathan", - "author_inst": "nference" - }, - { - "author_name": "Patrick J Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Pritha Ghosh", - "author_inst": "nference Labs" - }, - { - "author_name": "Tyler Feener", - "author_inst": "nference" - }, - { - "author_name": "Praveen Anand", - "author_inst": "nference Labs" - }, - { - "author_name": "Safak Simsek", - "author_inst": "nference" - }, - { - "author_name": "Rohit Suratekar", - "author_inst": "nference Labs" - }, - { - "author_name": "Travis K Hughes", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.24.21268370", "rel_title": "A novel methodology for the synchronous collection and multimodal visualisation of continuous neurocardiovascular and neuromuscular physiological data in adults with long COVID", @@ -439801,6 +438822,177 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.23.21268347", + "rel_title": "Ex-vivo mucolytic and anti-inflammatory activity of BromAc in tracheal aspirates from COVID-19", + "rel_date": "2021-12-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268347", + "rel_abs": "COVID-19 is a lethal disease caused by the pandemic SARS-CoV-2, which continues to be a public health threat. COVID-19 is principally a respiratory disease and is often associated with sputum retention, for which there are limited therapeutic options. In this regard, we evaluated the use of BromAc(R), a combination of Bromelain and Acetylcysteine (NAC). Both drugs present mucolytic effect and have been studied to treat COVID-19. Therefore, we sought to examine the mucolytic, antiviral, and anti-inflammatory effect of BromAc(R) in tracheal aspirate samples from critically ill COVID-19 patients requiring mechanical ventilation.\n\nMethodTracheal aspirate samples from COVID-19 patients were collected following next of kin consent and mucolysis, rheometry and cytokine storm analysis was performed.\n\nResultsBromAc(R) displayed a robust mucolytic effect in a dose dependent manner. BromAc(R) showed anti-inflammatory activity, reducing the action of cytokine storm, chemokines including MIP-1alpha, CXCL8, MIP-1b, MCP-1 and IP-10, and regulatory cytokines IL-5, IL-10, IL-13 IL-1RA and total reduction for IL-9 compared to NAC alone and control. BromAc(R) acted on IL-6, demonstrating a reduction in G-CSF and VEGF-D at concentrations of 125 and 250{micro}g.\n\nConclusionThese results indicate robust mucolytic and anti-inflammatory effect of BromAc(R) in tracheal aspirates from critically ill COVID-19 patients, indicating its potential as a therapeutic strategy to COVID-19.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Jordana Grazziela A. Coelho dos Reis", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Geovane Marques Ferreira", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Alice Aparecida Lourenco", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Agata Lopes Ribeiro", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Camila Pacheco da Silveira Martins da Mata", + "author_inst": "Risoleta Tolentino Neves Hospital, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Patricia de Melo Oliveira", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Daisymara Priscila de Almeida Marques", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Linziane Lopes Ferreira", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Felipe Alves Clarindo", + "author_inst": "Basic and Applied Virology Laboratory, Department of Microbiology, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Br" + }, + { + "author_name": "Murillo Ferreira da Silva", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil; Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cru" + }, + { + "author_name": "Heitor Portella Povoas Filho", + "author_inst": "Hospital de Ilheus, Ilheus, BA, Brazil" + }, + { + "author_name": "Nilson Roberto Ribeiro Oliveira Jr.", + "author_inst": "Department of Intensive Care Services, Hospital de Ilheus, Ilheus, BA, Brazil" + }, + { + "author_name": "Maisah Meyhr D Carmo Sodre", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil." + }, + { + "author_name": "Sandra Rocha Gadelha", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil; Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cru" + }, + { + "author_name": "George Rego Albuquerque", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil.\tDepartment of Agricultural and Enviro" + }, + { + "author_name": "Bianca Mendes Maciel", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil; Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cru" + }, + { + "author_name": "Ana Paula Melo Mariano", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil; Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cru" + }, + { + "author_name": "Mylene de Melo Silva", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil." + }, + { + "author_name": "Renato Fontana", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil; Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cru" + }, + { + "author_name": "Lauro Juliano Marin", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil;\tDepartment of Health Sciences (DCS), " + }, + { + "author_name": "Renata Santiago Alberto Carlos", + "author_inst": "Department of Agricultural and Environmental Sciences (DCAA), Santa Cruz State University (UESC), Ilheus, BA, Brazil" + }, + { + "author_name": "Amanda Teixeira Sampaio Lopes", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil" + }, + { + "author_name": "Fabricio Barbosa Ferreira", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil" + }, + { + "author_name": "Uener Ribeiro dos Santos", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil" + }, + { + "author_name": "Iris Terezinha Santos de Santana", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil" + }, + { + "author_name": "Hllytchaikra Ferraz Fehlberg", + "author_inst": "Laboratory of Pharmacogenomics and Molecular Epidemiology (LAFEM), Santa Cruz State University (UESC), Ilheus, BA, Brazil" + }, + { + "author_name": "Rachel Passos Rezende", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil" + }, + { + "author_name": "Joao Carlos T Dias", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil." + }, + { + "author_name": "Eduardo Gross", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil" + }, + { + "author_name": "Gisele Assis Castro Goulart", + "author_inst": "Department of Pharmaceuticals, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Marie Gabriele Santiago", + "author_inst": "Department of Pharmaceuticals, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Ana Paula Motta Lavigne de Lemos", + "author_inst": "Department of Intensive Care Services, Hospital de Ilheus, Ilheus, BA, Brazil" + }, + { + "author_name": "Aline O da Conceicao", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil." + }, + { + "author_name": "Carla Cristina Romano", + "author_inst": "Department of Intensive Care Services, Hospital de Ilheus, Ilheus, BA, Brazil" + }, + { + "author_name": "Luciana Debortoli de Carvalho", + "author_inst": "Department of Biological Sciences, Santa Cruz State University, Ilheus, BA, Brazil" + }, + { + "author_name": "Olindo Assis Martins Filho", + "author_inst": "Grupo Integrado de Pesquisas em Biomarcadores, Instituto Rene Rachou, Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil" + }, + { + "author_name": "Claudio Almeida Quadros", + "author_inst": "Sao Rafael Hospital and Bahia State University, Salvador, Bahia, Brazil" + }, + { + "author_name": "Sarah J Valle", + "author_inst": "Mucpharm Pty Ltd, Sydney NSW Australia; University of New South Wales, St George & Sutherland Hospital Clinical School, Sydney NSW Australia" + }, + { + "author_name": "David L Morris", + "author_inst": "Mucpharm Pty Ltd, Sydney NSW Australia; University of New South Wales, St George & Sutherland Hospital Clinical School, Sydney NSW Australia; Department of Surg" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.12.23.21268279", "rel_title": "Remote Covid Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.", @@ -440876,45 +440068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.23.21268343", - "rel_title": "Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268343", - "rel_abs": "Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in some countries, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Getting meaningful information from wastewater-based epidemiology in regions of low prevalence remains a key challenge. Here we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to February 2021 during the third wave of the COVID-19 outbreak in Japan. Viral RNA was below the limit of quantification in all samples. However, by counting the positive reactions in repeated qPCR of each sample, we found that the ratio of positive reactions to all tests in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during periods of both increasing and decreasing infection. Time-step analysis indicated that COVID-19 patients excreted large amounts of virus in their feces 2 days either side of symptom onset, which wastewater surveillance could detect. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.\n\nHighlightsO_LIPositive ratio by repeated qPCR of low target-molecule numbers correlated with number expected from Poisson distribution.\nC_LIO_LIPositive ratio by repeated RT-qPCR of SARS-CoV-2 RNA in wastewater tracked the infection dynamics of COVID-19 in a region of low prevalence.\nC_LIO_LIPositive ratios correlated with number of new cases by date of symptom onset.\nC_LIO_LICOVID-19 patients might excrete more virus in their feces in the period from 2 days before to 2 days after symptom onset.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bo Zhao", - "author_inst": "Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University" - }, - { - "author_name": "Zaizhi Yu", - "author_inst": "Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University" - }, - { - "author_name": "Tomonori Fujita", - "author_inst": "Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University" - }, - { - "author_name": "Yoshiaki Nihei", - "author_inst": "Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University" - }, - { - "author_name": "Hiroaki Tanaka", - "author_inst": "Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University" - }, - { - "author_name": "Masaru Ihara", - "author_inst": "Faculty of Agriculture and Marine Science, Graduate School of Integrated Arts and Sciences, Kochi University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.23.21268352", "rel_title": "Early Treatment with fluvoxamine among patients with COVID-19: a cost-consequence model", @@ -441823,6 +440976,149 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.21.473679", + "rel_title": "SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-weeks interval between doses", + "rel_date": "2021-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473679", + "rel_abs": "Continuous emergence of SARS-CoV-2 variants of concern (VOC) is fueling the COVID-19 pandemic. Omicron (B.1.1.529), is rapidly spreading worldwide. The large number of mutations in its Spike raised concerns about a major antigenic drift that could significantly decrease vaccine efficacy and infection-induced immunity. A long interval between BNT162b2 mRNA doses was shown to elicit antibodies that efficiently recognize Spikes from different VOCs. Here we evaluated the recognition of Omicron Spike by plasma from a cohort of SARS-CoV-2 naive and previously-infected individuals that received their BNT162b2 mRNA vaccine 16-weeks apart. Omicron Spike was recognized less efficiently than D614G, Alpha, Beta, Gamma and Delta Spikes. We compared to plasma activity from participants receiving a short (4-weeks) interval regimen. Plasma from individuals of the long interval cohort recognized and neutralized better the Omicron Spike compared to those that received a short interval. Whether this difference confers any clinical benefit against Omicron remains unknown.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Debashree Chatterjee", + "author_inst": "CRCHUM" + }, + { + "author_name": "Alexandra Tauzin", + "author_inst": "CRCHUM" + }, + { + "author_name": "Lorie Marchitto", + "author_inst": "CRCHUM" + }, + { + "author_name": "Shang Yu Gong", + "author_inst": "CRCHUM" + }, + { + "author_name": "Marianne Boutin", + "author_inst": "CRCHUM" + }, + { + "author_name": "Catherine Bourassa", + "author_inst": "CRCHUM" + }, + { + "author_name": "Guillaume Beaudoin-Bussieres", + "author_inst": "CRCHUM" + }, + { + "author_name": "Yuxia Bo", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Shilei Ding", + "author_inst": "CRCHUM" + }, + { + "author_name": "Annemarie Laumaea", + "author_inst": "CRCHUM" + }, + { + "author_name": "Dani Vezina", + "author_inst": "CRCHUM" + }, + { + "author_name": "Josee Perreault", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Laurie Gokool", + "author_inst": "CRCHUM" + }, + { + "author_name": "Chantal Morrisseau", + "author_inst": "CRCHUM" + }, + { + "author_name": "Pascale Arlotto", + "author_inst": "CRCHUM" + }, + { + "author_name": "Eric Fournier", + "author_inst": "INSPQ" + }, + { + "author_name": "Aurelie Guilbault", + "author_inst": "INSPQ" + }, + { + "author_name": "Benjamin Delisle", + "author_inst": "INSPQ" + }, + { + "author_name": "Ines Levade", + "author_inst": "INSPQ" + }, + { + "author_name": "Guillaume Goyette", + "author_inst": "CRCHUM" + }, + { + "author_name": "Gabrielle Gendron-Lepage", + "author_inst": "CRCHUM" + }, + { + "author_name": "Halima Medjahed", + "author_inst": "CRCHUM" + }, + { + "author_name": "Gaston De Serres", + "author_inst": "INSPQ" + }, + { + "author_name": "Cecile Tremblay", + "author_inst": "CRCHUM" + }, + { + "author_name": "Valerie Martel-Laferriere", + "author_inst": "CRCHUM" + }, + { + "author_name": "Daniel E Kaufmann", + "author_inst": "CRCHUM" + }, + { + "author_name": "Renee Bazin", + "author_inst": "Hema-Quebec" + }, + { + "author_name": "Jeremie Prevost", + "author_inst": "CRCHUM" + }, + { + "author_name": "Sandrine Moreira", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "CRCHUM" + }, + { + "author_name": "Marceline Cote", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Andres Finzi", + "author_inst": "CRCHUM" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.22.473949", "rel_title": "Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies", @@ -442761,81 +442057,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.21.473706", - "rel_title": "Anti-SARS-CoV-2 human antibodies retaining neutralizing activity against SARS-CoV-2 B.1.1.529 (omicron)", - "rel_date": "2021-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473706", - "rel_abs": "SARS-CoV-2 B.1.1.529, designated omicron, was recently identified as a new variant of concern by WHO and is rapidly replacing SARS-CoV-2 delta as the most dominant variant in many countries. Unfortunately, because of the high number of mutations present in the spike of SARS-CoV-2 omicron, most monoclonal antibodies (mAbs) currently approved for treatment of COVID-19 lose their in vitro neutralizing activity against this variant. We recently described a panel of human anti-SARS-CoV-2 mAbs that potently neutralize SARS-CoV-2 Wuhan, D614G and variants alpha, beta, gamma and delta. In this work, we evaluated our mAb panel for potential in vitro activity against SARS-CoV-2 delta and omicron. Three mAbs from our panel retain neutralizing activity against both delta and omicron, with mAb 3B8 still resulting in complete neutralization at a concentration as low as 0.02 g/ml for both variants. Overall, our data indicate that mAb 3B8 may have the potential to become a game-changer in the fight against the continuously evolving SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Maya Imbrechts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Winnie Kerstens", - "author_inst": "KU Leuven" - }, - { - "author_name": "Madina Rasulova", - "author_inst": "KU Leuven" - }, - { - "author_name": "Thomas Vercruysse", - "author_inst": "KU Leuven" - }, - { - "author_name": "Wim Maes", - "author_inst": "KU Leuven" - }, - { - "author_name": "Louanne Ampofo", - "author_inst": "KU Leuven" - }, - { - "author_name": "Karen Ven", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jeroen Lammertyn", - "author_inst": "KU Leuven" - }, - { - "author_name": "Karen Vanhoorelbeke", - "author_inst": "KU Leuven" - }, - { - "author_name": "Nico Callewaert", - "author_inst": "AZ Groeninge" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Kai Dallmeier", - "author_inst": "KU Leuven" - }, - { - "author_name": "Paul Declerck", - "author_inst": "KU Leuven" - }, - { - "author_name": "Hendrik Jan Thibaut", - "author_inst": "KU Leuven" - }, - { - "author_name": "Nick Geukens", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.21.473594", "rel_title": "Construction of a potent pan-vaccine based on the evolutionary tendency of SARS-CoV-2 spike protein.", @@ -443708,6 +442929,149 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.20.473557", + "rel_title": "mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant", + "rel_date": "2021-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473557", + "rel_abs": "The BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines generate potent neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the global emergence of SARS-CoV-2 variants with mutations in the spike protein, the principal antigenic target of these vaccines, has raised concerns over the neutralizing activity of vaccine-induced antibody responses. The Omicron variant, which emerged in November 2021, consists of over 30 mutations within the spike protein. Here, we used an authentic live virus neutralization assay to examine the neutralizing activity of the SARS-CoV-2 Omicron variant against mRNA vaccine-induced antibody responses. Following the 2nd dose, we observed a 30-fold reduction in neutralizing activity against the omicron variant. Through six months after the 2nd dose, none of the sera from naive vaccinated subjects showed neutralizing activity against the Omicron variant. In contrast, recovered vaccinated individuals showed a 22-fold reduction with more than half of the subjects retaining neutralizing antibody responses. Following a booster shot (3rd dose), we observed a 14-fold reduction in neutralizing activity against the omicron variant and over 90% of boosted subjects showed neutralizing activity against the omicron variant. These findings show that a 3rd dose is required to provide robust neutralizing antibody responses against the Omicron variant.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Venkata-Viswanadh Edara", + "author_inst": "Emory University" + }, + { + "author_name": "Kelly E Manning", + "author_inst": "Emory University" + }, + { + "author_name": "Madison Ellis", + "author_inst": "Emory University" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Kathryn M Moore", + "author_inst": "Emory University" + }, + { + "author_name": "Stephanie L Foster", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Meredith E Davis-Gardner", + "author_inst": "Emory University" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Emory University" + }, + { + "author_name": "Lindsay E Nyhoff", + "author_inst": "Emory University" + }, + { + "author_name": "Sarah Bechnack", + "author_inst": "Emory University" + }, + { + "author_name": "Ghina Alaaeddine", + "author_inst": "Emory University" + }, + { + "author_name": "Amal Naji", + "author_inst": "Emory University" + }, + { + "author_name": "Hady Samaha", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew Lee", + "author_inst": "Emory University" + }, + { + "author_name": "Laurel Bristow", + "author_inst": "Emory University" + }, + { + "author_name": "Laila Hussaini", + "author_inst": "Emory University" + }, + { + "author_name": "Caroline Rose Ciric", + "author_inst": "Emory University" + }, + { + "author_name": "Phuong-Vi Nguyen", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew Gagne", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Jesmine Roberts-Torres", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Amy R Henry", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Sucheta Godbole", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Arash Grakoui", + "author_inst": "Emory University" + }, + { + "author_name": "Marybeth Sexton", + "author_inst": "Emory University" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University" + }, + { + "author_name": "Jesse J Waggoner", + "author_inst": "Emory University" + }, + { + "author_name": "Daniel C Douek", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Evan J Anderson", + "author_inst": "Emory University" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.21.473528", "rel_title": "Immune escape of SARS-CoV-2 Omicron variant from mRNA vaccination-elicited RBD-specific memory B cells.", @@ -445179,185 +444543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267606", - "rel_title": "Context-specific emergence and growth of the SARS-CoV-2 Delta variant", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267606", - "rel_abs": "The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases1-3. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions4,5. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Deltas nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Deltas invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "John T. McCrone", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Verity Hill", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Sumali Bajaj", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - }, - { - "author_name": "Rosario Evans Pena", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - }, - { - "author_name": "Ben C. Lambert", - "author_inst": "Department of Computer Science, University of Oxford, Oxford, UK" - }, - { - "author_name": "Rhys Inward", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK & MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics" - }, - { - "author_name": "Samir Bhatt", - "author_inst": "MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK & 5.\tSection of Epid" - }, - { - "author_name": "Erik Volz", - "author_inst": "MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK" - }, - { - "author_name": "Christopher Ruis", - "author_inst": "Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK" - }, - { - "author_name": "Simon Dellicour", - "author_inst": "Spatial Epidemiology Lab (SpELL), Universit\u00e9 Libre de Bruxelles, Bruxelles, Belgium & Department of Microbiology, Immunology and Transplantation, Rega Institute" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Alexander E. Zarebski", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - }, - { - "author_name": "Adam Sadilek", - "author_inst": "Google, Mountain View, CA, USA" - }, - { - "author_name": "Neo Wu", - "author_inst": "Google, Mountain View, CA, USA" - }, - { - "author_name": "Aaron Schneider", - "author_inst": "Google, Mountain View, CA, USA" - }, - { - "author_name": "Xiang Ji", - "author_inst": "Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA" - }, - { - "author_name": "Jayna Raghwani", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - }, - { - "author_name": "Ben Jackson", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Rachel Colquhoun", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "\u00c1ine O'Toole", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Thomas P. Peacock", - "author_inst": "Department of Infectious Disease, Imperial College London, London, UK & UK Health Security Agency, London, UK" - }, - { - "author_name": "Kate Twohig", - "author_inst": "UK Health Security Agency, London, UK" - }, - { - "author_name": "Simon Thelwall", - "author_inst": "UK Health Security Agency, London, UK" - }, - { - "author_name": "Gavin Dabrera", - "author_inst": "UK Health Security Agency, London, UK" - }, - { - "author_name": "Richard Myers", - "author_inst": "UK Health Security Agency, London, UK" - }, - { - "author_name": "- The COVID-19 genomics UK (COG-UK) consortium", - "author_inst": "" - }, - { - "author_name": "Nuno R. Faria", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK & MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics" - }, - { - "author_name": "Carmen Huber", - "author_inst": "BlueDot, Toronto, Canada" - }, - { - "author_name": "Isaac I. Bogoch", - "author_inst": "Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada & 16.\tDepartment of Medicine, Divisio" - }, - { - "author_name": "Kamran Khan", - "author_inst": "BlueDot, Toronto, Canada & Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada & Departme" - }, - { - "author_name": "Louis du Plessis", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - }, - { - "author_name": "Jeffrey C. Barrett", - "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK" - }, - { - "author_name": "David M. Aanensen", - "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK & Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Departmen" - }, - { - "author_name": "Wendy S. Barclay", - "author_inst": "Department of Infectious Disease, Imperial College London, London, UK" - }, - { - "author_name": "Meera Chand", - "author_inst": "UK Health Security Agency, London, UK" - }, - { - "author_name": "Thomas Connor", - "author_inst": "Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK & School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK & Qu" - }, - { - "author_name": "Nicholas J. Loman", - "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Marc A. Suchard", - "author_inst": "Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA" - }, - { - "author_name": "Oliver G. Pybus", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK & Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Moritz U.G. Kraemer", - "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.16.473063", "rel_title": "Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses", @@ -446086,6 +445271,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.21.21268077", + "rel_title": "Quantitative detection of SARS-CoV-2 Omicron variant in wastewater through allele-specific RT-qPCR", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268077", + "rel_abs": "On November 26, 2021, the World Health Organisation classified the B.1.1.529 SARS-CoV-2 variant as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect VOCs (Alpha and Delta), here we report three allele-specific RT-qPCR assays that can quantitatively detect and discriminate the Omicron BA.1 and BA.2 variants in wastewater. The first assay targets the nine-nucleotide deletion at the L24-A27S of the spike protein for detection of BA.2. The second targets the six-nucleotide deletion at 69-70 of the spike protein for detection of the Omicron BA.1 variant, and the third targets the stretch of mutations from Q493R to Q498R for simultaneous detection of both Omicron BA.1 and BA.2. This method is open-sourced, can be implemented using commercially available RT-qPCR protocols, and would be an important tool for tracking the introduction and spread of the Omicron variants BA.1 and BA.2 in communities for informed public health responses.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Federica Armas", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Fuqing Wu", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Franciscus Chandra", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Hongjie Chen", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Amy Xiao", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Mats Leifels", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" + }, + { + "author_name": "Desmond F J Chua", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" + }, + { + "author_name": "Germaine W C Kwok", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" + }, + { + "author_name": "Joey Y R Tay", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Claire Y J Lim", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" + }, + { + "author_name": "Eric J Alm", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.21.21268171", "rel_title": "Breakthrough Covid-19 infections during periods of circulating Beta, Delta and Omicron variants of concern, among health care workers in the Sisonke Ad26.COV2.S vaccine trial, South Africa", @@ -447464,41 +446720,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.17.21268007", - "rel_title": "Outpatient therapies for COVID-19: How do we choose?", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21268007", - "rel_abs": "BackgroundSeveral outpatient COVID-19 therapies have reduced hospitalization in randomized controlled trials. The choice of therapy may depend on drug efficacy, toxicity, pricing, availability, and access to administration infrastructure. To facilitate comparative decision making, we evaluated the efficacy of each treatment in clinical trials and then estimated the associated cost per hospitalization prevented.\n\nMethodsWherever possible, we obtained relative risk for hospitalization from published randomized controlled trials. Otherwise, we extracted data from press releases, conference abstracts, government submissions, or preprints. If more than one study was published, the results were meta-analyzed. Using relative risk, we estimated the number needed to treat (NNT), assuming a baseline hospitalization risk of 5%. Drug pricing was based on Canadian formularies, government purchases, or manufacturer estimates.\n\nAdministrative and societal costs were not included. Results will be updated online as new studies emerge or final publication numbers become available.\n\nResultsAt a 5% risk of hospitalization the estimated NNTs were: 87 for colchicine, 80 for fluvoxamine, 72 for inhaled corticosteroids, 24 for nirmatrelvir/ritonavir, 25 for sotrovimab, 24 for remdesivir, 29 for casirivimab/imdevimab, 29 for bamlanivimab/etesevimab and 52 for molnupiravir. Colchicine, fluvoxamine, inhaled corticosteroids, and nirmatrelvir/ritonavir had cost per hospitalization prevented point estimates below the CIHI estimated cost of hospitalization ($23000).\n\nInterpretationCanada is fortunate to have access to several effective outpatient therapies to prevent COVID-19 hospitalization. Given differences in efficacy, toxicity, cost and administration complexities, this assessment serves as one tool to help guide policy makers and clinicians in their treatment selection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Todd C Lee", - "author_inst": "McGill University, Montreal, Canada" - }, - { - "author_name": "Andrew M Morris", - "author_inst": "Sinai Health System, Toronto, Canada" - }, - { - "author_name": "Steven A Grover", - "author_inst": "McGill University, Montreal, Canada" - }, - { - "author_name": "Srinivas Murthy", - "author_inst": "University of British Columbia, Vancouver, Canada" - }, - { - "author_name": "Emily G McDonald", - "author_inst": "McGill University, Montreal, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.17.21267362", "rel_title": "The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020", @@ -448107,6 +447328,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.20.21267832", + "rel_title": "PREVALENCE AND PREDICTORS OF STRESS AMONG COVID 19 HEALTH WORKERS IN KABWE DISTRICT: A CROSS SECTIONAL STUDY", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21267832", + "rel_abs": "OBJECTIVEThis study aimed at determining the magnitude of stress among COVID-19 health workers in Kabwe district.\n\nMETHODSThe study was a cross-sectional study which recruited 138 health care workers managing COVID-19 cases in Kabwe. Data were collected through structured questionnaires and in-depth interviews. Quantitative data was analyzed using SPSS version 16 while qualitative data was analyzed using Nvivo8.\n\nRESULTSThe study obtained 100% responses from the respondents and the prevalence of stress among the respondents was 73%. The nurses were more perceived to experience stress compared to the pharmacy personnel (28% vs. 3%). Similarly, women displayed a higher likelihood of experiencing stress compared to men. Lack of support, increased workload and fear were among the factors leading to stress.\n\nCONCLUSIONThe study went out to determine stress among healthcare workers in Kabwe district. It was established that nurses were more vulnerable than groups. And women were found to be more stressed than men. It is therefore recommended that effective and meaningful interventions be put in place to mitigate the impact of long-term psychological distress and physical well-being in healthcare workers during the COVID-19 pandemic and future outbreaks.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of the studyC_ST_ABSO_LIA cross-sectional study method was employed; it does not assist in determining the cause and effect, in addition, the timing of the snapshot may not guarantee representation of the situation overtime. Therefore, there may be need to evaluate the effects of the COVID-19 pandemic on health workers mental requirements using a longitudinal study design.\nC_LIO_LIThere might have been bias from respondents as the outcomes were self-reported. However, irrespective of the aforementioned limitations, this is a novel study in Kabwe describing stress among health workers in the district during the COVID-19 pandemic.\nC_LIO_LIThe study grants access to initial evidence on stress among health workers managing the COVID-19 pandemic in Kabwe district, with the expectation of drawing the attention to legislators, health facility supervisors and those involved in the response to COVID-19 or impending epidemics.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Leah L. Mukwasa", + "author_inst": "Ministry of Health" + }, + { + "author_name": "Emmy Nkhama", + "author_inst": "Levy Mwanawasa Medical University" + }, + { + "author_name": "Mowa Zambwe", + "author_inst": "University of Lusaka; Workers Compensation Fund Control Board" + }, + { + "author_name": "Richard Mutemwa", + "author_inst": "University of Lusaka" + }, + { + "author_name": "Peter J. Chipimo", + "author_inst": "University of Lusaka; Zambia National Public Health Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.12.20.21268141", "rel_title": "Field evaluation of Rapid SARS-Cov2 Antigen screening test on self-collected deep throat saliva samples in Malaysia", @@ -449374,29 +448630,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.16.472976", - "rel_title": "Single Amino Acid Change Mutation in the Hydrophobic Core of the N-terminal Domain of P22 TSP affects the Proteins Stability.", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472976", - "rel_abs": "The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly shifted the attention of researchers to critically investigate most viruses to understand specific characteristics that impart their virulence. For instance, the SARS-CoV-2 has undergone several mutations, with some variants classified as \"variants of concern\", e.g., the Omicron and Delta variant of SARS-CoV-2 are known for their rapid transmission and antigenicity due to mutation in the Spike protein. P22 bacteriophage is a bacterial virus that has a tailspike protein (TSP) that performs similar functions as the Spike protein of SARS-COV-2. We previously carried out a site-directed mutagenesis of the P22 TSP to bear disruptive mutations in the hydrophobic core of the N-terminal Domain (NTD), then partially characterized the properties of the mutant TSPs. In this process, the valine patch (triple valine residues that formed a hydrophobic core) was replaced with charged amino acids (Asp or lysine) or hydrophobic amino acids (Leucine or isoleucine). Some of the mutant TSPs characterized showed significant differences in migration in both native and SDS-PAGE. Mutants with such disruptive mutation are known to show non-native properties, and as expected, most of these mutants obtained showed significantly different properties from the WT P22 TSP. In this work, we further characterized these mutant species by computational and in vitro assays to demonstrate the validity of our previous inference that the valine patch is a critical player in the stability of the N-terminal domain of the P22 TSP.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Joseph A Ayariga", - "author_inst": "Alabama State University" - }, - { - "author_name": "Robert Villafane", - "author_inst": "Alabama State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.16.473030", "rel_title": "Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections", @@ -450189,6 +449422,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.16.472880", + "rel_title": "Unraveling the antiviral activity of plitidepsin by subcellular and morphological analysis", + "rel_date": "2021-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472880", + "rel_abs": "The pandemic caused by the new coronavirus SARS-CoV-2 has made evident the need for broad-spectrum, efficient antiviral treatments to combat emerging and re-emerging viruses. Plitidepsin is an antitumor agent of marine origin that has also shown a potent pre-clinical efficacy against SARS-CoV-2. Plitidepsin targets the host protein eEF1A (eukaryotic translation factor 1 alpha 1) and affects viral infection at an early, post-entry step. Because electron microscopy is a valuable tool to study virus-cell interactions and the mechanism of action of antiviral drugs, in this work we have used transmission electron microscopy (TEM) to evaluate the effects of plitidepsin in SARS-CoV-2 infection in cultured Vero E6 cells 24 and 48h post-infection. In the absence of plitidepsin, TEM morphological analysis showed double-membrane vesicles (DMVs), organelles that support coronavirus genome replication, single-membrane vesicles with viral particles, large vacuoles with groups of viruses and numerous extracellular virions attached to the plasma membrane. When treated with plitidepsin, no viral structures were found in SARS-CoV-2-infected Vero E6 cells. Immunogold detection of SARS-CoV-2 nucleocapsid (N) protein and double-stranded RNA (dsRNA) provided clear signals in cells infected in the absence of plitidepsin, but complete absence in cells infected and treated with plitidepsin. The present study shows that plitidepsin completely blocks the biogenesis of viral replication organelles and the morphogenesis of virus progeny. Electron microscopy morphological analysis coupled to immunogold labeling of SARS-CoV-2 products offers a unique approach to understand how antivirals such as plitidepsin work.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Martin Sachse", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + }, + { + "author_name": "Raquel Tenorio", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + }, + { + "author_name": "Isabel Fernandez de Castro", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + }, + { + "author_name": "Jordana Munoz-Basagoiti", + "author_inst": "IrsiCaixa" + }, + { + "author_name": "Daniel Perez-Zsolt", + "author_inst": "Irsicaixa" + }, + { + "author_name": "Dalia Raich-Regue", + "author_inst": "IrsiCaixa" + }, + { + "author_name": "Jordi Rodo", + "author_inst": "IRTA-CRESA" + }, + { + "author_name": "Alejandro Losada", + "author_inst": "Pharma Mar" + }, + { + "author_name": "Pablo Aviles", + "author_inst": "Pharma Mar" + }, + { + "author_name": "Carmen Cuevas", + "author_inst": "Pharma Mar" + }, + { + "author_name": "Roger Paredes", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Joaquim Segales", + "author_inst": "IRTA-CReSA" + }, + { + "author_name": "Bonaventura Clotet", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Julia Vergara-Alert", + "author_inst": "IRTA-CRESA" + }, + { + "author_name": "Nuria Izquierdo-Useros", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Cristina Risco", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.16.473096", "rel_title": "The rise and fall of SARS-CoV-2 variants and the mutational profile of Omicron", @@ -451020,57 +450332,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.12.17.21267961", - "rel_title": "Pseudotyped SARS-CoV-2 Omicron variant exhibits significant escape from neutralization induced by a third booster dose of vaccination", - "rel_date": "2021-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267961", - "rel_abs": "The Omicron Variant of Concern (B.1.1.529) has spread internationally and is raising serious concerns about reduced vaccine efficacy and the increased risk of reinfection. We assessed the serum neutralizing activity using a pseudovirus-based neutralization assay in 292 healthcare workers who had received a homologous booster dose of BBIBP-CorV vaccine, 8 to 9 months after completing the priming two-dose vaccination schedule, to investigate whether the newly identified Omicron variant can escape serum antibody neutralization induced by the booster vaccination. The booster dose of BBIBP-CorV rapidly induced a significantly high level of humoral immune response, and the neutralization geometric mean titer (GMT) against the wild-type strain on day 28 after the booster dose was 294.85 (252.99-343.65), 6.1 times higher than the level on day 28 after the second dose. The neutralization against the Omicron variant was also improved by the booster vaccination, although the GMT showed an approximately 20.1-fold reduction to 14.66 (12.30-17.48) when compared with the wild-type strain. This study demonstrated that a booster dose of BBIBP-CorV led to a significant rebound in neutralizing immune response against SARS-CoV-2, while the Omicron variant showed partial resistance to neutralizing antibodies induced by the booster vaccination.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xiaoqi Yu", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Dong Wei", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Wenxin Xu", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Yulong Li", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Xinxin Li", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Xin-xin Zhang", - "author_inst": "Ruijin Hospital,Shanghai Jiaotong University, School of Medicine" - }, - { - "author_name": "Jieming Qu", - "author_inst": "Ruijin hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Zhitao Yang", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Erzhen Chen", - "author_inst": "Ruijin Hospital, Shanghai Jiao Tong University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.17.21267996", "rel_title": "Antibody Responses to 3rd Dose mRNA Vaccines in Nursing Home and Assisted Living Residents", @@ -451735,6 +450996,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.17.21267980", + "rel_title": "How effective is vaccination protection?", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267980", + "rel_abs": "This short note provides a simple static model to assess the effect of vaccination against hospitalization.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "milan batista", + "author_inst": "university of ljubljana" + }, + { + "author_name": "Aleksej Turnsek", + "author_inst": "university of ljubljana" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.16.21267904", "rel_title": "Deficits in hospital care among clinically vulnerable children aged 0 to 4 years during the COVID-19 pandemic", @@ -453234,41 +452518,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.17.21267986", - "rel_title": "Magnitude, global variation, and temporal development of the COVID-19 infection fatality burden", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267986", - "rel_abs": "How deadly is an infection with SARS-CoV-2 worldwide over time? This information is critical for developing and assessing public health responses on the country and global levels. However, imperfect data have been the most limiting factor for estimating the COVID-19 infection fatality burden during the first year of the pandemic. Here we leverage recently emerged compelling data sources and broadly applicable modeling strategies to estimate the crude infection fatality rate (cIFR) in 77 countries from 28 March 2020 to 31 March 2021, using 2.4 million reported deaths and estimated 435 million infections by age, sex, country, and date. The global average of all cIFR estimates is 1.2% (10th to 90th percentile: 0.2% to 2.4%). The cIFR varies strongly across countries, but little within countries over time, and it is often lower for women than men. Cross-country differences in cIFR are largely driven by the age structures of both the general and the truly infected population. While the broad trends and patterns of the cIFR estimates are more robust, we show that their levels are uncertain and sensitive to input data and modeling choices. In consequence, increased efforts at collecting high-quality data are essential for accurately estimating the cIFR, which is a key indicator for better understanding the health and mortality consequences of this pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christina Bohk-Ewald", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Enrique Acosta", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Tim Riffe", - "author_inst": "Universidad del Pais Vasco" - }, - { - "author_name": "Christian Dudel", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Mikko Myrskyla", - "author_inst": "Max Planck Institute for Demographic Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.17.21267655", "rel_title": "Presentation, characteristics, treatments and outcomes of mechanically ventilated patients with COVID-19 in Bulgaria", @@ -453941,6 +453190,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.15.21267860", + "rel_title": "The impact of COVID-19 restrictions on older adults' loneliness: Evidence from high-frequency panel data", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267860", + "rel_abs": "BACKGROUNDIt is unclear how strong and long lasting the effects of (recurring) COVID-19 restrictions are on older adults loneliness.\n\nMETHODS469 retired older Austrians (60+) provided 9,732 repeated observations of loneliness across 30 waves of the Austrian Corona Panel Project between March 2020 and March 2022. Ordinal mixed regression models were used to estimate the effect of the strictness of COVID-19 restrictions (stringency index, range=0-100) on older adults loneliness.\n\nRESULTSThe proportion of older adults who reported to be often lonely correlated (r=0.45) with the stringency index over time: both peaked during lock-downs (stringency index=82, often lonely=10-13%) and were lowest during the summer of 2020 (stringency index=36, often lonely=4-6%). Results from regression models indicate, that when the stringency index increased, loneliness also increased. In turn, as COVID-19 restrictions loosened, levels of loneliness decreased again. Older adults who lived alone were more affected in terms of loneliness by COVID-19 restriction measures compared to those living with others.\n\nCONCLUSIONSMore stringent COVID-19 restrictions were associated with an increased in (situational) loneliness among older adults in Austria, and this effect was stronger among those who lived alone. Efforts should be made to enable older adults, in particular those who live alone, to have save in-person contact during periods of strict pandemic restriction measures.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erwin Stolz", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Hannes Mayerl", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Wolfgang Freidl", + "author_inst": "Medical University of Graz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.14.21251883", "rel_title": "S Gene Target Failure (SGTF) in Commercial Multiplex RT-PCR assay as indicator to detect SARS-CoV-2 VOC B.1.1.7 lineage in Tamil Nadu, India", @@ -454932,41 +454208,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.12.15.472822", - "rel_title": "Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma", - "rel_date": "2021-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472822", - "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, will inform our understanding of this disease and its treatment.\n\nKey PointsO_LIPlasma from COVID-19 patients exhibits prominent protein- and peptide-level changes\nC_LIO_LIProteins from COVID-19 patient plasma exhibit prominent changes in several key posttranslational modifications\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Pavan Vedula", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hsin-Yao Tang", - "author_inst": "Wistar Institute" - }, - { - "author_name": "- UPenn COVID Processing Unit", - "author_inst": "" - }, - { - "author_name": "David Speicher", - "author_inst": "Wistar Institute" - }, - { - "author_name": "Anna Kashina", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.12.14.21267742", "rel_title": "Impact of Population Mixing Between a Vaccinated Majority and Unvaccinated Minority on Disease Dynamics. Implications for SARS-CoV-2", @@ -456047,6 +455288,20 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.14.472614", + "rel_title": "Viral infection engenders bona fide and bystander lung memory B cell subsets through permissive selection", + "rel_date": "2021-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472614", + "rel_abs": "Lung-resident memory B cells (MBCs) provide localized protection against reinfection in the respiratory airways. Currently, the biology of these cells remains largely unexplored. Here, we combined influenza and SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs regardless of antigen specificity. scRNA-seq analysis and confocal imaging revealed that two main transcriptionally distinct subsets of MBCs colonize the lung peribronchial niche after infection. These subsets arise from different progenitors and are both class-switched, somatically mutated and intrinsically biased in their differentiation fate towards plasma cells. Combined analysis of antigen-specificity and B cell receptor repertoire unveiled a highly permissive selection process that segregates these subsets into \"bona fide\" virus-specific MBCs and \"bystander\" MBCs with no apparent specificity for eliciting viruses. Thus, diverse transcriptional programs in MBCs are not linked to specific effector fates but rather to divergent strategies of the immune system to simultaneously provide rapid protection from reinfection while diversifying the initial B cell repertoire.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.14.472719", "rel_title": "Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2", @@ -457258,105 +456513,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267039", - "rel_title": "Anti-SARS-CoV-2 cellular immunity in 571 vaccinees assessed using an interferon-\u03b3 release assay", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267039", - "rel_abs": "Generation of antigen-specific memory T cells has been analyzed only for few coronavirus disease 2019 (COVID-19) vaccinees, whereas antibody titers have been serologically measured for a large number of individuals. Here, we assessed the anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular immune response in a large cohort using interferon (IFN)-{gamma} release assays (IGRAs) based on short-term whole blood culture. The study included 571 individuals who received the viral spike (S) protein-expressing BNT162b2 mRNA SARS-CoV-2 vaccine. Serum IgG titers against the receptor-binding domain (RBD) of S protein were measured. Samples of 28 vaccinees were subjected to flow cytometry analysis of T cells derived from short-term whole blood culture. IFN-{gamma} production triggered by S antigens was observed in most individuals 8 weeks after receiving the second dose of the vaccine, indicating acquisition of T cell memory responses. The frequencies of activated T cell subsets were strongly correlated with IFN-{gamma} levels, supporting the usability of our approach. S antigen-stimulated IFN-{gamma} levels were weakly correlated with anti-RBD IgG titers and associated with pre-vaccination infection and adverse reactions after the second dose. Our approach revealed cellular immunity acquired after COVID-19 vaccination, providing insights regarding the effects and adverse reactions of vaccination.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine and Department of Infectious Diseases, Keio University School of Medicine" - }, - { - "author_name": "Masatoshi Wakui", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine" - }, - { - "author_name": "Yoko Yatabe", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Terumichi Nakagawa", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Akiko Sakai", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Toshinobu Kurafuji", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Ayako Shibata", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine" - }, - { - "author_name": "Yukari Tomita", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine" - }, - { - "author_name": "Masayo Noguchi", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Akiko Tanabe", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Tomoko Arai", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Akemi Ohno", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Hiromitsu Yokota", - "author_inst": "Clinical Laboratory, Keio University Hospital" - }, - { - "author_name": "Shunsuke Uno", - "author_inst": "Department of Infectious Diseases, Keio University School of Medicine" - }, - { - "author_name": "Wakako Yamasawa", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine" - }, - { - "author_name": "Yasunori Sato", - "author_inst": "Department of Epidemiology and Preventive Medicine, Keio University School of Medicine" - }, - { - "author_name": "Mari Ikeda", - "author_inst": "Department of Microbiology and Immunology, Keio University School of Medicine" - }, - { - "author_name": "Akihiko Yoshimura", - "author_inst": "Department of Microbiology and Immunology, Keio University School of Medicine" - }, - { - "author_name": "Naoki Hasegawa", - "author_inst": "Department of Infectious Diseases, Keio University School of Medicine" - }, - { - "author_name": "Hideyuki Saya", - "author_inst": "Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine" - }, - { - "author_name": "Mitsuru Murata", - "author_inst": "Department of Laboratory Medicine, Keio University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.15.21267834", "rel_title": "Comparison of the Immunogenicity of five COVID-19 vaccines in Sri Lanka", @@ -458497,6 +457653,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.13.472433", + "rel_title": "Production and secretion of functional full-length SARS-CoV-2 spike protein in Chlamydomonas reinhardtii", + "rel_date": "2021-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.13.472433", + "rel_abs": "The spike protein is the major protein on the surface of coronaviruses. It is therefore the prominent target of neutralizing antibodies and consequently the antigen of all currently admitted vaccines against SARS-CoV-2. Since it is a 1273-amino acids glycoprotein with 22 N-linked glycans, the production of functional, full-length spike protein was limited to mammalian and insect cells, requiring complex culture media. Here we report the production of full-length SARS-CoV-2 spike protein - lacking the C-terminal membrane anchor - as a secreted protein in the prefusion-stabilized conformation in the unicellular green alga Chlamydomonas reinhardtii. We show that the spike protein is efficiently cleaved at the furin cleavage site during synthesis in the alga and that cleavage is abolished upon mutation of the multi-basic cleavage site. We could enrich the spike protein from culture medium by ammonium sulfate precipitation and demonstrate its functionality based on its interaction with recombinant ACE2 and ACE2 expressed on human 293T cells. Chlamydomonas reinhardtii is a GRAS organism that can be cultivated at low cost in simple media at a large scale, making it an attractive production platform for recombinant spike protein and other biopharmaceuticals in low-income countries.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna Kiefer", + "author_inst": "TU Kaiserslautern" + }, + { + "author_name": "Justus Niemeyer", + "author_inst": "TU Kaiserslautern" + }, + { + "author_name": "Anna Probst", + "author_inst": "TU Kaiserslautern" + }, + { + "author_name": "Gerhard Erkel", + "author_inst": "TU Kaiserslautern" + }, + { + "author_name": "Michael Schroda", + "author_inst": "TU Kaiserslautern" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2021.12.13.21267716", "rel_title": "Age-specific Contribution of Contacts to Transmission of SARS-CoV-2 in Germany", @@ -459520,97 +458711,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.10.21267596", - "rel_title": "MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267596", - "rel_abs": "The SARS-CoV-2 infections are still imposing a great public health challenge despite the recent developments in vaccines and therapy. Searching for diagnostic and prognostic methods that are fast, low-cost and accurate is essential for disease control and patient recovery. The MALDI-TOF mass spectrometry technique is rapid, low cost and accurate when compared to other MS methods, thus its use is already reported in the literature for various applications, including microorganism identification, diagnosis and prognosis of diseases. Here we developed a prognostic method for COVID-19 using the proteomic profile of saliva samples submitted to MALDI-TOF and machine learning algorithms to train models for COVID-19 severity assessment. We achieved an accuracy of 88.5%, specificity of 85% and sensitivity of 91.5% for classification between mild/moderate and severe conditions. Then, we tested the model performance in an independent dataset, we achieved an accuracy, sensitivity and specificity of 67.18, 52.17 and 75.60% respectively. Saliva is already reported to have high inter-sample variation; however, our results demonstrates that this approach has the potential to be a prognostic method for COVID-19. Additionally, the technology used is already available in several clinics, facilitating the implementation of the method. Further investigation using a bigger dataset is necessary to consolidate the technique.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Lucas C. Lazari", - "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Rodrigo M Zerbinati", - "author_inst": "Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of Sao Paulo, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Livia Rosa-Fernandes", - "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Veronica Feijoli Santiago", - "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Klaise F. Rosa", - "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Claudia Blanes Angeli", - "author_inst": "GlycoProteomics Laboratory, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Grabriela Schwab", - "author_inst": "Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of Sao Paulo, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Michelle Palmieri", - "author_inst": "Department of Stomatology, School of Dentistry, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Dmity J.S. Sarmento", - "author_inst": "Department of Stomatology, School of Dentistry, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Claudio R. F. Marinho", - "author_inst": "Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Janete Dias Almeida", - "author_inst": "Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, Sao Paulo State University, Sao Jose dos Campos, Brazil" - }, - { - "author_name": "Kelvin Kai-Wang To", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Simone Giannecchini", - "author_inst": "University of Florence" - }, - { - "author_name": "Carsten Wrenger", - "author_inst": "Unit for Drug Discovery, Department of Parasitology, ICB, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Herculano Martinho", - "author_inst": "Universidade Federal do ABC, Santo Andre, Brazil" - }, - { - "author_name": "Jose A. L. Lindoso", - "author_inst": "Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of Sao Paulo, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Edison Luiz Durigon", - "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" - }, - { - "author_name": "Paulo Henrique Braz-Silva", - "author_inst": "School of Dentistry University of Sao Paulo" - }, - { - "author_name": "Giuseppe Palmisano", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.13.21267657", "rel_title": "Simple decision rules to predict local surges in COVID-19 hospitalizations during the winter and spring of 2022", @@ -460391,6 +459491,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.13.21267723", + "rel_title": "Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267723", + "rel_abs": "ObjectiveThis study aimed to estimate the incidence of new diabetes mellitus (DM) and cardiovascular diseases (CVD) up to one year after Covid-19 compared with matched controls.\n\nMethodsA cohort study was conducted using electronic records for 1,473 family practices with a population of 14.9 million. Covid-19 patients without DM or CVD were individually matched with controls and followed up to October 2021. A difference-in-difference analysis estimated the net effect of Covid-19 allowing for baseline differences and covariates.\n\nResultsThere were 372,816 Covid-19 patients, with 2,935 CVD and 3,139 DM events, and 372,816 matched controls with 1,193 CVD and 1,861 DM events following the index date. Net incidence of DM increased in acute Covid-19 up to four weeks from index date (adjusted rate ratio, RR 1.71, 1.40 to 2.10) and remained elevated in post-acute (five to 12 weeks from index date; RR 1.17, 1.01 to 1.36) and long-Covid-19 (13 to 52 weeks, 1.20, 1.09 to 1.31). Acute Covid-19 was associated with net increased CVD incidence (RR 6.02, 95% confidence interval 4.84 to 7.47) including pulmonary embolism (RR 14.5, 7.72 to 27.4), atrial arrythmias (6.58, 3.78 to 11.4) and venous thromboses (5.44, 3.22 to 9.17). CVD incidence declined in post-acute Covid-19 (1.68, 1.41 to 2.01) and showed no net increase in long Covid-19 (0.95, 0.85 to 1.06).\n\nConclusionsDM incidence remains elevated up to one year following Covid-19. CVD is increased early after Covid-19 mainly from pulmonary embolism, atrial arrhythmias and venous thromboses.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Emma Rezel-Potts", + "author_inst": "King's College London" + }, + { + "author_name": "Abdel Douiri", + "author_inst": "King's College London" + }, + { + "author_name": "Xiaohui Sun", + "author_inst": "King's College London" + }, + { + "author_name": "Phillip J Chowienczyk", + "author_inst": "King's College London" + }, + { + "author_name": "Ajay M Shah", + "author_inst": "King's College London" + }, + { + "author_name": "Martin C Gulliford", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.10.21267619", "rel_title": "COVID-19 vaccine effectiveness against laboratory confirmed symptomatic SARS-CoV-2 infection, COVID-19 related hospitalizations and deaths, among individuals aged 65 years or more in Portugal: a cohort study based on data-linkage of national registries February-September 2021", @@ -461422,77 +460561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.10.21267607", - "rel_title": "High correlation between binding IgG (anti-RBD/S) and neutralizing antibodies against SARS-CoV-2 six months after vaccination", - "rel_date": "2021-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267607", - "rel_abs": "Vaccination is considered the most important measure to control the COVID-19 pandemic. Extensive follow-up studies with distinct vaccines and populations are able to promote robust and reliable data to better understand the effectiveness of this pharmacologic strategy. In this sense, we present data regarding binding and neutralizing antibodies throughout time, from vaccinated and previously infected (PI) health care workers (HCW) in Portugal. We analyzed serum samples of 132 HCW, vaccinated and with previous SARS-CoV-2 infection. Samples were collected before vaccination (baseline, M1), at second dose vaccine uptake (M2), and 25-70 days (M3) and 150-210 days (M4) after the second dose for vaccinated individuals. The IgG (anti-RBD/S) antibody geometric mean titer found on vaccinated HCW at M2 (814.7 AU/ml; 95% CI 649.8-1021.5) were significantly higher than those found on PI HCW at recruitment (M1) (252.6 AU/ml; 95% CI 108.7 - 587.1), and the neutralizing antibodies (nAb) were similar between these groups, 93.2 UI/ml (95% CI 73.2-118.5) vs. 84.1 UI/ml (95% CI 40.4-155.9), respectively. We detected about 10-fold higher IgG (anti-RBD/S) antibodies titers in M3 when compared with M2, with a slightly but significant decrease in titers from 36 days after the second dose vaccine uptake. The increase of nAb titers were correlated with IgG (anti-RBD/S) antibodies titers, however, contrasting to IgG (anti-RBD/S) antibodies titers, we did not detect a decrease in nAb titer from 36 days after a second vaccine dose uptake. At M4, was observed a decrease of 8-fold in binding IgG (anti-RBD/S) and nAb. No significant differences in antibody titers were observed by sex, age or chronic diseases. Our results suggest that IgG (anti-RBD/S) antibodies titers and nAb titers could be correlated, but ongoing follow up of the cohort, is required to better understand this correlation, and the duration of the immune response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Raquel Guiomar", - "author_inst": "National Institute of Health Dr. Ricardo Jorge" - }, - { - "author_name": "Ana Joao Santos", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Aryse Melo", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Ines Costa", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Rita Matos", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Ana Paula Rodrigues", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Irina Kislaya", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Anabela S Silva", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Carla Roque", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Carla Silva", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Joaquim Aguiar", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Fatima Graca", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Antonio Graca", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - }, - { - "author_name": "Ausenda Machado", - "author_inst": "Instituto Nacional de Saude Doutor Ricardo Jorge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.10.21267613", "rel_title": "The impact of remote home monitoring of people with COVID-19 using pulse oximetry: a national population and observational study.", @@ -462189,6 +461257,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.12.10.472066", + "rel_title": "Structure of the 5' untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.10.472066", + "rel_abs": "2-5-Oligoadenylate synthetase 1 (OAS1) is one of the key enzymes driving the innate immune system response to SARS-CoV-2 infection whose activity has been related to COVID-19 severity. In particular, OAS1 is a sensor of endogenous RNA that triggers the 2-5 oligoadenylate/RNase L pathway in response to viral infections, ultimately activating the RNA-Lyase which cleaves endogenous and exogenous RNA impeding the viral maturation. Upon SARS-CoV-2 infection, OAS1 is responsible for the recognition of viral RNA and has been shown to possess a particularly high sensitivity for the 5-untranslated (5-UTR) RNA region, which is organized in a double-strand stem loop motif (SLA). Since the structure of the nucleic acid/protein complex has not been resolved, here we report its structure obtained by molecular modeling, including enhanced sampling approaches. We also pinpoint that the SL1 region enhances the interaction network with the enzyme, promoting specific hydrogen bonds, absent in normal double strand RNA fragments, hence rationalizing the high affinity for OAS1.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Emmanuelle Bignon", + "author_inst": "Universite de Lorraine" + }, + { + "author_name": "Tom Miclot", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Alessio Terenzi", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Giampaolo Barone", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Antonio Monari", + "author_inst": "Universite de Paris and CNRS, ITODYS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.12.10.472151", "rel_title": "Quantification of nuclear transport inhibition by SARS-CoV-2 ORF6 using a broadly applicable live-cell dose-response pipeline", @@ -463232,161 +462335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.09.21267557", - "rel_title": "Neutralizing Antibody Activity Against SARS-CoV-2 Variants in Gestational Age-Matched Mother-Infant Dyads", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267557", - "rel_abs": "Pregnancy confers unique immune responses to infection and vaccination across gestation. To date, there is limited data comparing vaccine versus infection-induced nAb to COVID-19 variants in mothers during pregnancy. We analyzed paired maternal and cord plasma samples from 60 pregnant individuals. Thirty women vaccinated with mRNA vaccines were matched with 30 naturally infected women by gestational age of exposure. Neutralization activity against the five SARS-CoV-2 Spike sequences was measured by a SARS-CoV-2 pseudotyped Spike virion assay. Effective nAbs against SARS-CoV-2 were present in maternal and cord plasma after both infection and vaccination. Compared to wild type or Alpha variant Spike, these nAbs were less effective against the Kappa, Delta, and Mu Spike variants. Vaccination during the third trimester induced higher nAb levels at delivery than infection during the third trimester. In contrast, vaccine-induced nAb levels were lower at the time of delivery compared to infection during the first trimester. The transfer ratio (cord nAb level/maternal nAb level) was greatest in mothers vaccinated in the second trimester. SARS-CoV-2 vaccination or infection in pregnancy elicit effective nAbs with differing neutralization kinetics that is impacted by gestational time of exposure. Vaccine induced neutralizing activity was reduced against the Delta, Mu, and Kappa variants.\n\nGraphic abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=155 HEIGHT=200 SRC=\"FIGDIR/small/21267557v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@4225dborg.highwire.dtl.DTLVardef@c35b5borg.highwire.dtl.DTLVardef@1a2d180org.highwire.dtl.DTLVardef@6863c2_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Yusuke Matsui", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Lin Li", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Mary Prahl", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Arianna G. Cassidy", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Nida Ozarslan", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Yarden Golan", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Veronica J. Gonzalez", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Christine Y. Lin", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Unurzul Jigmeddagva", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Megan A. Chidboy", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Mauricio Montano", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Taha Y. Taha", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Mir M. Khalid", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Bharath Sreekumar", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Jennifer M. Hayashi", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Pei-Yi Chen", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "G. Renuka Kumar", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Lakshmi Warrier", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Alan H.B. Wu", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Dongli Song", - "author_inst": "Santa Clara Valley Medical Center" - }, - { - "author_name": "Priya Jegatheesan", - "author_inst": "Santa Clara Valley Medical Center" - }, - { - "author_name": "Daljeet S. Rai", - "author_inst": "Stanford University" - }, - { - "author_name": "Balaji Govindaswami", - "author_inst": "Marshall University Joan C Edwards School of Medicine" - }, - { - "author_name": "Jordan Needens", - "author_inst": "Marshall University Joan C Edwards School of Medicine" - }, - { - "author_name": "Monica Rincon", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Leslie Myatt", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Ifeyinwa V. Asiodu", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Valerie J. Flaherman", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Yalda Afshar", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Vanessa L. Jacoby", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Amy P. Murtha", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Joshua F. Robinson", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Warner C. Greene", - "author_inst": "Gladstone Institues" - }, - { - "author_name": "Stephanie L. Gaw", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.08.21267452", "rel_title": "Accuracy and usability of saliva and nasal rapid antigen self-testing for detection of SARS-CoV-2 infection in the general population: a head-to-head comparison", @@ -464123,6 +463071,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.09.21267565", + "rel_title": "CalScope: Monitoring SARS-CoV-2 Seroprevalence from Vaccination and Prior Infection in Adults and Children in California May 2021 to July 2021", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267565", + "rel_abs": "ImportanceUnderstanding how SARS-CoV-2 seroprevalence varies regionally across California is critical to the public health response to the pandemic.\n\nObjectiveTo estimate how many Californians have antibodies against SARS-CoV-2 from prior infection or vaccination.\n\nDesignWave 1 of CalScope: a repeated cross-sectional serosurvey of adults and children enrolled between April 20, 2021 and June 16, 2021.\n\nSettingA population-based random sample of households in seven counties in California (Alameda, El Dorado, Kern, Los Angeles, Monterey, San Diego, and Shasta) were invited to complete an at-home SARS-CoV-2 antibody test and survey instrument.\n\nParticipantsInvitations were sent to 200,000 randomly selected households in the seven counties. From each household, 1 adult (18 years and older) and 1 child (aged 6 months to 17 years) could enroll in the study. There were no exclusion criteria.\n\nMain Outcome(s) and MeasuresAll specimens were tested for antibodies against the nucleocapsid and spike proteins of SARS-CoV-2. The primary outcome was serostatus category, which was determined based on antibody test results and self-reported vaccination status: seronegative, antibodies from infection only, antibodies from infection and vaccination, and antibodies from vaccination alone. We used inverse probability of selection weights and iterative proportional fitting to account for non-response.\n\nResults11,161 households enrolled in wave 1 of CalScope, with 7,483 adults and 1,375 children completing antibody testing. As of June 2021, 27% (95%CI [23%, 31%]) of adults and 30% (95%CI [24%, 36%]) of children had evidence of prior SARS-CoV-2 infection; 33% (95%CI [28%, 37%]) of adults and 57% (95%CI [48%, 66%]) of children were seronegative. Serostatus varied regionally. Californians 65 years or older were most likely to have antibodies from vaccine alone (59%; 95%CI [48%, 69%]) and children between 5-11 years old were most likely to have antibodies from prior infection alone (36%; 95%CI [21%, 52%]).\n\nConclusions and RelevanceAs of June 2021, a third of adults in California and most children under 18 remained seronegative. Seroprevalence varied regionally and by demographic group, suggesting that some regions or populations might remain more vulnerable to subsequent surges than others.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the prevalence of vaccine and infection derived antibodies against SARS-CoV-2 in adults and children in California?\n\nFindingsIn this population-based serosurvey that included 11,161 households, as of June 2021, 33% of adults and 57% of children were seronegative; 18% of adults and 26% of children had antibodies from infection alone; 9% of adults and 5% of children had antibodies from both infection and vaccination; and 41% of adults and 13% of children had antibodies from vaccination alone.\n\nMeaningSerostatus varied considerably across geographic regions, suggesting that certain areas might be at increased risk for future COVID-19 surges.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Megha L. Mehrotra", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Esther Lim", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Katherine Lamba", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Amanda Kamali", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Kristina W. Lai", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Erika Meza", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Irvin Szeto", + "author_inst": "Stanford University" + }, + { + "author_name": "Peter Robinson", + "author_inst": "Enable Biosciences" + }, + { + "author_name": "Cheng-ting Tsai", + "author_inst": "Enable Biosciences" + }, + { + "author_name": "David Gebhart", + "author_inst": "Enable Biosciences" + }, + { + "author_name": "Noemi Fonseca", + "author_inst": "Enable Biosciences" + }, + { + "author_name": "Andrew B. Martin", + "author_inst": "Stanford University" + }, + { + "author_name": "Catherine Ley", + "author_inst": "Stanford University" + }, + { + "author_name": "Steve Scherf", + "author_inst": "Gauss Surgical" + }, + { + "author_name": "James Watt", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "David Seftel", + "author_inst": "Enable Biosciences" + }, + { + "author_name": "Julie Parsonnet", + "author_inst": "Stanford University" + }, + { + "author_name": "Seema Jain", + "author_inst": "California Department of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.08.21267162", "rel_title": "Evaluating the number of unvaccinated people needed to exclude to prevent SARS-CoV-2 transmissions", @@ -465430,33 +464465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.12.09.21267022", - "rel_title": "(SARS-CoV-2) COVID 19: Genomic surveillance and evaluation of the impact on the population speaker of indigenous language in Mexico", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267022", - "rel_abs": "The importance of the working document is that it allows the analysis of information and cases associated with (SARS-CoV-2) COVID-19, based on the daily information generated by the Government of Mexico through the Secretariat of Health, responsible for the Epidemiological Surveillance System for Viral Respiratory Diseases (SVEERV). The information in the SVEERV is disseminated as open data, and the level of information is displayed at the municipal, state and national levels. On the other hand, the monitoring of the genomic surveillance of (SARS-CoV-2) COVID-19, through the identification of variants and mutations, is registered in the database of the Information System of the Global Initiative on Sharing All Influenza Data (GISAID) based in Germany. These two sources of information SVEERV and GISAID provide the information for the analysis of the impact of (SARS-CoV-2) COVID-19 on the population in Mexico. The first data source identifies information, at the national level, on patients according to age, sex, comorbidities and COVID-19 presence (SARS-CoV-2), among other characteristics. The data analysis is carried out by means of the design of an algorithm applying data mining techniques and methodology, to estimate the case fatality rate, positivity index and identify a typology according to the severity of the infection identified in patients who present a positive result. for (SARS-CoV-2) COVID-19. From the second data source, information is obtained worldwide on the new variants and mutations of COVID-19 (SARS-CoV-2), providing valuable information for timely genomic surveillance. This study analyzes the impact of (SARS-CoV-2) COVID-19 on the indigenous language-speaking population, it allows us to provide information, quickly and in a timely manner, to support the design of public policy on health.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Carlos Medel Ramirez", - "author_inst": "Universidad Veracruzana / IIESES" - }, - { - "author_name": "Hilario Medel-Lopez", - "author_inst": "Universidad Veracruzana / Instituto de Antropologia" - }, - { - "author_name": "Jennifer Lara-Merida", - "author_inst": "Universidad de Xalapa / Facultad de Derecho" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.12.09.21267203", "rel_title": "Reduced Odds of SARS-CoV-2 Reinfection after Vaccination among New York City Adults, June-August 2021", @@ -466253,6 +465261,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.08.471664", + "rel_title": "Combinatorial mRNA vaccination enhances protection against SARS-CoV-2 delta variant", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.08.471664", + "rel_abs": "Emergence of SARS-CoV-2 variants of concern (VOC), including the highly transmissible delta strain, has posed challenges to current COVID-19 vaccines that principally target the viral spike protein (S). Here, we report a nucleoside-modified mRNA vaccine that expresses the more conserved viral nucleoprotein (mRNA-N). We show that mRNA-N alone was able to induce a modest but significant control of SARS-CoV-2 in mice and hamsters. Critically, by combining mRNA-N with the clinically approved S-expressing mRNA vaccine (mRNA-S-2P), we found that combinatorial mRNA vaccination (mRNA-S+N) led to markedly enhanced protection against the SARS-CoV-2 delta variant compared to mRNA-S. In a hamster model, we demonstrated that while mRNA-S alone elicited significant control of the delta strain in the lungs ([~]45-fold reduction in viral loads compared to un-vaccinated control), its effectiveness in the upper respiratory tract was weak, whereas combinatorial mRNA-S+N vaccination induced markedly more robust control of the delta variant infection in the lungs ([~]450-fold reduction) as well as in the upper respiratory tract ([~]20-fold reduction). Immune analyses indicated that induction of N-specific immunity as well as augmented S-specific T-cell response and neutralizing antibody activity were collectively associated the enhanced protection against SARS-CoV-2 delta strain by combinatorial mRNA vaccination. These findings suggest that the combined effects of protection in the lungs and upper respiratory tract could both reduce the risk of severe disease as well as of infection and transmission.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Renee L Hajnik", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jessica A Plante", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yuejin Liang", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Mohamad-Gabriel Alameh", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jinyi Tang", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Chaojie Zhong", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Awadalkareem Adam", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Dionna Scharton", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Grace H Rafael", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yang Liu", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Nicholas C Hazell", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jiaren Sun", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Lynn Soong", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Tian Wang", + "author_inst": "The University of Texas Medical Branch" + }, + { + "author_name": "Jie Sun", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Drew Weissman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott C Weaver", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Kenneth S Plante", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Haitao Hu", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.07.471588", "rel_title": "Orally administered epeleuton inhibits SARS-CoV-2 viral load, replication and pathology in the Syrian Hamster model", @@ -467276,37 +466379,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.09.471953", - "rel_title": "The Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614 Mutant: Conformational Plasticity and Frustration-Driven Allostery as Energetic Drivers of Highly Transmissible Spike Variant", - "rel_date": "2021-12-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.09.471953", - "rel_abs": "The structural and functional studies of the SARS-CoV-2 spike protein variants revealed an important role of the D614G mutation that is shared across many variants of concern(VOCs), suggesting the effect of this mutation on the enhanced virus infectivity and transmissibility. The recent structural and biophysical studies provided important evidence about multiple conformational substates of the D614G spike protein. The development of a plausible mechanistic model which can explain the experimental observations from a more unified thermodynamic perspective is an important objective of the current work. In this study, we employed efficient and accurate coarse-grained simulations of multiple structural substates of the D614G spike trimers together with the ensemble-based mutational frustration analysis to characterize the dynamics signatures of the conformational landscapes. By combining the local frustration profiling of the conformational states with residue-based mutational scanning of protein stability and network analysis of allosteric interactions and communications, we determine the patterns of mutational sensitivity in the functional regions and sites of variants. We found that the D614G mutation may induce a considerable conformational adaptability of the open states in the SARS-CoV-2 spike protein without compromising folding stability and integrity of the spike protein. The results suggest that the D614G mutant may employ a hinge-shift mechanism in which the dynamic couplings between the site of mutation and the inter-protomer hinge modulate the inter-domain interactions, global mobility change and the increased stability of the open form. This study proposes that mutation-induced modulation of the conformational flexibility and energetic frustration at the inter-protomer interfaces may serve as an efficient mechanism for allosteric regulation of the SARS-CoV-2 spike proteins.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Steve Agajanian", - "author_inst": "Chapman University" - }, - { - "author_name": "Ryan Kassab", - "author_inst": "Chapman University" - }, - { - "author_name": "Keerthi Krishnan", - "author_inst": "Chapman University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.08.21267167", "rel_title": "Access to healthcare as an important moderating variable for understanding geography of immunity levels for COVID-19 - preliminary insights from Poland", @@ -467767,6 +466839,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.12.07.21267287", + "rel_title": "PROBABILITY OF HOSPITALIZATION AND DEATH AMONG COVID-19 PATIENTS WITH COMORBIDITY DURING OUTBREAKS OCCURRING IN MEXICO CITY.", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267287", + "rel_abs": "BackgroundWorldwide, it has been observed that there is a strong association between the severity of COVID-19 and with being over 40 years of age, having diabetes mellitus (DM), hypertension and/or obesity.\n\nObjectiveTo compare the probability of death caused by COVID-19 in patients with comorbidities during three periods defined for this study as follows: first wave (March 23 to July 12, 2020), interwave period (July 13 to October 25, 2020), and the second wave (October 26, 2020, to March 29, 2021) using the different fatality rates observed in Mexico City.\n\nMethodsThe cohort studied included individuals over 20 years of age. During the first wave (symptomatic), the interwave period, and the second wave (symptomatic and asymptomatic), participants were diagnosed using nasopharyngeal swabs taken in kiosks. Symptomatic individuals with risk factors for serious disease or death were referred to hospital. SARS-CoV-2 infection was defined by real time polymerase chain reaction in all hospitalized patients. All data from hospitalized patients and outpatients were added to the SISVER database.\n\nResultsThe total cohort size for this study was 2,260,156 persons (having a mean age of 43.1 years). Of these, 8.6% suffered from DM, 11.6% from hypertension, and 9.7% from obesity. Of the total of 2,260,156 persons, 666,694 tested positive (29.5%) to SARS CoV-2, (with a mean age of 45). During the first wave, 82,489 tested positive; in the interwave period, 112,115; and during the second wave, 472,090. That is, a considerable increase in the number of cases of infection was observed in all age groups between the first and second waves (an increase of +472% on the first wave).\n\nOf the infected persons, a total of 85,587 (12.8%) were hospitalized: 24,023 in the first wave (29.1% of those who tested positive in this period); 16,935 (15.1%) during the interwave period, and 44,629 (9.5%) in the second wave, which represents an increase of 85.77% on the first wave.\n\nOf the hospitalized patients, there were 42,979 deaths (50.2% of those hospitalized), in the first wave, 11,964 (49.8% of those hospitalized in this period), during the interwave period, 6,794 (40.1%), and in the second wave 24,221 (54.3%), an increase of +102.4% between the first wave and the second.\n\nWhile within the general population, the probability of a patient dying having both COVID-19 and one of the specified comorbidities (DM, obesity, or arterial hypertension) showed a systematic reduction across all age groups, the probability of death for a hospitalized patient with comorbidities increased across all age groups during the second wave. When comparing the fatality rate of hospitalized COVID-19 patients in the second wave with those of the first wave and the interwave period, a significant increase was observed across all age groups, even in individuals without comorbidities.\n\nConclusionThe data from this study show a considerable increase in the number of detected cases of infection in all age groups between the first and second waves. In addition, 12.8% of those infected were hospitalized for severe COVID-19, representing an increase of +85.9% from the first wave to the second. A high mortality rate was observed among hospitalized patients (>50%), as was a higher probability of death in hospitalized COVID-19 patients with comorbidities for all age groups during the second wave, although there had been a slight decrease during the interwave period.\n\nSUMMARY BOXO_ST_ABSWhat is already known?C_ST_ABSWorldwide the resurging of COVID-19 cases in waves has been observed. In Mexico, like in the rest of the world, we have observed surges of SARS CoV-2 infections, COVID-19 hospitalizations and fatal outcomes followed by decreases leading to local minima. Pre-existing health conditions such as being older, having diabetes mellitus (DM), hypertension and/or obesity has been observed to be associated with an increase in the severity of COVID-19.\n\nWhat are the new findings?O_LIBetween the first and second waves, considerable increases were observed in the number of detected cases of infection (+472%), in the number of hospitalized subjects (+85.9%), and the number of hospitalized subjects and deaths (+102.4%) in all age groups.\nC_LIO_LIWhen analysing only hospitalized individuals, with or without comorbidities, the Case Fatality Rate was high (50.2%), the probability of death increased considerably in all age groups between the first and second waves. This increase was more noticeable in those individuals with previously identified comorbidities (DM, hypertension, or obesity).\nC_LIO_LIAn increased probability of death among individuals without comorbidities was observed between the first and second waves.\nC_LI\n\nWhat do the new findings imply?During the second wave, demand for hospitalization increased, magnifying the impact of age and comorbidities as risk factors. This situation highlights the importance of decreasing the prevalence of comorbidities among the population.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jose Sifuentes-Osornio", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Ofelia Angulo-Guerrero", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "Guillermo de Anda-Jauregui", + "author_inst": "Instituto Nacional de Medicina Genomica" + }, + { + "author_name": "Juan Luis Diaz-De-Leon-Santiago", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "Enrique Hernandez-Lemus", + "author_inst": "Instituto Nacional de Medicina Genomica" + }, + { + "author_name": "Hector Benitez-Perez", + "author_inst": "Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, UNAM" + }, + { + "author_name": "Luis A. Herrera", + "author_inst": "Instituto Nacional de Medicina Genomica, Instituto de Investigaciones Biomedicas de la Universidad Autonoma de Mexico" + }, + { + "author_name": "Olivia Lopez-Arellano", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "Arturo Revuelta-Herrera", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "Ana R. Rosales-Tapia", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Manuel Suarez-Tapia", + "author_inst": "Instituto de Geografia, Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Rosaura Ruiz-Gutierrez", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "Claudia Sheinbaum-Pardo", + "author_inst": "Gobierno de la Ciudad de Mexico" + }, + { + "author_name": "David Kershenobich", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.06.471374", "rel_title": "Identifying protein sites contributing to vaccine escape via statistical comparisons of short-term molecular dynamics simulations", @@ -468594,189 +467737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.07.21267367", - "rel_title": "Diagnosis of COVID-19 Using CT image Radiomics Features: A Comprehensive Machine Learning Study Involving 26,307 Patients", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267367", - "rel_abs": "PurposeTo derive and validate an effective radiomics-based model for differentiation of COVID-19 pneumonia from other lung diseases using a very large cohort of patients.\n\nMethodsWe collected 19 private and 5 public datasets, accumulating to 26,307 individual patient images (15,148 COVID-19; 9,657 with other lung diseases e.g. non-COVID-19 pneumonia, lung cancer, pulmonary embolism; 1502 normal cases). Images were automatically segmented using a validated deep learning (DL) model and the results carefully reviewed. Images were first cropped into lung-only region boxes, then resized to 296x216 voxels. Voxel dimensions was resized to 1x1x1mm3 followed by 64-bin discretization. The 108 extracted features included shape, first-order histogram and texture features. Univariate analysis was first performed using simple logistic regression. The thresholds were fixed in the training set and then evaluation performed on the test set. False discovery rate (FDR) correction was applied to the p-values. Z-Score normalization was applied to all features. For multivariate analysis, features with high correlation (R2>0.99) were eliminated first using Pearson correlation. We tested 96 different machine learning strategies through cross-combining 4 feature selectors or 8 dimensionality reduction techniques with 8 classifiers. We trained and evaluated our models using 3 different datasets: 1) the entire dataset (26,307 patients: 15,148 COVID-19; 11,159 non-COVID-19); 2) excluding normal patients in non-COVID-19, and including only RT-PCR positive COVID-19 cases in the COVID-19 class (20,697 patients including 12,419 COVID-19, and 8,278 non-COVID-19)); 3) including only non-COVID-19 pneumonia patients and a random sample of COVID-19 patients (5,582 patients: 3,000 COVID-19, and 2,582 non-COVID-19) to provide balanced classes. Subsequently, each of these 3 datasets were randomly split into 70% and 30% for training and testing, respectively. All various steps, including feature preprocessing, feature selection, and classification, were performed separately in each dataset. Classification algorithms were optimized during training using grid search algorithms. The best models were chosen by a one-standard-deviation rule in 10-fold cross-validation and then were evaluated on the test sets.\n\nResultsIn dataset #1, Relief feature selection and RF classifier combination resulted in the highest performance (Area under the receiver operating characteristic curve (AUC) = 0.99, sensitivity = 0.98, specificity = 0.94, accuracy = 0.96, positive predictive value (PPV) = 0.96, and negative predicted value (NPV) = 0.96). In dataset #2, Recursive Feature Elimination (RFE) feature selection and Random Forest (RF) classifier combination resulted in the highest performance (AUC = 0.99, sensitivity = 0.98, specificity = 0.95, accuracy = 0.97, PPV = 0.96, and NPV = 0.98). In dataset #3, the ANOVA feature selection and RF classifier combination resulted in the highest performance (AUC = 0.98, sensitivity = 0.96, specificity = 0.93, accuracy = 0.94, PPV = 0.93, NPV = 0.96).\n\nConclusionRadiomic features extracted from entire lung combined with machine learning algorithms can enable very effective, routine diagnosis of COVID-19 pneumonia from CT images without the use of any other diagnostic test.", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Isaac Shiri", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Yazdan Salimi", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Abdollah Saberi", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Masoumeh Pakbin", - "author_inst": "Imaging Department, Qom University of Medical Sciences, Qum, Iran" - }, - { - "author_name": "Ghasem Hajianfar", - "author_inst": "Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran" - }, - { - "author_name": "Atlas Haddadi Avval", - "author_inst": "School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran" - }, - { - "author_name": "Amirhossein Sanaat", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Azadeh Akhavanallaf", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Shayan Mostafaei", - "author_inst": "Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Stockholm, Sweden" - }, - { - "author_name": "Zahra Mansouri", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Dariush Askari", - "author_inst": "Department of Radiology Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Mohammadreza Ghasemian", - "author_inst": "Department of Radiology, Shahid Beheshti Hospital, Qom University of Medical Sciences, Qum, Iran" - }, - { - "author_name": "Ehsan Sharifipour", - "author_inst": "Neuroscience Research Center, Qom University of Medical Sciences, Qum, Iran" - }, - { - "author_name": "Saleh Sandoughdaran", - "author_inst": "Mens Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Ahmad Sohrabi", - "author_inst": "Cancer control research center, Cancer control foundation, Iran University of medical sciences, Tehran, Iran" - }, - { - "author_name": "Elham Sadati", - "author_inst": "Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran" - }, - { - "author_name": "Somayeh Livani", - "author_inst": "Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran" - }, - { - "author_name": "Pooya Iranpour", - "author_inst": "Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran" - }, - { - "author_name": "Shahriar Kolahi", - "author_inst": "Department of Radiology, School of Medicine, Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Imam Khomeini Hospital, Tehran University " - }, - { - "author_name": "Bardia Khosravi", - "author_inst": "Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Maziar Khateri", - "author_inst": "Department of Medical Radiation Engineering, Science and Research Branch, Islamic Azad University, Tehran, Tehran, Iran" - }, - { - "author_name": "Salar Bijari", - "author_inst": "Department of Medical Physics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran" - }, - { - "author_name": "Mohammad Reza Atashzar", - "author_inst": "Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran" - }, - { - "author_name": "Sajad P. Shayesteh", - "author_inst": "Department of Physiology, Pharmacology and medical physics, Alborz University of Medical Sciences, Karaj, Iran" - }, - { - "author_name": "Mohammad Reza Babaei", - "author_inst": "Department of interventional radiology, Firouzgar hospital, Iran University of medical sciences, Tehran, Iran" - }, - { - "author_name": "Elnaz Jenabi", - "author_inst": "Research Centre for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Mohammad Hasanian", - "author_inst": "Department of Radiology, Arak University of Medical Sciences, Arak, Iran" - }, - { - "author_name": "Alireza Shahhamzeh", - "author_inst": "Clinical research development center, Qom University of Medical Sciences, Qum, Iran" - }, - { - "author_name": "Seyed Yaser Foroghi Gholami", - "author_inst": "Clinical research development center, Qom University of Medical Sciences, Qum, Iran" - }, - { - "author_name": "Abolfazl Mozafari", - "author_inst": "Department of Medical Sciences, Qom Branch, Islamic Azad University, Qum, Iran" - }, - { - "author_name": "Hesamaddin Shirzad-Aski", - "author_inst": "Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran" - }, - { - "author_name": "Fatemeh Movaseghi", - "author_inst": "Department of Medical Sciences, Qom Branch, Islamic Azad University, Qum, Iran" - }, - { - "author_name": "Rama Bozorgmehr", - "author_inst": "Clinical Research Development Unit, Shohadaye Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Neda Goharpey", - "author_inst": "Department of radiation oncology, Shohadaye Tajrish Hospital, Shahid Beheshti university of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Hamid Abdollahi", - "author_inst": "Department of Radiologic Technology, Faculty of Allied Medical Sciences, Kerman University of Medical Sciences, Kerman, Iran" - }, - { - "author_name": "Parham Geramifar", - "author_inst": "Research Center for Nuclear Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Amir Reza Radmard", - "author_inst": "Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Hossein Arabi", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - }, - { - "author_name": "Kiara Rezaei-Kalantari", - "author_inst": "Rajaie Cardiovascular, Medical & Research Center, Iran University of Medical Science, Tehran, Iran" - }, - { - "author_name": "Mehrdad Oveisi", - "author_inst": "Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Kings College London, London, United Kingdom" - }, - { - "author_name": "Arman Rahmim", - "author_inst": "Departments of Radiology and Physics, University of British Columbia, Vancouver BC, Canada" - }, - { - "author_name": "Habib Zaidi", - "author_inst": "Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.12.08.21267459", "rel_title": "Genetic overlap between idiopathic pulmonary fibrosis and COVID-19", @@ -469681,6 +468641,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.12.07.21267429", + "rel_title": "Clinical characteristics of Chilean patients with rheumatic diseases and COVID-19: data from the Covid-19 Global Rheumatology Alliance physician-reported registry", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267429", + "rel_abs": "ObjectiveThe coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), has registered more than 234 million confirmed cases and more than 4.7 million deaths throughout the world until October 2, 2021. During the last few months, a significant number of reports of COVID-19 in patients with rheumatic diseases have been published. In this study the objective is to report the clinical characteristics of Chilean patients with rheumatic diseases and COVID-19 reported in the \"Global Rheumatology Alliance\" (GRA) physician registration platform.\n\nMethodsChilean patients with rheumatic diseases and COVID-19 were included in the Covid-19 GRA physician-reported registry.\n\nResults54 patients were included. The most common primary rheumatic disease was rheumatoid arthritis (RA) with 28 cases (51.9%). 30 patients (55.6%) used corticosteroids, of which 20 (66.7%) used a dose of 10 mg or less. 33 patients (61.1%) only used conventional DMARDs, 4 (7.4%) only biological, and 6 (11.1%) the combination. A total of 35 patients (64.8%) had to be hospitalized. 2 patients (3.7%) died. 26 patients of the 35 hospitalized (74.2%) required some type of ventilatory support, of which 5 (19.2%) required non-invasive and 8 (30.8%) invasive mechanical ventilation or extracorporeal membrane oxygenation (ECMO).\n\nDiscussionMost of included Chilean rheumatic patients were hospitalized, with a low mortality rate but with a high percentage of patients requiring at least non-invasive mechanical ventilation.\n\nKey Points- The most common primary rheumatic disease was rheumatoid arthritis (RA) followed by lupus (LES)\n- Most of the included Chilean rheumatic patients were hospitalized, with a high percentage of patients requiring at least non-invasive mechanical ventilation, but with a low mortality rate.\n- Worsening of arthralgias or activation of the rheumatic disease was not reported.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Oriela Martinez", + "author_inst": "Hospital Padre Hurtado" + }, + { + "author_name": "Sebastian Ibanez", + "author_inst": "Hospital Padre Hurtado" + }, + { + "author_name": "Francisca Valenzuela", + "author_inst": "Hospital Padre Hurtado" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.12.03.471068", "rel_title": "The Petasites hybridus CO2-extract (Ze 339) blocks SARS-CoV-2 replication in vitro", @@ -470860,89 +469847,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.07.21267179", - "rel_title": "Significantly elevated antibody levels and neutralization titers in nursing home residents after SARS-CoV-2 BNT162b2 mRNA booster vaccination", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267179", - "rel_abs": "Nursing home (NH) residents have experienced significant morbidity and mortality to SARS-CoV-2 throughout the pandemic. Vaccines initially curbed NH resident morbidity and mortality, but antibody levels and protection have declined with time since vaccination, prompting introduction of booster vaccination. This study assesses humoral immune response to booster vaccination in 85 NH residents and 44 health care workers (HCW) that we have followed longitudinally since initial SARS-CoV-2 BNT162b2 mRNA vaccination. The findings reveal that booster vaccination significantly increased anti-spike, anti-receptor binding domain, and neutralization titers above the pre-booster levels in almost all NH residents and HCW to significantly higher levels than shortly after the completion of the initial vaccine series. These data support the CDC recommendation to offer vaccine boosters to HCWs and NH residents on an immunological basis. Notably, even the older, more frail and more multi-morbid NH residents have sizable antibody increases with boosting.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "David H. Canaday", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Oladayo A. Oyebanji", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Elizabeth M. White", - "author_inst": "Brown University School of Public Health" - }, - { - "author_name": "Debbie Keresztesy", - "author_inst": "CWRU" - }, - { - "author_name": "Michael Payne", - "author_inst": "CWRU" - }, - { - "author_name": "Dennis Wilk", - "author_inst": "CWRU" - }, - { - "author_name": "Lenore Carias", - "author_inst": "CWRU" - }, - { - "author_name": "Htin Aung", - "author_inst": "CWRU" - }, - { - "author_name": "Kerri St. Denis", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Maegan L. Sheehan", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Sarah D. Berry", - "author_inst": "Marcus Institute" - }, - { - "author_name": "Cheryl M. Cameron", - "author_inst": "CWRU" - }, - { - "author_name": "Mark J. Cameron", - "author_inst": "CWRU" - }, - { - "author_name": "Brigid M. Wilson", - "author_inst": "Cleveland VA" - }, - { - "author_name": "Alejandro B. Balazs", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Christopher L. King", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Stefan Gravenstein", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.07.21267293", "rel_title": "SPECIFIC DETECTION OF SARS-COV-2 B.1.1.529 (OMICRON) VARIANT BY FOUR RT-qPCR DIFFERENTIAL ASSAYS", @@ -471479,6 +470383,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.04.21267265", + "rel_title": "RT-PCR/MALDI-TOF diagnostic target performance reflects circulating SARS-CoV-2 variant diversity in New York City", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.04.21267265", + "rel_abs": "As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern (VOC) have emerged. New variants pose challenges for diagnostic platforms since sequence diversity can alter primer/probe binding sites (PBS), causing false-negative results. The Agena MassARRAY(R) SARS-CoV-2 Panel utilizes reverse-transcription polymerase chain reaction and mass-spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we utilize a dataset of 256 SARS-CoV-2-positive specimens collected between April 11, 2021-August 28, 2021 to evaluate target performance with paired sequencing data. During this timeframe, two targets in the N gene (N2, N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk (RR): 20.02; p<0.0001; 95% Confidence Interval (CI): 11.36-35.72). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3-mismatch to the N2 probe PBS and increases target dropout risk (RR: 11.92; p<0.0001; 95% CI: 8.17-14.06). These findings highlight the robust capability of Agena MassARRAY(R) SARS-CoV-2 Panel target results to reveal circulating virus diversity and underscore the power of multi-target design to capture VOC.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Matthew M. Hernandez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Radhika Banu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ana S. Gonzalez-Reiche", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brandon Gray", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Paras Shrestha", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Liyong Cao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Feng Chen", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Huanzhi Shi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ayman Hanna", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan David Ramirez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adriana van de Guchte", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert Sebra", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "- Mount Sinai Pathogen Surveillance Study Group", + "author_inst": "" + }, + { + "author_name": "Melissa R. Gitman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael D. Nowak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carlos Cordon-Cardo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ted E. Schutzbank", + "author_inst": "Agena Bioscience" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia M Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alberto E Paniz Mondolfi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.06.21267342", "rel_title": "Pharmacokinetics of \u03b2-d-N4-hydroxycytidine, the active metabolite of prodrug molnupiravir, in non-plasma compartments of patients with SARS-CoV-2 infection", @@ -472722,49 +471725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.05.21266089", - "rel_title": "Post-Vaccination Symptoms after A Third Dose of mRNA SARS-CoV-2 Vaccination in Patients with Inflammatory Bowel Disease", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.05.21266089", - "rel_abs": "Symptoms after SARS-CoV-2 primary vaccination among patients with inflammatory bowel disease (IBD) are generally of similar frequency, severity, and duration to those reported in the general population. The symptom profile after a 3rd mRNA vaccine dose in the predominantly immune-compromised IBD population is unknown. We aimed to assess symptomology after a 3rd or booster dose of mRNA vaccination in adults with IBD. We surveyed participants of the Coronavirus Risk Associations and Longitudinal Evaluation in IBD (CORALE-IBD) post-vaccination registry for symptom frequency and severity after a 3rd mRNA vaccine dose in an observational cohort study. In total, 524 participants (70% female, mean age 45 years) reported a third dose of mRNA vaccination through October 11, 2021. Overall, 41% reported symptoms after a third dose, with symptoms generally more frequent and more severe among participants younger than 55 years. The most frequent postvaccination symptoms were injection site pain (39%), fatigue or malaise (34%), and headache (23%). These symptoms were all less frequently reported after dose 3 than after dose 2. Gastrointestinal symptoms were reported by 8.8%, which was slightly more frequent than after dose 2 (7.8%). Those with severe symptoms after dose 2 were more likely to have severe symptoms after dose 3. These findings can reassure the IBD patient and provider communities that the likelihood and distribution of symptoms after a third mRNA vaccine dose are generally similar to those after a second dose, and that the frequency of postvaccination symptoms after dose 3 are generally lower than after dose 2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dalin Li", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Susan Cheng", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Philip Debbas", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Jonathan Braun", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Dermot P.B. McGovern", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Gil Y. Melmed", - "author_inst": "Cedars Sinai Medical Center" - }, - { - "author_name": "- CORALE-IBD Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.12.06.21267339", "rel_title": "Systematic review of cardiac adverse effects in children and young people un-der 18 years of age after SARS-CoV-2 vaccination", @@ -473317,6 +472277,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.03.470766", + "rel_title": "Pandemic-scale phylogenetics", + "rel_date": "2021-12-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.03.470766", + "rel_abs": "1.Phylogenetics has been central to the genomic surveillance, epidemiology and contact tracing efforts during the COVD-19 pandemic. But the massive scale of genomic sequencing has rendered the pre-pandemic tools inadequate for comprehensive phylogenetic analyses. Here, we discuss the phylogenetic package that we developed to address the needs imposed by this pandemic. The package incorporates several pandemic-specific optimization and parallelization techniques and comprises four programs: UShER, matOptimize, RIPPLES and matUtils. Using high-performance computing, UShER and matOptimize maintain and refine daily a massive mutation-annotated phylogenetic tree consisting of all SARS-CoV-2 sequences available in online repositories. With UShER and RIPPLES, individual labs - even with modest compute resources - incorporate newly-sequenced SARS-CoV-2 genomes on this phylogeny and discover evidence for recombination in real-time. With matUtils, they rapidly query and visualize massive SARS-CoV-2 phylogenies. These tools have empowered scientists worldwide to study the SARS-CoV-2 evolution and transmission at an unprecedented scale, resolution and speed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Cheng Ye", + "author_inst": "University of California San Deigo" + }, + { + "author_name": "Bryan Thornlow", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "Alexander Michael Kramer", + "author_inst": "Genomics Institute, University of California, Santa Cruz" + }, + { + "author_name": "Jakob McBroome", + "author_inst": "UC Santa Cruz" + }, + { + "author_name": "Angie S Hinrichs", + "author_inst": "University of California at Santa Cruz" + }, + { + "author_name": "Russell Corbett-Detig", + "author_inst": "UC Santa Cruz" + }, + { + "author_name": "Yatish Turakhia", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.01.21265957", "rel_title": "Long Term Humoral Immunity Decline in Hemodialysis Patients Following SARS-CoV-2 Vaccination", @@ -474400,49 +473403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.02.21267205", - "rel_title": "Time trends in social contacts of individuals according to comorbidity and vaccination status, before and during the COVID-19 pandemic: repeated cross-sectional population-based surveys", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267205", - "rel_abs": "BackgroundAs we are confronted with more transmissible/severe variants with immune escape and the waning of vaccine efficacy, it is particularly relevant to understand how the social contacts of individuals at greater risk of COVID-19 complications evolved over time. We described time trends in social contacts of individuals according to comorbidity and vaccination status before and during the first three waves of the COVID-19 pandemic in Quebec, Canada.\n\nMethodsWe used data from CONNECT, a repeated cross-sectional population-based survey of social contacts conducted before (2018/2019) and during the pandemic (April 2020 to July 2021). We recruited non-institutionalized adults from Quebec, Canada, by random digit dialling. We used a self-administered web-based questionnaire to measure the number of social contacts of participants (two-way conversation at a distance [≤]2 meters or a physical contact, irrespective of masking). We compared the mean number of contacts/day according to the comorbidity status of participants (pre-existing medical conditions with symptoms/medication in the past 12 months) and 1-dose vaccination status during the third wave. All analyses were performed using weighted generalized linear models with a Poisson distribution and robust variance.\n\nResultsA total of 1441 and 5185 participants with and without comorbidities, respectively, were included in the analyses. Contacts significantly decreased from a mean of 6.1 (95%CI 4.9-7.3) before the pandemic to 3.2 (95%CI 2.5-3.9) during the first wave among individuals with comorbidities, and from 8.1 (95%CI 7.3-9.0) to 2.7 (95%CI 2.2-3.2) among individuals without comorbidities. Individuals with comorbidities maintained fewer contacts than those without comorbidities in the second wave, with a significant difference before the Christmas 2020/2021 holidays (2.9 (95%CI 2.5-3.2) v 3.9 (95%CI 3.5-4.3); P<0.001). During the third wave, contacts were similar for individuals with (4.1, 95%CI 3.4- 4.7) and without comorbidities (4.5, 95%CI 4.1-4.9; P=0.27). This could be partly explained by individuals with comorbidities vaccinated with their first dose who increased their contacts to the level of those without comorbidities.\n\nConclusionsIt will be important to closely monitor COVID-19-related outcomes and social contacts by comorbidity and vaccination status to inform targeted or population-based interventions (e.g., booster doses of the vaccine).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Aurelie Godbout", - "author_inst": "Laval University, Quebec, Canada" - }, - { - "author_name": "Melanie Drolet", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval" - }, - { - "author_name": "Myrto Mondor", - "author_inst": "Centre de recherche du CHU de Quebec - Universite Laval" - }, - { - "author_name": "Marc Simard", - "author_inst": "Institut national de sante publique du Quebec" - }, - { - "author_name": "Chantal Sauvageau", - "author_inst": "Institut national de sante publique du Quebec" - }, - { - "author_name": "Gaston De Serres", - "author_inst": "Institut national de sante publique du Quebec" - }, - { - "author_name": "Marc Brisson", - "author_inst": "Laval University, Quebec, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.02.21267191", "rel_title": "Prevalence of SARS-CoV-2 infection among COVID-19 RT-PCR laboratory workers in Bangladesh", @@ -475315,6 +474275,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.01.21266680", + "rel_title": "A kinetic model considering the decline of antibody level and vaccination of COVID-19", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21266680", + "rel_abs": "In order to evaluate the decline in antibody levels and the impact of vaccination on the spread of the epidemic, we establish COVID-19 dynamic models that consider the decline in antibody levels and the effects of vaccination, and retrospectively evaluate the epidemic situation in England. Based on the epidemic data in England from September 1 to October 31, 2020, considering the continuous decline in the antibody level of COVID-19 recovers, an improved SEIR infectious disease dynamics model that considers the reinfection of recovers due to the decline in antibody levels is established. The kinetic parameters of the SEIR model are obtained by fitting. On this basis, a SEIRV infectious disease dynamic model with vaccination is established to study the impact of different vaccination rates and vaccine failure rates on the development of the epidemic in England. We obtain the lower the vaccine failure rate, the fewer new cases. When the vaccination rate is fixed at 0.005 (equivalent to 250000 people vaccinated every day), the peak of the epidemic will decrease with the decrease of vaccine failure rate. The peak value when the failure rate is 0.001 is 81.4% lower than the peak value when the failure rate is 0.01, and the peak value when the failure rate is 0.01 is 89.5% lower than the peak value when the failure rate is 0.02. When the failure rate is less than 0.01, the peak time will advance with the decrease of failure rate; when the failure rate is greater than 0.01, the peak time will be delayed with the decrease of failure rate; when the failure rate is 0.01, the peak time is 528 days later than that when the failure rate is 0.001 and 295 days later than that when the failure rate is 0.05. On the 60th day of vaccination, the vaccine failure rate of 0.002 decreases the number of cases by 5.8% compared with the vaccine failure rate of 0.01; on the 70th day of vaccination, the vaccine failure rate of 0.002 reduces the number of cases by 9.1% compared with the vaccine failure rate of 0.01. Therefore, with the extension of time, the vaccine with low failure rate has a more obvious effect on reducing the number of cases than the vaccine with high failure rate. When the vaccine failure rate is fixed at 0.005, we study the impact of different vaccination rates on the spread of the epidemic in England, the result shows that the peak of epidemic situation decreases with the increase of vaccination rate, and the peak time advance with the increase of vaccination rate, when the vaccination rate is 0.025, the peak decreases by 74.8% and the peak time was 114 days earlier than that when the vaccination rate is 0.005. Therefore, the higher the vaccine efficiency and vaccination rate, the lower the peak of the epidemic. On the basis of improving the effectiveness of vaccines, increasing the vaccination rate is of practical significance for controlling the spread of the epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chuan qing XU", + "author_inst": "Beijing University of Civil Engineering and Architecture" + }, + { + "author_name": "Xiaotong Huang", + "author_inst": "Beijing university of civil engineering and architecture" + }, + { + "author_name": "Zonghao Zhang", + "author_inst": "Beijinguniversity of civil engineering and architecture" + }, + { + "author_name": "Jingan Cui", + "author_inst": "Beijinguniversity of civil engineering and architecture" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.05.21267236", "rel_title": "Mental sequelae of the Covid-19 pandemic: Well-being one year into the crisis in children with and without complex medical histories and their parents", @@ -476166,53 +475157,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.01.470817", - "rel_title": "ScRNA-Seq study of neutrophils reveals vast heterogeneity and breadth of inflammatory responses in severe COVID-19 patients", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470817", - "rel_abs": "Severe cases of COVID-19 are characterized by dysregulated immune responses, but specific mechanisms contributing to the most severe outcomes remain unclear. Neutrophils are the most abundant leukocyte population in human hosts and reach markedly high numbers during severe COVID-19. However, a detailed examination of their responses has been largely overlooked in the COVID-19 literature to date. Here, we report for the first time a dedicated study of neutrophil responses using single-cell RNA sequencing (scRNA-Seq) of fresh leukocytes from 11 hospitalized adult patients with mild and severe COVID-19 disease and 5 healthy controls. We observed that neutrophils display a pronounced inflammatory profile, with dramatic disruption of predicted cell-cell interactions as the severity of the disease increases. We also identified unique mature and immature neutrophil subpopulations based on transcriptomic profiling, including an antiviral phenotype, and changes in the proportion of each population linked to the severity of the disease. Finally, pathway analysis revealed increased markers of oxidative phosphorylation and ribosomal genes, along with downregulation of many antiviral and host defense pathway genes during severe disease compared to mild infections. Collectively, our findings indicate that neutrophils are capable of mounting effective antiviral defenses but adopt a form of immune dysregulation characterized by excess cellular stress, thereby contributing to the pathogenesis of severe COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jintao Xu", - "author_inst": "University of Michigan/VA Ann Arbor Health System" - }, - { - "author_name": "Bing He", - "author_inst": "University of Michigan" - }, - { - "author_name": "Kyle Carver", - "author_inst": "University of Michigan" - }, - { - "author_name": "Debora Vanheyningen", - "author_inst": "University of Michigan" - }, - { - "author_name": "Brian Parkin", - "author_inst": "University of Michigan/VA Ann Arbor Health System" - }, - { - "author_name": "Lana Garmire", - "author_inst": "University of Michigan" - }, - { - "author_name": "Michal A Olszewski", - "author_inst": "University of Michigan/VA Ann Arbor Health System" - }, - { - "author_name": "Jane A Deng", - "author_inst": "University of Michigan/VA Ann Arbor Health System" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.01.470767", "rel_title": "A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike", @@ -476917,6 +475861,97 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.12.02.470987", + "rel_title": "Single immunization with recombinant ACAM2000 vaccinia viruses expressing the spike and the nucleocapsid proteins protect hamsters against SARS-CoV-2 caused clinical disease", + "rel_date": "2021-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.02.470987", + "rel_abs": "Increasing cases of SARS-CoV-2 breakthrough infections from immunization with predominantly spike protein based COVID-19 vaccines highlight the need for alternative vaccines using different platforms and/or antigens. In this study, we expressed SARS-CoV-2 spike and nucleocapsid proteins in a novel vaccinia virus ACAM2000 platform (rACAM2000). Following a single intramuscular immunization, the rACAM2000 co-expressing the spike and nucleocapsid proteins induced significantly improved protection against SARS-CoV-2 challenge in comparison to rACAM2000 expressing the individual proteins in a hamster model, as shown by reduced weight loss and quicker recovery time. The protection was associated with reduced viral loads, increased neutralizing antibody titre and reduced neutrophil-to-lymphocyte ratio. Thus, our study demonstrates that the rACAM2000 expressing a combination of the spike and nucleocapsid antigens is a promising COVID-19 vaccine candidate and further studies will investigate if the rACAM2000 vaccine candidate can induce a long lasting immunity against infection of SARS-CoV-2 variants of concern.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Jingxin Cao", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Yvon Deschambault", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Jessie Lynch", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Bryce Warner", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kevin Tierney", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Denise Huynh", + "author_inst": "Canadian Food Inspection Agency" + }, + { + "author_name": "Robert Vendramelli", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Nikesh Tailor", + "author_inst": "Canadian Food Inspection Agency" + }, + { + "author_name": "Stephanie Booth", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Babu Sajesh", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kathy Frost", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kyle LeBlanc", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Christine Layne", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Lisa Lin", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Daniel Beniac", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael Carpenter", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "David Safronetz", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Xuguang Li", + "author_inst": "Health Canada" + }, + { + "author_name": "Darwyn Kobasa", + "author_inst": "Public Health Agency of Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.01.21266982", "rel_title": "Humoral responses following SARS-CoV-2 breakthrough infection in COVID-19 vaccinated individuals", @@ -477848,33 +476883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.30.21267076", - "rel_title": "Accessibility of Canadian COVID-19 Testing Locations for People with Disabilities During the Third Wave of the COVID-19 Pandemic", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267076", - "rel_abs": "BackgroundCanadians with disabilities make up nearly a quarter of the population yet face barriers in accessing information about COVID-19 testing accessibility across the country.\n\nObjectiveNo known studies evaluate the online information about the accessibility of COVID-19 testing locations. This study aimed to understand the accessibility of COVID-19 testing sites in Canada based on online information in March 2021.\n\nMethodsKey accessibility features were identified to evaluate COVID-19 testing websites information on accessibility and data were extracted from the website to simulate the user experience of booking a COVID-19 test.\n\nResultsAll provinces and territories provided minimal accessibility information on their COVID-19 testing websites, except for Ontario. Out of 170 testing locations in Ontario, few had information about accessibility, with only 8.2% listing at least 3 of the 5 key accessibility features measured on their websites.\n\nConclusionsThis paper demonstrates that more than a year into the pandemic, there existed a clear lack of accessibility information for Canadian testing locations for people with disabilities.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sara Rotenberg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jane Cooper", - "author_inst": "University of Toronto Faculty of Law" - }, - { - "author_name": "Matthew B Downer", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.30.21267029", "rel_title": "Assessment of correlations between risk factors and symptom presentation among defined at-risk groups following a confirmed COVID-19 diagnosis", @@ -478479,6 +477487,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.29.21267009", + "rel_title": "Evaluation of Vaccination Strategies for the metropolitan area of Madrid", + "rel_date": "2021-12-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267009", + "rel_abs": "BackgroundThis work analyses the impact of different vaccination strategies on the propagation of COVID-19 within the Madrid metropolitan area starting the 27th of December 2020 and ending in the Summer of 2021. The predictions are based on simulation using EpiGraph, an agent-based COVID-19 simulator.\n\nMethodsWe briefly summarize the different interconnected models of EpiGraph and then we provide a comprehensive description of the vaccination model. We evaluate different vaccination strategies, and we validate the simulator by comparing the simulation results with real data from the metropolitan area of Madrid during the third wave.\n\nResultsWe consider the different COVID-19 propagation scenarios on a social environment consisting of the ten largest cities in the Madrid metropolitan area, with 5 million individuals. The results show that the strategy that fares best is to vaccinate the elderly first with the two doses spaced 56 days apart; this approach reduces the final infection rate and the number of deaths by an additional 6% and 3% with respect to vaccinating the elderly first at the interval between doses recommended by the vaccine producer.\n\nConclusionResults show that prioritizing the vaccination of young individuals would significantly increase the number of deaths. On the other hand, spacing out the first and second dose by 56 days would result in a slight reduction in the number of infections and deaths. The reason is the increase in the number of vaccinated individuals at any time during the simulation.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "David E. Singh", + "author_inst": "Universidad Carlos III de Madrid, Spain" + }, + { + "author_name": "Carmen Olmedo Luceron", + "author_inst": "Vaccine area. Spanish Health Ministry, Madrid. Spain" + }, + { + "author_name": "Aurora Limia Sanchez", + "author_inst": "Vaccine area. Spanish Health Ministry, Madrid. Spain" + }, + { + "author_name": "Miguel Guzman-Merino", + "author_inst": "Universidad Carlos III de Madrid, Spain" + }, + { + "author_name": "Christian Duran", + "author_inst": "Universidad Carlos III de Madrid, Spain" + }, + { + "author_name": "Concepcion Delgado-Sanz", + "author_inst": "CIBER en Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain; National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain." + }, + { + "author_name": "Diana Gomez-Barroso", + "author_inst": "CIBER en Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain; National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain." + }, + { + "author_name": "Jesus Carretero", + "author_inst": "Universidad Carlos III de Madrid, Spain" + }, + { + "author_name": "Maria Cristina Marinescu", + "author_inst": "Barcelona Supercomputing Center, Barcelona, Spain." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21267012", "rel_title": "Google Trends as a predictive tool for COVID-19 vaccinations in Italy: a retrospective infodemiological analysis.", @@ -479778,101 +478837,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.11.28.470250", - "rel_title": "Myeloid cell-driven nonregenerative pulmonary scarring is conserved in multiple nonhuman primate species regardless of SARS-CoV-2 infection modality", - "rel_date": "2021-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.28.470250", - "rel_abs": "The novel coronavirus SARS-CoV-2 has caused a worldwide pandemic resulting in widespread efforts in development of animal models that recapitulate human disease for evaluation of medical countermeasures, and to dissect COVID-19 immunopathogenesis. We tested whether route of experimental infection substantially changes COVID-19 disease characteristics in two species (Macaca mulatta; rhesus macaques; RM, Chlorocebus atheiops; African green monkeys; AGM) of nonhuman primates. Species-specific cohorts of RM and AGM Rhesus macaques (Macaca mulatta, RMs) and African green monkeys (Chlorocebus aethiops, AGMs) were experimentally infected with homologous SARS-CoV-2 by either direct mucosal instillation or small particle aerosol in route-discrete subcohorts. Both species demonstrated equivalent infection initially by either exposure route although the magnitude and duration of viral loading was greater in AGMs than that of the RM. Clinical onset was nearly immediate (+1dpi) in mucosally-exposed cohorts whereas aerosol-infected animals began to show signs +7dpi. Myeloid cell responses indicative of the development of pulmonary scarring and extended lack of regenerative capacity in the pulmonary compartment was a conserved pathologic response in both species by either exposure modality. This pathological commonality may be useful in future anti-fibrosis therapeutic evaluations and expands our understanding of how SARS-CoV-2 infection leads to ARDS and functional lung damage.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Alyssa C Fears", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Brandon J Beddingfield", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nicole R Chirichella", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nadia Slisarenko", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Stephanie Z Killeen", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Rachel K Redmann", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Kelly Goff", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Skye Spencer", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Breanna Picou", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nadia Golden", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Duane J Bush", - "author_inst": "Zalgen Laboratories" - }, - { - "author_name": "Luis M Branco", - "author_inst": "Zalgen Laboratories" - }, - { - "author_name": "Matthew L Boisen", - "author_inst": "Zalgen Laboratories" - }, - { - "author_name": "Hongmei Gao", - "author_inst": "Duke University" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Robert V Blair", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Lara A Doyle-Meyers", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Kasi E Russel-Lodrigue", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nicholas J Maness", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Chad J Roy", - "author_inst": "Tulane National Primate Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.24.469906", "rel_title": "Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines", @@ -480765,6 +479729,89 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.11.29.21267032", + "rel_title": "Use of heat-not-burn tobacco products, moderate alcohol drinking, and anti-SARS-CoV-2 IgG antibody titers after BNT162b2 vaccination among Japanese healthcare workers", + "rel_date": "2021-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267032", + "rel_abs": "BackgroundThe effect of heat-not-burn (HNB) tobacco product use and moderate alcohol drinking on immunogenicity to coronavirus disease (COVID-19) vaccines remain elusive. This study aimed to examine the association of tobacco product use and alcohol consumption with anti-SARS-CoV-2 spike IgG antibody titers after the BNT162b2 vaccine.\n\nMethodsParticipants were 3,457 fully vaccinated healthcare workers in the 4 national centers for advanced medical and research in Japan. Smoking status and alcohol consumption were assessed via a questionnaire, and anti-SARS-CoV-2 spike IgG titers were measured by chemiluminescent enzyme immunoassay using serum collected on the median of 64 days after the second vaccination. Multilevel linear regression models were used to estimate the geometric mean titers (GMT) and the ratios of means (RoM) between groups.\n\nResultsOf vaccinated participants, 99.5% (3,440/3,457) were seropositive. Compared with never-smokers (GMT=119), IgG antibody titers were significantly lower among HNB tobacco users (including those who also smoked cigarettes) (GMT=105; RoM=0.88 [95%CI: 0.78-0.99]) and exclusive cigarettes smokers (GMT=96; RoM=0.81 [95%CI: 0.71-0.92]). Compared with non-drinkers of alcohol (GMT=123), alcohol drinkers consuming <1 go/day (GMT=114; RoM=0.93 [95%CI: 0.88-0.98]), 1-1.9 go/day (GMT=105; RoM=0.85 [95%CI: 0.79-0.93]), and [≥]2 go/day (GMT=101; RoM=0.82 [95%CI: 0.72-0.94]) had significantly lower antibody titers (P for trend<0.01). Spline analysis showed a large reduction of antibody until around 1 go/day of alcohol consumption, and then they gradually decreased.\n\nConclusionsResults suggest that in addition to conventional cigarette smoking and heavy alcohol drinking, use of HNB tobacco products and moderate alcohol drinking may be predictors of lower immunological response to COVID-19 vaccine.\n\nKey MessagesO_LIEpidemiological evidence regarding the association of smoking status and alcohol drinking with COVID-19 vaccine-induced antibody levels is scarce.\nC_LIO_LIUsers of heat-not-burn (HNB) tobacco products, as well as cigarettes smokers, had lower antibody titers than never-smokers.\nC_LIO_LINot only high-dose but moderate-dose alcohol intake was also associated with decreased vaccine-induced antibody levels.\nC_LIO_LIHNB tobacco product use and moderate alcohol drinking may be modifiers of COVID-19 vaccine-induced immunogenicity.\nC_LI", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shohei Yamamoto", + "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Akihito Tanaka", + "author_inst": "Department of Laboratory Testing, Center Hospital of the National Center for the Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Koushi Yamaguchi", + "author_inst": "Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Tokyo, Japan" + }, + { + "author_name": "Kazue Ishitsuka", + "author_inst": "Department of social science, National Research Institute for Child Health and Development, Tokyo, Japan" + }, + { + "author_name": "Naho Morisaki", + "author_inst": "Department of social science, National Research Institute for Child Health and Development, Tokyo, Japan" + }, + { + "author_name": "Masayo Kojima", + "author_inst": "Department of Frailty Research, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan" + }, + { + "author_name": "Akihiko Nishikimi", + "author_inst": "Biosafety Division, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan" + }, + { + "author_name": "Haruhiko Tokuda", + "author_inst": "Bioresource Division, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan" + }, + { + "author_name": "Manami Inoue", + "author_inst": "Division of Prevention, National Cancer Center Institute for Cancer Control, Tokyo, Japan" + }, + { + "author_name": "Shiori Tanaka", + "author_inst": "Division of Prevention, National Cancer Center Institute for Cancer Control, Tokyo, Japan" + }, + { + "author_name": "Jun Umezawa", + "author_inst": "Division of Prevention, National Cancer Center Institute for Cancer Control, Tokyo, Japan" + }, + { + "author_name": "Ryo Okubo", + "author_inst": "Clinical Research & Education Promotion Division, National Center of Neurology and Psychiatry, Tokyo, Japan" + }, + { + "author_name": "Kunihiro Nishimura", + "author_inst": "Department of Preventive Medicine and Epidemiology, National Cerebral and Cardiovascular Center, Osaka, Japan" + }, + { + "author_name": "Maki Konishi", + "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Kengo Miyo", + "author_inst": "Center for Medical Informatics Intelligence, National Center for Global Health and Medicine, Tokyo, Japan" + }, + { + "author_name": "Tetsuya Mizoue", + "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.470421", "rel_title": "SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens", @@ -481644,113 +480691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.11.25.470011", - "rel_title": "Potent neutralizing anti-SARS-CoV-2 human antibodies cure infection with SARS-CoV-2 variants in hamster model", - "rel_date": "2021-11-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.25.470011", - "rel_abs": "Treatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants can escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent COVID-19 patient, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 Wuhan, alpha, beta, gamma and delta infection in vitro. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 g/ml, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Maya Imbrechts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Wim Maes", - "author_inst": "KU Leuven" - }, - { - "author_name": "Louanne Ampofo", - "author_inst": "KU Leuven" - }, - { - "author_name": "Nathalie Van den Berghe", - "author_inst": "KU Leuven" - }, - { - "author_name": "Bas Calcoen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Dominique Van Looveren", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sam Noppen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Kevin Hollevoet", - "author_inst": "KU Leuven" - }, - { - "author_name": "Thomas Vercruysse", - "author_inst": "KU Leuven" - }, - { - "author_name": "Xin Zhang", - "author_inst": "KU Leuven" - }, - { - "author_name": "Rana Abdelnabi", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Caroline Shi-Yan Foo", - "author_inst": "Katholieke Universiteit Leuven" - }, - { - "author_name": "Hendrik Jan Thibaut", - "author_inst": "KU Leuven" - }, - { - "author_name": "Dirk Jochmans", - "author_inst": "REGA Institute - KU Leuven" - }, - { - "author_name": "Karen Ven", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jeroen Lammertyn", - "author_inst": "KU Leuven" - }, - { - "author_name": "Karen Vanhoorelbeke", - "author_inst": "KU Leuven" - }, - { - "author_name": "Nico Callewaert", - "author_inst": "AZ Groeninge" - }, - { - "author_name": "Paul De Munter", - "author_inst": "UZ Leuven" - }, - { - "author_name": "Dominique Schols", - "author_inst": "KU Leuven" - }, - { - "author_name": "Johan Neyts", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Paul Declerck", - "author_inst": "KU Leuven" - }, - { - "author_name": "Nick Geukens", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.29.21266623", "rel_title": "Transient adverse events after REGN-CoV2 administration for mild COVID-19 patients and their potential predictive factors: a single center analysis", @@ -482331,6 +481271,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2021.11.26.21266650", + "rel_title": "Community healthcare workers' experiences during and after COVID-19 lockdown: a qualitative study from Aotearoa New Zealand", + "rel_date": "2021-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.26.21266650", + "rel_abs": "Shortly after the COVID-19 pandemic reached Aotearoa New Zealand, a stringent lockdown lasting seven weeks was introduced to manage community spread of the virus. This paper reports the findings of a qualitative study examining how lockdown policies impacted upon the lives of those caring for community-based patients. The study involved nationwide surveys and ethnographic interviews with 15 registered nurses (RN) employed in community settings, two community midwives, and five personal care assistants (PCAs).\n\nDuring the strict lockdown levels 4 and 3, RNs and PCAs in the community showed considerable courage in answering their \"call to duty\" by taking on heightened care responsibilities and going \"the extra mile\" to help others. They faced significant risks to personal and professional relationships when they were required to take on additional and complex responsibilities for community-based patients. Despite, and sometimes due to the hypervigilant monitoring of their personal protective equipment (PPE), the need to safeguard family and community members generated considerable stress and anxiety. Many also faced personal isolation and loneliness as a result of lockdown restrictions. Although care and kindness became social expectations throughout Aotearoa New Zealand during the lockdown, RNs and PCAs who were already doing care work in patient homes had to do more.\n\nThis article makes five core service delivery and policy recommendations for supporting community-based nurses and PCAs in respiratory disease pandemics: acknowledging the crucial role played by community-based carers and the associated stress and anxiety endured, through championing respect and compassion; demystifying the \"heroism\" or \"self-sacrifice\" projected onto care workers to facilitate boundary setting; the timely provision of adequate protective equipment; improving remuneration with adequate provision for time off; and regular counselling, peer support groups, and education on work-life balance delivered by support workers in recognition of stressors arising from these complex and isolated working conditions.\n\nWhat is known about the topicO_LINurses and personal care assistants play a pivotal role in community responses to pandemics.\nC_LIO_LIThe COVID-19 pandemic has intensified many community healthcare workers clinical duties.\nC_LIO_LIPandemics pose risks to healthcare workers physical and mental wellbeing.\nC_LI\n\nWhat this paper addsO_LICommunity healthcare workers pressured themselves to be a \"good carer\" or \"hero\" during the lockdown.\nC_LIO_LICaring for patients in the community also became about caring about patients, further intensifying workload.\nC_LIO_LIThe COVID-19 pandemic has negatively impacted community healthcare workers relationships, as well as their wellbeing. Impacts continued even once the virus was eliminated.\nC_LIO_LINeed for recognition of this workforce distinct from other care workers.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Eleanor HOLROYD", + "author_inst": "Auckland University of Technology" + }, + { + "author_name": "Nicholas J. LONG", + "author_inst": "London School of Economics and Political Science" + }, + { + "author_name": "Nayantara Sheoran APPLETON", + "author_inst": "Victoria University of Wellington" + }, + { + "author_name": "Sharyn Graham DAVIES", + "author_inst": "Monash University and Auckland University of Technology" + }, + { + "author_name": "Antje DECKERT", + "author_inst": "Auckland University of Technology" + }, + { + "author_name": "Edmond FEHOKO", + "author_inst": "University of Auckland" + }, + { + "author_name": "Megan LAWS", + "author_inst": "London School of Economics and Political Science" + }, + { + "author_name": "Nelly MARTIN-ANATIAS", + "author_inst": "Auckland University of Technology" + }, + { + "author_name": "Nikita SIMPSON", + "author_inst": "London School of Economics and Political Science" + }, + { + "author_name": "Rogena STERLING", + "author_inst": "University of Waikato" + }, + { + "author_name": "Susanna TRNKA", + "author_inst": "University of Auckland" + }, + { + "author_name": "Laumua TUNUFA'I", + "author_inst": "Auckland University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2021.11.25.21266251", "rel_title": "Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta Across Different Brazilian Regions", @@ -483574,53 +482577,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.24.21266820", - "rel_title": "Anatomy of the first six months of COVID-19 Vaccination Campaign in Italy", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266820", - "rel_abs": "We analyze the effectiveness of the first six months of vaccination campaign against SARS-CoV-2 in Italy by using a computational epidemic model which takes into account demographic, mobility, vaccines, as well as estimates of the introduction and spreading of the more transmissible Alpha variant. We consider six sub-national regions and study the effect of vaccines in terms of number of averted deaths, infections, and reduction in the Infection Fatality Rate (IFR) with respect to counterfactual scenarios with the actual non-pharmaceuticals interventions but no vaccine administration. Furthermore, we compare the effectiveness in counterfactual scenarios with different vaccines allocation strategies and vaccination rates. Our results show that, as of 2021/07/05, vaccines averted 29, 350 (IQR: [16, 454 - 42, 826]) deaths and 4, 256, 332 (IQR: [1, 675, 564 - 6, 980, 070]) infections and a new pandemic wave in the country. During the same period, they achieved a -22.2% (IQR: [-31.4%; -13.9%]) reduction in the IFR. We show that a campaign that would have strictly prioritized age groups at higher risk of dying from COVID-19, besides frontline workers, would have implied additional benefits both in terms of avoided fatalities and reduction in the IFR. Strategies targeting the most active age groups would have prevented a higher number of infections but would have been associated with more deaths. Finally, we study the effects of different vaccination intake scenarios by rescaling the number of available doses in the time period under study to those administered in other countries of reference. The modeling framework can be applied to other countries to provide a mechanistic characterization of vaccination campaigns worldwide.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nicol\u00f2 Gozzi", - "author_inst": "Networks and Urban Systems Centre, University of Greenwich, UK" - }, - { - "author_name": "Matteo Chinazzi", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" - }, - { - "author_name": "Jessica T. Davis", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" - }, - { - "author_name": "Kunpeng Mu", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" - }, - { - "author_name": "Ana Pastore y Piontti", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA" - }, - { - "author_name": "Nicola Perra", - "author_inst": "Networks and Urban Systems Centre, University of Greenwich, UK" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.24.21266809", "rel_title": "Pandemic inequity in a megacity: a multilevel analysis of individual, community, and health care vulnerability risks for COVID-19 mortality in Jakarta, Indonesia", @@ -484177,6 +483133,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.23.21266785", + "rel_title": "A RANDOMIZED CLINICAL TRIAL OF 2-WEEK METHOTREXATE DISCONTINUATION IN RHEUMATOID ARTHRITIS PATIENTS VACCINATED WITH INACTIVATED SARS-COV-2 VACCINE", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266785", + "rel_abs": "ObjectivesTo evaluate the effect on immunogenicity and safety of 2-week methotrexate(MTX) discontinuation after each dose of the Sinovac-CoronaVac vaccine versus MTX maintenance in rheumatoid arthritis(RA) patients.\n\nMethodsThis was a single-center, prospective, randomized, investigator-blinded, intervention study (#NCT04754698, CoronavRheum), including adult RA patients(stable CDAI<10, prednisone<7.5mg/day), randomized(1:1) to withdraw MTX(MTX-hold) for 2 weeks after each vaccine dose or maintain MTX(MTX-maintain), evaluated at D0, D28 and D69. Co-primary outcomes were anti-SARS-CoV-2 S1/S2 IgG seroconversion(SC) and neutralizing antibody(NAb) positivity at D69. Secondary outcomes were GMT and changes in disease activity scores. For immunogenicity analyses, we excluded patients with baseline positive IgG/NAb, and, for safety reasons, those unable to hold MTX twice(CDAI>10 at D28).\n\nResultsRandomization included 138 patients with 9 exclusions(5 COVID-19, 4 protocol violations). Safety evaluation included 60(MTX-hold) and 69(MTX-maintain) patients. Further exclusions consisted of 27 patients[13(21.7%) vs. 14(20.3%),p=0.848] with positive baseline IgG/NAb and 10 patients(21.3%) in MTX-hold with CDAI>10 at D28. At D69, a higher increase in SC[29(78.4%) vs 30(54.5%),p=0.019] was observed in MTX-hold(n=37) in comparison to MTX-maintain(n=55), with parallel augmentation in GMT[34.2(25.2-46.4) vs 16.8(11.9-23.6),p=0.006]. No differences were observed for NAb positivity[23(62.2%) vs 27(49.1%),p=0.217]. Longitudinal variations in disease activity scores were alike in both groups(CDAI,p=0.144; DAS28-CRP,p=0.718).\n\nConclusionWe provided novel data that 2-week MTX withdrawal after each vaccine dose improves anti-SARS-CoV-2 immunogenicity. The comparable longitudinal variations of disease activity in both groups suggest that discontinuation is a feasible and efficient strategy in well-controlled RA patients, and may be even safer for vaccines with longer interval between doses or single dose schedules.\n\nFundingFAPESP/CNPq/B3-Bolsa de Valores-Brasil.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Carlo Scognamiglio Renner Araujo", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Ana Cristina Medeiros-Ribeiro", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Carla G S Saad", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Karina Rossi Bonfiglioli", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Diogo Souza Domiciano", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Andrea Yukie Shimabuco", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Matheus Rodrigues Silva", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Emily Figueiredo Neves Yuki", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Sandra Gofinet Pasoto", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Tatiana Pedrosa", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Leonard de Vinci Kanda Kupa", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Gioanna Zou", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Rosa M. R. Pereira", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Clovis A Silva", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Nadia E Aikawa", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + }, + { + "author_name": "Eloisa Bonfa", + "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo-USP" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.11.21.21266561", "rel_title": "Reactogenicity of COVID-19 vaccine in hemodialysis patients: a single-center retrospective study", @@ -485200,89 +484235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.22.21266559", - "rel_title": "Factors associated with COVID-19 vaccine acceptance and hesitancy among residents of Northern California jails", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266559", - "rel_abs": "BackgroundCarceral facilities are high-risk settings for COVID-19 transmission. Understanding of factors associated with COVID-19 vaccine acceptance and hesitancy among incarcerated individuals is incomplete, especially for people living in jails.\n\nMethodsWe conducted a retrospective review of COVID-19 vaccination data from the electronic health record (EHR) of residents in two Northern California county jails to examine factors associated with vaccine uptake in this population. We additionally administered a survey in four jails to assess reasons for vaccine hesitancy, sources of COVID-19 information, and medical mistrust. We performed multivariate logistic regression to determine associations with vaccine uptake or hesitancy.\n\nResultsOf 2,584 jail residents offered a COVID-19 vaccine between March 19, 2021 and June 30, 2021, 1,464 (56.7%) accepted at least one dose. Among vaccinated residents, 538 (36.7%) initially refused the vaccine. Vaccine uptake was higher among older individuals, women, those with recent flu vaccination, and those living in shared cells or open dorms. Leading reasons for vaccine hesitancy included concerns around side effects and suboptimal efficacy. Television and friends/family were the most commonly cited and the most trusted sources of COVID-19 information, respectively. Vaccine acceptance was associated with increased trust in COVID-19 information sources and in medical personnel both in and out of jail.\n\nConclusionOngoing evidence-based COVID-19 vaccination efforts are needed in high-risk carceral settings. Effective interventions to improve vaccination rates in this population should utilize accessible and trusted sources of information to address concerns about vaccine side effects and efficacy and foster medical trust.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Yiran E Liu", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford, California, USA." - }, - { - "author_name": "Jillian Oto", - "author_inst": "Custody Health Services, Santa Clara Valley Health and Hospital System, San Jose, California, USA." - }, - { - "author_name": "John Will", - "author_inst": "Custody Health Services, Santa Clara Valley Health and Hospital System, San Jose, California, USA." - }, - { - "author_name": "Christopher LeBoa", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Alexis Doyle", - "author_inst": "Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Neil Rens", - "author_inst": "Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Shelley Aggarwal", - "author_inst": "Department of Pediatrics, Santa Clara Valley Health and Hospital System, San Jose, California, USA; Department of Medicine, Division of Custody Health, Santa Cl" - }, - { - "author_name": "Iryna Kalish", - "author_inst": "Custody Health Services, Santa Clara Valley Health and Hospital System, San Jose, California, USA." - }, - { - "author_name": "Marcela Rodriguez", - "author_inst": "Stanford Center for Clinical Research, Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Beruk Sherif", - "author_inst": "Stanford Center for Clinical Research, Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Chrisele Trinidad", - "author_inst": "Stanford Center for Clinical Research, Stanford University School of Medicine, Stanford, California, USA." - }, - { - "author_name": "Michael del Rosario", - "author_inst": "Division of Correctional Health Services, San Mateo County Health, Redwood City, California, USA." - }, - { - "author_name": "Sophie Allen", - "author_inst": "Stanford Law School, Stanford, California, USA; Department of Sociology, Stanford School of Humanities and Sciences, Stanford, California, USA." - }, - { - "author_name": "Robert Spencer", - "author_inst": "Division of Correctional Health Services, San Mateo County Health, Redwood City, California, USA." - }, - { - "author_name": "Carlos Morales", - "author_inst": "Division of Correctional Health Services, San Mateo County Health, Redwood City, California, USA." - }, - { - "author_name": "Alexander Chyorny", - "author_inst": "Department of Medicine, Division of Custody Health, Santa Clara Valley Health and Hospital System, San Jose, California, USA." - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.22.21266565", "rel_title": "Impacts of vaccination and asymptomatic testing on SARS-CoV-2 transmission dynamics in a university setting", @@ -486107,6 +485059,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.23.469695", + "rel_title": "Antiviral activity of molnupiravir precursor NHC against Variants of Concern (VOCs) and its therapeutic window in a human lung cell model", + "rel_date": "2021-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.23.469695", + "rel_abs": "Several regulatory agencies have either licensed or given emergency use approval for treatment of patients at risk of developing severe COVID-19 with the anti-viral drug, Molnupiravir. Recent trials involving Molnupiravir suggested the drug was not as efficacious as earlier studies suggested. This study aimed to: (i) determine the effectiveness of the Molnupiravir active metabolite (NHC) against different SARS-CoV-2 Variants of Concern (VoCs), (ii) establish the therapeutic window of NHC in a human lung cell model, and (iii) and evaluate the genetic barrier to resistance. Dose response assays were performed in parallel to determine the IC50 (the concentration required to inhibit virus titre by 50%) of NHC against different variants. Human ACE-2 A549 cells were treated with NHC at different time points either before, during or after infection with SARS-CoV-2. Multiple passaging in the presence or absence of drug was used to evaluate whether resistance occurred. To obtain genomic information, virus was sequenced at regular intervals. After 20 passages in the presence of the drug, dose response assays and sequencing showed the virus did not appear to have developed resistance. The drug had equivalent activity against four VOCs ranging from 0.04 to 0.16M IC50. The efficacy of the drug diminished when applied after 24 hours post-infection. Our results suggest that earlier administration in patients, perhaps pre- or post-exposure rather than symptom onset, would be a more effective treatment option.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tessa Prince", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Hannah Goldswain", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Rebekah Penrice-Randal", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Catherine Hartley", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Tom Fletcher", + "author_inst": "Liverpool School of Tropical Medicine, Liverpool, UK." + }, + { + "author_name": "Saye Khoo", + "author_inst": "Institute of systems, molecular and integrative biology, University of Liverpool, UK" + }, + { + "author_name": "Julian Alexander Hiscox", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.23.469747", "rel_title": "Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets", @@ -487010,37 +486005,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.24.469823", - "rel_title": "Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons", - "rel_date": "2021-11-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.24.469823", - "rel_abs": "As novel SARS-CoV-2 variants with different patterns of spike mutations have emerged, the susceptibility of these variants to neutralization by antibodies has been rapidly assessed. However, neutralization data are generated using different approaches and are scattered across different publications making it difficult for these data to be located and synthesized. The Stanford Coronavirus Resistance Database (CoV-RDB; https://covdb.stanford.edu) is designed to house comprehensively curated published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to monoclonal antibodies (mAbs), convalescent plasma (CP), and vaccinee plasma (VP). As of October 2021, CoV-RDB contains 186 publications including 64 (34%) containing 7,328 neutralizing mAb susceptibility results, 96 (52%) containing 11,390 neutralizing CP susceptibility results, and 125 (68%) containing 20,872 neutralizing VP results. The database also records which spike mutations are selected during in vitro passage of SARS-CoV-2 in the presence of mAbs and which emerge in persons receiving mAbs as treatment. The CoV-RDB interface interactively displays neutralizing susceptibility data at different levels of granularity by filtering and/or aggregating query results according to one or more experimental conditions. The CoV-RDB website provides a companion sequence analysis program that outputs information about mutations present in a submitted sequence and that also assists users in determining the appropriate mutation-detection thresholds for identifying non-consensus amino acids. The most recent data underlying the CoV-RDB can be downloaded in its entirety from a Github repository in a documented machine-readable format.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Philip L. Tzou", - "author_inst": "Stanford University" - }, - { - "author_name": "Kaiming Tao", - "author_inst": "Stanford University" - }, - { - "author_name": "Sergei L. Kosakovsky Pond", - "author_inst": "Temple University" - }, - { - "author_name": "Robert W. Shafer", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.11.17.21266461", "rel_title": "Space-time Classification Index for Assessing COVID-19 Hotspots", @@ -488017,6 +486981,93 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.19.469183", + "rel_title": "Self-assembling short immunostimulatory duplex RNAs with broad spectrum antiviral activity", + "rel_date": "2021-11-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.19.469183", + "rel_abs": "The current COVID-19 pandemic highlights the need for broad-spectrum antiviral therapeutics. Here we describe a new class of self-assembling immunostimulatory short duplex RNAs that potently induce production of type I and type III interferon (IFN-I and IFN-III), in a wide range of human cell types. These RNAs require a minimum of 20 base pairs, lack any sequence or structural characteristics of known immunostimulatory RNAs, and instead require a unique conserved sequence motif (sense strand: 5-C, antisense strand: 3-GGG) that mediates end-to-end dimer self-assembly of these RNAs by Hoogsteen G-G base-pairing. The presence of terminal hydroxyl or monophosphate groups, blunt or overhanging ends, or terminal RNA or DNA bases did not affect their ability to induce IFN. Unlike previously described immunostimulatory siRNAs, their activity is independent of TLR7/8, but requires the RIG-I/IRF3 pathway that induces a more restricted antiviral response with a lower proinflammatory signature compared with poly(I:C). Immune stimulation mediated by these duplex RNAs results in broad spectrum inhibition of infections by many respiratory viruses with pandemic potential, including SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza A, as well as the common cold virus HCoV-NL63 in both cell lines and human Lung Chips that mimic organ-level lung pathophysiology. These short dsRNAs can be manufactured easily, and thus potentially could be harnessed to produce broad-spectrum antiviral therapeutics at low cost.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Longlong Si", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Haiqing Bai", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Crystal Yuri Oh", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Tian Zhang", + "author_inst": "Department of Cell Biology, Harvard Medical School, Harvard University" + }, + { + "author_name": "Amanda Jiang", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Fan Hong", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Yongxin Ye", + "author_inst": "Department of Genetics, Harvard Medical School, Harvard University" + }, + { + "author_name": "Tristan X Jordan", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "James Logue", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Marisa McGrath", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Chaitra Belgur", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Atiq Nurani", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Wuji Cao", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Rani K Powers", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Rachelle Prantil-Baun", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Steven P Gygi", + "author_inst": "Department of Cell Biology, Harvard Medical School, Harvard University" + }, + { + "author_name": "Matthew Frieman", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Benjamin R tenOever", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.11.19.469229", "rel_title": "Characterization of SARS-CoV-2 public CD4+ \u03b1\u03b2 T cell clonotypes through reverse epitope discovery", @@ -488908,117 +487959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.19.21266572", - "rel_title": "Longitudinal analysis of antibody trajectories and humoral responses to a third dose of mRNA vaccines against SARS-CoV-2 in patients with a history of anti-CD20 therapy (RituxiVac 2.0)", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266572", - "rel_abs": "BackgroundMorbidity and mortality of COVID-19 is increased in patients with B-cell depleting therapies, the majority of which also show compromised vaccination-induced immune responses. Herein, we report on the trajectories of anti-SARS-CoV-2 antibodies in patients from the original RituxiVac study compared to healthy volunteers and investigate the immunogenicity of a third vaccination in previously non-responding patients.\n\nMethodsA follow-up evaluation was performed in volunteers and patients from the RituxiVac Study (NCT04877496), which investigated the humoral and cell-mediated immune response after SARS-CoV-2 mRNA vaccination in patients with a history with anti-CD20 depleting therapies (rituximab or ocrelizumab). The current population included 33 patients and 26 healthy volunteers with initial humoral vaccine response and 32 non-responding patients. Primary outcome was anti-SARS-CoV-2 antibody trajectories in vaccine responders 4.3 months (median; interquartile range [IQR]: 3.6 - 4.8 months) after first evaluation and humoral responses after a third vaccine dose in previous non-responders. Antibody decay rates were compared using analysis of covariance in linear regression.\n\nResultsIn patients with detectable anti-spike IgG antibodies after two-dose vaccination, circulating anti-spike IgG persisted in 88% (29/33) of patients 5.6 months after the second vaccination (median; IQR: 5.1-6.7) compared to 92% (24/26) of healthy volunteers 6.8 months after the second dose (IQR: 6.0-7.1) (p=0.7). Antibody decay rates were comparable between patients and controls with -0.54 signal/cut-off (s/c) units per month (IQR -0.72 to -0.45) and -0.60 s/c units per month (IQR: -0.88 to -0.44), p=0.70. Two-dose responders with loss of circulating antibodies at follow-up (n=4/33, 12%) had lower initial antibody concentrations (p<0.01). Biomarkers for immunocompetence, including CD3, CD4 or CD19 cell count at baseline did not predict anti-spike IgG persistence. In two-dose non-responders, a third dose of mRNA vaccine against SARS-CoV-2 elicited humoral response with detectable anti-spike IgG antibodies in 19% (6/32) participants. No clinical parameters nor biomarkers of immunocompetence predicted humoral response after a third vaccine dose.\n\nConclusionThe present study reveals comparable antibody reduction rates between patients with CD20-depleting treatment history and healthy volunteers, but inefficient humoral responses to a third dose of SARS-CoV-2 mRNA vaccines in the majority of two-dose non-responders. There is a need for individually tailored vaccination strategies in immunocompromised patients that could be stratified by B cell counts and initial level of antibody titers. (Funded by Bern University Hospital, ClinicalTrials.gov number, NCT04877496)", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Daniel Sidler", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Alexander Born", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Simeon Schietzel", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Michael P. Horn", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Daniel Aeberli", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Jennifer Amsler", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Burkhard Moeller", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Linet M Njue", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Cesare Medri", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Anne Angelillo-Scherrer", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Luca Borradori", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "S. Morteza Seyed Jafari", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Susanne Radonjic-Hoesli", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Andrew Chan", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Robert Hoepner", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Ulrike Bacher", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Laila-Yasmin Mani", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Joseena M. Iype", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Franziska Suter-Riniker", - "author_inst": "University of Bern" - }, - { - "author_name": "Cornelia Staehelin", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Michael Nagler", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Cedric Hirzel", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Britta Maurer", - "author_inst": "Inselspital University Hospital Bern" - }, - { - "author_name": "Matthias B. Moor", - "author_inst": "Inselspital University Hospital Bern" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.17.21266499", "rel_title": "Comprehensive genomic, immunological and clinical analysis of COVID-19 vaccine breakthrough infections: a prospective, comparative cohort study", @@ -489563,6 +488503,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.20.21266640", + "rel_title": "Patient experience with healthcare: Feedback for a Post COVID-19 clinic at a tertiary care center in rural area", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.20.21266640", + "rel_abs": "PurposePost-acute sequelae of SARS-CoV-2 (PASC) is a complex condition with multisystem involvement. We assessed patients perspectives and experience with a PASC clinic established at University of Iowa in June 2020.\n\nMethodsWe conducted a mixed-method survey in June 2021 to ask PASC clinic patients about 1) PASC symptoms and their impact on physical and mental health, and cognition using the PROMIS Global Health and Cognitive Function abilities items, and 2) satisfaction with clinic services and referrals, barriers to care, and recommended support resources.\n\nFindingsNinety-seven patients (97/277, 35% response rate) completed the survey. Most were women (67%, n=65/97), Caucasian (93%, n=90/97) and received outpatient care during acute COVID-19 illness (79%). Fifty percent reported wait time of 1-3 months and 40% traveled >1 hour for appointment. The most common symptoms >3 months from initial infection were fatigue (77%), \"brain fog\" (73%), exercise intolerance (73%), anxiety (63%), sleep difficulties (56%) and depression (44%). Qualitative analysis of open-ended answers added valuable context to quantitative results. A minority of patients reported significantly reduced functioning ([≥]1.5 SD below mean) of their physical health (22.5%), mental health (15.9%) and cognitive abilities (17.6%). Satisfaction with clinical services was high though participants identified barriers to care including scheduling delays and financial concerns. Respondents suggested potential strategies for optimizing recovery including continuity of care, a co-located multispecialty clinic and being provided with timely information from emerging research.\n\nConclusionOur study reports high PASC symptom burden, its impact on health and patient experience with healthcare. It is important that primary healthcare professionals listen to patients with empathy and support them during recovery. Healthcare systems and policymakers should focus on accessible, comprehensive, and patient-centered integrated care.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Alpana Garg MD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Maran Subramain PhD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Patrick B Barlow PhD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Lauren Garvin PhD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Karin F Hoth PhD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Kimberly Dukes PhD", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Richard M Hoffman MD,MPH", + "author_inst": "University of Iowa, Hospitals and clinics" + }, + { + "author_name": "Alejandro P Comellas MD", + "author_inst": "University of Iowa, Hospitals and clinics" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.11.19.21266555", "rel_title": "Antibody titers before and after booster doses of SARS-CoV-2 mRNA vaccines in healthy adults", @@ -490570,37 +489557,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.11.17.21266381", - "rel_title": "Encounters after Appointments Cancelled Due to COVID-19 in the Veterans Affairs Health Care System", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266381", - "rel_abs": "This statistical brief examines subsequent encounters after a cancellation due to COVID-19 in the Veterans Affairs System. We find that he vast majority of VA patients that had appointments cancelled in mid-March to mid-April of 2020 had another encounter within 180 days. The most common next encounter was a virtual visit with a VA provider on the same day of the original appointment. We also find that patients that saw a provider through VA community care had a lower median time to next encounter.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Linda Diem Tran", - "author_inst": "Health Economics Resource Center, Department of Veterans Affairs" - }, - { - "author_name": "Liam Rose", - "author_inst": "Health Economics Resource Center, Department of Veterans Affairs" - }, - { - "author_name": "Tracy Urech", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Anita Vashi", - "author_inst": "Center for Innovation to Implementation, VA Palo Alto Health Care System; Department of Emergency Medicine, University of California, San Francisco" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.11.16.21266408", "rel_title": "HLA-A*03:01 is associated with increased risk of fever, chills, and more severe reaction to Pfizer-BioNTech COVID-19 vaccination", @@ -491265,6 +490221,69 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.11.19.21266529", + "rel_title": "Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England", + "rel_date": "2021-11-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266529", + "rel_abs": "The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners (GPs) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Aleksandra J Borek", + "author_inst": "University of Oxford" + }, + { + "author_name": "Katherine Maitland", + "author_inst": "University of Oxford" + }, + { + "author_name": "Monsey Mcleod", + "author_inst": "Imperial College London" + }, + { + "author_name": "Anne Campbell", + "author_inst": "Imperia College London" + }, + { + "author_name": "Benedict Hayhoe", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christopher C Butler", + "author_inst": "University of Oxford" + }, + { + "author_name": "Liz Morrell", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laurence Roope", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alison Holmes", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Tonkin-Crine", + "author_inst": "University of Oxford" + }, + { + "author_name": "- the STEP-UP study team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.11.18.21266535", "rel_title": "Uptake of Covid-19 vaccines among frontline workers in California state prisons", @@ -492148,53 +491167,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.11.16.468893", - "rel_title": "BSG/CD147 and ACE2 receptors facilitate SARS-CoV-2 infection of human iPS cell-derived kidney podocytes", - "rel_date": "2021-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.16.468893", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the Coronavirus disease 2019 (COVID-19), which was declared a pandemic by the World Health Organization (WHO) in March 2020. The disease has caused more than 5.1 million deaths worldwide. While cells in the respiratory system are frequently the initial target for SARS-CoV-2, clinical studies suggest that COVID-19 can become a multi-organ disease in the most severe cases. Still, the direct affinity of SARS-CoV-2 for cells in other organs such as the kidneys, which are often affected in severe COVID-19, remains poorly understood.\n\nMethodIn this study, we employed a human induced pluripotent stem (iPS) cell-derived model to investigate the affinity of SARS-CoV-2 for kidney glomerular podocytes. We studied uptake of the live SARS-CoV-2 virus as well as pseudotyped viral particles by human iPS cell derived podocytes using qPCR, western blot, and immunofluorescence. Global gene expression and qPCR analyses revealed that human iPS cell-derived podocytes express many host factor genes (including ACE2, BSG/CD147, PLS3, ACTR3, DOCK7, TMPRSS2, CTSL CD209, and CD33) associated with SARS-CoV-2 binding and viral processing.\n\nResultInfection of podocytes with live SARS-CoV-2 or spike-pseudotyped lentiviral particles revealed viral uptake by the cells at low Multiplicity of Infection (MOI of 0.01) as confirmed by RNA quantification and immunofluorescence studies. Our results also indicate that direct infection of human iPS cell-derived podocytes by SARS-CoV-2 virus can cause cell death and podocyte foot process retraction, a hallmark of podocytopathies and progressive glomerular diseases including collapsing glomerulopathy observed in patients with severe COVID-19 disease. Additionally, antibody blocking experiments identified BSG/CD147 and ACE2 receptors as key mediators of spike binding activity in human iPS cell-derived podocytes.\n\nConclusionThese results show that SARS-CoV-2 can infect kidney glomerular podocytes in vitro. These results also show that the uptake of SARS-CoV-2 by kidney podocytes occurs via multiple binding interactions and partners, which may underlie the high affinity of SARS-CoV-2 for kidney tissues. This stem cell-derived model is potentially useful for kidney-specific antiviral drug screening and mechanistic studies of COVID-19 organotropism.\n\nSignificant statementMany patients with COVID19 disease exhibit multiorgan complications, suggesting that SARS-CoV-2 infection can extend beyond the respiratory system. Acute kidney injury is a common COVID-19 complication contributing to increased morbidity and mortality. Still, SARS-Cov-2 affinity for specialized kidney cells remain less clear. By leveraging our protocol for stem cell differentiation, we show that SARS-CoV-2 can directly infect kidney glomerular podocytes by using multiple Spike-binding proteins including ACE2 and BSG/CD147. Our results also indicate that infection by SARS-CoV-2 virus can cause podocyte cell death and foot process effacement, a hallmark of podocytopathies including collapsing glomerulopathy observed in patients with severe COVID-19 disease. This stem cell-derived model is potentially useful for kidney-specific antiviral drug screening and mechanistic studies of COVID-19 organotropism.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Titilola D Kalejaiye", - "author_inst": "Duke University" - }, - { - "author_name": "Rohan Bhattacharya", - "author_inst": "Duke University" - }, - { - "author_name": "Morgan A Burt", - "author_inst": "Duke University" - }, - { - "author_name": "Tatianna Travieso", - "author_inst": "Duke University" - }, - { - "author_name": "Arinze E Okafor", - "author_inst": "Duke University" - }, - { - "author_name": "Xingrui Mou", - "author_inst": "Duke University" - }, - { - "author_name": "Maria Blasi", - "author_inst": "Duke University" - }, - { - "author_name": "Samira Musah", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.11.17.468929", "rel_title": "Predicting SARS-CoV-2 epitope-specific TCR recognition using pre-trained protein embeddings", @@ -493023,6 +491995,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.15.21266157", + "rel_title": "Positive end expiratory pressure in invasive and non-invasive ventilation of COVID-19 acute respiratory distress syndrome: computational modeling illuminates the data", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266157", + "rel_abs": "Positive end expiratory pressure (PEEP) is routinely used as part of lung protective ventilation strategies in the treatment of acute respiratory distress syndrome (ARDS). In the case of ARDS arising due to COVID-19 (CARDS), there is some debate as to whether the atypical pathophysiological characteristics of the disease which lead to hypoxaemia could warrant a modified approach to ventilator management, particularly with regards to PEEP settings. Here we review the available evidence for the existence of a unique underlying lung pathophysiology in CARDS, and for the suitability of standard approaches to setting PEEP, in both the invasive and non-invasive ventilation settings. We show how detailed computational models informed by this evidence can shed light on the available data, and help to interpret recent results in the literature.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Liam Weaver", + "author_inst": "School of Engineering, University of Warwick, Coventry CV4 7AL, UK" + }, + { + "author_name": "Declan G. Bates", + "author_inst": "School of Engineering, University of Warwick, Coventry CV4 7AL, UK" + }, + { + "author_name": "Luigi Camporota", + "author_inst": "Department of Critical Care, Guy's and St Thomas NHS Foundation Trust, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.11.15.21266343", "rel_title": "Inhaled Prostacyclin Improves Oxygenation in Patients with COVID-19-induced Acute Respiratory Distress Syndrome", @@ -493962,53 +492961,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.14.21266295", - "rel_title": "Estimation of R0 for the spread of SARS-CoV-2 in Germany from Excess Mortality", - "rel_date": "2021-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266295", - "rel_abs": "For SARS-CoV-2, R0 calculations report usually 2-3, biased by PCR testing increases. Covid-19-induced excess mortality is less biased.\n\nWe used data from Robert Koch Institute on Covid incidence, deaths, and PCR tests and excess mortality to determine early, policy-free R0 estimates with a serial interval of 4.7 days.\n\nThe PCR-based R0 value was 2.56 (95% CI 2.52-2.60) for Covid-19 cases and 2.03 (95%CI 1.96-2.10) for Covid-19-related deaths. As the number of PCR tests increased, R0 values were corrected accordingly, yielding 1.86 for Covid-19 cases and 1.47 for Covid-19 deaths, excess deaths were 1.34 (95% CI 1.32-1.37).\n\nR0 is much lower than previously thought. This fits the observed seasonal pattern of infection across Europe in 2020-2021, including emergence of more contagious escape variants such as delta.\n\nOne-Sentence SummaryExcess mortality reveals infection speed in Covid-19 is surprisingly low with seasonal infection patterns and escape variants.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Juan Pablo Prada Salcedo", - "author_inst": "Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg" - }, - { - "author_name": "Luca Estelle Maag", - "author_inst": "Institute of Virology and Immunobiology, University of Wuerzburg" - }, - { - "author_name": "Laura Siegmund", - "author_inst": "Institute of Virology and Immunobiology, University of Wuerzburg" - }, - { - "author_name": "Elena Bencurova", - "author_inst": "Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg" - }, - { - "author_name": "Liang Chunguang", - "author_inst": "Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg" - }, - { - "author_name": "Eleni Koutsilieri", - "author_inst": "Institute of Virology and Immunobiology, University of Wuerzburg" - }, - { - "author_name": "Thomas Dandekar", - "author_inst": "Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg" - }, - { - "author_name": "Carsten Scheller", - "author_inst": "Institute of Virology and Immunobiology, University of Wuerzburg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.12.468428", "rel_title": "#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol", @@ -495025,6 +493977,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.15.21266187", + "rel_title": "Controlling SARS-CoV-2 in schools using repetitive testing strategies", + "rel_date": "2021-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266187", + "rel_abs": "SARS-CoV-2 remains a worldwide emergency. While vaccines have been approved and are widely administered, these are only available to adults and adolescents in Europe. Therefore, in order to mitigate the spread of more transmissible SARS-CoV-2 variants among children, the use of non-pharmaceutical interventions is still warranted. We investigate the impact of different testing strategies on the SARS-CoV-2 infection dynamics in a primary school environment, using an individual-based modelling approach. Specifically, we consider three testing strategies: 1) symptomatic isolation, where we test symptomatic individuals and isolate them when they test positive, 2) reactive screening, where a class is screened once one symptomatic individual was identified, and 3) repetitive screening, where the school in its entirety is screened on regular time intervals. Through this analysis, we demonstrate that repetitive testing strategies can significantly reduce the attack rate in schools, contrary to a reactive screening approach. Furthermore, we investigate the impact of these testing strategies on the average number of school days lost per child.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Andrea Torneri", + "author_inst": "Universiteit Hasselt" + }, + { + "author_name": "Lander Willem", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + }, + { + "author_name": "Cecile Kremer", + "author_inst": "Hasselt University" + }, + { + "author_name": "Christelle Meuris", + "author_inst": "Liege University Hospital" + }, + { + "author_name": "Gilles Darcis", + "author_inst": "Liege University Hospital" + }, + { + "author_name": "Niel Hens", + "author_inst": "Hasselt University and University of Antwerp" + }, + { + "author_name": "Pieter JK Libin", + "author_inst": "Vrije Universiteit Brussel" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.14.21266325", "rel_title": "Higher Vaccination Rate Predicts Reduction in SARS-CoV-2 Transmission across the United States", @@ -496156,57 +495155,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.14.21266318", - "rel_title": "Cost-effectiveness analysis of BNT162b2 COVID-19 booster vaccination in the United States", - "rel_date": "2021-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266318", - "rel_abs": "BackgroundOver 86% of older adults aged [≥]65 years are fully vaccinated against SARS-COV-2 in the United States (US). Waning protection of the existing vaccines promotes the new vaccination strategies, such as providing a booster shot for those fully vaccinated.\n\nMethodsWe developed a decision-analytic Markov model of COVID-19 to evaluate the cost-effectiveness of a booster strategy of Pfizer-BioNTech BNT162b2 (administered 6 months after 2nd dose) in those aged [≥]65 years, from a healthcare system perspective.\n\nFindingsCompared with 2-doses of BNT162b2 without a booster, the booster strategy in a 100,000 cohort of older adults would incur an additional cost of $3.4 million, but save $6.7 million in direct medical costs in 180 days. This corresponds to a benefit-cost ratio of 1.95 and a net monetary benefit of $3.4 million. Probabilistic sensitivity analysis indicates that with a COVID-19 incidence of 9.1/100,000 person-day, a booster strategy has a high chance (67%) of being cost-effective. The cost-effectiveness of the booster strategy is highly sensitive to the population incidence of COVID-19, with a cost-effectiveness threshold of 8.1/100,000 person-day. This threshold will increase with a decrease in vaccine and booster efficacies. Doubling the vaccination cost or halving the medical cost for COVID-19 treatment alone would not alter the conclusion of cost-effectiveness, but certain combinations of the two might render the booster strategy not cost-effective.\n\nInterpretationOffering BNT162b2 boosters to older adults aged [≥]65 years in the US is likely to be cost-effective. Less efficacious vaccines and boosters may still be cost-effective in settings of high SARS-COV-2 transmission.\n\nFundingNational Natural Science Foundation of China. Berlina and Bill Gates Foundation", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Rui Li", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Hanting Liu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Christopher Kit Fairley", - "author_inst": "China-Australia Joint Research Center for Infectious Diseases" - }, - { - "author_name": "Zhuoru Zou", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Li Xie", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Xinghui Li", - "author_inst": "Shaanxi University of Chinese Medicine" - }, - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yan Li", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.12.21266250", "rel_title": "Protection offered by mRNA-1273 versus BNT162b2 vaccines against SARS-CoV-2 infection and severe COVID-19 in Qatar", @@ -496919,6 +495867,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.11.21266119", + "rel_title": "Quantification and progress over time of specific antibodies against SARS-CoV-2 in breast milk of lactating women vaccinated with BNT162b2 Pfizer-BioNTech COVID-19 vaccine (LacCOVID)", + "rel_date": "2021-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266119", + "rel_abs": "ImportanceTo our knowledge, this is the first study to analyze long-term passage (6 months after immunization) of specific antibodies induced by BNT162b2 COVID-19 vaccine through breast milk.\n\nObjectivesMain objective: to determine SARS-CoV-2 vaccine induced antibody levels in the breast milk of lactating women 4 weeks after mRNA BNT162b2 Pfizer-BioNTech COVID-19 complete vaccination.\n\nSecondary objectives: to analyze SARS-CoV-2 antibody levels (breast milk and serum) at different time-points after vaccination, examine the correlation of SARS-CoV-2 antibody levels between serum and breast milk, describe adverse events related to vaccination (AErV) in both mothers and infants and determine the rate of COVID-19 infections.\n\nDesignProspective cohort study between February and September 2021.\n\nSettingParc Sanitari Sant Joan de Deu, an urban hospital in Spain.\n\nParticipantsDuring our health worker vaccination campaign at our hospital between January and March 2, we recruited 33 lactating women vaccinated with BNT162b2 Pfizer-BioNTech COVID-19.\n\nResultsA total of 33 volunteers were included in the study. The median (IQR) age of mothers was 38 (36-39) years and 15 (10-22) months for the infants.\n\nPrimary end-point: at 4 w after second dose median (IQR) IgG-S1 levels for serum-milk pairs were 12,478 (6,870-20,801) to 50.4 (24.3-104) arbitrary units (AU) per mL.\n\nSecondary end-pointsSARS-CoV-2 antibody levels at different time-points were (serum-milk): 519 (234-937) to 1 (0-2.9) AU/mL at 2w after first dose, 18,644 (9,923-29,264) to 78 (33.7-128) AU/mL at 2w, 4,094 (2,413-8,480) to 19.9 (10.8-51.9) AU/mL at 12w, and 1,350 (831-2,298) to 8.9 (7.8-31.5) at 24w after second dose.\n\nWe found a positive correlation of SARS-CoV-2 antibody levels between serum and breast milk (Pearson correlation coefficient 0.68).\n\nNo serious AErV were observed.\n\nWe found two (6%) COVID-19 vaccine breakthrough infections.\n\nConclusionsPfizer-BioNTech COVID-19 vaccination is safe during breastfeeding and it transmits antibodies into breast milk with a positive correlation with serum levels, and both decrease over time in a 6-month follow-up. Infants of breastfeeding vaccinated women could be protected for at least six months after vaccination and serum determination of SARS-CoV-2 IgG-S1 could indicate the breastmilk levels of antibodies during this period.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Erika Esteve-Palau", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "Araceli Gonzalez-Cuevas", + "author_inst": "Department of Microbiology at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "M. Eugenia Guerrero", + "author_inst": "Department of Microbiology at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "Clara Garcia-Terol", + "author_inst": "Department of Obstetrics and Gynecology at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "M. Carmen Alvarez", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "Geneva Garcia", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "Encarna Moreno", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "Francisco Medina", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + }, + { + "author_name": "David Casadevall", + "author_inst": "Cancer Research Program, Hospital del Mar Research Institute (Barcelona, Spain)" + }, + { + "author_name": "Vicens Diaz-Brito", + "author_inst": "Infectious Diseases Department at Parc Sanitari Sant Joan de Deu, Sant Boi (Barcelona, Spain)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.11.21266219", "rel_title": "Reducing false-positive SARS-CoV-2 diagnoses using long-range RT-qPCR", @@ -497906,29 +496909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.06.21266002", - "rel_title": "A prototype vaccination model for endemic Covid-19 under waning immunity and imperfect vaccine take-up", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.06.21266002", - "rel_abs": "In this paper, for an infectious disease such as Covid-19, we present a SIR model which examines the impact of waning immunity, vaccination rates, vaccine efficacy, and the proportion of the susceptible population who aspire to be vaccinated. Under an assumed constant control reproduction number, we provide simple conditions for the disease to be eliminated, and conversely for it to exhibit the more likely endemic behaviour. With regard to Covid-19, it is shown that if the control reproduction number is set to the basic reproduction number (say 6) of the dominant delta (B1.617.2) variant, vaccination alone, even under the most optimistic of assumptions about vaccine efficacy and high vaccine coverage, is very unlikely to lead to elimination of the disease. The model is not intended to be predictive but more an aid to understanding the relative importance of various biological and control parameters. For example, from a long-term perspective, it may be found that in the UK, through changes in societal behaviour (such as mask use, ventilation, and level of homeworking), without formal government interventions such as on-off lockdowns, the control reproduction number can still be maintained at a level significantly below the basic reproduction number. Even so, our simulations show that endemic behaviour ensues. The model obtains equilibrium values of the state variables such as the infection prevalence and mortality rate under various scenarios.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "John S Dagpunar", - "author_inst": "University of Southampton" - }, - { - "author_name": "ChenChen Wu", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.10.21266139", "rel_title": "The role of antiviral treatment in curbing the COVID-19 pandemic: a modeling study.", @@ -498893,6 +497873,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.05.467537", + "rel_title": "Transcriptome analysis of SARS-CoV-2 naive and recovered individuals vaccinated with inactivated vaccine", + "rel_date": "2021-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.05.467537", + "rel_abs": "The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naive individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the hosts molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yuwei Zhang", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Xingyu Guo", + "author_inst": "Shandong First Medical University & Shandong Academy of Medical Sciences" + }, + { + "author_name": "Cunbao Li", + "author_inst": "Lanshan Center for Disease Control and Prevention" + }, + { + "author_name": "Zengqiang Kou", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Lanfang Lin", + "author_inst": "Lanshan Center for Disease Control and Prevention" + }, + { + "author_name": "Mingxiao Yao", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Bo Pang", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaomei Zhang", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Qing Duan", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Xueying Tian", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Yufang Xing", + "author_inst": "Shandong Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaolin Jiang", + "author_inst": "Shandong Center for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.09.21266140", "rel_title": "Minimal in-school SARS-CoV-2 transmission with strict mitigation protocols at two independent schools in Nashville, TN", @@ -499887,73 +498930,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.05.21265890", - "rel_title": "Simultaneous identification of viruses and SARS-CoV-2 variants with programmable DNA nanobait", - "rel_date": "2021-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265890", - "rel_abs": "Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid read-out via nanopore sensing. Here, we show this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants, as we demonstrated for several key SARS-CoV-2 variants with single-nucleotide resolution. Lastly, we show that nanobait discriminates between samples extracted from oropharyngeal swabs from negative and positive SARS-CoV-2 patients without pre-amplification. Our system allows for multiplexed identification of native RNA molecules, providing a new scalable approach for diagnostics of multiple respiratory viruses in a single assay.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Filip Boskovic", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jinbo Zhu", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ran Tivony", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alexander Ohmann", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Kaikai Chen", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Mohammed Alawami", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Milan Djordjevic", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Niklas Ermann", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Joana Pereira Dias", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Michael Fairhead", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Howarth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephen Baker", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ulrich Felix Keyser", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.05.21265970", "rel_title": "Exploring Associations with Severe Hypoxemic Respiratory Failure in COVID-19 Patients upon Admission: A Model for Severe Hypoxemic Respiratory Failure in 329 Unvaccinated, Hospitalized COVID-19 Patients.", @@ -500622,6 +499598,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.05.21265900", + "rel_title": "Parents intention to vaccinate their 5-11 years old children with the COVID-19: vaccine rates, predictors and the role of incentives", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265900", + "rel_abs": "BackgroundOn September 20, 2021, Pfizer announced encouraging effectiveness and safety results from their COVID-19 vaccine clinical trials in 5-11 years old children. This study aims to assess parents perceptions and intention to vaccinate their 5-11 years old children and to determine the socio-demographic, health-related and behavioral factors, as well as the role of incentives beyond these factors, in predicting this intention.\n\nMethodsA cross-sectional representative online survey among parents of children aged 5-11 years in Israel (n=1,012). The survey was carried out between September 23 and October 4, 2021, at a critical time, immediately after Pfizers announcement. Two multivariate regressions were performed to determine predictors of parents intention to vaccinate their 5-11 years old children against COVID-19 in the coming winter and how soon they intend to do so.\n\nResultsOverall, 57% of the participants reported their intention to vaccinate their 5-11 years old children against COVID-19 in the coming winter. This intention was higher for participants over the age of 40. Perceived susceptibility, perceived benefits, perceived barriers, and cues to action, as well as two incentives - vaccine availability and receiving a green pass - were all significant predictors of this intention. When asked about how soon they intend to vaccinate their 5-11 years old children, 27% of the participants responded immediately; 26% within three months; and 24% within more than three months. Participants having a family member suffering from a chronic disease as well as those whose children were vaccinated against influenza in the previous winter intend to vaccinate their children sooner. Perceived susceptibility, perceived severity, perceived benefits, perceived barriers, and cues to action, were all found to be significant predictors of this sense of urgency. Similar to the intention to vaccinate children in the coming winter, while vaccine availability and receiving a green pass were found to be positive significant predictors of how soon parents intend to vaccinate their children, other incentives such as monetary rewards or monetary penalties were not found to be significant predictors. Parental concerns centered around the safety of the vaccine (64%), fear of severe side effects (60%), and fear that clinical trials and the authorization process were carried out too quickly (56%).\n\nConclusionsThis study provides up-to-date information on the rates of the intention of parents to vaccinate their 5-11 years old children, how soon they intend to do so, and the predictors of those intentions, which is essential for health policy makers and healthcare providers for planning vaccination campaigns. Moreover, as vaccine safety and side effects were found to be key parental concerns, it is important to release post-approval safety data regarding the vaccine to the public as soon as such is available. Finally, our findings underscore the important role of vaccine accessibility and receiving a green pass over other incentives in promoting parents intentions to vaccinate their children.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Liora Shmueli", + "author_inst": "Bar-Ilan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.11.05.21265978", "rel_title": "SARS-CoV-2 testing and COVID-19 related primary care use among people with citizenship, permanent residency, and temporary immigration status in British Columbia: Cross-sectional analysis of population-based administrative data", @@ -501501,49 +500496,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21266075", - "rel_title": "Neutralisation of SARS-CoV-2 Delta sub-lineage AY.4.2 and B.1.617.2+E484K by BNT162b2 mRNA vaccine-elicited sera", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266075", - "rel_abs": "Several factors may account for the recent increased spread of the SARS-CoV-2 Delta sublineage AY.4.2 in the United Kingdom, Romania, Poland, and Denmark. Here, we evaluate the sensitivity of AY.4.2 to neutralisation by sera from Pfizer/BioNTech (BNT162b2) vaccine recipients. AY.4.2 neutralisation was comparable to other circulating Delta lineages or sublineages. In contrast, the more rare B.1.617.2+E484K variant showed a significant >4-fold reduction in neutralisation that warrants surveillance of strains with the acquired E484K mutation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ria Lassauniere", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Charlotta Polacek", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Jannik Fonager", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Marc Bennedbaek", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Lasse Boding", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Morten Rasmussen", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Anders Fomsgaard", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.21266099", "rel_title": "A mathematical model for repetitive behaviors of Covid-19", @@ -502148,6 +501100,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.07.21266036", + "rel_title": "Association between long working hours and psychological distress: The effect of sick leave criteria in the workplace during the COVID-19 pandemic", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.07.21266036", + "rel_abs": "ObjectiveThis study investigated the effect of sick leave criteria on the association between long working hours and psychological distress.\n\nMethodsWe conducted a cross-sectional survey in December 2020, and 27,032 workers completed the questionnaire. First, after testing the interaction effect of overtime work hours and sick leave criteria on psychological distress, we conducted stratified analyses using sick leave criteria.\n\nResultsA significant interaction effect was found. When we conducted stratified analyses, the odds ratios increased with longer working hours, both with and without sick leave criteria groups; however, the risk was greater in the without sick leave criteria group, compared with the criteria group.\n\nConclusionWe revealed that working without sick leave criteria could strengthen the association between long working hours and psychological distress during the COVID-19 pandemic.\n\nClinical significanceWorkers working without sick leave criteria had a significantly higher risk of psychological distress due to long working hours than those who worked with the criteria. Our findings contribute to preventing the deterioration of mental health during the COVID-19 pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ayako Hino", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Akiomi Inoue", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Kosuke Mafune", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohisa Nagata", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Keiji Muramatsu", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.11.05.21265759", "rel_title": "Preventing the Transmission of COVID-19 in Older Adults Aged 60 Years and Above Living in Long-Term Care: Rapid Review Update", @@ -503471,69 +502474,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.11.02.21265750", - "rel_title": "Anti-membrane and anti-spike antibodies are long-lasting and together discriminate between past COVID-19 infection and vaccination", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.02.21265750", - "rel_abs": "The consequences of past COVID-19 infection for personal health and long-term population immunity are only starting to be revealed. Unfortunately, detecting past infection is currently a challenge, limiting clinical and research endeavors. Widely available anti-SARS-CoV-2 antibody tests cannot differentiate between past infection and vaccination given vaccine-induced anti-spike antibodies and the rapid loss of infection-induced anti-nucleocapsid antibodies. Anti-membrane antibodies develop after COVID-19, but their long-term persistence is unknown. Here, we demonstrate that anti-membrane IgG is a sensitive and specific marker of past COVID-19 infection and persists at least one year. We also confirm that anti-receptor binding domain (RBD) Ig is a long-lasting, sensitive, and specific marker of past infection and vaccination, while anti-nucleocapsid IgG lacks specificity and quickly declines after COVID-19. Thus, a combination of anti-membrane and anti-RBD antibodies can accurately differentiate between distant COVID-19 infection, vaccination, and naive states to advance public health, individual healthcare, and research goals.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Maya F Amjadi", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Ryan R Adyniec", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Srishti Gupta", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "S Janna Bashar", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Aisha M Mergaert", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Katarina M Braun", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Gage K Moreno", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "David H O'Connor", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Thomas C Friedrich", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Nasia Safdar", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Sara S McCoy", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Miriam A Shelef", - "author_inst": "University of Wisconsin - Madison" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.21265888", "rel_title": "SARS-CoV-2 Antibody Response is Associated with Age in Convalescent Outpatients", @@ -504254,6 +503194,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.04.467274", + "rel_title": "Prolonged and extended impacts of SARS-CoV-2 on the olfactory neurocircuit", + "rel_date": "2021-11-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.04.467274", + "rel_abs": "The impact of SARS-CoV-2 on the olfactory pathway was studied over several time points using Syrian golden hamsters. We found an incomplete recovery of the olfactory sensory neurons, prolonged activation of glial cells in the olfactory bulb, and a decrease in the density of dendritic spines within the hippocampus. These data may be useful for elucidating the mechanism underlying long-lasting olfactory dysfunction and cognitive impairment as a post-acute COVID-19 syndrome.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Shinji Urata", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Megumi Kishimoto-Urata", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Ryoji Kagoya", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Fumiaki Imamura", + "author_inst": "Penn State College of Medicine" + }, + { + "author_name": "Shin Nagayama", + "author_inst": "The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Rachel A Reyna", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Junki Maruyama", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Tatsuya Yamasoba", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Kenji Kondo", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Sanae Hasegawa-Ishii", + "author_inst": "Kyorin University" + }, + { + "author_name": "Slobodan Paessler", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2021.11.03.467186", "rel_title": "Stenoparib, an inhibitor of cellular poly (ADP-ribose) polymerases (PARPs), blocks in vitro replication of SARS-CoV-2 variants", @@ -505305,65 +504304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.11.01.466865", - "rel_title": "Low selectivity index of ivermectin and macrocyclic lactones on SARS-CoV2 replication in vitro argues against their therapeutic use for COVID-19.", - "rel_date": "2021-11-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.01.466865", - "rel_abs": "There are very limited antiviral therapeutic options for coronavirus infections, therefore global drug re-purposing efforts are paramount to identify available compounds that could provide clinical benefits to patients with COVID-19. Ivermectin was first approved for human use as an endectocide in the 1980s. It remains one of the most important global health medicines in history and has recently been shown to exert in vitro activity against SARS-CoV-2. However, the macrocyclic lactone family of compounds has not previously been evaluated for activity against SARS-CoV-2. The present study aims at comparing their anti-viral activity in relevant pulmonary cell lines in vitro. Here, in vitro antiviral activity of the avermectins (ivermectin and selamectin) and milbemycins (moxidectin and milbemycin oxime) were assessed against a clinical isolate from a CHU Montpellier patient infected with SARS-CoV-2 in 2020. Ivermectin demonstrated anti-SARS-CoV-2 activity in vitro in human pulmonary cells in comparison to VeroE6 (with EC50 of 1-3 M). Similarly, the other macrocyclic lactones moxidectin, milbemycin oxime and selamectin reduced SARS-CoV-2 replication in vitro (with EC50 of 2-5 M). Immunofluorescence assays with ivermectin and moxidectin showed a reduction in the number of infected and polynuclear cells suggesting a drug action on viral cell fusion. However, cellular toxicity of the avermectins and milbemycins during infection showed a very low selectivity index <10 for all compounds. In conclusion, none of these agents appears suitable for human use for its anti-SARS-CoV-2 activity per se, due to low selectivity index. This is discussed in regards to recent clinical COVID studies on ivermectin.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christine Chable-Bessia", - "author_inst": "CNRS" - }, - { - "author_name": "Charlotte Boull\u00e9", - "author_inst": "University Hospital of Montpellier" - }, - { - "author_name": "Aymeric Neyret", - "author_inst": "CNRS" - }, - { - "author_name": "Jitendriya M Swain", - "author_inst": "CNRS & University of Montpellier" - }, - { - "author_name": "Mathilde H\u00e9naut", - "author_inst": "CNRS" - }, - { - "author_name": "Peggy Merida", - "author_inst": "CNRS" - }, - { - "author_name": "Nathalie Gros", - "author_inst": "CNRS" - }, - { - "author_name": "Alain Makinson", - "author_inst": "CHU de Montpellier" - }, - { - "author_name": "Sebastien Lyonnais", - "author_inst": "CNRS" - }, - { - "author_name": "C\u00e9dric B Chesnais", - "author_inst": "Institut de Recherche pour le D\u00e9veloppement" - }, - { - "author_name": "Delphine Muriaux", - "author_inst": "CNRS & University of Montpellier" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.04.21265923", "rel_title": "How Do College Students with Disabilities Feel About Taking COVID-19 Vaccines?", @@ -505968,6 +504908,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.02.21265668", + "rel_title": "Black and Native Overdose Mortality Overtook that of White Individuals During the COVID-19 Pandemic", + "rel_date": "2021-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.02.21265668", + "rel_abs": "Drug overdose mortality rates have increased sharply during the COVID-19 pandemic. In recent years, overdose death rates were rising most rapidly among racial/ethnic minority communities. The pandemic has disproportionately affected communities of color in a wide swath of health, social, and economic outcomes. Careful attention is therefore warranted to trends in overdose mortality by race/ethnicity during COVID-19. We calculated total drug overdose death rates per 100,000 population by race/ethnicity for the 1999-2020 time period. We find that Black overdose mortality overtook that of White individuals in 2020 for the first time since 1999. Between 2019 and 2020 Black individuals had the largest percent increase in overdose mortality, of 48.8%, compared to 26.3% among White individuals. In 2020, Black overdose death rates rose to 36.8 per 100,000, representing 16.3% higher than the rate for White individuals for the same period. American Indian and Alaska Native (AI/AN) individuals experienced the highest rate of overdose mortality in 2020, of 41.4 per 100,000, representing 30.8% higher than the rate among White individuals. Our findings suggest that drug overdose mortality is increasingly becoming a racial justice issue in the United States and appears to have been exacerbated by the COVID-19 pandemic. Providing individuals with a safer supply of drugs, closing gaps in access to MOUD and harm reductions services, and ending routine incarceration of individuals with substance use disorders represent urgently needed, evidence-based strategies that can be employed to reduce rising inequalities in overdose.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Joseph Friedman", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Helena Hansen", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.02.21265831", "rel_title": "Multiplex Solid-Phase RPA Coupled CRISPR-Based Visual Detection of SARS-CoV-2", @@ -507335,73 +506298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.02.21265789", - "rel_title": "SARS-CoV-2 infection induces cross-reactive autoantibodies against angiotensin II", - "rel_date": "2021-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.02.21265789", - "rel_abs": "Patients infected with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can experience life-threatening respiratory distress, blood pressure dysregulation and thrombosis. This is thought to be associated with an impaired activity of angiotensin-converting enzyme-2 (ACE-2), which is the main entry receptor of SARS-CoV-2 and which also tightly regulates blood pressure by converting the vasoconstrictive peptide angiotensin II (AngII) to a vasopressor peptide. Here, we show that a significant proportion of hospitalized COVID-19 patients developed autoantibodies against AngII, whose presence correlates with lower blood oxygenation, blood pressure dysregulation, and overall higher disease severity. Anti-AngII antibodies can develop upon specific immune reaction to the SARS-CoV-2 proteins Spike or RBD, to which they can cross-bind, suggesting some epitope mimicry between AngII and Spike/RBD. These results provide important insights on how an immune reaction against SARS-CoV-2 can impair blood pressure regulation.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Priscilla S Briquez", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Sherin J Rouhani", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Jovian Yu", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Athalia R Pyzer", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Jonathan Trujillo", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Haley L Dugan", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Christopher T Stamper", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Siriruk Changrob", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Anne I Sperling", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Patrick C Wilson", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Thomas F Gajewski", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Jeffrey A Hubbell", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - }, - { - "author_name": "Melody A Swartz", - "author_inst": "The University of Chicago, Chicago, Illinois, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.01.21265766", "rel_title": "Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19", @@ -508482,6 +507378,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.01.466695", + "rel_title": "Antiviral activity of Pacific oyster (Crassostrea gigas) hemolymph against a human coronavirus.", + "rel_date": "2021-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.01.466695", + "rel_abs": "Coronaviruses can cause severe respiratory infections in humans. In this study we assessed the antiviral activity of Pacific oyster (Crassostrea gigas) hemolymph against a human coronavirus, HCoV-229E. An eight-fold reduction in infectivity of HCoV-229E on Huh-7 cells was observed in the presence of 10% C. gigas hemolymph. Antiviral activity of C. gigas hemolymph positively correlated with its concentration and appears to be active during an intracellular stage of HCoV-229E infection.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rebecca L Pedler", + "author_inst": "Flinders University" + }, + { + "author_name": "James Harris", + "author_inst": "Flinders University" + }, + { + "author_name": "Peter G Speck", + "author_inst": "Flinders University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.01.466863", "rel_title": "mRNA Vaccines Induce Rapid Antibody Responses in Mice", @@ -509517,77 +508440,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.30.466586", - "rel_title": "Visceral Fat Inflammation and Fat Embolism are associated with Lung's Lipidic Hyaline Membranes in COVID-19 patients", - "rel_date": "2021-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.30.466586", - "rel_abs": "BackgroundVisceral obesity is a critical determinant of severe coronavirus disease-2019 (COVID-19). Methods: In this study, we performed a comprehensive histomorphologic analysis of autoptic visceral adipose tissues (VAT), lungs and livers of 19 COVID-19 and 23 non-COVID-19 subjects.\n\nResultsAlthough there were no between-groups differences in body-mass-index and adipocytes size, higher prevalence of CD68+ macrophages in COVID-19 subjects VAT was detected (p=0.005) and accompanied by crown-like structures presence, signs of adipocytes stress and death. Consistently, human adipocytes were successfully infected by SARS-CoV2 in vitro and displayed lower cell viability. Being VAT inflammation associated with lipids spill-over from dead adipocytes, we studied lipids distribution employing Oil-Red-O staining (ORO). Lipids were observed within lungs and livers interstitial spaces, macrophages, endothelial cells, and vessels lumen, features suggestive of fat embolism syndrome, more prevalent among COVID-19 individuals (p<0.001). Notably, signs of fat embolism were more prevalent among obese (p=0.03) independently of COVID-19 diagnosis, suggesting that such condition may be an obesity complication, exacerbated by SARS-CoV2 infection. Importantly, all infected subjects lungs presented lipids-rich (ORO+) hyaline membranes, formations associated with COVID-19-related pneumonia, present only in one control with non-COVID-19 pneumonia.\n\nConclusionsThis study describes for the first time novel COVID-19-related features possibly underlying the unfavorable prognosis in obese SARS-CoV2-infected-subjects.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Georgia Colleluori", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Laura Graciotti", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Mauro Pesaresi", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Angelica Di Vincenzo", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Jessica Perugini", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Eleonora Di Mercurio", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Sara Caucci", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Patrizia Bagnarelli", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Cristina Maria Zingaretti", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Enzo Nisoli", - "author_inst": "University of Milan" - }, - { - "author_name": "Stefano Menzo", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Adriano Tagliabracci", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Antonio Giordano", - "author_inst": "Marche Polytechnic University" - }, - { - "author_name": "Saverio Cinti", - "author_inst": "Marche Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.10.31.466677", "rel_title": "Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)", @@ -510308,6 +509160,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.14.21264837", + "rel_title": "COVID-19 vaccine brand hesitancy and other challenges to vaccination in the Philippines", + "rel_date": "2021-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264837", + "rel_abs": "BackgroundCOVID-19 vaccines have been developed at a rapid and unprecedented pace to control the spread of the virus, and prevent hospitalisations and deaths. However, there are a series of events and factors that create barriers to vaccination. In this paper, we explore vaccination narratives and challenges experienced and observed by Filipinos during the early vaccination period in the Philippines.\n\nMaterial and methodsWe conducted 35 interviews from a subsample of 1,599 survey respondents ages 18 and older in the Philippines. The interviews were conducted in Filipino, Cebuano, and/or English via online platforms such as Zoom or via phone call. All interviews were recorded, transcribed verbatim, translated, and analysed using inductive content analysis. To highlight the complex reasons for delaying and/or refusing COVID-19 vaccines, we embedded our findings within the social ecological model.\n\nResultsOur analysis showed that individual perceptions play a major role on the decision to vaccinate. Such perceptions are shaped by exposure to (mis)information amplified by the media, the community, and the health system. Social networks may either positively or negatively impact vaccination uptake, depending on their views on vaccines. Political issues contribute to vaccine brand hesitancy, resulting to vaccination delays and refusals. Perceived inefficiencies and inflexibility of the system also create additional barriers to the vaccine rollout in the country, especially among vulnerable and marginalised groups.\n\nConclusionsChallenges to COVID-19 vaccination may be individual, interpersonal, and structural, which work individually and collectively. Among these barriers, our results suggest that many concerns regarding vaccination operate at the individual level. Vaccine brand hesitancy and misinformation are growing public health challenges in the country that need to be addressed. Recognising and addressing concerns at all levels are critical to solutions aimed at improving COVID-19 vaccination uptake and reach.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Arianna Maever L Amit", + "author_inst": "School of Medicine and Public Health, Ateneo de Manila University" + }, + { + "author_name": "Veincent Christian F Pepito", + "author_inst": "School of Medicine and Public Health, Ateneo de Manila University" + }, + { + "author_name": "Lourdes Sumpaico-Tanchanco", + "author_inst": "School of Medicine and Public Health, Ateneo de Manila University" + }, + { + "author_name": "Manuel M Dayrit", + "author_inst": "School of Medicine and Public Health, Ateneo de Manila University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.22.21265385", "rel_title": "COVID-19 Advanced Respiratory Care Educational Training Program for Healthcare Workers in Lesotho: An Observational Study", @@ -511151,109 +510034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.29.21265511", - "rel_title": "Blood cytokine analysis suggests that SARS-CoV-2 infection results in a sustained tumour promoting environment in cancer patients", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.29.21265511", - "rel_abs": "Cytokines, chemokines and (angiogenic) growth factors (CCGs) have been shown to play an intricate role in the progression of both solid and haematological malignancies. Recent studies have shown that SARS-CoV-2 infection leads to worse outcome in cancer patients, especially in haematological malignancy patients. Here, we investigated how SARS-CoV-2 infection impacts the already altered CCG levels in solid or haematological malignancies, specifically whether there is a protective effect or rather a potentially higher risk for major COVID-19 complications in cancer patients due to elevated CCGs linked to cancer progression. Serially analysing immune responses with 55 CCGs in cancer patients under active treatment with or without SARS-CoV-2 infection, we first showed that cancer patients without SARS-CoV-2 infection (n=54) demonstrate elevated levels of 35 CCGs compared to the non-cancer, non-infected control group of health care workers (n=42). Of the 35 CCGs, 19 were common to both solid and haematological malignancy groups and comprised previously described cytokines such as IL-6, TNF-, IL-1Ra, IL-17A, and VEGF, but also several less well described cytokines/chemokines such as Fractalkine, Tie-2, and T cell chemokine CTACK. Importantly, we show here that 7 CCGs are significantly altered in SARS-CoV-2 exposed cancer patients (n=52). Of these TNF-, IFN-{beta}, TSLP and sVCAM-1, identified to be elevated in haematological cancers, are also known tumour-promoting factors. Longitudinal analysis conducted over 3 months showed persistence of several tumour-promoting CCGs in SARS-CoV-2 exposed cancer patients. These data urge for increased vigilance for haematological malignancy patients as a part of long COVID follow-up.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Fien HR De Winter", - "author_inst": "University of Antwerp" - }, - { - "author_name": "An Hotterbeekx", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Manon Huizing", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Angelina Konnova", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Erik Fransen", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Bart 's Jongers", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Ravi Kumar Jairam", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Vincent Van averbeke", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Pieter Moons", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Ella Roelant", - "author_inst": "Antwerp University Hospital, University of Antwerp" - }, - { - "author_name": "Debbie Le Blon", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Wim Vanden Berghe", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Annelies Janssens", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Willem Lybaert", - "author_inst": "AZ Nikolaas, Belgium" - }, - { - "author_name": "Lieselot Croes", - "author_inst": "University of Antwerp, AZ Maria Middelares Ghent, Belgium" - }, - { - "author_name": "Christof Vulsteke", - "author_inst": "University of Antwerp, AZ Maria Middelares Ghent, Belgium, Antwerp University Hospital" - }, - { - "author_name": "Surbhi Malhotra-Kumar", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Herman Goossens", - "author_inst": "University of Antwerp, Antwerp University Hospital" - }, - { - "author_name": "Zwi Berneman", - "author_inst": "Antwerp University Hospital, University of Antwerp" - }, - { - "author_name": "Marc Peeters", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Peter van Dam", - "author_inst": "University of Antwerp, Antwerp University Hospital" - }, - { - "author_name": "Samir Kumar-Singh", - "author_inst": "University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2021.10.28.21265588", "rel_title": "Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine", @@ -512118,6 +510898,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.27.466067", + "rel_title": "Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro", + "rel_date": "2021-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.27.466067", + "rel_abs": "To date, COVID-19 is still a severe threat to public health, hence specific effective therapeutic drugs development against SARS-CoV-2 is urgent needed. 3CLpro and PLpro and RdRp are the enzymes required for the SARS-CoV-2 RNA synthesis. Therefore, binding to the enzyme may interfere the enzyme function. Before, we found that sulfated polysaccharide binding to 3CLpro might block the virus replication. Hence, we hypothesize that negative charged pectin glycan may also impede the virus replication. Here we show that 922 crude polysaccharide from Syzygium aromaticum may near completely block SARS-CoV-2 replication. The inhibition rate was 99.9% (EC50 : 0.90 M). Interestingly, 922 can associates with 3CLpro, PLpro and RdRp. We further show that the homogeneous glycan 922211 from 922 may specifically attenuate 3CL protease activity. The IC50s of 922 and 922211 against 3CLpro are 4.73 {+/-} 1.05 {micro}M and 0.18 {+/-} 0.01 {micro}M, respectively. Monosaccharide composition analysis reveals that 922211 with molecular weight of 78.7 kDa is composed of rhamnose, galacturonic acid, galactose and arabinose in the molar ratio of 8.21 : 37.81 : 3.58 : 4.49. The structure characterization demonstrated that 922211 is a homogalacturonan linked to RG-I pectin polysaccharide. The linear homogalacturonan part in the backbone may be partly methyl esterified while RG-I type part bearing 1, 4-linked -GalpA, 1, 4-linked -GalpAOMe and 1, 2, 4-linked -Rhap. There are four branches attached to C-1 or C4 position of Rhamnose glycosyl residues on the backbone. The branches are composed of 1, 3-linked {beta}-Galp, terminal (T)-linked {beta}-Galp, 1, 5-linked -Araf, T-linked -Araf, 4-linked -GalpA and/or 4-linked {beta}-GalpA. The above results suggest that 922 and 922211 might be a potential novel leading compound for anti-SARS-CoV-2 new drug development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Can Jin", + "author_inst": "Nanjing University of Chinese Medicine and Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Bo Feng", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Rong juan Pei", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Ya qi Ding", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Mei xia Li", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Xia Chen", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Zhen yun Du", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Yang xiao Ding", + "author_inst": "Shanghai High School International Division" + }, + { + "author_name": "Chun fan Huang", + "author_inst": "Nanjing University of Chinese Medicine and Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Bo Zhang", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Xin wen Chen", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Yi Zang", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Jia Li", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Kan Ding", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.10.27.465996", "rel_title": "Camel nanobodies broadly neutralize SARS-CoV-2 variants", @@ -513069,85 +511920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.26.21265261", - "rel_title": "Safety Monitoring of mRNA Vaccines Administered During the Initial 6 Months of the U.S. COVID-19 Vaccination Program: Reports to Vaccine Adverse Events Reporting System (VAERS) and v-safe", - "rel_date": "2021-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265261", - "rel_abs": "BackgroundIn December 2020, two mRNA-based COVID-19 vaccines were authorized for use in the United States. Vaccine safety was monitored using the Vaccine Adverse Event Reporting System (VAERS), a passive surveillance system, and v-safe, an active surveillance system.\n\nMethodsVAERS and v-safe data during December 14, 2020--June 14, 2021 were analyzed. VAERS reports were categorized as non-serious, serious, or death; reporting rates were calculated. Rates of reported deaths were compared to expected mortality rates by age. Proportions of v-safe participants reporting local and systemic reactions or health impacts the week following doses 1 and 2 were determined.\n\nFindingsDuring the analytic period, 298,792,852 doses of mRNA vaccines were administered in the United States. VAERS processed 340,522 reports; 92{middle dot}1% were non-serious; 6{middle dot}6%, serious, non-death; and 1{middle dot}3%, death. Over half of 7,914,583 v-safe participants self-reported local and systemic reactogenicity, more frequently after dose 2. Injection-site pain, fatigue, and headache were commonly reported during days 0-7 following vaccination. Reactogenicity was reported most frequently one day after vaccination; most reactions were mild. More reports of being unable to work or do normal activities occurred after dose 2 (32{middle dot}1%) than dose 1 (11{middle dot}9%); <1% of participants reported seeking medical care after vaccination. Rates of deaths reported to VAERS were lower than expected background rates by age group.\n\nInterpretationSafety data from >298 million doses of mRNA COVID-19 vaccine administered in the first 6 months of the U.S. vaccination program show the majority of reported adverse events were mild and short in duration.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Hannah G. Rosenblum", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Julianne M. Gee", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ruiling Liu", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Paige L. Marquez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Bicheng Zhang", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Penelope Strid", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Winston E. Abara", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Michael M. McNeil", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tanya R. Myers", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Anne M. Hause", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John R. Su", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Bethany Baer", - "author_inst": "Food and Drug Administration" - }, - { - "author_name": "David Menschik", - "author_inst": "Food and Drug Administration" - }, - { - "author_name": "Lauri E. Markowitz", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tom T. Shimabukuro", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David K. Shay", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.25.21265166", "rel_title": "Regional probabilistic situational awareness and forecasting of COVID-19", @@ -513896,6 +512668,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.10.26.21265363", + "rel_title": "Network analysis of England single parent household COVID-19 control policy impact; a proof-of-concept study", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265363", + "rel_abs": "Lockdowns have been a key infection control measure for many countries during the COVID-19 pandemic. In Englands first lockdown, children of single parent households (SPHs) were permitted to move between parental homes. By the second lockdown, SPH support bubbles between households were also permitted, enabling larger within-household networks. We investigated the combined impact of these approaches on household transmission dynamics, to inform policymaking for control and support mechanisms in a respiratory pandemic context.\n\nThis network modelling study applied percolation theory to a base model of SPHs constructed with population survey estimates of SPH family size. To explore putative impact, varying estimates were applied regarding extent of bubbling and proportion of Different-parentage SPHs (DSPHs) (in which children do not share both the same parents). Results indicate that the formation of giant components (in which Covid-19 household transmission accelerates) are more contingent on DSPHs than on formation of bubbles between SPHs; and that bubbling with another SPH will accelerate giant component formation where one or both are DSPHs. Public health guidance should include supportive measures that mitigate the increased transmission risk afforded by support bubbling among DSPHs. Future network, mathematical and epidemiological studies should examine both independent and combined impact of policies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Natalie L Edelman", + "author_inst": "University of Brighton" + }, + { + "author_name": "Peter Simon", + "author_inst": "Institute of Mathematics, Hungary" + }, + { + "author_name": "Jackie A Cassell", + "author_inst": "Brighton and Sussex Medical School" + }, + { + "author_name": "Istvan Kiss", + "author_inst": "University of Sussex" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.20.21265300", "rel_title": "Early COVID-related Acute Kidney Injury Recovery May Course with Hydroelectrolytic Disorders in Patients With High Risk of Insensible Fluid Loss", @@ -514843,45 +513646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.25.21265218", - "rel_title": "Ongoing use of SSRIs and the hospital course of COVID-19 patients: a retrospective outcome analysis", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265218", - "rel_abs": "BackgroundThe SARS-CoV2 virus continues to have devastating consequences worldwide. Though vaccinations have helped to reduce the impact of the virus, new strains still pose a threat to unvaccinated, and to a lesser extent vaccinated, individuals. Therefore, it is imperative to identify treatments that can prevent the development of severe COVID-19. Recently, acute use of SSRI antidepressants in COVID+ patients has been shown to reduce the severity of symptoms compared to placebo. Since SSRIs are a widely used anti-depressant, the aim of this study was to determine if COVID+ patients already on SSRI treatment upon admission to the hospital had reduced mortality compared to COVID+ patients not on chronic SSRI treatment.\n\nMethodsA retrospective observational study design was used. Electronic medical records of 9,043 patients with a laboratory-confirmed diagnosis of Covid-19 from 03/2020 to 03/2021from six hospitals were queried for demographic and clinical information. Using R, a logistic regression model was run with mortality as the outcome and SSRI status as the exposure. An adjusted logistic regression model was run to account for age category, gender, and race. All tests were considered significant at p of 0.05 or less.\n\nResultsIn this sample, no patients admitted on SSRIs had them discontinued. This is consistent with current recommendations. There was no significant difference in the odds of dying between COVID+ patients on chronic SSRIs vs COVID+ patients not taking SSRIs, after controlling for age category, gender, and race. The odds of COVID+ patients on SSRIs dying was 0.98 (95%CI: 0.81, 1.18) compared to COVID+ patients not on SSRIs (p=0.83).\n\nConclusionIn times of pandemics due to novel infectious agents it is difficult, but critical to evaluate safety and efficacy of drugs that might be repurposed for treatment. This large sample size of 9,043 patients suggests that there will be no significant benefit to use of SSRIs to decrease mortality rates for hospitalized patients with Covid-19 who are not currently on SSRI medications. This study shows the utility of large clinical databases in addressing the urgent issue of determining what commonly prescribed drugs might be useful in treating COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Steven H. Rauchman", - "author_inst": "Fresno Institute of Neuroscience" - }, - { - "author_name": "Sherri G. Mendelson", - "author_inst": "Providence Holy Cross Medical Center" - }, - { - "author_name": "Courtney Rauchman", - "author_inst": "Fresno Institute of Neuroscience" - }, - { - "author_name": "Lora J. Kasselman", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "Aaron Pinkhasov", - "author_inst": "NYU Long Island School of Medicine" - }, - { - "author_name": "Allison B. Reiss", - "author_inst": "NYU Long Island School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.23.21265402", "rel_title": "Severity of Illness Caused by Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern in Children: A Single-Center Retrospective Cohort Study", @@ -515766,6 +514530,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.25.21265500", + "rel_title": "Third doses of COVID-19 vaccines reduce infection and transmission of SARS-CoV-2 and could prevent future surges in some populations", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265500", + "rel_abs": "BackgroundVaccines have greatly reduced the impact of COVID-19, but vaccine protection against milder disease and infection have waned significantly, especially for the Delta variant (B.1.617.2). A third booster dose of two-dose vaccines could restore protection but the benefit of boosting immunity in younger healthy individuals and the resultant effects on transmission have not been quantified.\n\nMethodsWe develop relationships between neutralizing antibody titers and vaccine protection against both infection and transmission. We combine these relationships with data on waning and boosting of neutralizing antibody titers to examine the impact of third doses of Pfizer-BioNtech and Moderna vaccines on infection and transmission and the impact on the pathogen effective reproductive number Rt.\n\nFindingsWaning reduced protection of the Pfizer-BioNtech vaccine against all infections from 80.0% (95% CI: 77% to 83%) to 60.4% (95% CI: 53% to 67%), and for the Moderna vaccine from 83.8 (95% CI: 80 to 87%) to 65.9% (95% CI: 61-71%). A third dose increased neutralizing antibody titers 25.9-fold relative to waned levels for the Pfizer-BioNtech vaccine and 13-fold relative to waned levels for the Moderna vaccine. This increased protection against infection to 87.2% (95% CI: 83% to 91%) and 86.3% (95% CI: 82% to 90%) for Pfizer and Moderna, respectively. Increased protection against infection and transmission from third doses reduced Rt by 28% to 74% depending on vaccine coverage and previous infection and reduced Rt below 1 when vaccination coverage was high or contact rates were well below pre-pandemic levels.\n\nInterpretationA third vaccine dose could substantially reduce transmission of SARS-CoV-2 and prevent future surges, with the impact increasing with vaccine coverage and contact rates among individuals. Reducing transmission would reduce infection in both unvaccinated individuals and breakthrough infections in vaccinated individuals.\n\nFundingCalifornia Department of Health, National Science Foundation", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Billy J Gardner", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "A. Marm Kilpatrick", + "author_inst": "University of California, Santa Cruz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.25.21265475", "rel_title": "Optimising the balance of acute and intermediate care capacity for the complex discharge pathway: computer modelling study during COVID-19 recovery in England", @@ -516965,97 +515752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.10.21.21265158", - "rel_title": "Immune response to COVID-19 vaccination is attenuated by poor disease control and antimyeloma therapy with vaccine driven divergent T cell response", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265158", - "rel_abs": "BackgroundMyeloma patients frequently respond poorly to bacterial and viral vaccination. A few studies have reported poor humoral immune responses in myeloma patients to COVID-19 vaccination.\n\nMethodsUsing a prospective study of myeloma patients in UK Rudy Study cohort, we assessed humoral and Interferon gamma release assay (IGRA) cellular immune responses to COVID-19 vaccination post second COVID-19 vaccine administration.\n\nFindingsWe report data from 214 adults with myeloma (n=204) or smouldering myeloma (n=10) who provided blood samples at least 3 weeks after second vaccine dose. Positive Anti-Spike antibody levels (> 50 IU/ml) were detected in 189/203 (92.7%), positive IGRA responses were seen in 97/158 (61.4%) myeloma patients. Only 10/158 (6.3%) patients were identified to have both a negative IGRA and negative Anti-Spike protein antibody response. 95/158 (60.1%) patients produced positive results for both anti-Spike protein serology and IGRA. After adjusting for disease severity and myeloma therapy, poor humoral immune response was predicted by male gender. Predictors of poor IGRA included anti-CD38/ anti-BCMA therapy and Pfizer-BioNTech (PB) vaccination.\n\nInterpretationSignificant majority of myeloma patients elicit Anti-Spike protein antibody responses to COVID-19 vaccine with 60% of myeloma patients showing both humoral and T cell response. Predictors of a poor immune response included male gender, myeloma therapy regimen and administration of Pfizer-BioNTech vaccination. Further work is required to understand the clinical significance of divergent cellular response to vaccination.\n\nFundingFunding for this study has been received from Blood Cancer Vaccine Consortium and Janssen UK. RUDY platform has been funded by NIHR.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Karthik Ramasamy", - "author_inst": "Oxford University hospitals NHS FT" - }, - { - "author_name": "Ross Sadler", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Sally Jeans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Weeden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sherin Varghese", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Alison Turner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jemma Larham", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Nathanael Gray", - "author_inst": "University of Oxford" - }, - { - "author_name": "Oluremi Carti", - "author_inst": "Oxford University Hospitals NHS Trust" - }, - { - "author_name": "Joe Barrett", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stella Bowcock", - "author_inst": "Kings College Hospital NHS Trust" - }, - { - "author_name": "Gordon Cook", - "author_inst": "University of Leeds" - }, - { - "author_name": "Charalampia Kyriakou", - "author_inst": "University College London Hospitals NHS Trust" - }, - { - "author_name": "Mark Drayson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Supratik Basu", - "author_inst": "University of Wolverhampton" - }, - { - "author_name": "Sally Moore", - "author_inst": "Oxford University Hospitals NHS Trust, Bath Royal United Hospitals," - }, - { - "author_name": "Sarah Mcdonald", - "author_inst": "Myeloma UK" - }, - { - "author_name": "Sarah Gooding", - "author_inst": "The MRC Weatherall Institute of Molecular Medicine" - }, - { - "author_name": "Kassim Javid", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.10.21.21265340", "rel_title": "How different pre-existing mental disorders and their co-occurrence affects clinical outcomes of COVID-19? A study based on real-world data in the Southern United States", @@ -517768,6 +516464,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.21.21265322", + "rel_title": "Seroconversion rate and socioeconomic and ethnic risk factors for SARS-CoV-2 infection in children in a population-based cohort", + "rel_date": "2021-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265322", + "rel_abs": "IntroductionSocioeconomic and ethnic background have been discussed as possible risk factors for SARS-CoV-2 infections in children. Improved knowledge could lead way to tailored prevention strategies and help to improve infection control.\n\nMethodsObservational population-based cohort study in children (6mo. - 18 ys.) scheduled for legally required preventive examination and their parents in a metropolitan region in Germany. Primary endpoint was the SARS-CoV-2 seroconversion rate during study period. Risk factors assessed included age, pre-existing medical conditions, socioeconomic factors, and ethnicity.\n\nResults2124 children and their parents were included. Seroconversion rates among children in all age groups increased by 3-4-fold from 06/2020 to 02/2021. Only 41% of seropositive children were symptomatic. In 51% of infected children at least one parent was also SARS-CoV-2 positive.\n\nLow level of parental education (OR 3.13 (0.72-13.69)) significantly increased the risk of infection. Of the total cohort, 38.5% had a migration background. Specifically, 9% were of Turkish and 5% of Middle Eastern origin. These children had the highest risk for SARS-CoV-2 infections (OR 6.24 (1.38-28.12) and 6.44 (1.14-36.45) after adjustment for other risk factors.\n\nDiscussionSeroprevalence of SARS-CoV-2 infections in children increased by 3-4-fold within the study period. Frequently, more than one family member was infected. Children from families with lower socioeconomic status were at higher risk. The highest risk for SARS-CoV-2 infection was identified in families with Turkish or Middle Eastern background. Culture sensitive approaches are essential to improve infection control and serve as a blueprint for vaccination strategies in this population.\n\nTrial RegistrationBMBF funding registration 01KI20173 (Corkid)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Folke Brinkmann", + "author_inst": "University Hospital Bochum" + }, + { + "author_name": "Hans H Diebner", + "author_inst": "Ruhr-University-Bochum" + }, + { + "author_name": "Chantal Matenar", + "author_inst": "University Hospital Bochum" + }, + { + "author_name": "Anne Schlegtendal", + "author_inst": "University Hospital Bochum" + }, + { + "author_name": "Lynn Eitner", + "author_inst": "University Hospital Bochum" + }, + { + "author_name": "Nina Timmesfeld", + "author_inst": "Ruhr-University-Bochum" + }, + { + "author_name": "Christoph Maier", + "author_inst": "University- Hospital- Bochum" + }, + { + "author_name": "Thomas Luecke", + "author_inst": "University Hospital Bochum" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.10.24.21265451", "rel_title": "Main COVID-19 information sources in a culturally and linguistically diverse community in Sydney, Australia: A cross-sectional survey", @@ -519227,89 +517970,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.20.21265299", - "rel_title": "Collateral positives of COVID-19 for culturally and linguistically diverse communities in Western Sydney, Australia", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265299", - "rel_abs": "Issues addressedTo investigate whether culturally and linguistically diverse communities in Western Sydney have experienced any positive effects during the COVID-19 pandemic, and if so, what these were.\n\nMethodsA cross-sectional survey with ten language groups was conducted from 21st March to 9th July 2021 in Sydney, Australia. Participants were recruited through bilingual multicultural health staff and health care interpreter service staff and answered a question, In your life, have you experienced any positive effects from the COVID-19 pandemic? Differences were explored by demographic variables. Free-text responses were thematically coded using the Content Analysis method.\n\nResults707 people completed the survey, aged 18 to >70, 49% males and 51% females. Only 161 (23%) of those surveyed reported any positive impacts. There were significant differences in the proportion of those who reported positives based on age (p=0.004), gender (p=0.013), language (p=0.003), health literacy (p=0.014), English language proficiency (p=0.003), education (p=<0.001) and whether participants had children less than 18 years at home (p=0.001). Reporting of positive impacts ranged from 12% for people aged seventy years or older to 30% for the 30-49-year age group. Reporting of positive impacts for different language groups ranged from 9% to 42%. 18% of men reported positive impacts compared to 27% of women, and 18% of people with inadequate health literacy reported positive impacts compared to 26% with adequate health literacy. Content Analysis of open-ended responses showed that, of those that did report positives, the top themes were Family time (44%), Improved self-care (31%) and, Greater connection with others (17%).\n\nConclusionsFrom 21st March to July 9th, 2021, few surveyed participants reported finding any positives because of the COVID-19 pandemic. This finding is in stark contrast to related research in Australia in a population dominated by adults with English as their first language, carried out in June 2020, in which many more people experienced positives.\n\nSo whatThe needs of people from culturally and linguistically diverse backgrounds must inform future responses to community crises to facilitate an equitable effect of any collateral positives that may arise.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Samuel Cornell", - "author_inst": "University of Sydney" - }, - { - "author_name": "Julie Ayre", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Olivia A Mac", - "author_inst": "University of Sydney" - }, - { - "author_name": "Raveena Kapoor", - "author_inst": "University of Sydney" - }, - { - "author_name": "Kristen Pickles", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Carys Batcup", - "author_inst": "University of Sydney" - }, - { - "author_name": "Hankiz Dolan", - "author_inst": "University of Sydney" - }, - { - "author_name": "Carissa Bonner", - "author_inst": "University of Sydney" - }, - { - "author_name": "Erin Cvejic", - "author_inst": "University of Sydney" - }, - { - "author_name": "Dana Mouwad", - "author_inst": "Western Sydney Local Health District" - }, - { - "author_name": "Dipti Zacharia", - "author_inst": "Western Sydney Local Health District" - }, - { - "author_name": "Una Tularic", - "author_inst": "Nepean Blue Mountains Local Health District" - }, - { - "author_name": "Yvonne Santalucia", - "author_inst": "Southwestern Sydney Local Health District" - }, - { - "author_name": "Tingting Chen", - "author_inst": "Western Sydney Local Health District" - }, - { - "author_name": "Gordana Vasic", - "author_inst": "Western Sydney Local Health District" - }, - { - "author_name": "Kirsten J McCaffery", - "author_inst": "University of Sydney" - }, - { - "author_name": "Danielle M Muscat", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.20.21265295", "rel_title": "Predictors of SARS-CoV-2 infection following high-risk exposure: a test-negative design case-control study", @@ -520062,6 +518722,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.10.19.21265194", + "rel_title": "General Practitioner perspectives and wellbeing during the COVID-19 Pandemic: a mixed method social media analysis", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265194", + "rel_abs": "BackgroundGeneral practitioners (GPs) adapted their work practices rapidly in response to the COVID-19 pandemic. Limited research has explored their perspectives over this time, and factors that may affect their wellbeing.\n\nMethodWe conducted a social media analysis of NHS GPs practising in the UK during the COVID-19 pandemic to identify issues which may affect their wellbeing. To identify trends, we assessed 91,034 tweets from 185 GPs on Twitter who posted before and during the pandemic, (January 2019 to February 2021). To identify themes related to wellbeing, we analysed qualitatively 7145 tweets posted during the pandemic from 200 GPs.\n\nResultsWe identified inter-connecting themes that affect GP wellbeing, predominately around resources and support. Lack of personal protective equipment (PPE) and testing led to discussion of safety and risk, as well as increased workload resulting from staff isolating. Expressions of low morale and feeling undervalued were widespread, resulting from the perceived lack of support from the government, media and the general public at a time of staff shortages and high workload.\n\nTrends in themes were apparent, with emphasis on PPE, testing and safety March to May 2020 and morale, abuse, closed GP surgeries, testing, flu vaccines and overworked September to October 2020. From December 2020 the COVID-19 vaccine dominated posts.\n\nConclusionGPs experiences and perceptions as reflected in their social media posts during the pandemic have changed over time; perceived lack of support and resources, and negative public perceptions have exacerbated their concerns about existing underlying pressures.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Su Golder", + "author_inst": "University of York" + }, + { + "author_name": "Laura Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Elizabeth McHugh", + "author_inst": "University of York" + }, + { + "author_name": "Holly Essex", + "author_inst": "University of York" + }, + { + "author_name": "Claire Heathcote", + "author_inst": "University of York" + }, + { + "author_name": "Ana Cristina Castro-Avila", + "author_inst": "University of York" + }, + { + "author_name": "Veronica Dale", + "author_inst": "University of York" + }, + { + "author_name": "Christina Van Der Feltz-Cornelis", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.10.19.21265175", "rel_title": "Psychological distress of healthcare workers in Quebec (Canada) during the second and the third pandemic waves", @@ -521048,77 +519759,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.10.20.21265278", - "rel_title": "Multireader Evaluation of Radiologist Performance for COVID-19 Detection on Emergency Department Chest Radiographs", - "rel_date": "2021-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265278", - "rel_abs": "BackgroundChest radiographs (CXR) are frequently used as a screening tool for patients with suspected COVID-19 infection pending reverse transcriptase polymerase chain reaction (RT-PCR) results, despite recommendations against this. We evaluated radiologist performance for COVID-19 diagnosis on CXR at the time of patient presentation in the Emergency Department (ED).\n\nMaterials and MethodsWe extracted RT-PCR results, clinical history, and CXRs of all patients from a single institution between March and June 2020. 984 RT-PCR positive and 1043 RT-PCR negative radiographs were reviewed by 10 emergency radiologists from 4 academic centers. 100 cases were read by all radiologists and 1927 cases by 2 radiologists. Each radiologist chose the single best label per case: Normal, COVID-19, Other - Infectious, Other - Noninfectious, Non-diagnostic, and Endotracheal Tube. Cases labeled with endotracheal tube or non-diagnostic were excluded. Remaining cases were analyzed for label distribution, clinical history, and inter-reader agreement.\n\nResults1727 radiographs (732 RT-PCR positive, 995 RT-PCR negative) were included from 1,594 patients (51.2% male, 48.8% female, age 59 {+/-} 19 years). For 89 cases read by all readers, there was poor agreement for RT-PCR positive (Fleiss Score 0.36) and negative (Fleiss Score 0.46) exams. Agreement between two readers on 1,638 cases was 54.2% (373/688) for RT-PCR positive cases and 71.4% (679/950) for negative cases. Agreement was highest for RT-PCR negative cases labeled as Normal (50.4%, n= 479). Reader performance did not improve with clinical history or time between CXR and RT-PCR result.\n\nConclusionAt the time of presentation to the emergency department, emergency radiologist performance is non-specific for diagnosing COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Judy W. Gichoya", - "author_inst": "Emory University" - }, - { - "author_name": "Priyanshu Sinha", - "author_inst": "Indiana Univesity" - }, - { - "author_name": "Melissa Davis", - "author_inst": "Emory University" - }, - { - "author_name": "Jeffrey W. Dunkle", - "author_inst": "Indiana University" - }, - { - "author_name": "Scott A. Hamlin", - "author_inst": "Emory University" - }, - { - "author_name": "Keith D. Herr", - "author_inst": "Emory University" - }, - { - "author_name": "Carrie N. Hoff", - "author_inst": "Emory University" - }, - { - "author_name": "Haley P. Letter", - "author_inst": "University of Florida" - }, - { - "author_name": "Christopher R. McAdams", - "author_inst": "Emory University" - }, - { - "author_name": "Gregory D. Puthoff", - "author_inst": "Wake Forest University" - }, - { - "author_name": "Kevin L. Smith", - "author_inst": "Indiana University" - }, - { - "author_name": "Scott D. Steenburg", - "author_inst": "Indiana University" - }, - { - "author_name": "Imon Banerjee", - "author_inst": "Emory University" - }, - { - "author_name": "Hari Trivedi", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.10.20.21265283", "rel_title": "Food Security Impacts of the COVID-19 Pandemic: Following a Cohort of Vermonters During the First Year", @@ -522155,6 +520795,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.10.19.464931", + "rel_title": "Repurposed nystatin to inhibit SARS-CoV-2 and mutants in the GI tract", + "rel_date": "2021-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.19.464931", + "rel_abs": "The SARS-CoV-2 infections are considered as respiratory system diseases, mostly. In COVID-19, it might also be the infection of gastrointestinal (GI) tract too, especially at patients in severe clinical condition. SARS-CoV-2 can destroy the intestinal barrier, capable to spread into internal organs via blood and/or lymphatic circulation, and to cause serious damage there. Infected GI tract of COVID-19 patients is ideal environment for the coronavirus infection, replication and as virus reservoir might be the major source of pandemic reinfections, too. The process of virus budding is dependent on the host cell lipid rafts containing membrane-sterols, mainly cholesterol. The viral envelope may be challenged by polyene antibiotics, such as nystatin, which has strong affinity to sterols. Nystatin may block the establishment of the virus-host cell connection, too. In this study, the nystatin was investigated, as antiviral agent to SARS-CoV-2. We demonstrated by tests in Vero E6 cell based cytopathic assay, nystatin blocked the replication of SARS-CoV-2 in concentration 62.5 g/ml (IC50) at Wuhan and British mutant strains. No efficient SARS-CoV-2 antiviral agent is known so far to alleviate pandemic, to disinfect GI tract, where vaccines might have limited effect, only. Nystatin might be the first one with emergency use authorization, either, as a safe and efficient non-systemic antiviral drug, with well-established use, since decades.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Eszter Virag", + "author_inst": "Research Institute for Medicinal Plants and Herbs Ltd." + }, + { + "author_name": "Denes Seffer", + "author_inst": "Department of Research and Development, PannonPharma Pharmaceutical Ltd, Pecsvarad, Hungary" + }, + { + "author_name": "Agota Penzes-Huvos", + "author_inst": "Department of Research and Development, PannonPharma Pharmaceutical Ltd, Pecsvarad, Hungary" + }, + { + "author_name": "Krisztina Varajti", + "author_inst": "Department of Research and Development, PannonPharma Pharmaceutical Ltd, Pecsvarad, Hungary" + }, + { + "author_name": "Geza Hegedus", + "author_inst": "Department of Research and Development, PannonPharma Pharmaceutical Ltd, Pecsvarad, Hungary" + }, + { + "author_name": "Istvan Jankovics", + "author_inst": "Department of Coronavirus Diagnostics, Complex Medical Center, Budapest, Hungary" + }, + { + "author_name": "Jozsef Peter Pallos", + "author_inst": "Department of Research and Development, PannonPharma Pharmaceutical Ltd, Pecsvarad, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.10.19.465025", "rel_title": "Oral Lisinopril Raises Tissue Levels of ACE2, the SARS-CoV-2 Receptor, in Healthy Male and Female Mice", @@ -523194,101 +521877,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.18.21265113", - "rel_title": "Immune Responses in Fully Vaccinated Individuals Following Breakthrough Infection with the SARS-CoV-2 Delta Variant in Provincetown, Massachusetts", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265113", - "rel_abs": "BackgroundA cluster of over a thousand infections with the SARS-CoV-2 delta variant was identified in a predominantly fully vaccinated population in Provincetown, Massachusetts in July 2021. Immune responses in breakthrough infections with the SARS-CoV-2 delta variant remain to be defined.\n\nMethodsHumoral and cellular immune responses were assessed in 35 vaccinated individuals who were tested for SARS-CoV-2 in the Massachusetts Department of Public Health outbreak investigation.\n\nResultsVaccinated individuals who tested positive for SARS-CoV-2 demonstrated substantially higher antibody responses than vaccinated individuals who tested negative for SARS-CoV-2, including 28-fold higher binding antibody titers and 34-fold higher neutralizing antibody titers against the SARS-CoV-2 delta variant. Vaccinated individuals who tested positive also showed 4.4-fold higher Spike-specific CD8+ T cell responses against the SARS-CoV-2 delta variant than vaccinated individuals who tested negative.\n\nConclusionsFully vaccinated individuals developed robust anamnestic antibody and T cell responses following infection with the SARS-CoV-2 delta variant. These data suggest important immunologic benefits of vaccination in the context of breakthrough infections.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ai-ris Collier", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Catherine Brown", - "author_inst": "MA Department of Public Health" - }, - { - "author_name": "Katherine McMahan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jinyan Liu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Catherine Jacob-Dolan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Abishek Chandrashekar", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Dylan Tierney", - "author_inst": "MA Department of Public Health" - }, - { - "author_name": "Jessica Ansel", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Marjorie Rowe", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Daniel Sellers", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Kunza Ahmad", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Ricardo Aguayo", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Tochi Anioke", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Sarah Gardner", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Mazuba Siamatu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Lorraine Bermudez Rivera", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Michele Hacker", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Lawrence Madoff", - "author_inst": "MA Department of Public Health" - }, - { - "author_name": "Dan Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.14.21264762", "rel_title": "Longitudinal and comparative analysis of humoral response upon COVID-19 vaccination", @@ -523865,6 +522453,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.10.16.21264948", + "rel_title": "Impact of SARS-CoV-2 infection on longitudinal vaccine immune responses", + "rel_date": "2021-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.16.21264948", + "rel_abs": "People with previous SARS-CoV-2 infection mount potent immune responses to COVID-19 vaccination, but long-term effects of prior infection on these immune responses are unknown. We investigated the long-term impact of prior SARS-CoV-2 infection on humoral and cellular immune responses in healthcare workers receiving the mRNA BNT162b2 or the adenovirus vectored ChAdOx1 nCoV-19 vaccine. Vaccination with both vaccine platforms resulted in substantially enhanced T cell immune responses, antibody responses to spike and neutralizing antibodies effective against ten SARS-CoV-2 variants following SARS-CoV-2 infection, compared to in naive individuals. The enhanced immune responses sustained over seven months following vaccination. These findings imply that prior infection should be taken into consideration when planning booster doses and design of current and future COVID-19 vaccine programs.\n\nOne-Sentence SummarySARS-CoV-2 infection prior to vaccination leads to substantial and durable increases in immune memory responses.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Ulrika Marking", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Nina Greilert-Norin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Max Gordon", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Kim Blom", + "author_inst": "Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" + }, + { + "author_name": "Sara Mangsbo", + "author_inst": "Department of Pharmacy and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Mikael Aberg", + "author_inst": "Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.18.21265169", "rel_title": "Elevated antibody titers in Abdala vaccinees evaluated by Elecsys(R) anti-SARS-CoV-2 S highly correlate with UMELISA SARS-CoV-2 ANTI RBD, ACE-2 binding inhibition and viral neutralization assays.", @@ -524891,29 +523550,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.14.21265035", - "rel_title": "Modeling the influence of vaccine administration on COVID-19 testing strategies", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21265035", - "rel_abs": "Vaccination is considered the best strategy for limiting and eliminating the COVID-19 pandemic. The success of this strategy relies on the rate of vaccine deployment and acceptance across the globe. As these efforts are being conducted, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is continuously mutating, which leads to the emergence of variants with increased transmissibility, virulence, and lower response the vaccines. One important question is whether surveillance testing is still needed in order to limit SARS-CoV-2 transmission in an increasingly vaccinated population. In this study, we developed a multi-scale mathematical model of SARS-CoV-2 transmission in a vaccinated population and used it to predict the role of testing in an outbreak with alpha and delta variants. We found that, when the alpha variant is dominant, testing is effective when vaccination levels are low to moderate and its impact is diminished when vaccination levels are high. When the delta variant is dominant, widespread vaccination is necessary in order to prevent significant outbreaks. When only moderate vaccination can be achieved, frequent testing can significantly reduce the cumulative size of delta variant outbreak, with the impact of testing having maximum effects when focused on the non-vaccinated population.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jonathan Forde", - "author_inst": "Hobart and William Smith Colleges" - }, - { - "author_name": "Stanca Ciupe", - "author_inst": "Virginia Tech" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.15.21265006", "rel_title": "Vaccine effectiveness of Ad26.COV2.S against symptomatic COVID-19 and clinical outcomes in Brazil: a test-negative study design", @@ -525402,6 +524038,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.10.17.21265111", + "rel_title": "SARS-CoV-2 Pandemic Preventive Methods Efficacy - A Simulation Case Study", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265111", + "rel_abs": "The world has been facing the SARS-CoV-2, a.k.a. COVID-19, pandemic with different preventive methods including social distancing, face masking, screening tests (a.k.a. active surveillance), and vaccination. There are many publications and studies on the efficacy of each of these preventive methods for the last couple of years. Not all methods are readily available in each country and not all methods are accepted by all people in each society.\n\nIn this study, we explore the interaction of the three preventive methods: face masking, vaccinations, and screening tests. We study a confined space to represent schools, businesses, or healthcare facilities and we model the spread of the COVID-19 virus for a 60-day period among a sample population while varying the percentage of people adopting one or more of the three preventive methods.\n\nTo interpret the simulation results, we define a (Health Goal) target, for example achieving <5% infection rate, i.e., protecting 95% or more of the sample population. We then construct a (Decision Tree) that depicts all valid combinations that achieve this goal. Multiple scenarios are derived from the decision tree to guide decision makers in drawing effective policies to contain the virus spread. We demonstrate a ramping vaccination rate scenario, a removal of the face-masking mandate scenario, and a cost-minimizing goal scenario.\n\nThe study highlights the efficacy of combining the three prevention methods to constrain the virus spread among the sample population. For example, results show that a combination of 0% vaccination rate, 6% daily screening test rate, and 80% face masking rate will achieve the target [≥]95 protection rate, which can represent a scenario in which vaccination is not yet readily available. As the vaccination rate ramps up to 80% among the sample population, the screening test rate can be 0%, while the face masking rate can be as low as 5% to still achieve the health target. Many other scenarios are derived from this study to meet the defined health target, which represents the flexibility afforded to policy and decision makers when trying to adopt a combination of these preventive methods to contain virus spread.\n\nThe study also reveals the higher efficiency of either the vaccination or screening test over face masking under the assumed virus transmissibility rates in the study.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Malak Saad", + "author_inst": "Del Norte High School" + }, + { + "author_name": "Emad M Boctor", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.15.21265063", "rel_title": "Factors associated with severity of COVID-19 disease in a multicenter cohort of people with HIV in the United States, March-December 2020", @@ -526545,33 +525204,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.10.17.464720", - "rel_title": "Mapping Molecular Gene Signatures Among Respiratory Viruses Based on Large-Scale and Genome-wide Transcriptomics Analysis", - "rel_date": "2021-10-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.17.464720", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging RNA virus causing COVID-19 disease across the globe. SARS-CoV-2 infected patients exhibit acute respiratory distress syndrome which can be compounded by endemic respiratory viruses and thus highlighting the need to understand the genetic bases of clinical outcome under multiple respiratory infections. In this study, 42 individual datasets and a multi-parametric based selected list of over 12,000 genes against five medically important respiratory viruses (SARS-CoV-2, SARS-CoV-1, influenza A, respiratory syncytial virus (RSV) and rhinovirus were collected and analysed in an attempt to understand differentially regulated gene patterns and to cast genetic markers of individual and multiple co-infections. While a certain cohort of virus-specific genes were regulated (negatively and positively), notably results revealed a greatest correlation among gene regulation by SARS-CoV-2 and RSV. Furthermore, out of analysed genes, the MAP2K5 and NFKBIL1 were specifically and highly upregulated in SARS-CoV-2 infection in vivo or in vitro. In contrast, several genes including GPBAR1 and SC5DL were specifically downregulated in SARS-CoV-2 datasets. Additionally, we catalogued a set of genes that were conserved or differentially regulated across all the respiratory viruses. These finding provide foundational and genome-wide data to gauge the markers of respiratory viral infections individually and under co-infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thomas Smith", - "author_inst": "Division of Biomedical and Life Sciences, Lancaster University, Lancaster, Lancashire, LA1 4YG United Kingdom" - }, - { - "author_name": "Mohammed A. Rohaim", - "author_inst": "Division of Biomedical and Life Sciences, Lancaster University, Lancaster, Lancashire, LA1 4YG United Kingdom" - }, - { - "author_name": "Muhammad Munir", - "author_inst": "Division of Biomedical and Life Sciences, Lancaster University, Lancaster, Lancashire, LA1 4YG United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.13.21264855", "rel_title": "\"I had no life. I was only existing\". Factors shaping the mental health and wellbeing of people experiencing long Covid: a qualitative study.", @@ -527235,6 +525867,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.10.14.464320", + "rel_title": "Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids", + "rel_date": "2021-10-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.14.464320", + "rel_abs": "While pluripotent stem cell-derived kidney organoids are now being used to model renal disease, the proximal nephron remains immature with limited evidence for key functional solute channels. This may reflect early mispatterning of the nephrogenic mesenchyme and/or insufficient maturation. Here we show that enhanced specification to metanephric nephron progenitors results in elongated and radially aligned proximalised nephrons with distinct S1 - S3 proximal tubule cell types. Such PT-enhanced organoids possess improved albumin and organic cation uptake, appropriate KIM-1 upregulation in response to cisplatin, and improved expression of SARS-CoV-2 entry factors resulting in increased viral replication. The striking proximo-distal orientation of nephrons resulted from localized WNT antagonism originating from the organoid stromal core. PT-enhanced organoids represent an improved model to study inherited and acquired proximal tubular disease as well as drug and viral responses.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rajeev Rudraraju", + "author_inst": "Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia." + }, + { + "author_name": "Jessica Neil", + "author_inst": "Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia." + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.10.08.21264715", "rel_title": "One-shot immunization with Sputnik Light (the first component of Sputnik V vaccine) is effective against SARS-CoV-2 Delta variant: efficacy data on the use of the vaccine in civil circulation in Moscow", @@ -528646,49 +527305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.12.21264904", - "rel_title": "The impact of heating, ventilation, and air conditioning design features on the transmission of viruses, including the 2019 novel coronavirus: a systematic review of ultraviolet radiation", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264904", - "rel_abs": "Respiratory viruses are capable of transmitting via an aerosol route. Emerging evidence suggests that SARS-CoV-2 which causes COVID-19 can be spread through airborne transmission, particularly in indoor environments with poor ventilation. Heating, ventilation, and air conditioning (HVAC) systems can play a role in mitigating airborne virus transmission. We conducted a systematic review of the scientific literature examining the effectiveness of HVAC design features in reducing virus transmission--here we report results for ultraviolet (UV) radiation. Following international standards for systematic reviews, we conducted a comprehensive search and synthesized findings from 32 relevant studies published between 1936 and 2020. Research demonstrates that: viruses and bacteriophages are inactivated by UV radiation; increasing UV dose is associated with decreasing survival fraction of viruses and bacteriophages; increasing relative humidity is associated with decreasing susceptibility to UV radiation; UV dose and corresponding survival fraction are affected by airflow pattern, air changes per hour, and UV device location; and UV radiation is associated with decreased transmission in both animal and human studies. This comprehensive synthesis of the scientific evidence examining the impact of UV radiation on virus transmission can be used to guide implementation of systems to mitigate airborne spread and identify priorities for future research.\n\nPractical ImplicationsIn-duct ultraviolet germicidal irradiation (UVGI) addresses virus transmission throughout the heating, ventilation, and air conditioning (HVAC) system of a building as a whole; whereas, upper-room UVGI addresses virus transmission in one room of that building. The susceptibility of a virus is often determined from the relationship between UV dose and survival fraction of the virus, and can be affected by relative humidity. Modelling studies revealed that practical implementation of UVGI in HVAC systems should consider airflow patterns, air changes per hour, and UV device location. Future field studies of UVGI systems could address an existing research gap and provide important information on system performance in real-world situations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gail M. Thornton", - "author_inst": "University of Alberta" - }, - { - "author_name": "Brian A Fleck", - "author_inst": "University of Alberta" - }, - { - "author_name": "Natalie Fleck", - "author_inst": "University of Alberta" - }, - { - "author_name": "Emily Kroeker", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dhyey Dandnayak", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lexuan Zhong", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lisa Hartling", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.12.21264860", "rel_title": "SARS-CoV-2 vaccine antibody response and breakthrough infections in patients receiving dialysis", @@ -529573,6 +528189,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.10.12.21264898", + "rel_title": "Why one size fits all is not enough when designing immunity certificates for domestic use: a UK wide cross-sectional online survey", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264898", + "rel_abs": "ObjectivesThe present study explored publics willingness to use COVID-19 immunity certificates across six different domestic scenarios.\n\nDesignCross-sectional online survey.\n\nSettingUK representative survey conducted on the 3rd of August 2021.\n\nParticipants534 UK residents over 18 years old.\n\nInterventionsParticipants replied to the same set of questions.\n\nPrimary and secondary outcome measuresThe primary outcome measure was willingness to use immunity certificates across three different domestic settings (1. Visiting the GP for a non-urgent health issue, 2. Dining in a restaurant, and 3. Attending a performance in a theatre). For each setting two options, one prioritising convenience (option A) and the other privacy (option B), were offered. Our secondary outcome measures were computed indices from items adapted from the Health Belief Model; Attitudes towards sharing immunity status with service providers; Prior to COVID-19 lifestyle. In addition, we recorded data about respondents socio-demographic characteristics.\n\nResultsRespondents were more willing to use immunity certificates that prioritised convenience, rather than privacy, when visiting their GP (92%). However, privacy was more favorable (84%) in the other two settings (dining in a restaurant and going to a theatre) compared to convenience (39%). Personal beliefs about COVID-19 and immunity certificates were associated with variations in willingness to use these across all scenarios. No variations were observed across socio-demographics and lifestyle.\n\nConclusionsThe findings of this survey suggest that there is not one size fits all solution for designing immunity certificates. Immunity certificates are complex socio-technical systems, any attempt to implement these for domestic use should be tailored to different settings and user needs. The design of certification services requires a more evidence-based approach and further research is needed to understand how different settings, design elements (like convenience or privacy) and personal beliefs about the pandemic should inform their design.\n\nStrengths and limitations of this studyO_LIThis study presents unique knowledge about the publics willingness to use immunity certificates for domestic purposes where there is very little published research at the moment.\nC_LIO_LIThe study reports knowledge about the interaction between individual characteristics, domestic settings, and types of immunity certificate design on willingness to use these certificates.\nC_LIO_LIUK nationally representative sample for age, gender, and ethnic background, but limited to people who have the means and capacity to use digital technologies (survey administered using Prolific.co).\nC_LIO_LIWe present evidence-based recommendations for Public Health services and policy makers about the use of immunity certificates in different domestic settings.\nC_LIO_LISince, as to the writing of this paper, COVID-19 certification has not been mandated in the UK, the scenarios used in the survey were hypothetical.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Corina-Elena Niculaescu", + "author_inst": "Brunel University London" + }, + { + "author_name": "Isabel Karen Sassoon", + "author_inst": "Brunel University London" + }, + { + "author_name": "Irma Cecilia Landa-Avila", + "author_inst": "Loughborough University" + }, + { + "author_name": "Ozlem Colak", + "author_inst": "Loughborough University" + }, + { + "author_name": "Gyuchan Thomas Jun", + "author_inst": "Loughborough University" + }, + { + "author_name": "Panagiotis Balatsoukas", + "author_inst": "Loughborough University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.10.12.21264881", "rel_title": "Detection of neutralizing antibodies against SARS-CoV-2 by using a commercial surrogate virus neutralization ELISA: can it substitute the classical neutralization test?", @@ -530488,121 +529143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264755", - "rel_title": "High risk of SARS-CoV-2 infection among frontline healthcare workers in Northeast Brazil: a respondent-driven sampling approach", - "rel_date": "2021-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264755", - "rel_abs": "IntroductionThe disparities in the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among frontline health care workers (HCWs) and the unique work circumstances are poorly documented for low-and middle-income countries.\n\nMethodsWe assessed the frequency of SARS-CoV-2 infection, personal protective equipment (PPE) shortages, PPE use, and accidents involving biological material among HCWs in the Recife metropolitan area, Northeast Brazil. Using respondent driven sampling, we included HCWs attending suspected or confirmed COVID-19 patients from May 2020 to February 2021.\n\nResultsWe analyzed 1,525 HCWs (527 physicians, 471 registered nurses, 263 nursing assistants/technicians, and 264 physical therapists). Women predominated in all categories (81.1%). Nurses were older and had more comorbidities (hypertension and overweight/obesity) than the other HCWs. The overall prevalence of SARS-CoV-2 infection was 61.8% after adjustment for the cluster random effect, weighted by network, and reference population size. The independent risk factors for a positive RT-PCR test were being a nursing assistant (OR adjusted: 2.56), not always using all recommended PPE in routine practice (ORadj: 2.15), and reporting a splash of biological fluid/respiratory secretion in the eyes (ORadj: 3.37).\n\nConclusionsThe high risk of infection among HCWs reflects PPE shortages and younger, possibly less experienced, frontline HCWs. There were disparities in the risk of SARS-CoV-2 infection among HCWs, with nursing assistants being the most vulnerable, possibly due to their longer and frequent contact with COVID-19 patients.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Maria de Fatima Pessoa Militao de Albuquerque", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Wayner Vieira de Souza", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Ulisses Ramos Montarroyos", - "author_inst": "Pernambuco University, Pernambuco, Brazil" - }, - { - "author_name": "Cresio Romeu Pereira", - "author_inst": "Ministry of Health of Brazil" - }, - { - "author_name": "Cynthia Braga", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Thalia Velho Barreto de Araujo", - "author_inst": "Federal University of Pernambuco, Brazil" - }, - { - "author_name": "Ricardo Arraes de Alencar Ximenes", - "author_inst": "Federal University of Pernambuco and Pernambuco University, Brazil" - }, - { - "author_name": "Democrito Barros Miranda-Filho", - "author_inst": "Pernambuco University, Pernambuco, Brazil" - }, - { - "author_name": "Celia Landmann Szwarcwald", - "author_inst": "Institute of Scientific Communication and Information and Technological (ICIT), FIOCRUZ-RJ, Brazil" - }, - { - "author_name": "Paulo Roberto Borges de Souza-Junior", - "author_inst": "Institute of Scientific Communication and Information and Technological (ICIT), FIOCRUZ-RJ, Brazil" - }, - { - "author_name": "Morgana Nascimento Xavier", - "author_inst": "Federal University of Pernambuco, Pernambuco, Brazil" - }, - { - "author_name": "Clarice Neuenschwander Lins de Morais", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Gabriela Diniz Militao de Albuquerque", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Cristiane Bresani-Salvi", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Carolline Araujo Mariz", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Noemia Teixeira de Siquera", - "author_inst": "Department of Health Sciences, University of York, UK" - }, - { - "author_name": "Jadson Mendonca Galindo", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Claudio Luiz Franca-Neto", - "author_inst": "Pernambuco University, Brazil" - }, - { - "author_name": "Jessyka Mary Vasconcelos Barbosa", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - }, - { - "author_name": "Maria Amelia S M Veras", - "author_inst": "Faculty of Medical Sciences of Santa Casa de Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Luana Nepomuceno Gondim Costa Lima", - "author_inst": "State University of Para, Brazil" - }, - { - "author_name": "Luciane Nascimento Cruz", - "author_inst": "Institute of Health Technology Assessment (IATS)" - }, - { - "author_name": "Carl Kendall", - "author_inst": "Federal University of Ceara, Brazil and Tulane School of Public Health and Tropical Medicine, USA." - }, - { - "author_name": "Ligia Regina Franco Sansigolo Kerr", - "author_inst": "Federal University of Ceara, Ceara, Brazil." - }, - { - "author_name": "Celina Maria Turchi Martelli", - "author_inst": "Aggeu Magalhaes Institute /FIOCRUZ-PE, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.10.21264825", "rel_title": "Effects of Age, Sex, Serostatus and Underlying Comorbidities on Humoral Response Post-SARS-CoV-2 Pfizer-BioNTech Vaccination: A Systematic Review", @@ -531379,6 +529919,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.05.21264578", + "rel_title": "Ondansetron use is associated with lower COVID-19 mortality in a Real-World Data network-based analysis", + "rel_date": "2021-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264578", + "rel_abs": "ObjectiveThe COVID-19 pandemic generated a massive amount of clinical data, which potentially holds yet undiscovered answers related to COVID-19 morbidity, mortality, long term effects, and therapeutic solutions. The objective of this study was to generate insights on COVID-19 mortality-associated factors and identify potential new therapeutic options for COVID-19 patients by employing artificial intelligence analytics on real-world data.\n\nMethodsA Bayesian statistics-based artificial intelligence data analytics tool (bAIcis(R)) within Interrogative Biology(R) platform was used for network learning, inference causality and hypothesis generation to analyze 16,277 PCR positive patients from a database of 279,281 inpatients and outpatients tested for SARS-CoV-2 infection by antigen, antibody, or PCR methods during the first pandemic year in Central Florida. This approach generated causal networks that enabled unbiased identification of significant predictors of mortality for specific COVID-19 patient populations. These findings were validated by logistic regression, regression by least absolute shrinkage and selection operator, and bootstrapping.\n\nResultsWe found that in the SARS-CoV-2 PCR positive patient cohort, early use of the antiemetic agent ondansetron was associated with increased survival in mechanically ventilated patients.\n\nConclusionsThe results demonstrate how real world COVID-19 focused data analysis using artificial intelligence can generate valid insights that could possibly support clinical decision-making and minimize the future loss of lives and resources.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Gregory M Miller", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Austin J Ellis", + "author_inst": "National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA" + }, + { + "author_name": "Rangaprasad Sarangarajan", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Amay Parikh", + "author_inst": "Translational Research Institute, AdventHealth Research Institute, Orlando, FL 32804, USA" + }, + { + "author_name": "Leonardo O Rodrigues", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Can Bruce", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Nischal Mahaveer Chand", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Steven R Smith", + "author_inst": "Translational Research Institute, AdventHealth Research Institute, Orlando, FL 32804, USA" + }, + { + "author_name": "Kris Richardson", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Raymond Vazquez", + "author_inst": "AdventHealth Information Technology, Orlando, FL 32804" + }, + { + "author_name": "Michael A Kiebish", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Haneesh Chandran", + "author_inst": "Translational Research Institute, AdventHealth Research Institute, Orlando, FL 32804, USA" + }, + { + "author_name": "Elder Granger", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Judy Holtz", + "author_inst": "Translational Research Institute, AdventHealth Research Institute, Orlando, FL 32804, USA" + }, + { + "author_name": "Jacob Hinkle", + "author_inst": "Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA" + }, + { + "author_name": "Niven R Narain", + "author_inst": "BERG, Framingham, MA 01701" + }, + { + "author_name": "Bret Goodpaster", + "author_inst": "Translational Research Institute, AdventHealth Research Institute, Orlando, FL 32804, USA" + }, + { + "author_name": "Jeremy C Smith", + "author_inst": "UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA" + }, + { + "author_name": "Daniel S. Lupu", + "author_inst": "AdventHealth Translational Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.09.463766", "rel_title": "SARS-CoV-2 infects and replicates in photoreceptor and retinal ganglion cells of human retinal organoids", @@ -532177,61 +530808,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.08.21264752", - "rel_title": "Prospective predictors of risk and resilience trajectories during the early stages of the COVID-19 pandemic: a longitudinal study", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264752", - "rel_abs": "BackgroundThe COVID-19 pandemic is a rapidly evolving stressor with significant mental health consequences. We aimed to delineate distinct anxiety-response trajectories during the early stages of the pandemic and to identify baseline risk and resilience factors as predictors of anxiety responses.\n\nMethodsUsing a crowdsourcing website, we enrolled 1,362 participants, primarily from the United States (n = 1064) and Israel (n = 222) over three time-points from April-September 2020. We used latent growth mixture modeling to identify anxiety trajectories over time. Group comparison and multivariate regression models were used to examine demographic and risk and resilience factors associated with class membership.\n\nResultsA four-class model provided the best fit. The resilient trajectory (stable low anxiety) was the most common (n = 961, 75.08%), followed by chronic anxiety (n = 149, 11.64%), recovery (n = 96, 7.50%) and delayed anxiety (n = 74, 5.78%). While COVID-19 stressors did not differ between trajectories, resilient participants were more likely to be older, living with another person and to report higher income, more education, fewer COVID-19 worries, better sleep quality, and more dispositional resilience factors at baseline. Multivariate analyses suggested that baseline emotion regulation capabilities and low conflictual relationships uniquely distinguished participants in distinct trajectories.\n\nConclusionsConsistent with prior resilience research following major adversities, a majority of individuals showed stable low levels of low anxiety in response to the COVID-19 pandemic. Knowledge about dispositional resilience factors may prospectively inform mental health trajectories early in the course of ongoing adversity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tal Shilton", - "author_inst": "Sheba Medical Centre, Child Adolescent Psychiatry Division, Tel Aviv University Sackler School of Medicine, Israel" - }, - { - "author_name": "Anthony D Mancini", - "author_inst": "Department of Psychology, Pace University, Pleasantville, NY, USA" - }, - { - "author_name": "Samantha Perlstein", - "author_inst": "Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Grace E DiDomenico", - "author_inst": "Lifespan Brain Institute, Children's Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, PA, USA" - }, - { - "author_name": "Elina Visoki", - "author_inst": "Lifespan Brain Institute, Children's Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, PA, USA" - }, - { - "author_name": "David M Greenberg", - "author_inst": "Bar Ilan University, Israel" - }, - { - "author_name": "Lily A Brown", - "author_inst": "Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Raquel E Gur", - "author_inst": "Lifespan Brain Institute, Children's Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medi" - }, - { - "author_name": "Rebecca Waller", - "author_inst": "Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Ran Barzilay", - "author_inst": "Lifespan Brain Institute, Children's Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.07.21264204", "rel_title": "Decreased hospital visits and increased mortality rate in the emergency department during the COVID-19 pandemic: Evidence from Albania.", @@ -532748,6 +531324,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.08.21264760", + "rel_title": "Decline in prenatal buprenorphine/naloxone fills during the COVID-19 pandemic in the United States", + "rel_date": "2021-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264760", + "rel_abs": "Background and AimsPregnancy provides a critical opportunity to engage women with substance use disorder in care. Buprenorphine/naloxone treatment is associated with improved pregnancy and fetal outcomes, but prior to the COVID-19 pandemic, there were multiple barriers to accessing buprenorphine/naloxone during pregnancy. Care disruptions during the pandemic may have further exacerbated these already existing barriers. To quantify these changes, we examined trends in the number of individuals filling prescriptions for prenatal buprenorphine/naloxone prescriptions during the COVID-19 pandemic.\n\nMethodsWe estimated an interrupted time series model using linked national pharmacy claims and medical claims data from May 2019 to December 2020. We estimated changes in the level and trend in the monthly number of individuals filling prescriptions for prenatal buprenorphine/naloxone during the COVID-19 pandemic. We then stratified our analyses by payer.\n\nResultsWe identified 2,947 pregnant patients filling buprenorphine/naloxone prescriptions. Before the pandemic, there was positive growth in the monthly number of individuals filling prescriptions for prenatal buprenorphine/naloxone (4.83% (95% confidence interval (CI): 3.40% to 6.26%). During the pandemic, the monthly growth rate in individuals filling prescriptions for prenatal buprenorphine/naloxone declined for both patients on commercial insurance and patients on Medicaid (all payers: -5.53% (95% CI: -7.28% to -3.78%); Medicaid: -7.66% (95% CI: -10.42% to -4.90%); Commercial: -3.59% (95% CI: -5.53% to -1.66%)).\n\nConclusionThe number of pregnant individuals filling buprenorphine/naloxone prescriptions was increasing prior to the pandemic, but this growth has been lost during the pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ashley L O'Donoghue", + "author_inst": "Center for Healthcare Delivery Science, Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Alyse Reichheld", + "author_inst": "Center for Healthcare Delivery Science, Beth Israel Deaconess Medical Center, Boston, MA; Tufts University School of Medicine, Boston, MA" + }, + { + "author_name": "Timothy S Anderson", + "author_inst": "Center for Healthcare Delivery Science, Beth Israel Deaconess Medical Center, Boston, MA; Division of General Medicine, Beth Israel Deaconess Medical Center, Bo" + }, + { + "author_name": "Chloe A Zera", + "author_inst": "Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Tenzin Dechen", + "author_inst": "Center for Healthcare Delivery Science, Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Jennifer P Stevens", + "author_inst": "Center for Healthcare Delivery Science, Beth Israel Deaconess Medical Center, Boston, MA; Division for Pulmonary, Critical Care, and Sleep Medicine, Department " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2021.10.08.463699", "rel_title": "Immunity to SARS-CoV-2 up to 15 months after infection", @@ -534119,69 +532734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264595", - "rel_title": "COVID-19 Vaccine Effectiveness by Product and Timing in New York State", - "rel_date": "2021-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264595", - "rel_abs": "BackgroundUS population-based data on COVID-19 vaccine effectiveness (VE) for the 3 currently FDA-authorized products is limited. Whether declines in VE are due to waning immunity, the Delta variant, or other causes, is debated.\n\nMethodsWe conducted a prospective study of 8,834,604 New York adults, comparing vaccine cohorts defined by product, age, and month of full-vaccination to age-specific unvaccinated cohorts, by linking statewide testing, hospital, and vaccine registry databases. VE was estimated from May 1, 2021 for incident laboratory-confirmed COVID-19 cases (weekly life-table hazard rates through September 3) and hospitalizations (monthly incidence rates through August 31).\n\nResults155,092 COVID-19 cases and 14,862 hospitalizations occurred. Estimated VE for cases declined contemporaneously across age, products, and time-cohorts, from high levels beginning May 1 (1.8% Delta variant prevalence), to a nadir around July 10 (85.3% Delta), with limited changes thereafter (>95% Delta). Decreases were greatest for Pfizer-BioNTech (-24.6%, -19.1%, -14.1% for 18-49, 50-64 years, and [≥]65 years, respectively), and similar for Moderna (-18.0%, -11.6%, -9.0%, respectively) and Janssen (-19.2%, -10.8, -10.9%, respectively). VE for hospitalization for adults 18-64 years was >86% across cohorts, without time trend. Among persons [≥]65 years, VE declined from May to August for Pfizer-BioNTech (95.0% to 89.2%) and Moderna (97.2% to 94.1%). VE was lower for Janssen, without trend, ranging 85.5%-82.8%.\n\nConclusionsDeclines in VE for cases may have been primarily driven by factors other than waning. VE for hospitalizations remained high, with modest declines limited to Pfizer-BioNTech and Moderna recipients [≥]65 years, supporting targeted booster dosing recommendations.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Eli Rosenberg", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Vajeera Dorabwila", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Delia Easton", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Ursula Bauer", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Jessica Kumar", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Rebecca Hoen", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Dina Hoefer", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Meng Wu", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Emily Lutterloh", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Mary Beth Conroy", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Danielle Greene", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Howard A Zucker", - "author_inst": "New York State Department of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.08.21264716", "rel_title": "COVID-19 Pandemic Impact on Sexually Transmitted Infection Testing in a College Setting", @@ -534746,6 +533298,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.05.21264555", + "rel_title": "Seropositivity to Nucleoprotein to detect SARS-CoV-2 infections: a tool to detect breakthrough infections after COVID-19 vaccination", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264555", + "rel_abs": "BackgroundWith COVID-19 vaccine roll-out ongoing in many countries globally, monitoring of breakthrough infections is of great importance. Antibodies persist in the blood after a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Since COVID-19 vaccines induce immune response to the Spike protein of the virus, which is the main serosurveillance target to date, alternative targets should be explored to distinguish infection from vaccination.\n\nMethodsMultiplex immunoassay data from 1,513 SARS-CoV-2 RT-qPCR-tested individuals (352 positive and 1,161 negative) with a primary infection and no vaccination history were used to determine the accuracy of Nucleoprotein-specific immunoglobulin G (IgG) in detecting past SARS-CoV-2 infection. We also described Spike S1 and Nucleoprotein-specific IgG responses in 230 COVID-19 vaccinated individuals (Pfizer/BioNTech).\n\nResultsThe sensitivity of Nucleoprotein seropositivity was 85% (95% confidence interval: 80-90%) for mild COVID-19 in the first two months following symptom onset. Sensitivity was lower in asymptomatic individuals (67%, 50-81%). Participants who had experienced a SARS-CoV-2 infection up to 11 months preceding vaccination, as assessed by Spike S1 seropositivity or RT-qPCR, produced 2.7-fold higher median levels of IgG to Spike S1 [≥]14 days after the first dose as compared to those unexposed to SARS-CoV-2 at [≥]7 days after the second dose (p=0.011). Nucleoprotein-specific IgG concentrations were not affected by vaccination in naive participants.\n\nConclusionsSerological responses to Nucleoprotein may prove helpful in identifying SARS-CoV-2 infections after vaccination. Furthermore, it can help interpret IgG to Spike S1 after COVID-19 vaccination as particularly high responses shortly after vaccination could be explained by prior exposure history.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Lotus Leonie van den Hoogen", + "author_inst": "RIVM" + }, + { + "author_name": "Gaby Smits", + "author_inst": "RIVM" + }, + { + "author_name": "Cheyenne CE van Hagen", + "author_inst": "RIVM" + }, + { + "author_name": "Denise Wong", + "author_inst": "RIVM" + }, + { + "author_name": "Eric RA Vos", + "author_inst": "RIVM" + }, + { + "author_name": "Michiel van Boven", + "author_inst": "RIVM" + }, + { + "author_name": "Hester E de Melker", + "author_inst": "RIVM" + }, + { + "author_name": "Jeffrey van Vliet", + "author_inst": "RIVM" + }, + { + "author_name": "Marjan Kuijer", + "author_inst": "RIVM" + }, + { + "author_name": "Linde Woudstra", + "author_inst": "RIVM" + }, + { + "author_name": "Alienke J Wijmenga-Monsuur", + "author_inst": "RIVM" + }, + { + "author_name": "Corine H Geurts van Kessel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Susanne P Stoof", + "author_inst": "Dijklander ziekenhuis" + }, + { + "author_name": "Daphne Reukers", + "author_inst": "RIVM" + }, + { + "author_name": "Lisa A Wijsman", + "author_inst": "RIVM" + }, + { + "author_name": "Adam Meijer", + "author_inst": "RIVM" + }, + { + "author_name": "Chantal BEM Reusken", + "author_inst": "RIVM" + }, + { + "author_name": "Nynke Y Rots", + "author_inst": "RIVM" + }, + { + "author_name": "Fiona RM van der Klis", + "author_inst": "RIVM" + }, + { + "author_name": "Robert S van Binnendijk", + "author_inst": "RIVM" + }, + { + "author_name": "Gerco den Hartog", + "author_inst": "RIVM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.05.21264557", "rel_title": "Rotational worker vaccination provides indirect protection to vulnerable groups in regions with low COVID-19 prevalence", @@ -536121,73 +534772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.06.21264407", - "rel_title": "Minority and Rural Coronavirus Insights Study (MRCIS): The Need for Targeted COVID-19 Vaccination Efforts in Minority Populations", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264407", - "rel_abs": "ImportanceRacial and ethnic minority populations have been disproportionately affected in terms of hospitalizations and deaths during the COVID-19 pandemic. Vaccine uptake remains a barrier to full population inoculation against this highly infectious disease.\n\nObjectiveThe purpose of this report is to describe SARS-CoV-2 vaccine interest rates in a racially, geographically, and ethnically diverse study cohort and characterize vaccine interest across a racially, ethnically, and geographically diverse study population.\n\nDesignThis report describes responses to a survey administered between November 2020 and May 2021 using a community convenience sample through a partnership between the National Minority Quality Forum (NMQF) and Federally Qualified Health Centers (FQHCs) as part of the Minority and Rural Coronavirus Insights Study (MRCIS). Analysis of survey responses from 3,624 participants are provided.\n\nResultsEarly data from the MRCIS cohort suggest that \"SARS-CoV-2 vaccine hesitancy\" is more prevalent in Black versus Non-Hispanic Whites survey respondents, and the Hispanic community has positive interest in the vaccine, to a similar degree as Whites. The persistent presence of \"vaccine undecideds\" across different sites and racial/ethnic groups uncovers the need for more public health efforts to influence positive views about vaccination.\n\nConclusionThese findings highlights the urgent need for interventional educational campaigns targeted at populations at risk of low vaccine interest. Focused efforts are needed to combat misinformation and explain the vaccines safety and effectiveness to promote its uptake and avoid low inoculation rates. Public health communication must consider differences in population groups, regions, and social determinants of health to fully address vaccine uptake disparities and overcome alleged hesitancy.\n\nKey PointsO_LIWillingness to receive the SARS CoV-2 varies among minority populations.\nC_LIO_LI\"SARS-CoV-2 vaccine hesitancy\" is more prevalent in the non-Hispanic Black population than the non-Hispanic White and Hispanic populations.\nC_LIO_LIPublic health infrastructure is needed in underserved communities for efficient assessment and targeted communication of public health priorities such as the SARS CoV-2 vaccination.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Latrice Landry", - "author_inst": "Harvard" - }, - { - "author_name": "LaTasha Lee", - "author_inst": "National Minority Quality Forum" - }, - { - "author_name": "William Meyer", - "author_inst": "Quest Diagnostics" - }, - { - "author_name": "Gary Puckrein", - "author_inst": "National Minority Quality Forum" - }, - { - "author_name": "Nishanth Chalasani", - "author_inst": "National Minority Quality Forum" - }, - { - "author_name": "Liou Xu", - "author_inst": "National Minority Quality Forum" - }, - { - "author_name": "Taylor Stair", - "author_inst": "National Minority Quality Forum" - }, - { - "author_name": "Gary Wiltz", - "author_inst": "Teche Action Clinic" - }, - { - "author_name": "Marian Sampson", - "author_inst": "Osceola Community Health Service" - }, - { - "author_name": "Paul Gregerson", - "author_inst": "John Wesley Community Health Institute" - }, - { - "author_name": "Charles Barron", - "author_inst": "Aunt Martha's Health and Wellness" - }, - { - "author_name": "Jeffrey Marable", - "author_inst": "Primary One Health" - }, - { - "author_name": "Ola Akinboboye", - "author_inst": "Queens Heart Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.05.21264559", "rel_title": "Effectiveness and Safety of MSC Cell Therapies for Hospitalized Patients with COVID-19: A Systematic Review and Meta-analysis", @@ -537140,6 +535724,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.10.07.21264626", + "rel_title": "Protection Across Age Groups of BNT162b2 Vaccine Booster against Covid-19", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264626", + "rel_abs": "BACKGROUNDFollowing administration to persons 60+ years of age, the booster vaccination campaign in Israel was gradually expanded to younger age groups who received a second dose >5 months earlier. We study the booster effect on COVID-19 outcomes.\n\nMETHODSWe extracted data for the period July 30, 2021 to October 6, 2021 from the Israeli Ministry of Health database regarding 4,621,836 persons. We compared confirmed Covid-19 infections, severe illness, and death of those who received a booster [≥]12 days earlier (booster group) with a nonbooster group. In a secondary analysis, we compared the rates 3-7 days with [≥]12 days after receiving the booster dose. We used Poisson regressions to estimate rate ratios after adjusting for possible confounding factors.\n\nRESULTSConfirmed infection rates were {approx}10-fold lower in the booster versus nonbooster group (ranging 8.8-17.6 across five age groups) and 4.8-11.2 fold lower in the secondary analysis. Severe illness rates in the primary and secondary analysis were 18.7-fold (95% CI, 15.7-22.4) and 6.5-fold (95% CI, 5.1-8.3) lower for ages 60+, and 22.0-fold (95% CI, 10.3-47.0) and 3.2-fold (95% CI, 1.1-9.6) lower for ages 40-60. For ages 60+, COVID-19 associated death rates were 14.7-fold (95% CI, 9.4-23.1) lower in the primary analysis and 4.8-fold (95% CI, 2.8-8.2) lower in the secondary analysis.\n\nCONCLUSIONSAcross all age groups, rates of confirmed infection and severe illness were substantially lower among those who received a booster dose of the BNT162b2 vaccine.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yinon M. Bar-On", + "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Yair Goldberg", + "author_inst": "Technion - Israel Institute of Technology, Israel" + }, + { + "author_name": "Micha Mandel", + "author_inst": "The Hebrew University of Jerusalem, Israel" + }, + { + "author_name": "Omri Bodenheimer", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Laurence Freedman", + "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" + }, + { + "author_name": "Sharon Alroy-Preis", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Nachman Ash", + "author_inst": "Israel Ministry of Health, Israel" + }, + { + "author_name": "Amit Huppert", + "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" + }, + { + "author_name": "Ron Milo", + "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.07.21264681", "rel_title": "Monitoring sociodemographic inequality in COVID-19 vaccination coverage in England: a national linked data study", @@ -538243,177 +536878,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.10.05.463282", - "rel_title": "SARS-CoV-2 hijacks neutralizing dimeric IgA for enhanced nasal infection and injury", - "rel_date": "2021-10-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.05.463282", - "rel_abs": "Robust severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in nasal turbinate (NT) accounts for high viral transmissibility, yet whether neutralizing IgA antibodies can control it remains unknown. Here, we evaluated receptor binding domain (RBD)-specific monomeric B8-mIgA1 and B8-mIgA2, and dimeric B8-dIgA1 and B8-dIgA2 against intranasal SARS-CoV-2 challenge in Syrian hamsters. These antibodies exhibited comparably potent neutralization against authentic virus by competing with human angiotensin converting enzyme-2 (ACE2) receptor for RBD binding. While reducing viruses in lungs, pre-exposure intranasal B8-dIgA1 or B8-dIgA2 led to 81-fold more infectious viruses and severer damage in NT than placebo. Virus-bound B8-dIgA1 and B8-dIgA2 could engage CD209 as an alternative receptor for entry into ACE2-negative cells and allowed viral cell-to-cell transmission. Cryo-EM revealed B8 as a class II neutralizing antibody binding trimeric RBDs in 3-up or 2-up/1-down conformation. Therefore, RBD-specific neutralizing dIgA engages an unexpected action for enhanced SARS-CoV-2 nasal infection and injury in Syrian hamsters.", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Biao Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Runhong Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jasper Fuk-Woo Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jianwei Zeng", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Qi Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Li Liu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "R\u00e9my Robinot", - "author_inst": "Institute Pasteur" - }, - { - "author_name": "Sisi Shan", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jiwan Ge", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Hugo Yat-Hei Kwong", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dongyan Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Haoran Xu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Chung-Sing Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Vincent Kwok-Man Poon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hin Chu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ming Yue", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ka-Yi Kwan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chun-Yin Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Na Liu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Chun-Yiu Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kenn Ka-Heng Chik", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Zhenglong Du", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ka-Kit Au", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Haode Huang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hiu-On Man", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jianli Cao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Cun Li", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ziyi Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jie Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Youqiang Song", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Man-Lung Yeung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kelvin Kai-Wang To", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "David D. Ho", - "author_inst": "Columbia University" - }, - { - "author_name": "Lisa A. Chakrabarti", - "author_inst": "Institute Pasteur" - }, - { - "author_name": "Xinquan Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Linqi Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Kwok-Yung Yuen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Zhiwei Chen", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.06.21263384", "rel_title": "SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame", @@ -539470,6 +537934,141 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.10.04.463121", + "rel_title": "Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients", + "rel_date": "2021-10-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.04.463121", + "rel_abs": "Multiple studies have identified an association between neutrophils and COVID-19 disease severity; however, the mechanistic basis of this association remains incompletely understood. Here we collected 781 longitudinal blood samples from 306 hospitalized COVID-19+ patients, 78 COVID-19- acute respiratory distress syndrome patients, and 8 healthy controls, and performed bulk RNA-sequencing of enriched neutrophils, plasma proteomics, cfDNA measurements and high throughput antibody profiling assays to investigate the relationship between neutrophil states and disease severity or death. We identified dynamic switches between six distinct neutrophil subtypes using non-negative matrix factorization (NMF) clustering. At days 3 and 7 post-hospitalization, patients with severe disease had an enrichment of a granulocytic myeloid derived suppressor cell-like state gene expression signature, while non-severe patients with resolved disease were enriched for a progenitor-like immature neutrophil state signature. Severe disease was associated with gene sets related to neutrophil degranulation, neutrophil extracellular trap (NET) signatures, distinct metabolic signatures, and enhanced neutrophil activation and generation of reactive oxygen species (ROS). We found that the majority of patients had a transient interferon-stimulated gene signature upon presentation to the emergency department (ED) defined here as Day 0, regardless of disease severity, which persisted only in patients who subsequently died. Humoral responses were identified as potential drivers of neutrophil effector functions, as enhanced antibody-dependent neutrophil phagocytosis and reduced NETosis was associated with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirmed that while patient-derived IgG antibodies mostly drove neutrophil phagocytosis and ROS production in healthy donor neutrophils, patient-derived IgA antibodies induced a predominant NETosis response. Overall, our study demonstrates neutrophil dysregulation in severe COVID-19 and a potential role for IgA-dominant responses in driving neutrophil effector functions in severe disease and mortality.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Thomas J. LaSalle", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard" + }, + { + "author_name": "Anna L. K. Gonye", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard" + }, + { + "author_name": "Samuel S. Freeman", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Department of Biomedical Informatics, Ha" + }, + { + "author_name": "Paulina Kaplonek", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Irena Gushterova", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard" + }, + { + "author_name": "Kyle R. Kays", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Kasidet Manakongtreecheep", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Center for Immunology and Inflammatory D" + }, + { + "author_name": "Jessica Tantivit", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Center for Immunology and Inflammatory D" + }, + { + "author_name": "Maricarmen Rojas-Lopez", + "author_inst": "Department of Medicine, Harvard Medical School; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital; Department of Microbiol" + }, + { + "author_name": "Brian C. Russo", + "author_inst": "Department of Medicine, Harvard Medical School; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital; Department of Microbiol" + }, + { + "author_name": "Nihaarika Sharma", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Molly F. Thomas", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Center for Immunology and Inflammatory D" + }, + { + "author_name": "Kendall M. Lavin-Parsons", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Brendan M. Lilly", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Brenna N. Mckaig", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Nicole C. Charland", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Hargun K. Khanna", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Carl L. Lodenstein", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Justin D. Margolin", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Emily M. Blaum", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard" + }, + { + "author_name": "Paola B. Lirofonis", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Abraham Sonny", + "author_inst": "Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Roby P. Bhattacharyya", + "author_inst": "Broad Institute of MIT and Harvard; Department of Medicine, Harvard Medical School; Division of Infectious Diseases, Department of Medicine, Massachusetts Gener" + }, + { + "author_name": "Blair Alden Parry", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital" + }, + { + "author_name": "Marcia B. Goldberg", + "author_inst": "Broad Institute of MIT and Harvard; Department of Medicine, Harvard Medical School; Division of Infectious Diseases, Department of Medicine, Massachusetts Gener" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Michael R. Filbin", + "author_inst": "Broad Institute of MIT and Harvard; Department of Emergency Medicine, Massachusetts General Hospital; Department of Emergency Medicine, Harvard Medical School" + }, + { + "author_name": "Alexandra Chloe Villani", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Center for Immunology and Inflammatory D" + }, + { + "author_name": "Nir Hacohen", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Department of Medicine, Harvard Medical " + }, + { + "author_name": "Moshe Sade-Feldman", + "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital; Broad Institute of MIT and Harvard; Department of Medicine, Harvard Medical " + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.10.04.463028", "rel_title": "B.1.617.3 SARS CoV-2 spike E156G/\u0394157-158 mutations contribute to reduced neutralization sensitivity and increased infectivity", @@ -540365,37 +538964,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.03.462911", - "rel_title": "Unique Peptide Signatures Of SARS-CoV-2 Against Human Proteome Reveal Variants' Immune Escape And Infectiveness", - "rel_date": "2021-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.03.462911", - "rel_abs": "SARS-CoV-2 pandemic has emerged the necessity of the identification of sequences sites in viral proteome appropriate as antigenic sites and treatment targets. In the present study, we apply a novel approach for deciphering the virus-host organism interaction, by analyzing the Unique Peptides of the virus with a minimum amino acid sequence length defined as Core Unique Peptides (CrUPs) not of the virus per se, but against the entire proteome of the host organism. The result of this approach is the identification of the CrUPs of the virus itself, which do not appear in the host organism proteome. Thereby, we analyzed the SARS-CoV-2 proteome for identification of CrUPs against the Human Proteome and they are defined as C/H-CrUPs. We found that SARS-CoV-2 include 7.503 C/H-CrUPs, with the SPIKE_SARS2 being the protein with the highest density of C/H-CrUPs. Extensive analysis indicated that the P681R mutation produces new C/H-CrUPs around the R685 cleavage site, while the L452R mutation induces the loss of antigenicity of the NF9 peptide and the strong(er) binding of the virus to ACE2 receptor protein. The simultaneous existence of these mutations in variants like Delta results in the immune escape of the virus, its massive entrance into the host cell, a notable increase in virus formation, and its massive release and thus elevated infectivity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vasileios Pierros", - "author_inst": "Biomedical Research Foundation of the Academy of Athens, Greece" - }, - { - "author_name": "Evangelos Kontopodis", - "author_inst": "Department of Biology, School of Science, National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "Dimitrios Stravopodis", - "author_inst": "Department of Biology, School of Science, National and Kapodistrian University of Athens, Greece" - }, - { - "author_name": "George Theodore Tsangaris", - "author_inst": "Biomedical Research Foundation of the Academy of Athens" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.03.21264494", "rel_title": "Why a Globally Fair COVID-19 Vaccination? An Analysis based on Agent-Based Simulation", @@ -541060,6 +539628,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.30.21264344", + "rel_title": "Development and validation of a questionnaire to measure attitudes toward COVID-19 vaccination and pandemic", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.30.21264344", + "rel_abs": "BackgroundAccurate measurement of individuals attitudes toward COVID-19 vaccination and pandemic is critical to understand the way that people respond during a major crisis such as the COVID-19 pandemic.\n\nObjectiveTo develop and validate a questionnaire to assess attitudes toward COVID-19 vaccination and pandemic.\n\nMethodsWe performed a reliability and validity study in a sample of the general population in Greece. Data were collected online through social media between 15 August and 7 September 2021. Thus, a convenience sample was obtained. Reliability and validity of the questionnaire were assessed with a Delphi study, an exploratory factor analysis, and a test-retest study. Also, we calculated Cronbachs coefficient alpha for the factors that emerged from the exploratory factor analysis.\n\nResultsThe final study included 1959 adults from the general population in Greece. Our four-factor model explained 73% of the variance and confirmed out initial hypothesis regarding the factors of the questionnaire. In particular, we found the following four factors: (a) fear against the COVID-19 (five items), (b) information regarding the COVID-19 (two items), (c) compliance with hygiene measures (two items), and (d) trust in COVID-19 vaccination (seven items). Cronbachs coefficients alpha for the four factors that emerged from the exploratory factor analysis were greater than 0.82. Pearsons correlation coefficients for the 16 items and the four factors were greater than 0.67 (p-value<0.001 in all cases).\n\nConclusionsWe developed a reliable and valid questionnaire to measure attitudes toward COVID-19 vaccination and pandemic. Further studies should be conducted to expand our knowledge and infer more valid results.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Petros A Galanis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Irene Vraka", + "author_inst": "P & A Kyriakou Children's Hospital" + }, + { + "author_name": "Olga Siskou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Olympia Konstantakopoulou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Aglaia Katsiroumpa", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Ioannis Moisoglou", + "author_inst": "General Hospital of Lamia" + }, + { + "author_name": "Daphne Kaitelidou", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.30.21264337", "rel_title": "Risk-benefit analysis of the AstraZeneca COVID-19 vaccine in Australia using a Bayesian network modelling framework", @@ -542179,33 +540790,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.29.21264304", - "rel_title": "Evaluation of liver function tests and C-reactive protein in COVID-19 (SARS Cov-2) positive patients diagnosed by Real-time PCR", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264304", - "rel_abs": "BACKGROUND AND AIMSThe SARS-CoV-2 pandemic, has caused an unconventional social and economic impact globally. To date, there was limited data regarding the effect of COVID-19 infection on the trend of RT-PCR Ct value, risk factors for disease, effect on liver enzymes, etc. This study aimed to assess the frequency of COVID-19 infection in different age groups and genders. Association of cycle threshold (Ct) values with disease severity and to describe the effect of COVID-19 infection on LFT, Deritis ratio, and CRP. That can be used as indicators for COVID-19 infection diagnosis, the guidance for treatment decisions, and prognosis in infected individuals.\n\nMETHODSThis was a cross-sectional study conducted in the Molecular Biology and Chemical Pathology sections of the Pathology Department, Shalamar Teaching Hospital Lahore from November 2020 to March 2021.\n\nResultsMales 51% were more likely to be infected by SARS-CoV-2. Most of the infected individuals 36.5% were in the age group 20-40. Age and underlying comorbidities are important factors that play a significant role in COVID-19 severity. The uppermost number of the patients had symptoms of fever 78.3%, cough 50.4% and myalgias 50.1% RT-PCR low Ct value could be an important indicator related with the disease severity and mortality risk p value < 0.001 and 0.003 respectively. Bilirubin indirect, ALT, AST, and CRP were significantly associated with disease severity. Deritis ratio and CRP was found to be significantly associated with the risk of mortality.\n\nCONCLUSIONSReal-Time PCR results along with Ct values for SARS-CoV-2 may have benefit for clinicians in patient management decisions. Several risk factors e.g., age and comorbidities for developing severe disease and mortality risk have been identified. These biochemical laboratory parameters ALT, AST, Deritis ratio and CRP can be used as predictive biomarkers for progression towards severe disease and risk of mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fatima Khurshid", - "author_inst": "Shalamar medical and dental college" - }, - { - "author_name": "Sajad Iqbal", - "author_inst": "Shalamar medical and dental college" - }, - { - "author_name": "Madiha Mumtaz", - "author_inst": "School of Biological Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.01.21264408", "rel_title": "Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests", @@ -542846,6 +541430,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.30.21264363", + "rel_title": "SARS-CoV-2 infections elicit higher levels of original antigenic sin antibodies compared to SARS-CoV-2 mRNA vaccinations", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.30.21264363", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccines elicit higher levels of antibodies compared to natural SARS-CoV-2 infections in most individuals; however, the specificities of antibodies elicited by vaccination versus infection remain incompletely understood. Here, we characterized the magnitude and specificity of SARS-CoV-2 spike-reactive antibodies from 10 acutely infected health care workers and 23 participants who received mRNA-based SARS-CoV-2 vaccines. We found that infection and primary mRNA vaccination elicited S1 and S2-reactive antibodies, while secondary vaccination boosted mostly S1 antibodies. Using magnetic bead-based absorption assays, we found that SARS-CoV-2 infections elicited a large proportion of original antigenic sin-like antibodies that bound efficiently to common seasonal human coronaviruses but poorly to SARS-CoV-2. In converse, vaccination only modestly boosted antibodies reactive to common seasonal human coronaviruses and these antibodies bound efficiently to SARS-CoV-2. Our data indicate that SARS-CoV-2 mRNA vaccinations elicit fundamentally different antibody responses compared to SARS-CoV-2 infections.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC=\"FIGDIR/small/21264363v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@1352972org.highwire.dtl.DTLVardef@13419bcorg.highwire.dtl.DTLVardef@18595a5org.highwire.dtl.DTLVardef@1238eac_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISARS-CoV-2 mRNA vaccines elicit higher levels of antibodies compared to SARS-CoV-2 infections\nC_LIO_LIThe first dose of an mRNA vaccine generates both S1 and S2 responses while the second dose boosts primarily S1-specific antibodies\nC_LIO_LISARS-CoV-2 infections, but not mRNA vaccinations, elicit high levels of antibodies that bind strongly to seasonal coronaviruses but weakly to SARS-CoV-2\nC_LI", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Elizabeth M. Anderson", + "author_inst": "Penn" + }, + { + "author_name": "Theresa Eiloa", + "author_inst": "Penn" + }, + { + "author_name": "Eileen Goodwin", + "author_inst": "Penn" + }, + { + "author_name": "Marcus J. Bolton", + "author_inst": "Penn" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "Penn" + }, + { + "author_name": "Rishi R. Goel", + "author_inst": "Penn" + }, + { + "author_name": "Mark M Painter", + "author_inst": "Penn" + }, + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "Penn" + }, + { + "author_name": "Divij Mathew", + "author_inst": "Penn" + }, + { + "author_name": "Debora Dunbar", + "author_inst": "Penn" + }, + { + "author_name": "Danielle Fiore", + "author_inst": "Penn" + }, + { + "author_name": "Amanda Brock", + "author_inst": "Penn" + }, + { + "author_name": "JoEllen Weaver", + "author_inst": "Penn" + }, + { + "author_name": "John S. Millar", + "author_inst": "Penn" + }, + { + "author_name": "Stephanie DerOhannessian", + "author_inst": "Penn" + }, + { + "author_name": "- The UPenn COVID Processing Unit", + "author_inst": "" + }, + { + "author_name": "Allison R. Greenplate", + "author_inst": "Penn" + }, + { + "author_name": "Ian Frank", + "author_inst": "Penn" + }, + { + "author_name": "Daniel J Rader", + "author_inst": "Penn" + }, + { + "author_name": "E John Wherry", + "author_inst": "Penn" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "Penn" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264319", "rel_title": "Adaptive data-driven age and patch mixing in contact networks with recurrent mobility", @@ -543753,201 +542436,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.29.21264272", - "rel_title": "Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study", - "rel_date": "2021-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264272", - "rel_abs": "BackgroundThe COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with seven SARS-CoV-2 variants.\n\nMethodsOur study includes individuals with positive SARS-CoV-2 RT-PCR in the Washington Disease Reporting System with available viral genome data, from December 1, 2020 to January 14, 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination.\n\nFindings58,848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95%CI 2.40-4.26), Beta (HR 2.85, 95%CI 1.56-5.23), Delta (HR 2.28 95%CI 1.56-3.34) or Alpha (HR 1.64, 95%CI 1.29-2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95%CI 0.56-1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination.\n\nConclusionInfection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.\n\nSummaryHospitalization risk following infection with SARS-CoV-2 variant remains unclear. We find a higher hospitalization risk in cases infected with Alpha, Beta, Gamma, and Delta, but not Omicron, with vaccination lowering risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Miguel I. Paredes", - "author_inst": "Department of Epidemiology, University of Washington, Seattle, WA, USA , Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattl" - }, - { - "author_name": "Stephanie Lunn", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling, Bellevue, WA, USA" - }, - { - "author_name": "Lauren A. Frisbie", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Ian Painter", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Roy Burstein", - "author_inst": "Institute for Disease Modeling, Bellevue, WA, USA" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Laboratory Medicine and Pathology, Univ" - }, - { - "author_name": "Hong Xie", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Shah A. Mohamed Bakhash", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Ricardo Perez", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Maria Lukes", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Sean Ellis", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Saraswathi Sathees", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Patrick C Mathias", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Alexander Greninger", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Laboratory Medicine and Pathology, Univ" - }, - { - "author_name": "Lea M. Starita", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Chris D. Frazar", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Erica Ryke", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Weizhi Zhong", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Luis Gamboa", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Machiko Threlkeld", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Jover Lee", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA" - }, - { - "author_name": "Evan McDermot", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Melissa Truong", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Deborah A. Nickerson", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA USA" - }, - { - "author_name": "Daniel L. Bates", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "Matthew E. Hartman", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA; Department of Cardiovascular Services, Swedish Medical Center, Seattle, WA USA" - }, - { - "author_name": "Eric Haugen", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "Truong N. Nguyen", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "Joshua D. Richards", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "Jacob L. Rodriguez", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "John Stamatoyannopoulos", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Eric Thorland", - "author_inst": "Altius Institute for Biomedical Sciences, Seattle, WA USA" - }, - { - "author_name": "Geoff Melly", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Philip E. Dykema", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Drew C. MacKellar", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Hannah K. Gray", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Avi Singh", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "JohnAric MoonDance Peterson", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Denny Russell", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Laura Marcela Torres", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Scott Lindquist", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Trevor Bedford", - "author_inst": "Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle" - }, - { - "author_name": "Krisandra J. Allen", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - }, - { - "author_name": "Hanna N. Oltean", - "author_inst": "Washington State Department of Health, Shoreline, WA USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.29.21264305", "rel_title": "Determinants of sleep quality in adults during the COVID-19 pandemic: COVID-Inconfidentes, a population-based study", @@ -545100,6 +543588,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.29.21264061", + "rel_title": "A PTX3/LDH/CRP signature correlates with lung injury CTs scan severity and disease progression in paucisymptomatic COVID-19", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264061", + "rel_abs": "BackgroundQuantitative CT (QCT) analysis is an invaluable diagnostic tool to assess lung injury and predict prognosis of patients affected by COVID-19 pneumonia. PTX3 was recently described as one of the most reliable serological predictors of clinical deterioration and short-term mortality. The present study was designed to evaluate a correlation between serological biomarkers of inflammation and lung injury measured by QCT.\n\nMethodsThis retrospective monocentric study analysed a cohort of patients diagnosed with COVID-19 and admitted because of respiratory failure, or significant radiological involvement on chest CT scan. All patients, males and non-pregnant females older than 18 years, underwent chest CT scan and laboratory testing at admission. Exclusion criteria were defined by concurrent acute pathological processes and ongoing specific treatments which could interfere with immune activity. The cohort was stratified based on severity in mild and severe forms. Compromised lung at QCT was then correlated to serological biomarkers representative of SARS-CoV-2. We further developed a multivariable logistic model to predict CT data and clinical deterioration based on a specific molecular signature. Internal cross-validation led to evaluate discrimination, calibration, and clinical utility of the tool that was provided by a score to simplify its application.\n\nFindings592 patients were recruited between March 19th and December 1st, 2020. Applying exclusion criteria which consider confounders, the cohort resulted in 366 individuals characterized by 177 mild and 189 severe forms. In our predictive model, blood levels of PTX3, CRP and LDH were found to correlate with QCT values in mild COVID-19 disease. A signature of these three biomarkers had a high predictive accuracy in detecting compromised lungs as assessed by QCT. The score was elaborated and resulted representative of lung CT damage leading to clinical deterioration and oxygen need in mild disease.\n\nInterpretationThe LDH, PTX3, CRP blood signature can serve as a strong correlate of compromised lung in COVID-19, possibly integrating cellular damage, systemic inflammation, myeloid and endothelial cell activation.\n\nFundingThis work was supported by a philanthropic donation by Dolce & Gabbana fashion house (to A.M., C.G.) and by a grant from Italian Ministry of Health for COVID-19 (to A.M. and C.G.).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSBesides nasopharyngeal swab and serological test, chest CT scan represents one of the most useful tools to confirm COVID-19 diagnosis; moreover, QCT has been demonstrated to foresee oxygen need as well as deterioration of health status. Several clinical and serological parameters have been studied alone or combined in scores to be applied as prognostic tools of SARS-CoV-2 pneumonia; however, no one has yet reached the everyday practice. Recently, our group has investigated the expression and clinical significance of PTX3 in COVID-19 demonstrating the correlation with short-term mortality independently of confounders. The result was confirmed by other studies in different settings increasing evidence of PTX3 as a strong biomarker of severity; noteworthy, a recent report analysed proteomic data with a machine learning approach identifying age with PTX3 or SARS-CoV-2 RNAemia as the best binary signatures associated to 28-days mortality.\n\nAdded value of this studyThe present study was designed to investigate associations between markers of damage and the CT extension of SARS-CoV-2 pneumonia in order to provide a biological footprint of radiological results in paucisymptomatic patients. QCT data were considered in a binary form identifying a threshold relevant for clinical deterioration, as already proved by literature. Our findings demonstrate a significant correlation with three peripheral blood proteins (PTX3, LDH and CRP) which result representative of COVID-19 severity. The study presents a predictive model of radiological lung involvement which performs with a high level of accuracy (cvAUC of 0{middle dot}794{+/-}0{middle dot}107; CI 95%: 0{middle dot}74-0{middle dot}87) and a simple score was provided to simplify the interpretation of the three biomarkers. Besides additional finding on PTX3 role in SARS-CoV2 pathology, its prognostic value was confirmed by data on clinical deterioration; indeed, paucisymptomatic subjects showed a 11{middle dot}9% deaths. The model offers the possibility to quickly assess patients resulted positive for SARS-CoV-2 and estimate people at risk of deterioration despite normal clinical and blood gases analysis, with potential to identify those who need better clinical monitoring and interventions.\n\nImplications of all the available evidencePredicting the extension, severity, and clinical deterioration in COVID-19 patients its pivotal to allocate enough resources in emergency and to avoid health system burden. Despite the urgent clinical need of biomarkers, SARS-CoV-2 pneumonia still lacks something able to provide an easy measure of its severity. Some multiparametric scores have been proposed for severe COVID-19 and rely on deep assessment of patients status (clinical, serological, and radiological data). Our model represents an unprecedented effort to provide a tool which could predict CT pneumonia extension, oxygen requirement and clinical deterioration in mild COVID-19. Based on the measurement of three proteins on peripheral blood, this score could improve early assessment of asymptomatic patients tested positive by SARS-CoV2 specifically in first level hospitals as well in developing countries.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Marco Folci", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Enrico Brunetta", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Ezio Lanza", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Barbara Bottazzi", + "author_inst": "Humanitas Clinical and Research Center IRCCS" + }, + { + "author_name": "Alessandro Protti", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Gaia Messana", + "author_inst": "Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Costanza Lisi", + "author_inst": "Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Roberto Leone", + "author_inst": "IRCCS Humanitas Clinical and Research Center" + }, + { + "author_name": "Marina Sironi", + "author_inst": "IRCCS Humanitas Clinical and Research Center" + }, + { + "author_name": "Elena Generali", + "author_inst": "Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Stefano Rodolfi", + "author_inst": "Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Michele Sagasta", + "author_inst": "Dept. Biomedical Sciences Humanits University" + }, + { + "author_name": "Antonio Voza", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Michele Ciccarelli", + "author_inst": "IRCCS Humanitas Clinical and Research Center" + }, + { + "author_name": "Cecilia Garlanda", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Luca Balzarini", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "Alberto Mantovani", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University; William Harvey Research Institute, Queen Mary University, Lond" + }, + { + "author_name": "Maurizio Cecconi", + "author_inst": "IRCCS Humanitas Clinical and Research Center and Dept. Biomedical Sciences, Humanitas University" + }, + { + "author_name": "- Humanitas COVID-19 Task Force", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.28.21264262", "rel_title": "No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups Infected with SARS-CoV-2 Delta Variant", @@ -545867,81 +544446,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.09.28.21264240", - "rel_title": "Predicting hospital-onset COVID-19 infections using dynamic networks of patient contacts: an observational study", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264240", - "rel_abs": "BackgroundReal-time prediction is key to prevention and control of healthcare-associated infections. Contacts between individuals drive infections, yet most prediction frameworks fail to capture the dynamics of contact. We develop a real-time machine learning framework that incorporates dynamic patient contact networks to predict patient-level hospital-onset COVID-19 infections (HOCIs), which we test and validate on international multi-site datasets spanning epidemic and endemic periods.\n\nMethodsOur framework extracts dynamic contact networks from routinely collected hospital data and combines them with patient clinical attributes and background contextual hospital data to forecast the infection status of individual patients. We train and test the HOCI prediction framework using 51,157 hospital patients admitted to a UK (London) National Health Service (NHS) Trust from 01 April 2020 to 01 April 2021, spanning UK COVID-19 surges 1 and 2. We then validate the framework by applying it to data from a non-UK (Geneva) hospital site during an epidemic surge (40,057 total inpatients) and to data from the same London Trust from a subsequent period post surge 2, when COVID-19 had become endemic (43,375 total inpatients).\n\nFindingsBased on the training data (London data spanning surges 1 and 2), the framework achieved high predictive performance using all variables (AUC-ROC 0{middle dot}89 [0{middle dot}88-0{middle dot}90]) but was almost as predictive using only contact network variables (AUC-ROC 0{middle dot}88 [0{middle dot}86-0{middle dot}90]), and more so than using only hospital contextual (AUC-ROC 0{middle dot}82 [0{middle dot}80-0{middle dot}84]) or patient clinical (AUC-ROC 0{middle dot}64 [0{middle dot}62-0{middle dot}66]) variables. The top three risk factors we identified consisted of one hospital contextual variable (background hospital COVID-19 prevalence) and two contact network variables (network closeness, and number of direct contacts to infectious patients), and together achieved AUC-ROC 0{middle dot}85 [0{middle dot}82-0{middle dot}88]. Furthermore, the addition of contact network variables improved performance relative to hospital contextual variables on both the non-UK (AUC-ROC increased from 0{middle dot}84 [0{middle dot}82-0{middle dot}86] to 0{middle dot}88 [0{middle dot}86-0{middle dot}90]) and the UK validation datasets (AUC-ROC increased from 0{middle dot}52 [0{middle dot}49-0{middle dot}53] to 0{middle dot}68 [0{middle dot}64-0{middle dot}70]).\n\nInterpretationOur results suggest that dynamic patient contact networks can be a robust predictor of respiratory viral infections spreading in hospitals. Their integration in clinical care has the potential to enhance individualised infection prevention and early diagnosis.\n\nFundingMedical Research Foundation, World Health Organisation, Engineering and Physical Sciences Research Council, National Institute for Health Research, Swiss National Science Foundation, German Research Foundation.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Ashlegh C Myall", - "author_inst": "Imperial College London" - }, - { - "author_name": "James Richard Price", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert L Peach", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mohamed Abbas", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Siddharth Mookerjee", - "author_inst": "Imperial College London NHS Trust" - }, - { - "author_name": "Nina Zhu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Isa Ahmad", - "author_inst": "Imperial College London" - }, - { - "author_name": "Damien Keng Yen Ming", - "author_inst": "Imperial College London" - }, - { - "author_name": "Farzan Ramzan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Daniel Teixeira", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Christophe Graf", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Andrea Y Wiesse", - "author_inst": "The University of Edinburgh" - }, - { - "author_name": "Stephan Harbarth", - "author_inst": "University Hospital of Geneva" - }, - { - "author_name": "Alison Holmes", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mauricio Barahona", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.09.28.21264207", "rel_title": "Durability of ChAdOx1 nCov-19 (AZD1222) vaccination in people living with HIV - responses to SARS-CoV-2, variants of concern and circulating coronaviruses", @@ -547066,6 +545570,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.28.462109", + "rel_title": "Use of eVLP-based vaccine candidates to broaden immunity against SARS-CoV-2 variants", + "rel_date": "2021-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.28.462109", + "rel_abs": "Rapid emergence of SARS-CoV-2 variants is a constant threat and a major hurdle to reach heard immunity. We produced VBI-2905a, an enveloped virus-like particle (eVLP)-based vaccine candidate expressing prefusion spike protein from the Beta variant that contains several escape mutations. VBI-2905a protected hamsters against infection with a Beta variant virus and induced high levels of neutralizing antibodies against Beta RBD. In a heterologous vaccination regimen, a single injection of VBI-2905a in animals previously immunized with VBI-2902, a vaccine candidate expressing S from ancestral SARS-CoV-2, hamsters were equally protected against Beta variant infection. As an alternate strategy to broaden immunity, we produced a trivalent vaccine expressing the prefusion spike protein from SARS-CoV-2 together with unmodifed S from SARS-CoV-1 and MERS-CoV. Relative to immunity induced against the ancestral strain, the trivalent vaccine VBI-2901a induced higher and more consistent antibody binding and neutralizing responses against a panel of variants including Beta, Delta, Kappa, and Lambda, with evidence for broadening of immunity rather than just boosting cross-reactive antibodies.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jasminka Bozic", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Tanvir Ahmed", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Barthelemy Ontsouka", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Anne-Catherine Fluckiger", + "author_inst": "VBIvaccines" + }, + { + "author_name": "Abebaw Diress", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Tamara Berthoud", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Xiaoyang Yuan", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Lanjian Yang", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Francisco Diaz-Mitoma", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "David E Anderson", + "author_inst": "VBI Vaccines" + }, + { + "author_name": "Catalina Soare", + "author_inst": "VBI Vaccines" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.27.462074", "rel_title": "A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in rhesus macaques", @@ -548069,33 +546632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.25.21264099", - "rel_title": "Induction of robust neutralizing antibodies against the COVID-19 Delta variant with ChAdOx1 nCoV-19 or BNT162b2 as a booster following a primary vaccination series with CoronaVac", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264099", - "rel_abs": "We determined the antibody response among CoronaVac vaccinees who were boosted with either BNT162b2 or ChAdOx1 nCoV-19. Increase in anti-S-RBD antibodies and surrogate neutralizing antibodies against the Delta variant was higher in BNT162b2 recipients than in ChAdOx1 nCoV-19 recipients. High proportions of reactogenicity were seen for both booster regimens.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Samadhi Patamatamkul", - "author_inst": "Mahasarakham University" - }, - { - "author_name": "Benjaporn Buranrat", - "author_inst": "Mahasarakham University" - }, - { - "author_name": "Sutthiwan Thammawat", - "author_inst": "Mahasarakham University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.26.21264153", "rel_title": "COVID-19 Vaccination Strategies Considering Hesitancy Using Particle-Based Epidemic Simulation", @@ -548664,6 +547200,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.27.461930", + "rel_title": "Milk casein prevents inactivation effect of black tea galloylated theaflavins on SARS-CoV-2 in vitro", + "rel_date": "2021-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.27.461930", + "rel_abs": "Repeated emergence of highly contagious and potentially immune-evading variant SARS-CoV-2 is posing global health and socioeconomical threats. For suppression of the spread of the virus infection among people, a procedure to inactivate virus in saliva may be useful, because saliva of infected persons is the major origin of droplets and aerosols that mediate viral transmission to nearby persons. We previously reported that SARS-CoV-2 is rapidly and remarkably inactivated by treatment in vitro with tea including green tea, roasted green tea, oolong tea and black tea. Tea catechin-derived compounds including theaflavins (TFs) with (a) galloyl moiety(ies) showed this activity. Although black tea is popularly consumed worldwide, a lot of people consume it with sugar, milk, lemon juice, and so on. But it has not been determined whether these ingredients may influence the inactivation effect of black tea against SARS-CoV-2. Moreover, it has not been revealed whether black tea is capable of inactivating variant viruses such as delta variant. Here we examined the effect of black tea on some variants in the presence or absence of sugar, milk, and lemon juice in vitro. Black tea and galloylated TFs remarkably inactivated alpha, gamma, delta and kappa variants. Intriguingly, an addition of milk but not sugar and lemon juice totally prevented black tea from inactivating alpha and delta variant viruses. The suppressive effect was also exerted by milk casein. These results suggest the possibility that intake of black tea without milk by infected persons may result in inactivation of the virus in saliva and attenuation of spread of SARS-CoV-2 to nearby persons through droplets. Clinical studies are required to investigate this possibility.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eriko Ohgitani", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Masaharu Shin-Ya", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Masaki Ichitani", + "author_inst": "ITO EN, Ltd." + }, + { + "author_name": "Makoto Kobayashi", + "author_inst": "ITO EN, Ltd." + }, + { + "author_name": "Takanobu Takihara", + "author_inst": "ITO EN, Ltd." + }, + { + "author_name": "Motoki Saito", + "author_inst": "Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Hitoshi Kinugasa", + "author_inst": "ITO EN, Ltd." + }, + { + "author_name": "Osam Mazda", + "author_inst": "Kyoto Prefectural University of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.27.461855", "rel_title": "Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities", @@ -549595,173 +548178,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.18.21263630", - "rel_title": "The International Sexual Health And Reproductive Health Survey (I-SHARE-1): A Cross-Sectional Multi-Country Analysis of Adults from 30 Countries Prior to and During the Initial COVID-19 Wave", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263630", - "rel_abs": "BackgroundThe COVID-19 pandemic forced billions of people to shelter in place, altering social and sexual relationships worldwide. In many settings, COVID-19 threatened already precarious health services. However, there is limited evidence to date about changes to sexual and reproductive health (SRH) during the initial wave of COVID-19 disease. To address this gap, our team organized a multi-country, cross-sectional online survey as part of a global consortium.\n\nMethodsConsortium research teams conducted online surveys in 30 countries. Sampling methods included convenience, online panels, and population-representative. Primary outcomes included sexual behaviors, partner violence, and SRH service utilization, and we compared three months prior to and three months after policy measures to mitigate COVID-19. We used established indicators and analyses pre-specified in our protocol. We conducted meta-analyses for primary outcomes and graded the certainty of the evidence using Cochrane methods. Descriptive analyses included 22,724 individuals in 25 countries. Five additional countries with sample sizes <200 were included in descriptive meta-analyses.\n\nResultsRespondents were mean age 34 years; most identified as women (15160; 66.7%), cis-gender (19432; 86.6%) and heterosexual (16592; 77.9%). Among 4546 respondents with casual partners, condom use stayed the same for 3374 (74.4%) people and 640 (14.1%) people reported a decline. Fewer respondents reported physical or sexual partner violence during COVID-19 measures (1063/15144, 7.0%) compared to the period before COVID-19 measures (1469/15887, 9.3%). COVID-19 measures impeded access to condoms (933/10790, 8.7%), contraceptives (610/8175, 7.5%), and HIV/STI testing (750/1965, 30.7%). Pooled estimates from meta-analysis indicate during COVID-19 measures, 32.3% (95% CI 23.9-42.1) of people needing HIV/STI testing had hindered access, 4.4% (95% CI 3.4-5.4) experienced partner violence, and 5.8% (95% CI 5.4-8.2) decreased casual partner condom use (moderate certainty of evidence for each outcome). Meta-analysis findings were robust in sensitivity analyses that examined country income level, sample size, and sampling strategy.\n\nConclusionOpen science methods are feasible to organize research studies as part of emergency responses. The initial COVID-19 wave impacted SRH behaviors and access to services across diverse global settings.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Jennifer Toller Erausquin", - "author_inst": "University of North Carolina at Greensboro, Greensboro, NC, USA" - }, - { - "author_name": "Rayner K.J. Tan", - "author_inst": "Dermatology Hospital of Southern Medical University, Guangzhou, China; University of North Carolina Project-China, Guangzhou, China" - }, - { - "author_name": "Maximiliane Uhlich", - "author_inst": "University of Fribourg, Fribourg, Switzerland" - }, - { - "author_name": "Joel M. Francis", - "author_inst": "University of Witwatersrand, Johanessburg, South Africa" - }, - { - "author_name": "Navin Kumar", - "author_inst": "Yale University, New Haven, CT, USA" - }, - { - "author_name": "Linda Campbell", - "author_inst": "University of Antwerp, Antwerp, Belgium; University of Ghent, Ghent, Belgium" - }, - { - "author_name": "Wei-Hong Zhang", - "author_inst": "University of Ghent, Ghent, Belgium; Universite Libre de Bruxelles, Brussels, Belgium" - }, - { - "author_name": "Takhona G. Hlatshwako", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Priya Kosana", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Sonam Shah", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Erica M. Brenner", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC" - }, - { - "author_name": "Lore Remmerie", - "author_inst": "University of Ghent, Ghent, Belgium" - }, - { - "author_name": "Aamirah Mussa", - "author_inst": "Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana" - }, - { - "author_name": "Katerina Klapilova", - "author_inst": "Charles University, Prague, Czech Republic; National Institute of Mental Health, Klecany, Czech Republic" - }, - { - "author_name": "Kristen Mark", - "author_inst": "University of Minnesota Medical School, Minneapolis, MN, USA" - }, - { - "author_name": "Gabriela Perotta", - "author_inst": "University of Buenos Aires, Buenos Aires, Argentina" - }, - { - "author_name": "Amanda Gabster", - "author_inst": "Gorgas Memorial Institute for Health Studies, Panama City, Panama; London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Edwin Wouters", - "author_inst": "University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Sharyn Burns", - "author_inst": "Curtin University, Perth, Australia" - }, - { - "author_name": "Jacqueline Hendriks", - "author_inst": "Curtin University, Perth, Australia" - }, - { - "author_name": "Devon J. Hensel", - "author_inst": "Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Purdue University Indianapolis, Indianapolis, IN, USA" - }, - { - "author_name": "Simukai Shamu", - "author_inst": "Foundation for Professional Development, Pretoria, South Africa; University of Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Jenna Marie Strizzi", - "author_inst": "University of Copenhagen, Copenhagen, Denmark" - }, - { - "author_name": "Tammary Esho", - "author_inst": "End FGM/C Centre of Excellence, Amref Health Africa, Nairobi, Kenya" - }, - { - "author_name": "Chelsea Morroni", - "author_inst": "Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Stefano Eleuteri", - "author_inst": "Sapienzo University, Rome, Italy" - }, - { - "author_name": "Norhafiza Sahril", - "author_inst": "Ministry of Health Malaysia, Putrajaya, Malaysia" - }, - { - "author_name": "Wah Yun Low", - "author_inst": "Universiti Malaya, Kuala Lumpur, Malaysia" - }, - { - "author_name": "Leona Plasilova", - "author_inst": "Charles University, Prague, Czech Republic; National Institute of Mental Health, Klecany, Czech Republic" - }, - { - "author_name": "Gunta Lazdane", - "author_inst": "Riga Stradins University, Riga, Latvia" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Adesola Olumide", - "author_inst": "University of Ibadan, Ibadan, Nigeria" - }, - { - "author_name": "Amr Abdelhamed", - "author_inst": "Department of Dermatology, Venereology & Andrology, Sohag University, Sohag, Egypt" - }, - { - "author_name": "Alejandra Lopez Gomez", - "author_inst": "Department of Psychology, University of the Republic, Montevideo, Uruguay" - }, - { - "author_name": "Kristien Michielsen", - "author_inst": "University of Ghent, Ghent, Belgium" - }, - { - "author_name": "Caroline Moreau", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; CESP, INSERM 1018, Villejuif, France" - }, - { - "author_name": "Joseph D Tucker", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC; London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "- I-SHARE research consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.24.21263766", "rel_title": "The Report on China-Spain Joint Clinical Testing for Rapid COVID-19 Risk Screening by Eye-region Manifestations", @@ -550810,6 +549226,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2021.09.21.21263898", + "rel_title": "The Impact of New SARS-CoV-2 Variants on Vaccine Breakthrough: a pilot study on spreading infection in the communities", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263898", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) vaccines are effective at helping protect against severe disease and death from variants; however, incident of breakthrough infection in vaccinated patients has been increased. Therefore, we aimed to assess the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) new variants of concern in the communities and investigate vaccine breakthrough cases on our laboratory (Ayass Bioscience LLC) confirmed detection of COVID-19 variants in Dallas-Fort Worth (DFW), Texas.\n\nMethodsEpidemiologic study has been performed at our laboratory. We studied the viral whole-genome sequence and genotyping analysis on 166 symptomatic cases of COVID-19 which were randomly selected from nasal swab positive cases assessed from June 1st to August 30th, 2021, by reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values. COVID-19 variants were identified to be dominated by B.1.617.2 (89.2%) and followed by AY.3 (1.8%), B.1.1.7 (4.8%), a combination of B.1.526.1 and B.1.617.2 (3%), B.1.621 (0.6%), and P.2 (0.6%).\n\nResultThe CT values showed significant difference among the three age groups: <30 years, 31-60 years, and >60 years by one-way ANOVA (N1: F (2, 118) =4.96, p=0.009; N2: F (2, 118) =4.95, p=0.009). No significant difference was observed by symptom, status of immunization, or vaccine manufacturer. A two-way ANOVA was performed to examine the effect of gender and variant group (Delta and other variants) on the CT values. The analyses revealed a statistically significant interaction between the effect of gender and variant group (N1, F (1.117) = 3.906, p = 0.05; N2, F (1, 117) = 7.402, p = 0.008).\n\nConclusionOur study shows that Delta, the dominant variant of COVID-19, is spreading in the communities, and vaccine breakthrough cases occurred in the majority of Delta variant (91%) followed by AY.3 (5%), B.1.1.7 (2%) and 2% of the double variant of B.1.526.1 and B.1.617.2. The incidence of the breakthrough cases was not linked to a specific manufacturer. The CT value is likely to associate with age. This study also supports our laboratorys ongoing efforts to sequence the SARS-CoV-2 virus from positive patient samples to identify the new viral variants and possible vaccine breakthrough mutations in the community.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mohamad Ammar Ayass", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Jin Zhang", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Kevin Zhu", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Wanying Cao", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Natalya Griko", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Victor Pashkov", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Jun Dai", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Trivendra Tripathi", + "author_inst": "Ayass Bioscience LLC" + }, + { + "author_name": "Lina Abi Mosleh", + "author_inst": "Ayass Bioscience LLC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.22.21263946", "rel_title": "Association of comorbidities with COVID-19 infection rate and severity: nationwide cohort study with propensity score matching", @@ -551777,33 +550244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.23.21263864", - "rel_title": "COVID-19 Vaccine Breakthrough Infections in the Veterans Health Administration.", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21263864", - "rel_abs": "BackgroundVaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been accompanied by rising concern of vaccine breakthrough due to SARS-CoV-2 variants, waning protection over time, differential vaccine effectiveness, and regional resurgence of Coronavirus 2019 (COVID-19). Characterizing the frequency and drivers of vaccine breakthrough is necessary to inform COVID-19 control efforts.\n\nMethodsWe performed a retrospective cohort study of vaccine breakthrough infections in fully vaccinated persons in Veterans Health Administration. We applied Cox proportional hazard models to estimate cumulative incidence, assess differences in outcomes by vaccine, and identify associations with individual characteristics as well as time-dependent geographic variation in COVID-19 incidence, proportion of delta variant, and vaccine coverage.\n\nResultsAmong 3,032,561 fully vaccinated persons, documented SARS-CoV-2 infection occurred in 11,197 (0.37%) and COVID-19 hospitalization occurred in 2,080 (0.07%). Compared to Ad26.COV2.S, BNT162b2 and mRNA-1273 had lower occurrence of documented SARS-CoV-2 infection (aHR 0.54, 95% confidence interval (CI) 0.51-0.58; aHR 0.36; 95% CI 0.33-0.38; respectively) and COVID-19 hospitalization (aHR 0.56, 95% CI 0.47-0.66; aHR 0.30; 0.25-0.35; respectively). Documented SARS-CoV-2 infection and COVID-19 hospitalization were associated with younger age, Hispanic or Latino ethnicity, number of comorbidities, and previous SARS-CoV-2 infection. Regional proportion of delta variant and county-level COVID-19 incidence were predictors of vaccine breakthrough events; county-level vaccine coverage was inversely associated.\n\nConclusionsVaccine breakthrough was rare among fully vaccinated persons. mRNA-1273 and BNT162b2 were more protective against documented SARS-CoV-2 infection and COVID-19 hospitalization compared to Ad26.COV2.S. Efforts to limit COVID-19 transmission and bolster vaccine coverage would also curtail vaccine breakthrough.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aditya Sharma", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Gina Oda", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Mark Holodniy", - "author_inst": "Department of Veterans Affairs" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.14.21263403", "rel_title": "Evaluation Of A New All In One Sars-Cov-2 Antigen-Detecting Rapid Diagnostic Test And Self-Test: Diagnostic Performance And Usability On Child And Adult Population", @@ -552520,6 +550960,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.25.461776", + "rel_title": "LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein", + "rel_date": "2021-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.25.461776", + "rel_abs": "The interactions between severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to COVID-19. The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary ACE2 receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was restricted to SARS-CoV-2, suggesting LRRC15 represents a novel class of spike binding interaction. We localized the interaction to the C-terminus of the S1 domain, and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19.\n\nIn briefWe present evidence from genome-wide screening that the spike protein of SARS-CoV-2 interacts with human cells expressing LRRC15. The interaction is distinct from previously known classes of spike attachment factors, and appears to have emerged recently within the coronavirus family. Although not sufficient for cell invasion, this interaction can modulate viral infection. Our data point to an unappreciated host factor for SARS-CoV-2, with potential relevance to COVID-19.\n\nHighlights- Two systematic cell-based screens for SARS-CoV-2 spike protein binding identify LRRC15 as a human host factor\n- Interaction with LRRC15 is reproducible in different human cell lines and independent of known glycan or ACE2 binding pathways\n- The C-terminal S1 domain of SARS-CoV-2 spike binds LRRC15 with sub-micromolar affinity, while related coronavirus spikes do not\n- LRRC15 is expressed in tissues with high ACE2 levels and may modulate infection", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jarrod Shilts", + "author_inst": "Wellcome Trust Sanger Institute" + }, + { + "author_name": "Thomas M. Crozier", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ana Teixeira-Silva", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ildar Gabaev", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Edward J.D. Greenwood", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Samuel James Watson", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Brian M. Ortmann", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Christian M. Gawden-Bone", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Tekle Pauzaite", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "German Primate Center, G\u00f6ttingen" + }, + { + "author_name": "James A. Nathan", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Stefan P\u00f6hlmann", + "author_inst": "German Primate Center, G\u00f6ttingen" + }, + { + "author_name": "Paul J. Lehner", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Gavin J. Wright", + "author_inst": "Wellcome Trust Sanger Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.09.17.21263549", "rel_title": "A systematic review of COVID-19 vaccine efficacy and effectiveness against SARS-CoV-2 infection and disease", @@ -553639,37 +552150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.17.21263464", - "rel_title": "Profiles of US Hispanics Unvaccinated for COVID-19", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263464", - "rel_abs": "BackgroundThe COVID-19 pandemic has disproportionately impacted Hispanics in the US with increased rates of SARS-Cov2 infections, hospitalizations, and deaths. The objective of this report was to characterize the demographics and beliefs of unvaccinated Hispanics to help address their concerns that lead to vaccine hesitancy.\n\nMethodsOf 1,011 potential participants from a national online panel, 22.3% (N=225, 51.6% female, age = 40.5) met inclusion criteria of Hispanic adults and not receiving at least one dose of the COVID-19 vaccine. The 30-item survey included items about demographics, political affiliations, sources of news (e.g., Fox vs. CNN), reasons for being unvaccinated, and ratings (0 = strongly disagree, 100 = strongly agree) of 10 controversial statements regarding COVID-19.\n\nResultsOver three-fifths (62.6%) identified side effects and safety concerns while almost one-third (30.5%) a lack of efficacy as their top reasons for being unvaccinated. Agreement to \"The developers of the COVID-19 vaccine rushed the development and cut-corners\" was rated highest (63.22) which was significantly (p < .001) higher than the other nine statements (e.g., \"The COVID-19 vaccine does not work\"). Many vaccine attitudes differed significantly by political party affiliation and some by gender and news source. Republicans (59.9 {+/-} 4.2) scored higher than Democrats (38.5 {+/-} 4.2, p [≤] .001) to \"If Ive already had COVID-19, I dont need the vaccine.\"\n\nConclusionsThis study identified heterogeneity in COVID-19 vaccine attitudes among Hispanics. Further research is needed to determine if the subgroups identified are differentially receptive to interventions to facilitate reconsideration of prior vaccination decisions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Brian J Piper", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Bianca V Sanchez", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Joshua D. Madera", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Michael A Sulzinski", - "author_inst": "Geisinger Commonwealth School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.19.21263807", "rel_title": "RNA-extraction-free diagnostic method to detect SARS-CoV-2: an assessment from two States, India", @@ -554206,6 +552686,41 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.09.22.461286", + "rel_title": "Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor", + "rel_date": "2021-09-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.22.461286", + "rel_abs": "Interferons establish an antiviral state in responding cells through the induction of hundreds of interferon-stimulated genes (ISGs). ISGs antagonize viral pathogens directly through diverse mechanisms acting at different stages of viral life cycles, and indirectly by modulating cell cycle and promoting programmed cell death. The mechanisms of action and viral specificities for most ISGs remain incompletely understood. To enable the high throughput interrogation of ISG antiviral functions in pooled genetic screens while mitigating the potentially confounding effects of endogenous IFN and potential antiproliferative/proapoptotic ISG activities, we adapted a CRISPR-activation (CRISPRa) system for inducible ISG induction in isogenic cell lines with and without the capacity to respond to IFN. Engineered CRISPRa cell lines demonstrated inducible, robust, and specific gRNA-directed expression of ISGs, which are functional in restricting viral infection. Using this platform, we screened for ISGs that restrict SARS-CoV-2, the causative agent of the COVID-19 pandemic. Results included ISGs previously described to restrict SARS-CoV-2 as well as multiple novel candidate antiviral factors. We validated a subset of candidate hits by complementary targeted CRISPRa and ectopic cDNA expression infection experiments, which, among other hits, confirmed OAS1 as a SARS-CoV-2 restriction factor. OAS1 exhibited strong antiviral effects against SARS-CoV-2, and these effects required OAS1 catalytic activity. These studies demonstrate a robust, high-throughput approach to assess antiviral functions within the ISG repertoire, exemplified by the identification of multiple novel SARS-CoV-2 restriction factors.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Oded Danziger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Roosheel S Patel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emma J DeGrace", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mikaela R Rosen", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brad R Rosenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.22.21263964", "rel_title": "Impact of the COVID-19 pandemic on treatment patterns for US patients with metastatic solid cancer", @@ -555117,65 +553632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.09.20.21263812", - "rel_title": "Health-Related Quality of Life and psychological distress of adolescents during the COVID-19 pandemic in Geneva", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263812", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPurposeC_ST_ABSOur objective was to assess adolescents Health-Related Quality of Life (HRQoL) and psychological distress, from their own and their parents perspective, and to examine associated risk factors during the COVID-19 pandemic in Geneva, Switzerland.\n\nMethodsA random sample of adolescents, aged 14-17 years, and their families was invited to a serosurvey in November and December 2020. Adolescents HRQoL was evaluated using the validated adolescent-reported KIDSCREEN-10 and parent-reported KINDL(R) scales. Psychological distress was assessed with self-reported sadness and loneliness, and using the KINDL(R) emotional well-being scale. Risk factors for adolescents low HRQoL and psychological distress were identified using generalized estimating equations and both adolescents and their parents perceptions were compared.\n\nResultsAmong 240 adolescents, 11% had a low HRQoL, 35% reported sadness and 23% reported loneliness. Based on parents perception, 12% of the adolescents had a low HRQoL and 16% a low emotional well-being. Being a girl (aOR=3.29; 95%CI: 1.64-6.57), increased time on social media (aOR=2.05; 95%CI: 1.08-3.88), parents average to poor mood (aOR=2.81; 95%CI: 1.21-6.56) and average to poor household financial situation (aOR=2.30; 95%CI: 1.00-5.29) were associated with an increased risk of sadness. Mismatches between adolescents and their parents perception of HRQoL were more likely for girls (aOR=2.88; 95%CI: 1.54-5.41) and in households with lower family well-being (aOR=0.91; 95%CI: 0.86-0.96).\n\nConclusionA meaningful proportion of adolescents experienced low well-being during the second wave of COVID-19. Adolescents living in underprivileged or distressed families seemed particularly affected. Monitoring is necessary to evaluate the long-term effects of the pandemic on adolescents.\n\nImplications and ContributionThis study describes the psychological well-being of a population-based sample of adolescents in Geneva, Switzerland amid the COVID-19 pandemic, and identifies adolescents at risk of distress. This study provides further insight by comparing adolescents well-being as reported by themselves and their parents.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Roxane Dumont", - "author_inst": "Unit of Population epidemiology - Geneva university hospital" - }, - { - "author_name": "Viviane Richard", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Helene Baysson", - "author_inst": "University of Geneva - HUG" - }, - { - "author_name": "Elsa Lorthe", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Giovanni Piumatti", - "author_inst": "Institute of Public Health, Faculty of BioMedicine, Universita della Svizzera Italiana, Lugano, Switzerland" - }, - { - "author_name": "Stephanie Schrempft", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Ania Wisniak", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Remy Barbe", - "author_inst": "Division of Child and Adolescent Psychiatry, Department of Woman, Child, and Adolescent Medicine, Geneva University Hospitals, Switzerland" - }, - { - "author_name": "Klara Posfay Barbe", - "author_inst": "Division of General Pediatrics, Department of Woman, Child, and Adolescent Medicine, Geneva University Hospitals, Switzerland" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.20.21263566", "rel_title": "Health-care workers in gastrointestinal endoscopy are at higher risk for SARS-CoV-2 infection compared to other aerosol-generating disciplines", @@ -556188,6 +554644,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.20.21263836", + "rel_title": "HUMORAL AND CELLULAR IMMUNOGENICITY and SAFETY UP TO 4 MONTHS AFTER VACCINATION WITH BNT162B2 mRNA COVID-19 VACCINE IN HEART AND LUNG TRANSPLANTED YOUNG ADULTS", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263836", + "rel_abs": "BackgroundImmunizations among vulnerable population, including solid organ transplant recipients (SOT), present suboptimal responses at vaccination and over time. We investigated safety and immunogenicity of the BNT162B2 mRNA COVID-19 vaccine in 34 SOT young adults as compared to 36 healthy controls (HC).\n\nMethodsimmunogenicity was measured through the analysis of anti SARS-CoV2 IgG Antibodies and antigen specific CD4 T cells (CD40L+), detected by flow cytometry before vaccination, 21 days after priming (T21), 7 days after booster dose (T28) and 2-4 months after priming (T120). Baseline T and B cell immune phenotype was deeply investigated. The safety profile was investigated by close monitoring and self-reported diary.\n\nResultsAnti-S and anti-Trimeric Ab responses were significantly lower in SOT vs HC at T21 (p<0.0001) and at T28 (p<0.0001). Ten out of 34 SOT (29%) at T28 and 3 out of 33 (9%) at T120 had undetectable SARS-CoV-2 IgG. The analysis of SARS-CoV-2 specific CD4 T cells showed lower CD40L expression after in vitro stimulation in SOT compared to HC. Lower frequencies of memory B cells were found in patients not responding to vaccination. Lack of seroconversion was higher in patients treated with mycophenolate (p=0.0005). The vaccination was safe and well tolerated. Only short-term adverse events, were reported and no hospitalization or graft rejection were observed after vaccinations.\n\nConclusionsThese data show that SOT have a suboptimal immune response following mRNA vaccinations as compared to HC. Alternative strategies should be investigated to improve the immunization against SARS-CoV-2 in these patients.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nicola Cotugno", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Chiara Pighi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Elena Morrocchi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Alessandra Ruggiero", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Donato Amodio", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Chiara Medri", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Luna Colagrossi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Silvia Di Cesare", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Veronica Santilli", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Emma Concetta Manno", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Paola Zangari", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Carmela Giancotta", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Stefania Bernardi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Luciana Nicolosi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Marta Ciofi degli Atti", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Massimiliano Raponi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Salvatore Zaffina", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Sara Alfieri", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Richard Kirk", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Carlo Federico Perno", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Paolo Rossi", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "- Convers Study Team", + "author_inst": "" + }, + { + "author_name": "Antonio Amodeo", + "author_inst": "Bambino Gesu Children Hospital" + }, + { + "author_name": "Paolo Palma", + "author_inst": "Bambino Gesu Children Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263527", "rel_title": "Long Term Accuracy of SARS-CoV-2 Interferon-\u03b3 Release Assay and its Application in Household Investigation", @@ -556872,29 +555439,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.20.21263869", - "rel_title": "Genomic Surveillance in Japan of AY.29--A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263869", - "rel_abs": "In the present study, we report a new sub-lineage of the SARS-CoV-2 Delta variant called AY.29, which has C5239T and T5514C mutations. We investigated the monthly trend of AY.29 in Japan within 37,737 Delta variants downloaded on October 2, 2021. Among the total Japanese Delta variants, the AY.29 sub-lineage accounted for 95.1%. In terms of monthly trends, the sequences became predominant in June, and accounted for 95.4%, 97.6% and 90.5% of the reported sequences in July, August and September, respectively. Furthermore, the number of Delta variants imported from abroad during the Tokyo 2020 Olympics and Paralympics (held in August 2021) was extremely low during the fifth wave in Japan. Therefore, the epidemic of the new Delta variant is attributable to a newly occurring mutation in Japan.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Takashi Abe", - "author_inst": "Niigata University" - }, - { - "author_name": "Masanori Arita", - "author_inst": "National Institute of Genetics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.14.21263300", "rel_title": "Predictors of COVID-19 vaccine uptake in healthcare workers: a cross-sectional study in Greece", @@ -557647,6 +556191,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.16.21263678", + "rel_title": "Association of inflammatory markers with severity of disease and mortality in COVID-19 patients: a systematic review and meta-analysis", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263678", + "rel_abs": "PurposeLiterature suggests association of inflammatory markers with the severity and mortality related to COVID-19, but there are varying conclusions available. We aimed to provide an overview of the association of inflammatory markers with the severity and mortality of COVID-19 patients.\n\nMethodsWe searched Medline (via PubMed), Cochrane, Clinicaltrials.gov databases until Sept 1, 2020.\n\nResultsA total of 21 studies comprising 4023 patients with COVID-19 were included in our analysis. Levels of IL-6 (WMD=18.17 95%CI 3.38 to 32.96, p=0.016), IL-8 (WMD=12.09 95%CI 4.41 to 19.77, p=0.002), MCP-1 (WMD=146.66 95%CI 88.16 to 205.16, p<0.001), CRP (WMD=31.09 95%CI 10.08 to 52.10, p=0.004), PCT (WMD= -31.23 95%CI -37.70 to -24.76, p<0.001), IL-2R (WMD=861.93 95%CI 275.45 to 1448.41, p=0.004), ferritin (WMD= 1083.34 95%CI 431.99 to 1734.70, p=0.001) were found significantly higher in the severe group compared with the non-severe group of COVID-19 patients. Moreover, non-survivors had a higher levels of IL-2R (WMD= -666.06 95%CI -782.54 to -549.59, p<0.001), IL-8 (WMD= -26.63 95%CI -33.031 to -20.236, p<0.001), IL-10 (WMD= -7.60 95%CI -8.93 to -6.26, p<0.001), TNF- (WMD= -4.60 95%CI -5.71 to -3.48, p<0.001), IL-1{beta} (WMD=22.66 95%CI 8.13 to 37.19, p=0.002), CRP (WMD= -96.40 95%CI -117.84 to -74.97, p<0.001), and ferritin (WMD= -937.60 95%CI -1084.15 to -791.065, p<0.001) when compared to the non-survivor group.\n\nConclusionThis meta-analysis highlights the association of inflammatory markers with the severity and mortality of COVID-19 patients. Measurement of these inflammatory markers may assist clinicians to monitor and evaluate the severity and prognosis of COVID-19 thereby reducing the mortality rate.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sara Khan", + "author_inst": "Jamia Hamdard" + }, + { + "author_name": "Pinki Mishra", + "author_inst": "Jamia Hamdard" + }, + { + "author_name": "Rizwana Parveen", + "author_inst": "Jamia Hamdard" + }, + { + "author_name": "Ram Bajpai", + "author_inst": "Keele University, UK" + }, + { + "author_name": "Mohd Ashif Khan", + "author_inst": "Jamia Hamdard" + }, + { + "author_name": "Nidhi Bharal Agarwal", + "author_inst": "Jamia Hamdard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.17.21262959", "rel_title": "Assessment of Environmental and Occupational Risk Factors for the Mitigation and Containment of a COVID-19 Outbreak in a Meat Processing Plant", @@ -558362,65 +556945,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.17.460814", - "rel_title": "A BioID-derived proximity interactome for SARS-CoV-2 proteins", - "rel_date": "2021-09-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.17.460814", - "rel_abs": "The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here we use BioID to map the SARS-CoV-2 virus-host interactome using human lung cancer derived A549 cells expressing individual SARS-CoV-2 viral proteins. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are in association with SARS-CoV-2 proteins. We have also established a website to host the proteomic data to allow for public access and continued analysis of host-viral protein associations and whole-cell proteomes of cells expressing the viral-BioID fusion proteins. Collectively, these studies provide a valuable resource to potentially uncover novel SARS-CoV-2 biology and inform development of antivirals.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Danielle G May", - "author_inst": "Sanford Research" - }, - { - "author_name": "Laura Martin-Sancho", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Valesca Anschau", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Sophie Liu", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Rachel J Chrisopulos", - "author_inst": "Sanford Research" - }, - { - "author_name": "Kelsey L Scott", - "author_inst": "Sanford Research" - }, - { - "author_name": "Charles T Halfmann", - "author_inst": "Sanford Research" - }, - { - "author_name": "Ramon Diaz Pena", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Dexter Pratt", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Alexandre R Campos", - "author_inst": "SBP Medical Discovery Intitute" - }, - { - "author_name": "Kyle J Roux", - "author_inst": "Sanford Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.09.17.21263528", "rel_title": "Dichotomy between the humoral and cellular responses elicited by mRNA and adenoviral vector vaccines against SARS-CoV-2.", @@ -559057,6 +557581,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.09.16.21263704", + "rel_title": "Real-world serologic responses to Extended-interval and Heterologous COVID-19 mRNA vaccination in Frail Elderly - Interim report from a prospective observational cohort study", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263704", + "rel_abs": "BackgroundThe Coronavirus disease 2019 (Covid-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted accelerated vaccines development. Their use was prioritized to protect the most vulnerable, notably, the elderly. Because of fluctuations in vaccine availability, strategies such as delayed second dose and heterologous prime-boost have been employed. The effectiveness of these strategies in the frail elderly are unknown.\n\nMethodsIn this real-world vaccination study, under a government-decreed rationing strategy, elderly adults residing in long-term care facilities, with or without previously-documented SARS-CoV-2 infection, were administered homologous or heterologous mRNA vaccines, with an extended 16-week interval between doses. Clinical data and blood were serially collected during and after this interval period. Sera were tested for SARS-CoV-2-specific IgG antibodies (to trimeric S; RBD; nucleocapsid) by automated chemiluminescent ELISA.\n\nFindingsAfter a significant increase 4 weeks post-prime dose, there was a significant decline in anti-RBD and anti-S IgG levels until the boost dose, followed by an increase 4 weeks later. Previously uninfected individuals exhibited lower antibody responses up to 16 weeks post-prime dose, but achieved comparable levels to previously infected counterparts by 4 weeks post-second dose. Individuals primed with BNT162b2 exhibited larger decrease in anti-RBD and anti-S IgG levels with 16-week interval between doses, compared to those who received mRNA-1273. No differences in antibody levels 4 weeks after the second dose were noted between the two vaccines, in either homologous or heterologous combinations.\n\nInterpretationsThese interim results of this ongoing longitudinal study show that, among frail elderly, neither age, sex, nor comorbidity affect antigenicity of mRNA-based COVID vaccines, but previous SARS-CoV-2 infection and type of mRNA vaccine influenced antibody responses when used with a 16-week interval between doses. Homologous/heterologous use of mRNA vaccines was not associated with significant differences in antibody responses 4 weeks following second dose, supporting their interchangeability.\n\nFundingThis project was supported by funding from the Public Health Agency of Canada, through the Vaccine Surveillance Reference group and the COVID-19 Immunity Task Force (CITF).", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Donald C Vinh", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada Division of Infectious Di" + }, + { + "author_name": "Jean-Philippe Gouin", + "author_inst": "Centre de recherche de l'Institut de g\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Canada Department of Psychology, Faculty of Arts and Sciences, Concordia University, Montr" + }, + { + "author_name": "Diana Cruz-Santiago", + "author_inst": "Centre de recherche de l'Institut de g\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Canada" + }, + { + "author_name": "Michelle Canac-Marquis", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "St\u00e9phane Bernier", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Florian Bobeuf", + "author_inst": "Centre de recherche de l'Institut de g\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Canada" + }, + { + "author_name": "Avik Sengupta", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Jean-Philippe Brassard", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Alyssa Guerra", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Rob Dziarmaga", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Anna Perez", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Yichun Sun", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Yongbiao Li", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Lucie Roussel", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Melanie Langelier", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Danbing Ke", + "author_inst": "Infectious Diseases and Immunity in Global Health program, Research Institute of the McGill University Health Centre, Montreal, Canada" + }, + { + "author_name": "Corey Arnold", + "author_inst": "Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada" + }, + { + "author_name": "Martin Pelchat", + "author_inst": "Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada uOttawa Center for Infection, Immunity an" + }, + { + "author_name": "Marc-Andr\u00e9 Langlois", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Timothy G. Evans", + "author_inst": "School of Population and Global Health, McGill University" + }, + { + "author_name": "Xun Zhang", + "author_inst": "Centre for Outcomes Research and Evaluation, Research Institute of McGill University Health Centre, Montreal, QC, Canada." + }, + { + "author_name": "Bruce D. Mazer", + "author_inst": "Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Canada Division of Allergy, Immunology, and Dermatology, Dep" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/423467", "rel_title": "An epi-evolutionary model to predict spore-producing pathogens adaptation to quantitative resistance in heterogeneous environments", @@ -560296,85 +558923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.09.15.21263618", - "rel_title": "SARS-CoV-2 variants in Paraguay: Detection and surveillance with a readily modifiable, multiplex real-time RT-PCR", - "rel_date": "2021-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263618", - "rel_abs": "ObjectivesThe objective of the current study was to develop a lower-cost and scalable protocol to identify and monitor SARS-CoV-2 variants in Paraguay by pairing real-time RT-PCR detection of spike mutations with amplicon Sanger sequencing and whole-genome Nanopore sequencing.\n\nMethods201 acute-phase nasopharyngeal samples from SARS-CoV-2-positive individuals were tested with two rRT-PCRs: 1) N2RP assay to confirm SARS-CoV-2 RNA detection (CDC N2 target), and 2) the Spike SNP assay to detect mutations in the spike receptor binding domain. The assay was performed with probes to identify mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S).\n\nResultsAll samples were positive for SARS-CoV-2 in the N2RP assay (mean Ct, 20.8; SD 5.6); 198/201 (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%) and most consistent with P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%); and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). Results were confirmed by Sanger sequencing in 181/181 samples (100%) with high-quality amplicon sequences, and variant calls were consistent with Nanopore sequencing in 29/29 samples.\n\nConclusionsThe Spike SNP assay provides accurate detection of mutations associated with SARS-CoV-2 variants. This can be implemented in laboratories performing rRT-PCR to improve population-level surveillance for these mutations and inform the judicious use of scarce sequencing resources.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Magaly Martinez", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Phuong-Vi Nguyen", - "author_inst": "Emory University, Department of Medicine, Division of Infectious Diseases" - }, - { - "author_name": "Maxwell Su", - "author_inst": "Emory University, Department of Medicine, Division of Infectious Diseases" - }, - { - "author_name": "Fatima Cardozo", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Adriana Valenzuela", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Laura Franco", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Maria Eugenia Galeano", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Leticia Elizabeth Rojas", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Chyntia Carolina Diaz Acosta", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Jonas Fernandez", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Joel Ortiz", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Florencia del Puerto", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Laura Mendoza", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Eva Nara", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Alejandra Rojas", - "author_inst": "Universidad Nacional de Asuncion, Instituto de Investigaciones en Ciencias de la Salud" - }, - { - "author_name": "Jesse Waggoner", - "author_inst": "Emory University, Department of Medicine, Division of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.16.460716", "rel_title": "The supramolecular organization of SARS-CoV and SARS-CoV-2 virions revealed by coarse-grained models of intact virus envelopes", @@ -561411,6 +559959,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.09.14.21263545", + "rel_title": "Widening Disparities in Online Information Access during the COVID-19 Pandemic", + "rel_date": "2021-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263545", + "rel_abs": "The COVID-19 pandemic has stimulated a staggering increase in online information access (1, 2), but the extent to which different communities of internet users enlist digital resources to meet everyday needs varies (2-4). We analyze 55 billion everyday web search interactions across 25,150 US ZIP codes and demonstrate that there were disparate impacts of the pandemic on online information access across several information domains, including health and pandemic-relevant online resources (e.g., online learning, online food delivery). Among many findings, we show that ZIP codes associated with higher proportions of Black residents intensified their access to unemployment resources, and ZIP codes associated with lower income reduced their access to health information resources relative to their counterpart ZIP codes. Because these disparate impacts on the access to online information may result in downstream offline gaps in health, education, employment, and well-being (3), public health interventions should target potential barriers to accessing the necessary digital resources and provide adequate support to meet the intensified digital resource needs.\n\nOne Sentence SummaryLarge-scale web search logs reveal disparate impacts on online health, education, unemployment, and food information access.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jina Suh", + "author_inst": "Microsoft Research; University of Washington" + }, + { + "author_name": "Eric Horvitz", + "author_inst": "Microsoft Research; University of Washington" + }, + { + "author_name": "Ryen W. White", + "author_inst": "Microsoft Research; University of Washington" + }, + { + "author_name": "Tim Althoff", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.14.21263603", "rel_title": "Predominance of Distinct Autoantibodies in Response to SARS-CoV-2 Infection", @@ -562574,53 +561153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.13.21263473", - "rel_title": "Adverse reactions to BNT162b2 mRNA COVID-19 vaccine in medical staffs with a history of allergy.", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263473", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) vaccination is progressing globally. Several adverse reactions have been reported with vaccination against COVID-19. It is unknown whether adverse reactions to COVID-19 vaccination are severe in individuals with allergies. We administered the COVID-19 vaccine to the medical staff at Yamagata University Hospital from March to August 2021. Subsequently, we conducted an online questionnaire-based survey to investigate the presence of allergy and adverse reactions after vaccination and examined the association between allergy and adverse reactions after immunization.\n\nResponses were collected from 1586 subjects after the first vaccination and 1306 subjects after the second administration of the BNT162b2 mRNA COVID-19 vaccine. Adverse reactions included injection site pain, injection site swelling, fever, fatigue or malaise, headache, chills, nausea, muscle pain outside the injection site, and arthralgia. The frequency and severity of most adverse reactions were higher after the second vaccination compared to the first. The frequency of some adverse reactions and their severity were higher, and the duration of symptoms was longer in subjects with allergies than in subjects without allergies. Although several participants visited the emergency room for treatment after the first and second vaccinations, nobody was diagnosed with anaphylaxis.\n\nGiven the serious consequence of COVID-19 and the reported high efficacy of this vaccine against this disease, we conclude that vaccination of allergic individuals is generally recommended.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sumito Inoue", - "author_inst": "Department of Cardiology, Pulmonology, and Nephrology, Yamagata University Faculty of Medicine, Japan" - }, - { - "author_name": "Akira Igarashi", - "author_inst": "Department of Cardiology, Pulmonology, and Nephrology, Yamagata University Faculty of Medicine, Japan" - }, - { - "author_name": "Keita Morikane", - "author_inst": "Division of Clinical Laboratory and Infection Control, Yamagata University Hospital, Japan" - }, - { - "author_name": "Osamu Hachiya", - "author_inst": "Division of Infection Control, Yamagata University Hospital, Japan" - }, - { - "author_name": "Masafumi Watanabe", - "author_inst": "Department of Cardiology, Pulmonology, and Nephrology, Yamagata University Faculty of Medicine, Japan" - }, - { - "author_name": "Seiji Kakehata", - "author_inst": "Department of Otolaryngology Head and Neck Surgery, Yamagata University Faculty of Medicine, Japan" - }, - { - "author_name": "Shinya Sato", - "author_inst": "Yamagata University Hospital, Yamagata University Faculty of Medicine, Japan" - }, - { - "author_name": "Yoshiyuki Ueno", - "author_inst": "Department of Gastroenterology, Yamagata University Faculty of Medicine, Japan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.13.21263497", "rel_title": "Factors Influencing The First and Second Peak of COVID-19 Global Cases: A Survival Analysis", @@ -563453,6 +561985,125 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.09.16.460663", + "rel_title": "Neutralizing antibody-independent immunity to SARS-CoV-2 in hamsters and hACE-2 transgenic mice immunized with a RBD/Nucleocapsid fusion protein", + "rel_date": "2021-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.16.460663", + "rel_abs": "The nucleocapsid (N) and the receptor binding domain (RBD) of the Spike (S) proteins elicit robust antibody and T cell responses either in vaccinated or COVID-19 convalescent individuals. We generated a chimeric protein that comprises the sequences of RBD from S and N antigens (SpiN). SpiN was highly immunogenic and elicited a strong IFN{gamma} response from T cells and high levels of antibodies to the inactivated virus, but no neutralizing antibodies. Importantly, hamsters and the human Angiotensin Convertase Enzyme-2-transgenic mice immunized with SpiN were highly resistant to challenge with the wild type SARS-CoV-2, as indicated by viral load, clinical outcome, lung inflammation and lethality. Thus, the N protein should be considered to induce T-cell-based immunity to improve SARS-CoV-2 vaccines, and eventually to circumvent the immune scape by variants.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Julia Castro", + "author_inst": "Plataforma de Medicina Translacional da Fundacao Oswaldo Cruz e Faculdade de Medicina de Ribeirao Preto" + }, + { + "author_name": "Marcilio Fumagalli", + "author_inst": "Faculdade de Medicina de Ribeirao Preto" + }, + { + "author_name": "Natalia Hojo-Souza", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Patrick Azevedo", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Natalia Salazar", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Bruna Rattis", + "author_inst": "Faculdade de Medicina de Ribeirao Preto" + }, + { + "author_name": "Simone Ramos", + "author_inst": "Faculdade de Medicina de Ribeirao Preto" + }, + { + "author_name": "Lidia Faustino", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Gregorio Almeida", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Livia Oliveira", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Tomas Marcal", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Marconi Augusto", + "author_inst": "Fundacao Hospitalar do Estado de Minas Gerais" + }, + { + "author_name": "Rubens Daniel Miserani Magalhaes", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Bruno Cassaro", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Gabriela Burle", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Daniel Doro", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Jorge Kalil", + "author_inst": "Instituto do Coracao, Universidade de Sao Paulo" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" + }, + { + "author_name": "Andres Salazar", + "author_inst": "Oncovir, Inc; Orygen Biotecnologia" + }, + { + "author_name": "Otavia Caballero", + "author_inst": "Oncovir, Inc; Orygen Biotecnologia" + }, + { + "author_name": "Alexandre Machado", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + }, + { + "author_name": "Joao da Silva", + "author_inst": "Plataforma de Medicina Translacional da Fundacao Oswaldo Cruz e Faculdade de Medicina de Ribeirao Preto" + }, + { + "author_name": "Flavio da Fonseca", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Ana Paula Fernandes", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Santuza Teixeira", + "author_inst": "Centro de Tecnologia de Vacinas, Parque Tecnologico de Belo Horizonte" + }, + { + "author_name": "Ricardo Gazzinelli", + "author_inst": "Fundacao Oswaldo Cruz - Minas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.13.21263432", "rel_title": "Geographic and Phylodynamic Distribution of SARS-CoV-2 from Environmental Origin", @@ -564496,33 +563147,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.27.457922", - "rel_title": "Role of sleep quality in the acceleration of biological aging and its potential for preventive interaction on air pollution insults: findings from the UK Biobank cohort", - "rel_date": "2021-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.27.457922", - "rel_abs": "BackgroundSleep has been associated with aging and relevant health outcomes, but their causal relationship remains inconclusive.\n\nMethodsIn this study, we investigated the associations of sleep behaviors with biological ages (BAs) among 363,886 middle and elderly-aged adults from UK Biobank. Sleep index (0 [worst]-6 [best]) of each participant was retrieved from six sleep behaviors: snoring, chronotype, daytime sleepiness, sleep duration, insomnia, and difficulties in getting up. Two BAs, the KDM-biological age and PhenoAge, were estimated by corresponding algorithms based on clinical traits, and their discrepancies with chronological age were defined as the age accelerations (AAs).\n\nResultsWe first observed negative associations between the sleep index and the two AAs, and demonstrated that the change of AAs could be the consequence of sleep quality using Mendelian randomization with genetic risk scores of sleep index and BAs. Particularly, one unit increase in sleep index was associated with 0.105- and 0.125-year decreases in KDM-biological age acceleration and PhenoAge acceleration, respectively. Furthermore, we observed significant independent and joint effects of sleep and air pollution (i.e. PM2.5 and NO2), another key driver of aging, on BAs. Sleep quality also showed modifying effect on the associations of elevated PM2.5 and NO2 levels with accelerated aging. For instance, an interquartile range increase in PM2.5 level was associated with 0.011-, 0.047-, and 0.078-year increase in PhenoAge acceleration among people with high (5-6), medium (3-4), and low (0-2) sleep index, respectively.\n\nConclusionsOur findings elucidate that better sleep quality could lessen accelerated biological aging resulting from exogenous exposures including air pollution.\n\nFundingPeking University Start-up Grant (BMU2021YJ044)", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xu Gao", - "author_inst": "Peking University" - }, - { - "author_name": "Ninghao Huang", - "author_inst": "Peking University" - }, - { - "author_name": "Tao Huang", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.09.13.21263476", "rel_title": "Association between work attendance when experiencing fever or cold symptoms and company characteristics and socioeconomic status in the COVID-19 pandemic in Japanese workers: a cross-sectional study", @@ -565239,6 +563863,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.12.21263291", + "rel_title": "Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263291", + "rel_abs": "In this study we conducted RNA sequencing on two brain regions (olfactory bulb and amygdala) from subjects who died from COVID-19 or who died of other causes. We found several-fold more transcriptional changes in the olfactory bulb than in the amygdala, consistent with our own work and that of others indicating that the olfactory bulb may be the initial and most common brain region infected. To some extent our results converge with pseudotime analysis towards common processes shared between the brain regions, possibly induced by the systemic immune reaction following SARS-CoV-2 infection. Changes in amygdala emphasized upregulation of interferon-related neuroinflammation genes, as well as downregulation of synaptic and other neuronal genes, and may represent the substrate of reported acute and subacute COVID-19 neurological effects. Additionally, and only in olfactory bulb, we observed an increase in angiogenesis and platelet activation genes, possibly associated with microvascular damages induced by neuroinflammation. Through coexpression analysis we identified two key genes (CAMK2B for the synaptic neuronal network and COL1A2 for the angiogenesis/platelet network) that might be interesting potential targets to reverse the effects induced by SARS-CoV-2 infection. Finally, in olfactory bulb we detected an upregulation of olfactory and taste genes, possibly as a compensatory response to functional deafferentation caused by viral entry into primary olfactory sensory neurons. In conclusion, we were able to identify transcriptional profiles and key genes involved in neuroinflammation, neuronal reaction and olfaction induced by direct CNS infection and/or the systemic immune response to SARS-CoV-2 infection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ignazio S Piras", + "author_inst": "Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ" + }, + { + "author_name": "Matt Huentelman", + "author_inst": "Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ" + }, + { + "author_name": "Jessica Walker", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Richard Arche", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Michael Glass", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Daisy Vargas", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Lucia Sue", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Anthony Intorcia", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Courtney Nelson", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Katsuko Suszczewicz", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Claryssa Borja", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Marc Desforges", + "author_inst": "Centre Hospitalier Universitaire Sainte-Justine, Laboratory of Virology, Montreal, Canada" + }, + { + "author_name": "Michael Deture", + "author_inst": "Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, FL" + }, + { + "author_name": "Dennis Dicksond", + "author_inst": "Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, FL" + }, + { + "author_name": "Thomas Beach", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + }, + { + "author_name": "Geidy Serrano", + "author_inst": "Banner Sun Health Research Institute, Sun City, AZ" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.12.21263448", "rel_title": "Efficacy of vaccination against severe COVID-19 in relation to Delta variant and time since second dose: the REACT-SCOT case-control study", @@ -566538,41 +565241,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.09.21263140", - "rel_title": "Trends of COVID-19 pediatric admissions number during the first 24 weeks of COVID-19 vaccination in Rio de Janeiro, Brazil", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263140", - "rel_abs": "ObjectiveTo describe trends of COVID-19 pediatric admissions number during the first 24 weeks of COVID-19 vaccination.\n\nDesignA retrospective study was conducted in children (0-18 years), admitted in two pediatric hospitals of Rio de Janeiro city, between January 17 and July 3, 2021 with confirmed COVID-19 by reverse transcription polymerase chain reaction or serological tests. Trends of COVID-19 pediatric admissions number during the first 24 weeks of COVID-19 vaccination in Rio de Janeiro, Brazil and the pre-vaccine period were measured by linear regression.\n\nParticipantsChildren admitted in pediatric hospitals in Rio de Janeiro, city, Brazil\n\nResultsThe number of total admitted patients (with all diseases) were 5340 during the pre-vaccine period, being 94 (1.8%) of them with confirmed COVID-19, and 4182 children admitted during the vaccine period, with 86 confirmed COVID-19 patients (2.1 %) (p=0.29). Media of cases admitted per/week were 2.02 in pre-vaccine period and 3.6 during the first 24 weeks of COVID vaccination (p=0.009). One death was reported in the pre-vaccine period and four in the vaccine period (p=0.14). Trends of increase in the number of admitted cases were verified both in the pre-vaccine period as in the vaccine period, being more expressive in the last one.\n\nConclusionThere was trend of increase in number of children admitted with confirmed COVID-19 during the first 24 weeks of COVID-vaccination in Rio de Janeiro, city. Considering that few people were fully vaccinated, reducing of number of admitted children with confirmed COVID-19 was not verified.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andre Ricardo Araujo da Silva", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Monica Del Monaco Esteves", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Bernardo Rodrigues Rosa de Carvalho", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Cristina Vieira Souza", - "author_inst": "Prontobaby Group" - }, - { - "author_name": "Cristiane Henriques Teixeira", - "author_inst": "Prontobaby Group" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.09.04.21262932", "rel_title": "A Comparative Study Between Nasopharyngeal/Oropharyngeal, Faecal and Saliva Viral Shedding In Ghanaian COVID-19 Patients attending KATH from October-December, 2020", @@ -567385,6 +566053,49 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.09.08.21263296", + "rel_title": "SARS-CoV-2 infection fatality rates in India: systematic review, meta-analysis and model-based estimation", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263296", + "rel_abs": "IntroductionFervorous investigation and dialogue surrounding the true number of SARS-CoV-2 related deaths and implied infection fatality rates in India have been ongoing throughout the pandemic, and especially pronounced during the nations devastating second wave. We aim to synthesize the existing literature on the true SARS-CoV-2 excess deaths and infection fatality rates (IFR) in India, through a systematic search followed by viable meta-analysis. We then provide updated epidemiological model-based estimates of the wave 1, wave 2 and combined IFRs using an extension of the Susceptible-Exposed-Infected-Removed (SEIR) model, using data from April 1, 2020 to June 30, 2021.\n\nMethodsFollowing PRISMA guidelines, the databases PubMed, Embase, Global Index Medicus, as well as BioRxiv, MedRxiv, and SSRN for preprints (accessed through iSearch), were searched on July 3, 2021 (with results verified through August 15, 2021). Altogether using a two-step approach, 4,765 initial citations were screened resulting in 37 citations included in the narrative review and 19 studies with 41 datapoints included in the quantitative synthesis. Using a random effects model with DerSimonian-Laird estimation, we meta-analyze IFR1 which is defined as the ratio of the total number of observed reported deaths divided by the total number of estimated infections and IFR2 (which accounts for death underreporting in the numerator of IFR1). For the latter, we provide lower and upper bounds based on the available range of estimates of death undercounting, often arising from an excess death calculation. The primary focus is to estimate pooled nationwide estimates of IFRs with the secondary goal of estimating pooled regional and state-specific estimates for SARS-CoV-2 related IFRs in India. We also try to stratify our empirical results across the first and the second wave. In tandem, we present updated SEIR model estimates of IFRs for waves 1, 2, and combined across the waves with observed case and death count data from April 1, 2020 to June 30, 2021.\n\nResultsFor India countrywide, underreporting factors (URF) for cases (sourced from serosurveys) range from 14.3-29.1 in the four nationwide serosurveys; URFs for deaths (sourced from excess deaths reports) range from 4.4-11.9 with cumulative excess deaths ranging from 1.79-4.9 million (as of June 2021). Nationwide pooled IFR1 and IFR2 estimates for India are 0.097% (95% confidence interval [CI]: 0.067 - 0.140) and 0.365% (95% CI: 0.264 - 0.504) to 0.485% (95% CI: 0.344 - 0.685), respectively, again noting that IFR2 changes as excess deaths estimates vary. Among the included studies in this meta-analysis, the IFR1 generally appear to decrease over time from the earliest study end date to the latest study end date (from 4 June 2020 to 6 July 2021, IFR1 changed from 0.199 to 0.055%), whereas a similar trend is not as readily evident for IFR2 due to the wide variation in excess death estimates (from 4 June 2020 to 6 July 2021, IFR2 ranged from (0.290-1.316) to (0.241-0.651) %).\n\nNationwide SEIR model-based combined estimates for IFR1 and IFR2 are 0.101% (95% CI: 0.097 - 0.116) and 0.367% (95% CI: 0.358 - 0.383), respectively, which largely reconcile with the empirical findings and concur with the lower end of the excess death estimates. An advantage of such epidemiological models is the ability to produce daily estimates with updated data with the disadvantages being that these estimates are subject to numerous assumptions, arduousness of validation and not directly using the available excess death data. Whether one uses empirical data or model-based estimation, it is evident that IFR2 is at least 3.6 times more than IFR1.\n\nConclusionWhen incorporating case and death underreporting, the meta-analyzed cumulative infection fatality rate in India varies from 0.36%-0.48%, with a case underreporting factor ranging from 25-30 and a death underreporting factor ranging from 4-12. This implies, by June 30, 2021, India may have seen nearly 900 million infections and 1.7-4.9 million deaths when the reported numbers stood at 30.4 million cases and 412 thousand deaths (covid19india.org) with an observed case fatality rate (CFR) of 1.35%. We reiterate the need for timely and disaggregated infection and fatality data to examine the burden of the virus by age and other demographics. Large degrees of nationwide and state-specific death undercounting reinforce the call to improve death reporting within India.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lauren Zimmermann", + "author_inst": "University of Michigan" + }, + { + "author_name": "Subarna Bhattacharya", + "author_inst": "University of Michigan" + }, + { + "author_name": "Soumik Purkayastha", + "author_inst": "University of Michigan" + }, + { + "author_name": "Ritoban Kundu", + "author_inst": "Indian Statistical Institute" + }, + { + "author_name": "Ritwik Bhaduri", + "author_inst": "Indian Statistical Institute" + }, + { + "author_name": "Parikshit Ghosh", + "author_inst": "Delhi School of Economics" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.14.459961", "rel_title": "Development of a novel, pan-variant aerosol intervention for COVID-19", @@ -568408,41 +567119,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.06.21263166", - "rel_title": "Trends in Covid-19 hospital mortality in women and men", - "rel_date": "2021-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21263166", - "rel_abs": "IntroductionIt remains unclear if the development of health services, clinical management, and scientific evidence, during the pandemic is associated with better medical outcomes, sustained in the long term, for Covid-19 patients of each gender. This study presents the trends in mortality associated with Covid-19 for women and men during the first year of the pandemic.\n\nMethodsThis study was based in 17 Spanish hospitals. Sociodemographic, clinical, and mortality data from all patients with Covid-19, who had been discharged alive, or had died after being admitted, between March 2020 and February 2021, were used.\n\nThe association between time of admission and mortality was examined with multivariate logistic regression models.\n\nResults3390 Covid-19 patients were included in the study, of which 1330 were women, the age was M(SD): 66.55(16.55) Death was reported for 451 patients. There was a significant decreasing trend in mortality by time of admission for the whole year with an OR: 0.86(0.77-0.96) p=0.005. No significant trend in mortality for women was observed OR: 1.00(0.85-1.19) p=0.959, while there was a significant decreasing trend for men OR: 0.78 (0.68-0.90) p=0.001\n\nDiscussionThe health policies put in place, the scientific evidence developed by researchers, and the experienced acquired by clinicians, are likely to explain this improvement in mortality. More epidemiological and clinical studies addressing trends of mortality in patients with different sociodemographic and clinical profile and the improvement of clinical outcomes are required. Future research may address the safety and efficacy of interventions specifically in female patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Luis Ayerbe", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Carlos Risco-Risco", - "author_inst": "Hospital Universitario HM Sanchinarro. Madrid, Spain" - }, - { - "author_name": "Diego Martinez-Urbistondo", - "author_inst": "Hospital Universitario HM Sanchinarro. Madrid. Spain" - }, - { - "author_name": "Maria Elena Caro-Tinoco", - "author_inst": "Hospital Universitario HM Sanchinarro" - }, - { - "author_name": "Salma Ayis", - "author_inst": "School of Population Health and Environmental Sciences, King's College London, London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.06.21262027", "rel_title": "A simple, sensitive and quantitative FACS-based test for SARS-CoV-2 serology in humans and animals", @@ -569115,6 +567791,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.09.21262542", + "rel_title": "Indirect effects of peaks in COVID admissions on access to surgery in the English NHS, differential effects by operation type, ethnicity and socio-economic status: a database study", + "rel_date": "2021-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21262542", + "rel_abs": "ObjectivesDuring the COVID pandemic the UK saw two peaks in the prevalence of hospital admissions resulting in disruption of routine hospital services in the English National Health Service. This study aimed to track the effect of these peaks on various types of surgery representing differences in urgency, importance, and complexity.\n\nDesignDatabase study using the Hospital Episode Statistics database and surgical operations selected purposively, to represent different combinations of urgency, importance and complexity.\n\nSettingAll hospitals within England that carried out procedures funded by the National Health Service.\n\nMain Outcome MeasuresNumber of emergency routine surgeries; cancer-removal surgeries; transplant surgeries; renal transplants Deceased and living donors); and elective routine surgeries carried out prior to and during the COVID pandemic.\n\nResultsWhile all surgeries declined, emergency or urgent operations held up better than elective cases. There was rapid rebound between peaks. Among emergency cases, coronary angioplasty for acute myocardial infarction held up well in contrast to appendectomy, where indications for surgery are more elastic. Among urgent cancer and transplant operations, those with the most complex pathways were the most severely affected. The pandemic affected socio-economic and ethnic groups similarly. Disruption during the second peak was slightly less than during the first peak despite even greater COVID admission rates.\n\nConclusionThe NHS titrated its response appropriately to the pandemic by prioritising emergency and urgent cases over elective cases. However, complex time critical conditions like organ transplants and certain cancers are also disrupted with implications for third peaks in hospital admissions that many countries are experiencing.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sandra Remsing", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "Felicity Evison", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "Ravinder S Vohra", + "author_inst": "Nottingham City Hospital" + }, + { + "author_name": "Dion Morton", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Peter J Chilton", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Richard J Lilford", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.09.07.21263206", "rel_title": "Safety and efficacy of the mRNA BNT162b2 vaccine against SARS-CoV-2 in five groups of immunocompromised patients and healthy controls in a prospective open-label clinical trial", @@ -569914,41 +568633,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.09.08.21263248", - "rel_title": "Low dose prime and delayed boost can improve COVID-19 vaccine efficacies by increasing B cell selection stringency in germinal centres", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263248", - "rel_abs": "The efficacy of COVID-19 vaccines appears to depend in complex ways on the vaccine dosage and the interval between the prime and boost doses. Unexpectedly, lower dose prime and longer prime-boost intervals have yielded higher efficacies in clinical trials. To elucidate the origins of these effects, we developed a stochastic simulation model of the germinal centre (GC) reaction and predicted the antibody responses elicited by different vaccination protocols. The simulations predicted that a lower dose prime could increase the selection stringency in GCs due to reduced antigen availability, resulting in the selection of GC B cells with higher affinities for the target antigen. The boost could relax this selection stringency and allow the expansion of the higher affinity GC B cells selected, improving the overall response. With a longer dosing interval, the decay in the antigen with time following the prime could further increase the selection stringency, amplifying this effect. The effect remained in our simulations even when new GCs following the boost had to be seeded by memory B cells formed following the prime. These predictions offer a plausible explanation of the observed paradoxical effects of dosage and dosing interval on vaccine efficacy. Tuning the selection stringency in the GCs using prime-boost dosages and dosing intervals as handles may help improve vaccine efficacies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Amar K Garg", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Soumya Mittal", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Pranesh Padmanabhan", - "author_inst": "University of Queensland" - }, - { - "author_name": "Rajat Desikan", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Narendra M Dixit", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21263222", "rel_title": "Elevated plasma levels of CXCL16 in severe COVID-19 patients", @@ -570737,6 +569421,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.08.21263027", + "rel_title": "Autoantibodies against IL-1-receptor-antagonist in multisystem inflammatory syndrome in children", + "rel_date": "2021-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263027", + "rel_abs": "Multisystem inflammatory syndrome in children (MIS-C or PIMS) is a rare but serious complication after an infection with SARS-CoV-2. A possible involvement of pathogenetically relevant autoantibodies has been discussed. Recently neutralizing autoantibodies against anti-inflammatory receptor antagonists progranulin (PGRN) and IL-1-receptor antagonist (IL-1-Ra) were discovered in adult patients with critical COVID-19.\n\nPlasma of an index case with severe PIMS/MIS-C was analyzed for autoantibodies against IL-1-Ra and PGRN. The study was extended by a case series of 12 additional patients. In addition to ELISA for of antibodies, IL-1-Ra plasma levels were determined and IL-1-Ra was analyzed by Western-blot and isoelectric focusing. Functional activity of the autoantibodies was examined in vitro with IL-1{beta} reporter assays.\n\nAntibodies against IL-1-Ra could be detected in 10 of 13 (76.9%) patients with PIMS/MIS-C, but not in controls. In contrast to critical COVID-19 in adults, no IL-1-Ra antibodies of the IgM class were detected in PIMS/MIS-C. IL-1-Ra-antibodies exclusively belonged to IgG1. No antibodies directed against PGRN were detected. Western blots and ELISA showed a concomitant reduction of free IL-1-Ra plasma levels in the presence of IL-1-Ra-antibodies. The antibodies inhibited IL-1-Ra function in IL-1{beta} reporter cell assays. Notably, an additional, hyperphosphorylated, transiently occurring atypical isoform of IL-1-Ra was observed in all IL-1-Ra autoantibody-positive patients.\n\nTo conclude, IL-1-Ra autoantibodies were observed in high frequency in children with PIMS/MIS-C. They may represent a diagnostic and pathophysiologically relevant marker for PIMS/MIS-C. Their generation is likely to be triggered by an atypical, hyperphosphorylated isoform of IL-1-Ra.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Jochen Pfeifer", + "author_inst": "Department of Pediatric Cardiology, Saarland University, Homburg, Germany" + }, + { + "author_name": "Bernhard Thurner", + "author_inst": "Department of Pediatrics, Klinikum Kempten, Germany" + }, + { + "author_name": "Christoph Kessel", + "author_inst": "Department of Pediatric Rheumatology and Immunology, University Children's Hospital Muenster" + }, + { + "author_name": "Natalie Fadle", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Evi Regitz", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Marie-Christin Hoffmann", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Igor Kos", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Klaus-Dieter Preuss", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Yvan Fischer", + "author_inst": "Institute of Physiology, Medical Faculty, RWTH Aachen, D-52057 Aachen, Germany" + }, + { + "author_name": "Klaus Roemer", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Stefan Lohse", + "author_inst": "Institute of Virology, University of Saarland, Homburg, Germany" + }, + { + "author_name": "Kristina Heyne", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Marie-Claire Detemple", + "author_inst": "Department of Pediatrics, Klinikum Saarbruecken, Germany" + }, + { + "author_name": "Michael Fedlmeier", + "author_inst": "Department of Pediatrics, Klinikum Kempten, Germany" + }, + { + "author_name": "Hendrik Juenger", + "author_inst": "Department of Pediatrics, Klinikum Kempten, Germany" + }, + { + "author_name": "Harald Sauer", + "author_inst": "Department of Pediatrics, Saarland University Medical Center, Homburg/Saar, Germany" + }, + { + "author_name": "Sascha Meyer", + "author_inst": "Department of Pediatrics, Saarland University Medical Center, Homburg/Saar, Germany" + }, + { + "author_name": "Tilman Rohrer", + "author_inst": "Department of Pediatrics, Saarland University Medical Center, Homburg/Saar, Germany" + }, + { + "author_name": "Helmut Wittkowski", + "author_inst": "Department of Pediatric Rheumatology and Immunology, University Children Hospital Muenster" + }, + { + "author_name": "Katja Masjosthusmann", + "author_inst": "Department of Pediatric Rheumatology and Immunology, University Children Hospital Muenster" + }, + { + "author_name": "Soeren Leif Becker", + "author_inst": "Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany" + }, + { + "author_name": "Sigrun Smola", + "author_inst": "Institute of Virology, University of Saarland, Homburg, Germany" + }, + { + "author_name": "Moritz Bewarder", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Michael Boehm", + "author_inst": "Department of Internal Medicine III, Saarland University Medical School, Homburg/Saar, Germany" + }, + { + "author_name": "Jordi Anton", + "author_inst": "Department of Pediatric Rheumatology, Hospital Sant Joan de Deu, Universitat de Barcelona, Barcelona, Spain" + }, + { + "author_name": "Rosa Maria Pino-Ramirez", + "author_inst": "Department of pediatrics, Hospital Sant Joan de Deu, Universitat de Barcelona, Barcelona, Spain" + }, + { + "author_name": "Hashim Abdul-Khaliq", + "author_inst": "Department of Pediatric Cardiology, Saarland University, Homburg, Germany" + }, + { + "author_name": "Dirk Foell", + "author_inst": "Department of Pediatric Rheumatology and Immunology, University Children Hospital Muenster" + }, + { + "author_name": "Lorenz Thurner", + "author_inst": "Jose Carreras Center for Immuno- and Gene Therapy and Department of Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.09.09.21263351", "rel_title": "The anticipated artificial increase in life expectancy from COVID-19", @@ -572056,61 +570871,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.05.21263141", - "rel_title": "Metabolic and immune markers for precise monitoring of COVID-19 severity and treatment", - "rel_date": "2021-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.05.21263141", - "rel_abs": "Deep understanding of the SARS-CoV-2 effects on host molecular pathways is paramount for the discovery of early biomarkers of outcome of coronavirus disease 2019 (COVID-19) and the identification of novel therapeutic targets. In that light, we generated metabolomic data from COVID-19 patient blood using high-throughput targeted nuclear magnetic resonance (NMR) spectroscopy and high-dimensional flow cytometry. We find considerable changes in serum metabolome composition of COVID-19 patients associated with disease severity, and response to tocilizumab treatment. We built a clinically annotated, biologically-interpretable space for precise time-resolved disease monitoring and characterize the temporal dynamics of metabolomic change along the clinical course of COVID-19 patients and in response to therapy. Finally, we leverage joint immuno-metabolic measurements to provide a novel approach for patient stratification and early prediction of severe disease. Our results show that high-dimensional metabolomic and joint immune-metabolic readouts provide rich information content for elucidation of the hosts response to infection and empower discovery of novel metabolic-driven therapies, as well as precise and efficient clinical action.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Andre Figueiredo Rendeiro", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Charles Kyriakos Vorkas", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Jan Krumsiek", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Harjot Singh", - "author_inst": "weill cornell medicine" - }, - { - "author_name": "Shashi N Kapadia", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Luca Vincenzo Cappelli", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Maria Teresa Cacciapuoti", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Giorgio Inghirami", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Olivier Elemento", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mirella Salvatore", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.03.21262551", "rel_title": "A Learning Health System Randomized Trial of Monoclonal Antibodies for Covid-19", @@ -573043,6 +571803,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.04.21262907", + "rel_title": "Perceptions towards mask use in school children during the SARS-CoV-2 pandemic: the Ciao Corona Study", + "rel_date": "2021-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.04.21262907", + "rel_abs": "BackgroundMask wearing contributes to the reduction of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In Switzerland, compulsory use of masks was introduced in indoor public spaces and later in schools. In the canton of Zurich, masks were introduced for secondary school children (grades 7-9) from November 2020, and for primary school children (grades 4-6) from February 2021- along with other protective measures against SARS-CoV-2. This study explored perceptions towards the usefulness of masks in school and public in a cohort of children and adolescents in the canton of Zurich, Switzerland, in January - May 2021.\n\nMethodsSchool children aged 10 to 17 years enrolled in Ciao Corona, a prospective school-based cohort study, responded to nested online surveys between January 12 to March 24 2021 (Q1) and March 10 to May 16 2021 (Q2). Secondary school children were surveyed at Q1 and Q2, and primary school children at Q2 only. Surveys for parents and their children included questions on childrens perception of the usefulness of masks and mask wearing behavior. Associations between perceived usefulness of masks and childs school level, gender, and parents educational attainment were analyzed with Pearsons and McNemars chi-squared tests. Free-text comments provided by children were classified into categories of expressed attitude towards mask wearing.\n\nResults595 (54% girls) and 1118 (52% girls) school children responded to online questionnaires at Q1 and Q2, respectively. More than half of school children perceived masks to be useful at school (Q1:60% and Q2:57%) and in public (Q1:69% and Q2:60%). Girls perceived masks as useful more often than boys (at Q2 at school: 61% versus 53%, in public: 64% versus 57%), and children of parents with high educational attainment more often than those of parents with lower educational attainment (at Q2 at school: 61% versus 49%, in public: 63% versus 54%). There were no differences in the perceived usefulness of masks among children in primary versus secondary school. At Q1 and Q2 each, about 20% of children provided individual statements about masks, of which 36% at Q1 and 16% at Q2 reported side-effects and discomfort such as skin irritations, headache or difficulties breathing during physical education.\n\nConclusionApproximately 60% of school children perceived masks at school and in public places as useful. A small but non-negligible proportion of children reported discomfort and side-effects that should be considered to ensure high adherence to mask wearing among school children.\n\nTrial registrationClinicalTrials.gov NCT04448717 https://clinicaltrials.gov/ct2/show/NCT04448717\n\nCONTRIBUTION TO THE FIELD STATEMENTWorldwide about 150 countries fully closed their schools at some point during the coronavirus pandemic, while other countries - such as Switzerland - kept schools open almost all the time. However, among other protective measures, children in secondary school (aged approximately 14-16 years) had to wear masks since November 2020, and older children in primary school (aged 11-13 years) - since February 2021.\n\nAs part of the large study Ciao Corona based in schools in Switzerland, we wanted to learn how children perceive the usefulness of masks in school and public. Children and their parents completed questionnaires in January-March (595 secondary school children) and March-May 2021 (1118 secondary and primary school children).\n\nWe found that about 60% of children perceived masks to be useful at school and in public. Girls perceived masks as useful more often than boys, and children of parents with university or college education more often than those of parents with lower education. About 7- 9% of children reported side-effects and discomfort such as skin irritations, headache or difficulties breathing during physical education. Although side-effects were not frequently reported, they should be considered to ensure high adherence to mask wearing among school children.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Priska Ammann", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Agne Ulyte", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Sarah R Haile", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Milo A Puhan", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Susi Kriemler", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Thomas Radtke", + "author_inst": "Department of Epidemiology, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.09.04.21263121", "rel_title": "Previous COVID-19 infection and antibody levels after vaccination", @@ -574270,53 +573069,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21263088", - "rel_title": "SARS-CoV-2 circulation in the school setting: A systematic review and meta-analysis", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263088", - "rel_abs": "BackgroundThe contribution of children to viral spread in schools is still under debate.\n\nWe conducted a systematic review and meta-analysis of studies to investigate SARS-CoV-2 transmission in the school setting.\n\nMethodsLiterature searches from April, 2021 and repeated on May, 15th 2021 yielded a total of 1088 publications: screening, contact tracing and seroprevalence studies.\n\nMOOSE guidelines were followed and data analyzed using random-effects models.\n\nResultsFrom screening studies involving more than 120,000 subjects, we estimated 0.31% (95% Confidence Interval [CI] 0.05-0.81%) SARS-CoV-2 point prevalence in schools. Contact tracing studies, involving a total of 112,622 contacts of children and adults, showed that onward viral transmission was limited (2.54%; 95%CI 0.76-5.31). Young index cases were found to be 74% significantly less likely than adults to favor viral spread (Odds Ratio [OR]=0.26; 95%CI 0.11-0.63) and were less susceptible to infection (OR=0.60; 95% CI 0.25-1.47). Finally, from seroprevalence studies, with a total of 17,879 subjects involved, we estimated that children are 43% significantly less likely than adults to test positive for antibodies (OR=0.57; 95%CI: 0.49-0.68).\n\nIn conclusion, testing all subjects in schools, independently of symptoms, students less likely than adults favor viral spread and SARS-CoV-2 circulation in schools was found to be limited.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat is the infectivity and susceptibility of students and staff exposed to SARS-CoV-2 in the school setting?\n\nFindingsThis systematic review and meta-analysis of all available data shows that SARS-CoV-2 viral spread is limited and child-to-adult transmission in the school setting scarce.\n\nSummary estimates indicate that young index cases were 74% significantly less likely than adults to favor viral spread and children are 43% less susceptible than adults.\n\nMeaningOverall, SARS-CoV-2 circulation in schools was limited and could be reasonably controlled with appropriate mitigation measures.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Chiara Martinoli", - "author_inst": "European Institute of Oncology" - }, - { - "author_name": "Carlo La Vecchia", - "author_inst": "University Statale di Milano" - }, - { - "author_name": "Sara Raimondi", - "author_inst": "European institute of Oncology" - }, - { - "author_name": "Federica Bellerba", - "author_inst": "European institute of Oncology" - }, - { - "author_name": "Clementina Sasso", - "author_inst": "INAF-Capodimonte Astronomical Observatory, Salita Moiariello 16, 80131 Napoli, Italy" - }, - { - "author_name": "Alessandra Basso", - "author_inst": "Academy of Finland Centre of Excellence in the Philosophy of the Social Sciences, University of Helsinki, PL 24 00014 Helsinki, Finland" - }, - { - "author_name": "Giulio Cammarata", - "author_inst": "European institute of Oncology" - }, - { - "author_name": "sara Gandini", - "author_inst": "European Institute of oncology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.03.21262874", "rel_title": "Detection of SARS CoV-2 contamination in the Operating Room and Birthing Room Setting: Risks to attending health care workers", @@ -575053,6 +573805,73 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.09.04.21263115", + "rel_title": "Durability analysis of the highly effective BNT162b2 vaccine against COVID-19", + "rel_date": "2021-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.04.21263115", + "rel_abs": "SARS-CoV-2 breakthrough infections have been increasingly reported in fully vaccinated individuals. We conducted a test-negative case-control study to assess the durability of protection after full vaccination with BNT162b2, defined as 14 days after the second dose, against polymerase chain reaction (PCR)-confirmed symptomatic SARS-CoV-2 infection, in a national medical practice between February 1, 2021 and August 22, 2021. We fit conditional logistic regression (CLR) models stratified on residential county and calendar time of testing to assess the association between time elapsed since vaccination and the odds of symptomatic infection or non-COVID-19 hospitalization (negative control), adjusted for several covariates. The primary population included 652 individuals who had a positive symptomatic test after full vaccination with BNT162b2 (cases) and 5,946 individuals with at least one negative symptomatic test after full vaccination (controls). The adjusted odds of symptomatic infection were higher 120 days after full vaccination versus at the date of full vaccination (Odds Ratio [OR]: 3.21, 95% confidence interval [CI]: 1.33-7.74). Importantly, the odds of infection were still lower 150 days after the first BNT162b2 dose as compared to 4 days after the first dose (OR: 0.3, 95% CI: 0.19-0.45), when immune protection approximates the unvaccinated status. Low rates of COVID-19 associated hospitalization or death in this cohort precluded analyses of these severe outcomes. The odds of experiencing a non-COVID-19 hospitalization decreased with time since vaccination, suggesting a possible underestimation of waning protection by this approach due to confounding factors. Taken together, these data constitute an early signal for waning protection against symptomatic illness while also providing reassurance that BNT162b2 continues to protect against symptomatic SARS-CoV-2 infection several months after full vaccination. Continued surveillance of COVID-19 vaccine durability, particularly against severe disease, is critical to guide effective and equitable strategies to respond to the pandemic, including distribution of booster doses, development of new vaccines, and implementation of both pharmaceutical and nonpharmaceutical interventions.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Patrick Lenehan", + "author_inst": "nference" + }, + { + "author_name": "John C O'Horo", + "author_inst": "Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota 55902, USA" + }, + { + "author_name": "Michiel JM Niesen", + "author_inst": "nference" + }, + { + "author_name": "Abinash Virk", + "author_inst": "Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota 55902, USA" + }, + { + "author_name": "Melanie D Swift", + "author_inst": "Division of Aerospace, Occupational and Preventive Medicine, Mayo Clinic, Rochester, Minnesota 55902, USA" + }, + { + "author_name": "Walter Kremers", + "author_inst": "Division of Biomedical Statistics, Mayo Clinic, Rochester, Minnesota 55902, USA" + }, + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Joel E Gordon", + "author_inst": "Department of Family Medicine, Mayo Clinic Health System, Mankato, Minnesota 56001, USA" + }, + { + "author_name": "Holly L Geyer", + "author_inst": "Division of Hospital Internal Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA" + }, + { + "author_name": "Leigh Lewis Speicher", + "author_inst": "Division of General Internal Medicine, Mayo Clinic, Jacksonville, Florida 32224, USA" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.06.459206", "rel_title": "The vaccinia-based Sementis Copenhagen Vector COVID-19 vaccine induces broad and durable cellular and humoral immune responses", @@ -575816,105 +574635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.03.21263062", - "rel_title": "Heterologous prime-boost immunization with CoronaVac and Convidecia", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263062", - "rel_abs": "BackgroundThe safety and immunogenicity of heterologous prime-boost COVID-19 vaccine regimens with one shot of a recombinant adenovirus type-5-vectored COVID-19 vaccine Convidecia has not been reported.\n\nMethodsWe conducted a randomized, controlled, observer-blinded trial of heterologous prime-boost immunization with CoronaVac and Convidecia in healthy adults 18-59 years of age. Eligible participants who were primed with one or two doses of CoronaVac were randomly assigned at a 1:1 ratio to receive a booster dose of Convidecia or CoronaVac. Participants were masked to the vaccine received but not to the three-dose or two-dose regimen. The occurrences of adverse reactions within 28 days after the vaccination were documented. The geometric mean titers of neutralizing antibodies against live SARS-CoV-2 virus were measured at 14 and 28 days after the booster vaccination.\n\nResultsBetween May 25 and 26, 2021, a total of 300 participants were enrolled. Participants who received a booster shot with a heterologous dose of Convidecia reported increased frequencies of solicited injection-site reactions than did those received a homogeneous dose of CoronaVac, but frequencies of systemic reactions. The adverse reactions were generally mild to moderate. The heterologous immunization with Convidecia induced higher live viral neutralizing antibodies than did the homogeneous immunization with CoronaVac (197.4[167.7, 232.4] vs. 33.6[28.3, 39.8] and 54.4[37. 9, 78.0] vs. 12.8[9.3, 17.5]) at day 14 in the three- and two-dose regimen cohort, respectively.\n\nConclusionsThe heterologous prime-boost regimen with Convidecia after the priming with CoronaVac was safe and significantly immunogenic than a homogeneous boost with CoronaVac (ClinicalTrials.gov, number NCT04892459).", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Jingxin Li", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Lihua Hou", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Xiling Guo", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Pengfei Jin", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Shipo Wu", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Jiahong Zhu", - "author_inst": "Lianshui County Center for Disease Control and Prevention" - }, - { - "author_name": "Hongxing Pan", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Xue Wang", - "author_inst": "Tianjin CanSino Biotechnology Inc" - }, - { - "author_name": "Zhizhou Song", - "author_inst": "Lianshui County Center for Disease Control and Prevention" - }, - { - "author_name": "Jingxuan Wan", - "author_inst": "Tianjin CanSino Biotechnology Inc" - }, - { - "author_name": "Lunbiao Cui", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Junqiang Li", - "author_inst": "Tianjin CanSino Biotechnology Inc" - }, - { - "author_name": "Xuewen Wang", - "author_inst": "Canming Medical Technology Co." - }, - { - "author_name": "Lairun Jin", - "author_inst": "Southeast university" - }, - { - "author_name": "Jingxian Liu", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Fengjuan Shi", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Xiaoyu Xu", - "author_inst": "Vazyme Biotech Co." - }, - { - "author_name": "Yin Chen", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Tao Zhu", - "author_inst": "Tianjin CanSino Biotechnology Inc" - }, - { - "author_name": "Wei Chen", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Fengcai Zhu", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.01.21262540", "rel_title": "Analysis of the Dynamics, Outcome, and Prerequisites of the first German SARS-CoV-2 Superspreading Event", @@ -576527,6 +575247,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, + { + "rel_doi": "10.1101/2021.09.02.21263019", + "rel_title": "The association between SARS-CoV-2 infection and neuronal damage: A population-based nested case-control study", + "rel_date": "2021-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263019", + "rel_abs": "ObjectiveTo assess whether severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with changes in plasma levels of neurofilament light chain (NfL), an extremely sensitive marker of neuroaxonal damage, in community-dwelling individuals.\n\nSettingThis study was embedded within the Rhineland Study, an ongoing community-based cohort study in Bonn, Germany\n\nDesignCross-sectional nested case-control study.\n\nParticipantsParticipants were selected based on results from a previously conducted seroprevalence survey within the framework of the Rhineland Study. Cases were defined as those individuals who had had two positive confirmatory test results, including a recombinant spike-based immunofluorescence assay and a plaque reduction neutralization test (N=21). As controls, a random sample of individuals with a negative ELISA test result (Controls I, N=1117), and those with a borderline or positive ELISA test result who failed confirmatory testing (Controls II, N=68), were selected.\n\nOutcome measuresPlasma levels of NfL at the time of measurement, as well as change in plasma NfL levels compared to previously measured pre-pandemic levels\n\nResultsAfter adjustment for age, sex and batch effects, serologically confirmed SARS-CoV-2 infection was neither associated with cross-sectional NfL levels, nor with the magnitude of change from pre-pandemic levels, compared to either of the two control groups. Similarly, after adjustment for age, sex and batch effects, self-reported neurological symptoms - including altered sense of smell or taste, headache, myalgia and fever - were not associated with changes in NfL levels in participants with a serologically confirmed SARS-CoV-2 infection (all p [≥] 0.56).\n\nConclusionsOur findings indicate that mild-to-moderate coronavirus disease-19 is unlikely to be associated with a clinically relevant degree of neuroaxonal damage, even in those cases associated with neurological symptoms.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "N. Ahmad Aziz", + "author_inst": "Population Health Sciences, German Center for Neurodegenerative diseases (DZNE), Bonn, Germany & Department of Neurology, Faculty of Medicine, University of Bon" + }, + { + "author_name": "Marina L.S. Santos", + "author_inst": "Population Health Sciences, German Center for Neurodegenerative diseases (DZNE), Bonn, Germany." + }, + { + "author_name": "Monique M.B. Breteler", + "author_inst": "Population Health Sciences, German Center for Neurodegenerative diseases (DZNE), Bonn, Germany & Institute for Medical Biometry, Informatics and Epidemiology (I" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.08.28.21262753", "rel_title": "Comparative quantitative analysis of SARS-CoV-2 Spike neutralizing antibody titers following two anti COVID-19 vaccines in India", @@ -577442,61 +576189,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2021.08.30.21262844", - "rel_title": "The impact of mental health and substance use issues on COVID-19 vaccine readiness: a cross sectional community-based survey in Ontario, Canada", - "rel_date": "2021-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262844", - "rel_abs": "BackgroundCOVID-19 vaccines have been approved for use in Canada since December 2020. However, data about factors associated with vaccine hesitancy and the impact of mental health and/or substance use (MHSU) issues on vaccine uptake are currently not available. The goal of this study was to explore factors, particularly MHSU factors, that impact COVID-19 vaccination intentions in Ontario, Canada.\n\nMethodsA community-based cross-sectional survey with recruitment based on age, gender, and geographical location (to ensure a representative population of Ontario), was conducted in February 2021. Multinomial logistic regression was used to test the relationship between COVID-19 vaccination status and plans and sociodemographic background, social support, anxiety about contracting COVID-19, and MHSU concerns.\n\nResultsOf the total sample of 2528 respondents, 1932 (76.4%) were vaccine ready, 381 (15.1%) were hesitant, and 181 (7.1%) were resistant. Significant independent predictors of vaccine hesitancy compared with vaccine readiness included younger age (OR=2.11, 95%CI=1.62-2.74), female gender (OR=1.36, 95%CI=1.06-1.74), Black ethnicity (OR=2.11, 95%CI=1.19-3.75), lower education (OR=1.69, 95%CI=1.30-2.20), lower SES status (OR=.88, 95%CI=.84-.93), lower anxiety about self or someone close contracting COVID-19 (OR=2.06, 95%CI=1.50-2.82), and lower depression score (OR=.90, 95%CI=.82-.98). Significant independent predictors of vaccine resistance compared with readiness included younger age (OR=1.72, 95%CI=1.19-2.50), female gender (OR=1.57, 95%CI=1.10-2.24), being married (OR=1.50, 95%CI=1.04-2.16), lower SES (OR=.80, 95%CI=.74-.86), lower satisfaction with social support (OR=.78, 95%CI=.70-.88), lower anxiety about contracting COVID-19 (OR=7.51, 95%CI=5.18-10.91), and lower depression score (OR=.85, 95%CI=.76-.96).\n\nInterpretationCOVID-19 vaccination intention is affected by sociodemographic factors, anxiety about contracting COVID-19, and select mental health issues.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kamna Mehra", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Roula Markoulakis", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Sugy Kodeeswaran", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Donald Redelmeier", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Mark Sinyor", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "James MacKillop", - "author_inst": "McMaster University" - }, - { - "author_name": "Amy Cheung", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Emily E Levitt", - "author_inst": "McMaster University" - }, - { - "author_name": "Tracey Addison", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Anthony J Levitt", - "author_inst": "Sunnybrook Health Sciences Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.08.31.21262891", "rel_title": "Strengthening public COVID-19 response with private facilities in Kisumu, Kenya", @@ -578269,6 +576961,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.28.21262692", + "rel_title": "Pharmacokinetic /Pharmacodynamic Considerations of Alternate Dosing Strategies of Tocilizumab in COVID-19", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.28.21262692", + "rel_abs": "Tocilizumab is one of few treatments that have been shown to improve mortality in patients with COVID-19, but increased demand has led to relative global shortages. Recently, it has been suggested that lower doses, or fixed doses, of tocilizumab could be a potential solution to conserve the limited global supply while conferring equivalent therapeutic benefit to the dosing regimens studied in major trials. The relationship between tocilizumab dose, exposure, and response in COVID-19 has not been adequately characterized. There are a number of pharmacokinetic (PK) parameters which likely differ between patients with severe COVID-19 and patients in whom tocilizumab was studied during the FDA approval process. Likewise, it is unclear whether a threshold exposure is necessary for tocilizumab efficacy. The safety and efficacy of fixed versus weight-based dosing of tocilizumab has been evaluated outside of COVID-19, but it is uncertain if these observations are generalizable to severe or critical COVID-19. In the current review, we consider the potential advantages and limitations of alternative tocilizumab dosing strategies. Leveraging PK models and simulation analyses, we demonstrate that a fixed single dose of tocilizumab 400 mg is unlikely to produce PK exposures equivalent to those achieved in the REMAP-CAP trial, though weight-stratified dosing appears to produce more uniform exposure distribution. Data from current and future trials could provide PK/PD insight to better inform dosing strategies at the bedside. Ultimately, rational dosing strategies that balance available limited supply with patient needs are required.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elizabeth Leung", + "author_inst": "Department of Pharmacy, St. Michael's Hospital, Unity Health, Toronto, Toronto, ON, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, " + }, + { + "author_name": "Sarah C.J. Jorgensen", + "author_inst": "Department of Pharmacy, Mount Sinai Hospital, Toronto, ON, Canada" + }, + { + "author_name": "Ryan L. Crass", + "author_inst": "Ann Arbor Pharmacometrics Group, Ann Arbor, MI, USA" + }, + { + "author_name": "Sumit Raybardhan", + "author_inst": "Department of Pharmacy, North York General, Toronto, ON, Canada" + }, + { + "author_name": "Bradley Langford", + "author_inst": "Public Health Ontario, Toronto, ON, Canada" + }, + { + "author_name": "W. Justin Moore", + "author_inst": "Department of Pharmacy, Northwestern Medicine, Chicago, IL, USA" + }, + { + "author_name": "Nathaniel J. Rhodes", + "author_inst": "Department of Pharmacy, Northwestern Medicine, Chicago, IL, USA; Department of Pharmacy Practice, College of Pharmacy Downers Grove Campus, Midwestern Universit" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.31.21262538", "rel_title": "Fine analysis of lymphocyte subpopulations in SARS-CoV-2 infected patients: toward a differential profiling of patients with severe outcome", @@ -579384,73 +578119,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.02.458774", - "rel_title": "Structural and Biochemical Rationale for Enhanced Spike Protein Fitness in Delta and Kappa SARS-CoV-2 Variants", - "rel_date": "2021-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.02.458774", - "rel_abs": "The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a novel head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "James W. Saville", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Dhiraj Mannar", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Xing Zhu", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Shanti S. Srivastava", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Alison M. Berezuk", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Jean-Philippe Demers", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Steven Zhou", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Katharine Tuttle", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Andrew Kim", - "author_inst": "UPMC" - }, - { - "author_name": "Wei Li", - "author_inst": "UPMC" - }, - { - "author_name": "Dimitrov S. Dimiter", - "author_inst": "UPMC" - }, - { - "author_name": "Sriram Subramaniam", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.09.02.21262965", "rel_title": "Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19", @@ -580415,6 +579083,125 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2021.09.01.457774", + "rel_title": "Mapping interindividual dynamics of innate immune response at single-cell resolution", + "rel_date": "2021-09-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.01.457774", + "rel_abs": "Common genetic variants modulate the cellular response to viruses and are implicated in a range of immune pathologies, including infectious and autoimmune diseases. The transcriptional antiviral response is known to vary between infected cells from a single individual, yet how genetic variants across individuals modulate the antiviral response (and its cell-to-cell variability) is not well understood. Here, we triggered the antiviral response in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-seq. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), the first statistical approach designed to identify dynamic eQTLs across a transcriptional trajectory of cell populations, without aggregating single-cell data into pseudo-bulk. This allows us to uncover the underlying architecture and variability of antiviral response across responding cells, and to identify more than two thousands eQTLs modulating the dynamic changes during this response. Many of these eQTLs colocalise with risk loci identified in GWAS of infectious and autoimmune diseases. As a case study, we focus on a COVID-19 susceptibility locus, colocalised with the antiviral OAS1 splicing QTL. We validated it in blood cells from a patient cohort and in the infected nasal cells of a patient with the risk allele, demonstrating the utility of GASPACHO to fine-map and functionally characterise a genetic locus. In summary, our novel analytical approach provides a new framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Natsuhiko Kumasaka", + "author_inst": "Wellcome Trust Sanger Institute" + }, + { + "author_name": "Raghd Rostom", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Ni Huang", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Krzysztof Polanski", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Kerstin Meyer", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Sharad Patel", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Rachel Boyd", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Celine Gomez", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Sam Barnett", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Nikolaos Panousis", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Jeremy Schwartzentruber", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Maya Ghoussaini", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + }, + { + "author_name": "Paul A. Lyons", + "author_inst": "Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK" + }, + { + "author_name": "Fernando J. Calero-Nieto", + "author_inst": "Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Berthold G\u00f6ttgens", + "author_inst": "Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK" + }, + { + "author_name": "Josephine L. Barnes", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, UK" + }, + { + "author_name": "Kaylee B. Worlock", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, UK" + }, + { + "author_name": "Masahiro Yoshida", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, UK" + }, + { + "author_name": "Marko Nikolic", + "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, UK" + }, + { + "author_name": "Emily Stephenson", + "author_inst": "Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK" + }, + { + "author_name": "Gary Reynolds", + "author_inst": "Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK" + }, + { + "author_name": "Muzlifah Haniffa", + "author_inst": "Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK" + }, + { + "author_name": "John Marioni", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK" + }, + { + "author_name": "Oliver Stegle", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK" + }, + { + "author_name": "Tzachi Hagai", + "author_inst": "Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel" + }, + { + "author_name": "Sarah A. Teichmann", + "author_inst": "Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.08.22.21262024", "rel_title": "Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR", @@ -581442,45 +580229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.29.21262792", - "rel_title": "Short Term Reduction in the Odds of Testing Positive for SARS-CoV-2; a Comparison Between Two Doses and Three doses of the BNT162b2 Vaccine", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21262792", - "rel_abs": "With the evidence of waning immunity of the BNT162b2 vaccine, a national third dose vaccination campaign was initiated in Israel during August 2021; other countries have announced their intention to administer a booster shot as well. Leveraging data from Maccabi Healthcare Services, we conducted a preliminary retrospective study aimed at evaluating initial short-term effectiveness of a three dose versus a two dose regimen against infection due to the Delta variant of SARS-CoV-2, using two complementary approaches; a test-negative design and a matched case-control design. We found that 7-13 days after the booster shot there is a 48-68% reduction in the odds of testing positive for SARS-CoV-2 infection and that 14-20 days after the booster the marginal effectiveness increases to 70-84%. Further studies are needed to determine the duration of protection conferred by the third dose and its effect on severe disease.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tal Patalon", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Sivan Gazit", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Virginia E. Pitzer", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Ottavia Prunas", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Joshua L. Warren", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Daniel M. Weinberger", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.29.21262799", "rel_title": "The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the evolutionary rate", @@ -582309,6 +581057,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.30.21262865", + "rel_title": "Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262865", + "rel_abs": "At the end of 2019 Wuhan witnessed an outbreak of \"atypical pneumonia\" that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus - SARS-CoV-2. Herein, to provide a snapshot of the pathogens in pneumonia-associated respiratory samples from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid samples from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their \"total infectome\", including viruses, bacteria and fungi. Consequently, we identified 37 pathogen species, comprising 15 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (12.8%). However, SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen - Chlamydia psittaci. Samples from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of individual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more diverse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016-2017.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Mang Shi", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai, China." + }, + { + "author_name": "Su Zhao", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Bin Yu", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China." + }, + { + "author_name": "Wei-Chen Wu", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai, China." + }, + { + "author_name": "Yi Hu", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Jun-Hua Tian", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China." + }, + { + "author_name": "Wen Yin", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Fang Ni", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Hong-Ling Hu", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Shuang Geng", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Li Tan", + "author_inst": "The Central Hospital of Wuhan, Wuhan, China" + }, + { + "author_name": "Ying Peng", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China." + }, + { + "author_name": "Zhi-Gang Song", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai, China." + }, + { + "author_name": "Wen Wang", + "author_inst": "Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China." + }, + { + "author_name": "Yan-Mei Chen", + "author_inst": "Shanghai Public Health Clinical Center,, Fudan University, Shanghai, China." + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Yong-Zhen Zhang", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai, China." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.31.21262680", "rel_title": "Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India", @@ -583280,25 +582111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.30.21262814", - "rel_title": "National Excess Mortality from Sub-National data: Method and Application for Argentina", - "rel_date": "2021-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262814", - "rel_abs": "Currently, many countries have not yet reported 2020 or 2021 mortality data to allow an estimate of excess mortality during the COVID-19 pandemic. However, some countries have sub-national mortality data, at the state, province or city level. I present a simple method to allow estimation of national level mortality and excess mortality from sub-national data, using the case of Argentina and projecting excess mortality up to August 2021.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ariel Karlinsky", - "author_inst": "Hebrew University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.28.458041", "rel_title": "Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays", @@ -584135,6 +582947,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.08.25.21262417", + "rel_title": "Prolonged SARS-CoV-2 infection in patients with lymphoid malignancies", + "rel_date": "2021-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262417", + "rel_abs": "Coronavirus disease 2019 (COVID-19) infection results in high mortality rates in patients with hematologic malignancies. Persistent and/or recurrent COVID-19 has not yet been demonstrated in this population. We identified patients with B-cell lymphomas as having a particularly high risk for persistent SARS-CoV-2 positivity. Subsequent analysis of patients with lymphoid malignancies and COVID-19 identified discrete risk factors for severity of primary infection as compared to disease chronicity. Active therapy and diminished T-cell counts were key drivers of acute mortality in lymphoma patients with COVID-19 infection. Conversely, B-cell depleting therapy was the primary driver of re-hospitalization for COVID-19. In patients with persistent SARS-CoV-2 positivity, we observed high levels of viral entropy consistent with intrahost viral evolution, particularly in patients with impaired CD8+ T-cell immunity. These results suggest that persistent COVID-19 infection is likely to remain a risk in patients with impaired adaptive immunity and that additional therapeutic strategies are needed to enable viral clearance in this high-risk population.\n\nStatement of SignificanceWe establish persistent symptomatic COVID-19 infection as a novel clinical syndrome in patients with lymphoid malignancies and identify B-cell depletion as the key immunologic driver of persistent infection. Furthermore, we demonstrate ongoing intrahost viral evolution in patients with persistent COVID-19 infection, particularly in patients with impaired CD8+ T-cell immunity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Christina Y Lee", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Monika K Shah", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "David Hoyos", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Alexander Solovyov", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Melanie Douglas", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Ying Taur", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Peter G Maslak", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "N Esther Babady", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Benjamin Greenbaum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Mini Kamboj", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Santosha A Vardhana", + "author_inst": "Memorial Sloan Kettering Cancer Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.27.21262741", "rel_title": "A Systematic Review of the Protective Effect of Prior SARS-CoV-2 Infection on Repeat Infection", @@ -585186,61 +584057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.23.21262500", - "rel_title": "Effectiveness of the WHO-authorized Covid-19 Vaccines: a Rapid Review of Global Reports till June 30, 2021", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262500", - "rel_abs": "ObjectiveLarge clinical trials have proved the efficacy of Covid-19 vaccine, and the number of literature about the effectiveness is rapidly growing in the first half of year after mass vaccination was administrated globally. This rapid review aims to provide evidence syntheses as a means to complement the current evidence on the vaccine effectiveness (VE) against various outcomes in real-world settings.\n\nMethodsThis review is conducted based on the updated guideline of PRISMA 2020. Databases (PubMed, EMBASE, and MedRxiv) were searched up to 30 June 2021, (PROSPERO ID: 266866). The studies that assessed the VE of the 6 WHO-authorized vaccines (BNT162b2, ChAdOx1, Ad26.COV2.S, mRNA-1273, BBIBP-CorV, and CoronaVac) were eligible to be included. Quality assessment was performed based on ROBINS-I by 2 independent reviewers.\n\nFindingsA total of 39 studies were included, covering over 15 million of participants from 11 nations. Among the general population after 2 doses of vaccination, the VE against symptomatic SARS-CoV-2 infection was estimated at 89%-97%, 92% (95% CI, 78%-97%) and 94% (95% CI, 86%-97%) for BNT162b2, ChAdOx1 and mRNA-1273, respectively. As for the protective effects against B.1.617.2 related symptomatic infection, the VE was 88% (95% CI, 85.3%-90.1%) by BNT162b2 and 67.0% (95% CI, 61.3%-71.8%) by ChAdOx1 after fully vaccination.\n\nConclusionThis review revealed a consistently high effectiveness of vaccines among the general population in real-world settings. Further studies are needed to provide the information on different races/ethnicity, the effects against SARS-CoV-2 variants, and the duration of protection with longer study time.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Chang-Jie Cheng", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Chun-Yi Lu", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Ya-Hui Chang", - "author_inst": "National Cheng Kung University" - }, - { - "author_name": "Yu Sun", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Hai-Jui Chu", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Chun-Yu Lee", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Chang-Hsiu Liu", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Cheng-Huai Lin", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Chien-Jung Lu", - "author_inst": "En Chu Kong Hospital" - }, - { - "author_name": "Chung-Yi Li", - "author_inst": "National Cheng Kung University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.26.21262697", "rel_title": "Mental health and substance use associated with hospitalization among people with laboratory confirmed diagnosis of COVID-19 in British Columbia: a population-based cohort study", @@ -586213,6 +585029,89 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.08.21.21262401", + "rel_title": "An in-depth statistical analysis of the COVID-19 pandemic's initial spread in the WHO African region", + "rel_date": "2021-08-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.21.21262401", + "rel_abs": "During the first wave of the COVID-19 pandemic, sub-Saharan African countries experienced comparatively lower rates of SARS-CoV-2 infections and related deaths than in other parts of the world, the reasons for which remain unclear. Yet, there was also considerable variation between countries. Here, we explored potential drivers of this variation among 46 of the 47 World Health Organization African region member states in a cross-sectional study. We described five indicators of early COVID-19 spread and severity for each country as of 29 November 2020: delay in detection of the first case, length of the early epidemic growth period, cumulative and peak attack rates, and crude case fatality ratio (CFR). We tested the influence of 13 pre-pandemic and pandemic response predictor variables on the country-level variation in the spread and severity indicators using multivariate statistics and regression analysis. We found that wealthier African countries, with larger tourism industries and older populations, had higher peak (p < 0.001) and cumulative (p < 0.001) attack rates, and lower CFRs (p = 0.021). More urbanized countries also had higher attack rates (p < 0.001 for both indicators). Countries applying more stringent early control policies experienced greater delay in detection of the first case (p < 0.001), but the initial propagation of the virus was slower in relatively wealthy, touristic African countries (p = 0.023). Careful and early implementation of strict government policies were likely pivotal to delaying the initial phase of the pandemic, but did not have much impact on other indicators of spread and severity. An over-reliance on disruptive containment measures in more resource-limited contexts is neither effective nor sustainable. We thus urge decision-makers to prioritize the reduction of resource-based health disparities, and surveillance and response capacities in particular, to ensure global resilience against future threats to public health and economic stability.\n\nSummary BoxO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LICOVID-19 trajectories varied widely across the world, and within the African continent.\nC_LIO_LIThere is significant heterogeneity in the surveillance and response capacities among WHO African region member states.\nC_LI\n\nWhat are the new findings?O_LICumulative and peak attack rates during the first wave of COVID-19 were higher in WHO African region member states with higher per-capita GDP, larger tourism industries, older and more urbanized populations, and higher pandemic preparedness scores.\nC_LIO_LIAlthough better-resourced African countries documented higher attack rates, they succeeded in limiting rapid early spread and mortalities due to COVID-19 infection.\nC_LIO_LIAfrican countries that had more stringent early COVID-19 response policies managed to delay the onset of the outbreak at the national level. However, this phenomenon is partially explained by a lack of detection capacity, captured in low pandemic preparedness scores, and subsequent initial epidemic growth rates were slower in relatively well-resourced countries.\nC_LI\n\nWhat do the new findings imply?Careful implementation of strict government policies can aid in delaying an epidemic, but investments in public health infrastructure and pandemic preparedness are needed to better mitigate its impact on the population as a whole.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Ananthu James", + "author_inst": "Indian Institute of Science, Bangalore; The Global Research and Analysis for Public Health (GRAPH) Network (https://thegraphnetwork.org), Association Actions en" + }, + { + "author_name": "Jyoti Dalal", + "author_inst": "The Global Research and Analysis for Public Health (GRAPH) Network (https://thegraphnetwork.org), Association Actions en Sante, Geneve, Switzerland" + }, + { + "author_name": "Timokleia Kousi", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland; The Global Research and Analysis for Public Health (GRAPH) Network (" + }, + { + "author_name": "Daniela Vivacqua", + "author_inst": "Department of Pediatric Infectious Diseases, UFRJ, Rio de Janeiro, Brazil; The Global Research and Analysis for Public Health (GRAPH) Network (https://thegraphn" + }, + { + "author_name": "Daniel Cardoso Portela Camara", + "author_inst": "Nucleo Operacional Sentinela de Mosquitos Vetores - NOSMOVE, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; The Global Research and Analysis for Public Health (" + }, + { + "author_name": "Izabel Cristina dos Reis", + "author_inst": "Nucleo Operacional Sentinela de Mosquitos Vetores - NOSMOVE, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; The Global Research and Analysis for Public Health (" + }, + { + "author_name": "Sara Botero-Mesa", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland; The Global Research and Analysis for Public Health (GRAPH) Network (" + }, + { + "author_name": "Wingston Ng'ambi", + "author_inst": "Health Economics Policy Unit, Department of Health Systems and Policy, College of Medicine, University of Malawi, Lilongwe, Malawi" + }, + { + "author_name": "Papy Ansobi", + "author_inst": "Research and Training Unit in Ecology and Control of Infectious Diseases (URF-ECMI), Faculty of Medicine, University of Kinshasa, Kinshasa, Republic Democratic" + }, + { + "author_name": "Beat Stoll", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Cleophas Chimbetete", + "author_inst": "Newlands Clinic, Harare, Zimbabwe" + }, + { + "author_name": "Franck Mboussou", + "author_inst": "World Health Organization, Regional Office for Africa, Brazzaville, Congo" + }, + { + "author_name": "Benido Impouma", + "author_inst": "World Health Organization, Regional Office for Africa, Brazzaville, Congo" + }, + { + "author_name": "Cristina Barroso Hofer", + "author_inst": "Department of Pediatric Infectious Diseases, UFRJ, Rio de Janeiro, Brazil; The Global Research and Analysis for Public Health (GRAPH) Network (https://thegraphn" + }, + { + "author_name": "Flavio Codeco Coelho", + "author_inst": "School of Applied Mathematics, Getulio Vargas Foundation, Rio de Janeiro, Brazil; The Global Research and Analysis for Public Health (GRAPH) Network (https://th" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland; The Global Research and Analysis for Public Health (GRAPH) Network (" + }, + { + "author_name": "Jessica L Abbate", + "author_inst": "UMI TransVIHMI (Institut de Recherche pour le Developpement, Institut National de la Sante et de la Recherche Medicale, Universite de Montpellier), Montpellier," + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.14.21262064", "rel_title": "Predicting COVID-19 Incidences from Patients Viral Load using Deep-Learning", @@ -587344,81 +586243,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.25.457692", - "rel_title": "The Lambda variant of SARS-CoV-2 has a better chance than the Delta variant to escape vaccines", - "rel_date": "2021-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.25.457692", - "rel_abs": "The newly emerging variants of SARS-CoV-2 from India (Delta variant) and South America (Lambda variant) have led to a higher infection rate of either vaccinated or unvaccinated people. We found that sera from Pfizer-BioNTech vaccine remain high reactivity toward the receptor binding domain (RBD) of Delta variant while it drops dramatically toward that of Lambda variant. Interestingly, the overall titer of antibodies of Pfizer-BioNTech vaccinated individuals drops 3-fold after 6 months, which could be one of major reasons for breakthrough infections, emphasizing the importance of potential third boost shot. While a therapeutic antibody, Bamlanivimab, decreases binding affinity to Delta variant by ~20 fold, it fully lost binding to Lambda variant. Structural modeling of complexes of RBD with human receptor, Angiotensin Converting Enzyme 2 (ACE2), and Bamlanivimab suggest the potential basis of the change of binding. The data suggest possible danger and a potential surge of Lambda variant in near future.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Haolin Liu", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Pengcheng Wei", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Qianqian Zhang", - "author_inst": "China Agriculture University" - }, - { - "author_name": "Katja Aviszus", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Jared Linderberger", - "author_inst": "University of Colorado, Anschutz Medical Campus" - }, - { - "author_name": "John Yang", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Junfeng Liu", - "author_inst": "China Agriculture University" - }, - { - "author_name": "Zhongzhou Chen", - "author_inst": "China Agriculture University" - }, - { - "author_name": "Hassan Waheed", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Lyndon Reynoso", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Gregory Downey", - "author_inst": "National Jewish Helath" - }, - { - "author_name": "Stephen Frankel", - "author_inst": "National Jewish Health" - }, - { - "author_name": "John Kappler", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Philippa Marrack", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Gongyi Zhang", - "author_inst": "National Jewish Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.24.21262580", "rel_title": "The efficacy and safety of bamlanivimab treatment against COVID-19: A meta-analysis", @@ -588011,6 +586835,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.08.26.21262468", + "rel_title": "Long-term immunogenicity of BNT162b2 vaccination in the elderly and in younger health care workers", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262468", + "rel_abs": "COVID-19 mRNA vaccine BNT162b2 is highly immunogenic and effective, but recent studies have indicated waning anti-SARS-CoV-2 immune responses over time. Increasing infection rates has led authorities in several countries to initiate booster campaigns for vulnerable populations, including the elderly. However, the durability of vaccine-induced immunity in the elderly is currently unknown. Here, we describe interim results of a prospective cohort study comparing immune responses in a cohort of vaccinated elderly persons to those in healthcare workers (HCW), measured six months after first immunisation with BNT162b2. Anti-SARS-CoV-2 S1-, full Spike- and RBD-IgG seropositivity rates and IgG levels at six months were significantly lower in the elderly compared to HCW. Serum neutralization of Delta VOC measured by pseudovirus neutralisation test was detectable in 43/71 (60.6%, 95%CI: 48.9-71.1) in the elderly cohort compared to 79/83 in the HCW cohort (95.2%, 95%CI: 88.3-98.1) at six months post vaccination. Consistent with the overall lower antibody levels, SARS-CoV-2-S1 T cell reactivity was reduced in the elderly compared to HCW (261.6 mIU/ml, IQR:141.5-828.6 vs 1198.0 mIU/ml, IQR: 593.9-2533.6, p<0.0001).\n\nCollectively, these findings suggest that the established two-dose vaccination regimen elicits less durable immune responses in the elderly compared to young adults. Given the recent surge in hospitalisations, even in countries with high vaccination rates such as Israel, the current data may support booster vaccinations of the elderly. Further studies to determine long-term effectiveness of COVID-19 vaccines in high-risk populations and the safety and effectiveness of additional boosters are needed.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Pinkus Tober-Lau", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Tatjana Schwarz", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Kanika Vanshylla", + "author_inst": "Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "David Hillus", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Henning Gruell", + "author_inst": "Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "- EICOV/COVIM Study Group", + "author_inst": "" + }, + { + "author_name": "Norbert Suttorp", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Irmgard Landgraf", + "author_inst": "Hausarztpraxis am Agaplesion Bethanien Sophienhaus" + }, + { + "author_name": "Kai Kappert", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Joachim Seybold", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Florian Klein", + "author_inst": "University of Cologne" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Charite Universistaetsmedizin Berlin" + }, + { + "author_name": "Victor M Corman", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Leif Erik M Sander", + "author_inst": "Charite Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.21.21262393", "rel_title": "Global disparities in SARS-CoV-2 genomic surveillance", @@ -589378,41 +588277,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.25.457645", - "rel_title": "Structure-based screening of drug candidates targeting the SARS-CoV-2 envelope protein", - "rel_date": "2021-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.25.457645", - "rel_abs": "The COVID-19 (coronavirus disease 2019) pandemic is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). SARS-CoV-2 produces a small hydrophobic envelope (E) protein which shares high homology with SARS-CoV E protein. By patch-clamp recording, the E protein is demonstrated to be a cation-selective ion channel. Furthermore, the SARS-CoV-2 E protein can be blocked by a SARS-CoV E protein inhibitor hexamethylene amiloride. Using structural model and virtual screening, another E protein inhibitor AZD5153 is discovered. AZD5153 is a bromodomain protein 4 inhibitor against hematologic malignancies in clinical trial. The E protein amino acids Phe23 and Val29 are key determinants for AZD5153 sensitivity. This study provides two promising lead compounds and a functional assay of SARS-CoV-2 E protein for the future drug candidate discovery.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xin Xia", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Yuwei Zhang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Songling Li", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Hengwei Lin", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Zhiqiang Yan", - "author_inst": "Shenzhen Bay Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.24.457397", "rel_title": "Direct RNA sequencing reveals SARS-CoV-2 m6A sites and possible differential DRACH motif methylation among variants", @@ -590208,6 +589072,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.16.21262135", + "rel_title": "Assessing the impact of adherence to Non-pharmaceutical interventions and indirect transmission on the dynamics of COVID-19: a mathematical modelling study", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262135", + "rel_abs": "Adherence to public health policies such as the non-pharmaceutical interventions implemented against COVID-19 plays a major role in reducing infections and controlling the spread of the diseases. In addition, understanding the transmission dynamics of the disease is also important in order to make and implement efficient public health policies. In this paper, we developed an SEIR-type compartmental model to assess the impact of adherence to COVID-19 non-pharmaceutical interventions and indirect transmission on the dynamics of the disease. Our model considers both direct and indirect transmission routes and stratifies the population into two groups: those that adhere to COVID-19 non-pharmaceutical interventions (NPIs) and those that do not adhere to the NPIs. We compute the control reproduction number and the final epidemic size relation for our model and study the effect of different parameters of the model on these quantities. Our results show that direct transmission has more effect on the reproduction number and final epidemic size, relative to indirect transmission. In addition, we showed that there is a significant benefit in adhering to the COVID-19 NPIs.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sarafa Adewale Iyaniwura", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Musa Abolade Rabiu", + "author_inst": "School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa" + }, + { + "author_name": "Jummy David", + "author_inst": "Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada." + }, + { + "author_name": "Jude Dzevela Kong", + "author_inst": "York University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.18.21262237", "rel_title": "Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK", @@ -591235,97 +590130,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.08.24.457520", - "rel_title": "Immunization with SARS-CoV-2 nucleocapsid protein triggers a pulmonary immune response in rats", - "rel_date": "2021-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457520", - "rel_abs": "The SARS-CoV-2 pandemic have been affecting millions of people worldwide, since the beginning of 2020. COVID-19 can cause a wide range of clinical symptoms, which varies from asymptomatic presentation to severe respiratory insufficiency, exacerbation of immune response, disseminated microthrombosis and multiple organ failure, which may lead to dead. Due to the rapid spread of SARS-CoV-2, the development of vaccines to minimize COVID-19 severity in the world population is imperious. One of the employed techniques to produce vaccines against emerging viruses is the synthesis of recombinant proteins, which can be used as immunizing agents. Based on the exposed, the aim of the present study was to verify the systemic and immunological effects of IM administration of recombinant Nucleocapsid protein (NP), derived from SARS-CoV-2 and produced by this research group, in 2 different strains of rats (Rattus norvegicus); Wistar and Lewis. For this purpose, experimental animals received 4 injections of NP, once a week, and were submitted to biochemical and histological analysis. Our results showed that NP inoculations were safe for the animals, which presented no clinical symptoms of worrying side effects, nor laboratorial alterations in the main biochemical and histological parameters, suggesting the absence of toxicity induced by NP. Moreover, NP injections successfully triggered the production of specific anti-SARS-CoV-2 IgG antibodies by both Wistar and Lewis rats, showing the sensitization to have been well sufficient for the immunization of these strains of rats. Additionally, we observed the local lung activation of the Bronchus-Associated Lymphoid Tissue (BALT) of rats in the NP groups, suggesting that NP elicits specific lung immune response. Although pre-clinical and clinical studies are still required, our data support the recombinant NP produced by this research group as a potential immunizing agent for massive vaccination, and may represent advantages upon other recombinant proteins, since it seems to induce specific pulmonary protection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Everidiene K. V. B. Silva Sr.", - "author_inst": "FM-USP" - }, - { - "author_name": "Camila G Bomfim Sr.", - "author_inst": "ICB-USP" - }, - { - "author_name": "Ana P Barbosa Sr.", - "author_inst": "ICB-USP" - }, - { - "author_name": "Paloma Noda Sr.", - "author_inst": "FM-USP" - }, - { - "author_name": "Irene L Noronha", - "author_inst": "FM-USP" - }, - { - "author_name": "Bianca H V Fernandes", - "author_inst": "FM-USP" - }, - { - "author_name": "Rafael R.G Machado", - "author_inst": "ICB-USP" - }, - { - "author_name": "Edison L Durigon", - "author_inst": "ICB-USP" - }, - { - "author_name": "Sergio Catanozi", - "author_inst": "FM-USP" - }, - { - "author_name": "Leticia G Rodrigues", - "author_inst": "FM-USP" - }, - { - "author_name": "Fabiana Pieroni", - "author_inst": "Labinbraz Comercial Ltda" - }, - { - "author_name": "Sergio Lima", - "author_inst": "Labinbraz Comercial Ltda" - }, - { - "author_name": "Zelita A. J. Queiroz", - "author_inst": "FM-USP" - }, - { - "author_name": "Ives Charlie-Silva", - "author_inst": "ICB-USP" - }, - { - "author_name": "Lizandre K. R. Silveira", - "author_inst": "FM-USP" - }, - { - "author_name": "Walcy T Teodoro", - "author_inst": "FM-USP" - }, - { - "author_name": "Vera L Capelozzi", - "author_inst": "FM-USP" - }, - { - "author_name": "Cristiane R Guzzo", - "author_inst": "ICB-USP" - }, - { - "author_name": "Camilla Fanelli", - "author_inst": "FM-USP" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.24.457457", "rel_title": "Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response", @@ -592114,6 +590918,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.15.21262074", + "rel_title": "Comparison of the inhomogeneous SEPIR model and data from the COVID-19 outbreak in South Carolina", + "rel_date": "2021-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262074", + "rel_abs": "During the COVID-19 pandemic authorities have been striving to obtain reliable predictions for the spreading dynamics of the disease. We recently developed a multi-\"sub-populations\" (multi-compartments: susceptible, exposed, pre-symptomatic, infectious, recovered) model, that accounts for the spatial in-homogeneous spreading of the infection and shown, for a variety of examples, how the epidemic curves are highly sensitive to location of epicenters, non-uniform population density, and local restrictions. In the present work we test our model against real-life data from South Carolina during the period May 22 to July 22 (2020). During this period, minimal restrictions have been employed, which allowed us to assume that the local basic reproduction number is constant in time. We account for the non-uniform population density in South Carolina using data from NASA, and predict the evolution of infection heat-maps during the studied period. Comparing the predicted heat-maps with those observed, we find high qualitative resemblance. Moreover, the Pearsons correlation coefficient is relatively high thus validating our model against real-world data. We conclude that the model accounts for the major effects controlling spatial in-homogeneous spreading of the disease. Inclusion of additional sub-populations (compartments), in the spirit of several recently developed models for COVID-19, can be easily performed within our mathematical framework.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rony Granek", + "author_inst": "Ben-Gurion University of the Negev" + }, + { + "author_name": "Yoav Tsori", + "author_inst": "Ben-Gurion University of the Negev" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.15.21262071", "rel_title": "Improving the reproduction number calculation by treating for daily variations of SARS-CoV-2 cases", @@ -593493,49 +592320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.20.21262326", - "rel_title": "Disability-adjusted life years (DALYs) due to the direct health impact of COVID-19 in India, 2020", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262326", - "rel_abs": "COVID-19 has affected all countries. Its containment represents a unique challenge for India due to a large population (>1.38 billion) across a wide range of population densities. Assessment of the COVID-19 disease burden is required to put the disease impact into context and support future pandemic policy development. Here, we present the national-level burden of COVID-19 in India in 2020 that accounts for differences across urban and rural regions and across age groups. Disability-adjusted life years (DALY) due to COVID-19 were estimated in the Indian population in 2020, comprised of years of life lost (YLL) and years lived with disability (YLD). Scenario analyses were conducted to account for excess deaths not recorded in the official data and for reported COVID-19 deaths. The direct impact of COVID-19 in 2020 in India was responsible for 14,106,060 (95% uncertainty interval [UI] 14,030,129-14,213,231) DALYs, consisting of 99.2% (95% UI 98.47-99.64%) YLLs and 0.80% (95% UI 0.36-1.53) YLDs. DALYs were higher in urban (56%; 95% UI 56-57%) than rural areas (44%; 95% UI 43.4-43.6) and in males (64%) than females (36%). In absolute terms, the highest DALYs occurred in the 51-60-year-old age group (28%) but the highest DALYs per 100,000 persons were estimated for the 71-80 year old age group (5,481; 95% UI 5,464-5,500 years). There were 4,823,791 (95% UI 4,760,908-4,924,307) DALYs after considering reported COVID-19 deaths only. The DALY estimations have direct and immediate implications not only for public policy in India, but also internationally given that India represents one sixth of the worlds population.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Balbir Bagicha Singh", - "author_inst": "Guru Angad Dev Veterinary & Animal Sciences University" - }, - { - "author_name": "Brecht Devleesschauwer", - "author_inst": "Department of Epidemiology and Public Health, Sciensano, Rue Juliette Wytsman 14, BE-1050, Brussels, Belgium" - }, - { - "author_name": "Mehar S Khatkar", - "author_inst": "Sydney School of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570 NSW, Australia" - }, - { - "author_name": "Mark Lowerison", - "author_inst": "Dept. of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1" - }, - { - "author_name": "Baljit Singh", - "author_inst": "University of Saskatchewan, Saskatoon, SK, Canada" - }, - { - "author_name": "Navneet K Dhand", - "author_inst": "Sydney School of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570 NSW, Australia" - }, - { - "author_name": "Herman W Barkema", - "author_inst": "Dept. of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.19.21262296", "rel_title": "Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia", @@ -594156,6 +592940,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.19.21262304", + "rel_title": "Bias as a source of inconsistency in ivermectin trials for COVID-19: A systematic review", + "rel_date": "2021-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262304", + "rel_abs": "Background and purposeThe objective of this systematic review is to summarize the effects of ivermectin for the prevention and treatment of patients with COVID-19 and to assess inconsistencies in results from individual studies with focus on risk of bias due to methodological limitations.\n\nEvidence reviewWe searched the L.OVE platform through July 6, 2021 and included randomized trials (RCTs) comparing ivermectin to standard or other active treatments. We conducted random-effects pairwise meta-analysis, assessed the certainty of evidence using the GRADE approach and performed sensitivity analysis excluding trials with risk of bias.\n\nResultsWe included 29 RCTs which enrolled 5592 cases. Overall, the certainty of the evidence was very low to low. Compared to standard of care, ivermectin may reduce mortality, may increase symptom resolution or improvement, may increase viral clearance, may reduce infections in exposed individuals and may decrease hospitalizations (Risk difference (RD) 21 fewer per 1000, 95%CI: 35 fewer to 4 more). However, after excluding trials classified as \"high risk\" or \"some concerns\" in the risk of bias assessment, most estimates of effect changed substantially: Compared to standard of care, low certainty evidence suggests that ivermectin may not significantly reduce mortality (RD 7 fewer per 1000, 95%CI: 77 fewer to 108 more) nor mechanical ventilation (RD 6 more per 1000, 95%CI: 43 fewer to 86 more), and moderate certainty evidence shows that it probably does not significantly increase symptom resolution or improvement (RD 14 more per 1000, 95%CI: 29 fewer to 71 more) nor viral clearance (RD 12 fewer per 1000, 95%CI: 84 fewer to 76 more). It is uncertain if ivermectin increases or decreases severe adverse events and symptomatic infections in exposed individuals.\n\nConclusions and RelevanceIvermectin may not improve clinically important outcomes in patients with COVID-19 and its effects as a prophylactic intervention in exposed individuals are uncertain. Previous reports concluding significant benefits associated with ivermectin are based on potentially biased results reported by studies with substantial methodological limitations. Further research is needed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ariel Izcovich", + "author_inst": "Incident Management System for the Covid-19 Response. Pan American Health Organization" + }, + { + "author_name": "Sasha Peiris", + "author_inst": "Incident Management System for the Covid-19 Response. Pan American Health Organization" + }, + { + "author_name": "Mart\u00edn Ragusa", + "author_inst": "Evidence and Intelligence for Action in Health Department. Pan American Health Organization" + }, + { + "author_name": "Fernando Tortosa", + "author_inst": "Evidence and Intelligence for Action in Health Department. Pan American Health Organization" + }, + { + "author_name": "Gabriel Rada", + "author_inst": "Fundaci\u00f3n Epistemonikos" + }, + { + "author_name": "Sylvain Aldighieri", + "author_inst": "Incident Management System for the Covid-19 Response. Pan American Health Organization" + }, + { + "author_name": "Ludovic Reveiz", + "author_inst": "Incident Management System for the Covid-19 Response. Pan American Health Organization" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.18.21262248", "rel_title": "Regional comparisons of COVID reporting rates, burden, and mortality age-structure using auxiliary data sources", @@ -595043,69 +593870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.17.21262169", - "rel_title": "SARS-CoV-2 aerosol transmission in schools: the effectiveness of different interventions", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262169", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSIndoor aerosol transmission of SARS-CoV-2 has been widely recognized, especially in schools where children remain in closed indoor spaces and largely unvaccinated. Measures such as strategic natural ventilation and high efficiency particulate air (HEPA) filtration remain poorly implemented and mask mandates are often progressively lifted as vaccination rollout is enhanced.\n\nMethodsWe adapted a previously developed aerosol transmission model to study the effect of interventions (natural ventilation, face masks, HEPA filtration, and their combinations) on the concentration of virus particles in a classroom of 160 m3 containing one infectious individual. The cumulative dose of viruses absorbed by exposed occupants was calculated.\n\nResultsThe most effective single intervention was natural ventilation through the full opening of six windows all day during the winter (14-fold decrease in cumulative dose), followed by the universal use of surgical face masks (8-fold decrease). In the spring/summer, natural ventilation was only effective ([≥] 2-fold decrease) when windows were fully open all day. In the winter, partly opening two windows all day or fully opening six windows at the end of each class was effective as well ([≥] 2-fold decrease). Opening windows during yard and lunch breaks only had minimal effect ([≤] 1.2-fold decrease). One HEPA filter was as effective as two windows partly open all day during the winter (2.5-fold decrease) while two filters were more effective (4-fold decrease). Combined interventions (i.e., natural ventilation, masks, and HEPA filtration) were the most effective ([≥] 30-fold decrease). Combined interventions remained highly effective in the presence of a super-spreader.\n\nConclusionsNatural ventilation, face masks, and HEPA filtration are effective interventions to reduce SARS-CoV-2 aerosol transmission. These measures should be combined and complemented by additional interventions (e.g., physical distancing, hygiene, testing, contact tracing, and vaccination) to maximize benefit.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jennifer Villers", - "author_inst": "Global Studies Institute" - }, - { - "author_name": "Andre Henriques", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Serafina Calarco", - "author_inst": "Foundation for Innovative New Diagnostics (FIND)" - }, - { - "author_name": "Markus Rognlien", - "author_inst": "Norwegian University of Science and Technology (NTNU)" - }, - { - "author_name": "Nicolas Mounet", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "James Devine", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Gabriella Azzopardi", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Philip Elson", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Marco Andreini", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Nicola Tarocco", - "author_inst": "European Organization for Nuclear Research (CERN)" - }, - { - "author_name": "Claudia C Vassella", - "author_inst": "Federal Office of Public Health, Consumer Protection Directorate, Indoor Pollutants Unit" - }, - { - "author_name": "Olivia Keiser", - "author_inst": "Institute of Global Health, University of Geneva" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.18.21262166", "rel_title": "Changes in the serial interval and transmission dynamics associated with the SARS-CoV-2 Delta variant in South Korea", @@ -595850,6 +594614,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.19.456973", + "rel_title": "Modeling Coronavirus Spike Protein Dynamics: Implications for Immunogenicity and Immune Escape", + "rel_date": "2021-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.19.456973", + "rel_abs": "The ongoing COVID-19 pandemic is a global public health emergency requiring urgent development of efficacious vaccines. While concentrated research efforts are underway to develop antibody-based vaccines that would neutralize SARS-CoV-2, and several first-generation vaccine candidates are currently in Phase III clinical trials or have received emergency use authorization, it is forecasted that COVID-19 will become an endemic disease requiring second-generation vaccines. The SARS-CoV-2 surface Spike (S) glycoprotein represents a prime target for vaccine development because antibodies that block viral attachment and entry, i.e. neutralizing antibodies, bind almost exclusively to the receptor binding domain (RBD). Here, we develop computational models for a large subset of S proteins associated with SARS-CoV-2, implemented through coarse-grained elastic network models and normal mode analysis. We then analyze local protein domain dynamics of the S protein systems and their thermal stability to characterize structural and dynamical variability among them. These results are compared against existing experimental data, and used to elucidate the impact and mechanisms of SARS-CoV-2 S protein mutations and their associated antibody binding behavior. We construct a SARS-CoV-2 antigenic map and offer predictions about the neutralization capabilities of antibody and S mutant combinations based on protein dynamic signatures. We then compare SARS-CoV-2 S protein dynamics to SARS-CoV and MERS-CoV S proteins to investigate differing antibody binding and cellular fusion mechanisms that may explain the high transmissibility of SARS-CoV-2. The outbreaks associated with SARS-CoV, MERS-CoV, and SARS-CoV-2 over the last two decades suggest that the threat presented by coronaviruses is ever-changing and long-term. Our results provide insights into the dynamics-driven mechanisms of immunogenicity associated with coronavirus S proteins, and present a new approach to characterize and screen potential mutant candidates for immunogen design, as well as to characterize emerging natural variants that may escape vaccine-induced antibody responses.\n\nSTATEMENT OF SIGNIFICANCEWe present novel dynamic mechanisms of coronavirus S proteins that encode antibody binding and cellular fusion properties. These mechanisms may offer an explanation for the widespread nature of SARS-CoV-2 and more limited spread of SARS-CoV and MERS-CoV. A comprehensive computational characterization of SARS-CoV-2 S protein structures and dynamics provides insights into structural and thermal stability associated with a variety of S protein mutants. These findings allow us to make recommendations about the future mutant design of SARS-CoV-2 S protein variants that are optimized to elicit neutralizing antibodies, resist structural rearrangements that aid cellular fusion, and are thermally stabilized. The integrated computational approach can be applied to optimize vaccine immunogen design and predict escape of vaccine-induced antibody responses by SARS-CoV-2 variants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Genevieve Kunkel", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Mohammad Madani", + "author_inst": "University of Connecticut" + }, + { + "author_name": "S. J. White", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Paulo Verardi", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Anna Tarakanova", + "author_inst": "University of Connecticut" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.08.12.21261955", "rel_title": "Cardiac Inflammation after COVID-19 mRNA Vaccines: A Global Pharmacovigilance Analysis", @@ -596937,89 +595736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.15.21262067", - "rel_title": "Significant reduction in humoral immunity among healthcare workers and nursing home residents 6 months after COVID-19 BNT162b2 mRNA vaccination", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262067", - "rel_abs": "High COVID-19 mortality among nursing home (NH) residents led to their prioritization for SARS-CoV-2 vaccination; most NH residents received BNT162b2 mRNA vaccination under the Emergency Use Authorization due to first to market and its availability. With NH residents poor initial vaccine response, the rise of NH breakthrough infections and outbreaks, characterization of the durability of immunity to inform public health policy on the need for boosting is needed. We report on humoral immunity from 2 weeks to 6-months post-vaccination in 120 NH residents and 92 ambulatory healthcare worker controls with and without pre-vaccination SARS-CoV-2 infection. Anti-spike and anti-receptor binding domain (RBD) IgG, and serum neutralization titers, were assessed using a bead-based ELISA method and pseudovirus neutralization assay. Anti-spike, anti-RBD and neutralization levels dropped more than 84% over 6 months time in all groups irrespective of prior SARS-CoV-2 infection. At 6 months post-vaccine, 70% of the infection-naive NH residents had neutralization titers at or below the lower limit of detection compared to 16% at 2 weeks after full vaccination. These data demonstrate a significant reduction in levels of antibody in all groups. In particular, those infection-naive NH residents had lower initial post-vaccination humoral immunity immediately and exhibited the greatest declines 6 months later. Healthcare workers, given their younger age and relative good-health, achieved higher initial antibody levels and better maintained them, yet also experienced significant declines in humoral immunity. Based on the rapid spread of the delta variant and reports of vaccine breakthrough in NH and among younger community populations, boosting NH residents may be warranted.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "David H. Canaday", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Oladayo Oyebanji", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Debbie Keresztesy", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Michael Payne", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Dennis Wilk", - "author_inst": "Case Wesern Reserve University" - }, - { - "author_name": "Lenore Caris", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Htin Aung", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Kerri St. Denis", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Evan Lam", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Christopher Rowley", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Sarah Berry", - "author_inst": "Marcus Institute for Aging Research" - }, - { - "author_name": "Cheryl Cameron", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Mark Cameron", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Brigid Wilson", - "author_inst": "Cleveland VA" - }, - { - "author_name": "Alejandro Balazs", - "author_inst": "Ragon Institute" - }, - { - "author_name": "Christopher King", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Stefan Gravenstein", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.14.21257136", "rel_title": "Worldwide association of lifestyle related factors and COVID-19 mortality", @@ -597652,6 +596368,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.17.456707", + "rel_title": "An Endogenously activated antiviral state restricts SARS-CoV-2 infection in differentiated primary airway epithelial cells", + "rel_date": "2021-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.17.456707", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-19 (COVID-19) pandemic, was identified in late 2019 and went on to cause over 3.3 million deaths in 15 months. To date, targeted antiviral interventions against COVID-19 are limited. The spectrum of SARS-CoV-2 infection ranges from asymptomatic to fatal disease. However, the reasons for varying outcomes to SARS-CoV-2 infection are yet to be elucidated. Here we show that an endogenously activated interferon lambda (IFN{lambda}) pathway leads to resistance against SARS-CoV-2 infection. Using a well-differentiated primary nasal epithelial cell (WD-PNEC) model from multiple adult donors, we discovered that susceptibility to SARS-CoV-2 infection, but not respiratory syncytial virus (RSV) infection, varied. One of four donors was resistant to SARS-CoV-2 infection. High baseline IFN{lambda} expression levels and associated interferon stimulated genes correlated with resistance to SARS-CoV-2 infection. Inhibition of the JAK/STAT pathway in WD-PNECs with high endogenous IFN{lambda} secretion resulted in higher SARS-CoV-2 titres. Conversely, prophylactic IFN{lambda} treatment of WD-PNECs susceptible to infection resulted in reduced viral titres. An endogenously activated IFN{lambda} response, possibly due to genetic differences, may be one explanation for the differences in susceptibility to SARS-CoV-2 infection in humans. Importantly, our work supports the continued exploration of IFN{lambda} as a potential pharmaceutical against SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Guillermo Lopez Campos", + "author_inst": "Queens University Belfast" + }, + { + "author_name": "Sheerien Manzoor", + "author_inst": "Queens University Belfast" + }, + { + "author_name": "David Courtney", + "author_inst": "Queens University Belfast" + }, + { + "author_name": "Ahlam Ali", + "author_inst": "Queens University Belfast" + }, + { + "author_name": "Olivier Touzelet", + "author_inst": "Queens University Belfast" + }, + { + "author_name": "Conall McCaughey", + "author_inst": "Belfast Health and Social Care Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.17.456704", "rel_title": "Protein-based RBD-C-tag COVID-19 Vaccination Candidate Elicits Protection Activity against SARS-COV-2 Variant Infection", @@ -598719,37 +597474,6 @@ "type": "confirmatory results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.16.456510", - "rel_title": "Age-related susceptibility of ferrets to SARS-CoV-2 infection", - "rel_date": "2021-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.16.456510", - "rel_abs": "Susceptibility to SARS-CoV-2 and the outcome of COVID-19 have been linked to underlying health conditions and the age of affected individuals. Here we assessed the effect of age on SARS-CoV-2 infection using a ferret model. For this, young (6-month-old) and aged (18-to-39-month-old) ferrets were inoculated intranasally with various doses of SARS-CoV-2. By using infectious virus shedding in respiratory secretions and seroconversion, we estimated that the infectious dose of SARS-CoV-2 in aged animals is [~]32 plaque forming units (PFU) per animal while in young animals it was estimated to be [~]100 PFU. We showed that viral replication in the upper respiratory tract and shedding in respiratory secretions is enhanced in aged ferrets when compared to young animals. Similar to observations in humans, this was associated with higher expressions levels of two key viral entry factors - ACE2 and TMPRSS2 - in the upper respiratory tract of aged ferrets.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mathias Martins", - "author_inst": "Cornell University College of Veterinary Medicine" - }, - { - "author_name": "Maureen H.V. Fernandes", - "author_inst": "Cornell University College of Veterinary Medicine" - }, - { - "author_name": "Lok R Joshi", - "author_inst": "Cornell University" - }, - { - "author_name": "Diego Diel", - "author_inst": "Cornell University College of Veterinary Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.13.454991", "rel_title": "A screening pipeline identifies a broad-spectrum inhibitor of bacterial AB toxins with cross protection against influenza A virus H1N1 and SARS-CoV-2", @@ -599374,6 +598098,65 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.08.09.21261738", + "rel_title": "Beneficial Effects of novel Aureobasidium Pullulans strains produced Beta-1,3-1,6 Glucans on Interleukin-6 and D-Dimer levels in COVID-19 patients; results of a randomized multiple-arm pilot clinical study", + "rel_date": "2021-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261738", + "rel_abs": "ObjectiveCytokine storm and Coagulopathy have been implicated as major causes of morbidity and mortality in COVID-19 patients. A black yeast Aureobasidium pullulans AFO-202 strain produced beta 1,3-1,6 glucan has been reported to offer potential immune enhancement and metabolism balancing, as well as mitigation of coagulopathy risks. The N-163 strain produced beta glucan is an efficient anti-inflammatory immune modulator. In this pilot clinical study, we report the beneficial effects of these two beta glucans on the biomarkers for cytokine storm and coagulopathy in COVID-19 patients.\n\nMethodsA total of 24 RT-PCR positive COVID-19 patients were recruited (Age range: 18[~]62; 17 males and 7 females). Patients were randomly divided into three groups (Gr): Gr. 1 control (n=8); Gr. 2: AFO-202 beta glucan (n=8); and Gr. 3, a combination of AFO-202 and N-163 beta glucans (n=8). All three groups received the standard care while groups 2 and 3 received additional supplementation of beta glucans for 30 days. In addition to basic clinical parameters, we periodically evaluated D-Dimer, IL-6, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), the neutrophil to lymphocyte ratio (NLR), the lymphocyte to CRP ratio (LCR) and the leukocyte-CRP ratio (LeCR).\n\nResultsThe duration of hospital stay for all three groups was nearly equivalent. There was no mortality of the subjects in any of the groups. Intermittent oxygen was administered from day of admission for up to four to five days with mask (two to four Lpm) to two subjects in Gr. 2 and one subject in Gr. 3. None of the subjects required ventilation. The D-Dimer values in Gr. 1, which was on average 751 ng/ml at baseline, decreased to 143.89 ng/ml on day 15, but increased to 202.5 ng/ml on day 30, which in groups 2 and 3 decreased on day 15 and continued to remain at normal levels until day 30. IL-6 levels decreased on day 15 from an average of 7.395 pg/ml to 3.16 pg/ml in the control, 26.18 pg/ml to 6.94 pg/ml in Gr. 2 and 6.25 pg/ml to 5.22 pg/ml in Gr. 3. However, when measured on day 30, in Gr. 1, the IL-6 increased to 55.37 pg/ml while there was only slight marginal increase in Gr. 2 but within normal range, and the levels further decreased to less than 0.5 pg/ml in Gr. 3. The same trend was observed with ESR. LCR and LeCR increased significantly in Gr. 3. NLR decreased significantly in groups 2 and 3. There was no difference in CRP within the groups.\n\nConclusionIn this exploratory study, consumption of Aureobasidium pullulans produced beta glucans for thirty days, results in a significant control of IL6, D-Dimer and NLR, a significant increase in LCR, LeCR and marginal control of ESR in COVID-19 patients. As these beta glucans are well known food supplements with decades of a track record for safety, based on these results, we recommend larger multi-centric clinical studies to validate their use as an adjunct in the management of COVID-19 and the ensuing long COVID-19 syndrome.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kadalraja Raghavan", + "author_inst": "Dept of Paediatric Neurology, Kenmax Healthcare Services Pvt Ltd, Madurai, India" + }, + { + "author_name": "Vidyasagar Devaprasad Dedeepiya", + "author_inst": "Mary-Yoshio Translational Hexagon (MYTH), Nichi-In Centre for Regenerative Medicine (NCRM), Chennai, India." + }, + { + "author_name": "Vaddi Suryaprakash", + "author_inst": "Department of Urology, Yashoda Hospitals, Hyderabad, India" + }, + { + "author_name": "Kosagi-Sharaf Rao", + "author_inst": "Instituto de Investigaciones Cientificas y Servicios de Alta Tecnologia (INDICASAT AIP), City of Knowledge, Panama" + }, + { + "author_name": "Nobunao Ikewaki", + "author_inst": "Dept. of Medical Life Science, Kyushu University of Health and Welfare, Japan" + }, + { + "author_name": "Tohru Sonoda", + "author_inst": "Institute of Immunology, Junsei Educational Institute, Nobeoka, Miyazaki, Japan" + }, + { + "author_name": "Gary A. Levy", + "author_inst": "Professor Emeritus, Medicine and Immunology, University of Toronto, Ontario, Canada" + }, + { + "author_name": "Masaru Iwasaki", + "author_inst": "Centre for Advancing Clinical Research (CACR), University of Yamanashi - School of Medicine, Chuo, Japan" + }, + { + "author_name": "Rajappa Senthilkumar", + "author_inst": "Fujio-Eiji Academic Terrain (FEAT), Nichi-In Centre for Regenerative Medicine (NCRM), Chennai, India" + }, + { + "author_name": "Senthilkumar Preethy", + "author_inst": "Fujio-Eiji Academic Terrain (FEAT), Nichi-In Centre for Regenerative Medicine (NCRM), Chennai, India" + }, + { + "author_name": "Samuel JK Abraham", + "author_inst": "Yamanashi University-Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.06.21261665", "rel_title": "The impact of seasonal factors on the COVID-19 pandemic waves", @@ -600361,49 +599144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.11.21261877", - "rel_title": "Serological detection of SARS-CoV-2 IgG using a commercially available enzyme immunoassays on dried blood spots collected from patients", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261877", - "rel_abs": "Serological testing for SARS-CoV-2 antibodies provides important research and diagnostic information relating to COVID-19 immune response and surveillance. A major challenge when addressing protection post-infection or vaccination is the difficulty of specimen collection from infants and children. Dried blood spots (DBS) collected by finger prick or heel prick are a minimally invasive sample collection alternative previously used to detect antibodies to other viruses. In this study we evaluated DBS for the detection of SARS-CoV-2 antibodies on three commercially available enzyme (EIA) and chemiluminescent (CLIA) immunoassays by analysing paired DBS and serum samples collected from 54 subjects. We demonstrate that testing of DBS samples was highly sensitive and specific, and quantitative results strongly correlated with those of paired serum. These results suggest that DBS derived blood is a viable alternative to plasma or serum for use in EIAs and CLIAs, and has particular utility as a minimally invasive collection tool for COVID-19 serological testing of infants and children.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gregory J Walker", - "author_inst": "Prince of Wales Hospital" - }, - { - "author_name": "Rebecca Davis", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Zin Naing", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Brad McEntee", - "author_inst": "NSW Health" - }, - { - "author_name": "Yonghui Lu", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Tatijana Denadija", - "author_inst": "NSW Health" - }, - { - "author_name": "William D Rawlinson", - "author_inst": "Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261876", "rel_title": "SARS-CoV-2 variants: levels of neutralisation required for protective immunity", @@ -601224,6 +599964,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.12.21261981", + "rel_title": "COVID-19 vaccine uptake among older people in relation to sociodemographic factors: cohort results from southern Sweden", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261981", + "rel_abs": "The aim of this cohort study was to investigate sociodemographic determinants of COVID-19 vaccine uptake in the 70+ age group in Sk[a]ne county, Sweden (n = 216 243 at baseline). Uptake of the first dose was high (91.9%) overall, but markedly lower (75.3%) among persons born outside the Nordic countries. Vaccine uptake was generally satisfactory among native Swedes also in areas with lower socioeconomic status, but dropped substantially among non-Nordic born in those areas. The identified clusters of unvaccinated older people, mainly representing ethnic minorities in disadvantaged areas, warrants intensified efforts regarding tailored communication, easier vaccine access and local engagement.\n\nKey pointsO_LICOVID-19 vaccine uptake in the 70+ age group in Sk[a]ne county, Sweden, was high (91.9%) overall, but markedly lower (75.3%) within the group born outside the Nordic countries\nC_LIO_LIInverse associations between indicators of neighbourhood deprivation and vaccine uptake were observed, which lowered the uptake among persons born outside the Nordic countries further\nC_LIO_LIThe identified clusters of unvaccinated older people, mainly representing ethnic minorities in disadvantaged areas, warrants intensified efforts regarding tailored communication, easier vaccine access and local engagement\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Malin Inghammar", + "author_inst": "Lund University" + }, + { + "author_name": "Mahnaz Moghaddassi", + "author_inst": "Lund University" + }, + { + "author_name": "Magnus Rasmussen", + "author_inst": "Lund University" + }, + { + "author_name": "Ulf Malmqvist", + "author_inst": "Region Skane" + }, + { + "author_name": "Fredrik Kahn", + "author_inst": "Lund University" + }, + { + "author_name": "Jonas Bjork", + "author_inst": "Lund University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.13.21261959", "rel_title": "Factors influencing wellbeing in young people during COVID-19.", @@ -602319,97 +601098,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.08.11.21261899", - "rel_title": "Saliva molecular testing bypassing RNA extraction is suitable for monitoring and diagnosing SARS-CoV-2 infection in children", - "rel_date": "2021-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261899", - "rel_abs": "Structured abstractO_ST_ABSIMPORTANCEC_ST_ABSAdults are being vaccinated against SARS-CoV-2 worldwide, but the longitudinal protection of these vaccines is uncertain, given the ongoing appearance of SARS-CoV-2 variants. Children are susceptible to infection, and some studies reported that they actively transmit the virus even when asymptomatic, thus affecting the community. Methods to easily test infected children and track the virus they carry are in demand.\n\nOBJECTIVETo determine if saliva is an effective sample for detecting SARS-CoV-2 RNA and antibodies in children aged 10 years and under, and associate viral RNA levels to infectivity.\n\nDESIGN, SETTING, AND PARTICIPANTSIn this cross-sectional study, saliva SARS-CoV-2 RT-qPCR tests, with and without RNA extraction, were validated in 49 hospitalized adults. The test was then applied to 85 children, aged 10 years and under, admitted to the hospital regardless of COVID-19 symptomatology. Amongst 85 children, 29 (63.0%) presented at least one COVID-19 symptom, 46 (54.1%) were positive for SARS-CoV-2 infection, 28 (32.9%) were under the age of 1 and the mean (SD) age was 3.8 (3.4) years. Saliva samples were collected up to 48 h after a positive test by nasopharyngeal (NP) swab-RT-qPCR.\n\nEXPOSUREInfection by SARS-COV-2 in adults up to 8 days post-symptom onset. Children admitted to hospital for any reason and therefore with unclear onset of SARS-CoV-2 infection.\n\nMAIN OUTCOMES AND MEASURESSaliva RT-qPCR up to CT<37 accurately identifies SARS-CoV-2 infected children, with viral infectivity in tissue culture restricted to CT<26.\n\nRESULTSIn adults, the accuracy of the saliva SARS-CoV-2 RT-qPCR test was 98.0% (95% confidence intervals [CI]: 89.3%-100%) as compared to NP-RT-qPCR. In children, the sensitivity, specificity, and accuracy of saliva-RT-qPCR tests compared to NP swab-RT-qPCR were, respectively, 84.8% (71.8%-92.4%), 100% (91.0%-100%), and 91.8% (84.0%- 96.6%) with RNA extraction and 81.8% (68.0%-90.5%), 100% (91.0%-100%), and 90.4% (82.1%-95.0%) without RNA extraction. The threshold for rescuing infectious particles from saliva was CT<26. There were significant IgM positive responses to the spike protein and its receptor-binding domain (RBD) among children positive for SARS-CoV-2 by NP swab and negative by saliva compared to other groups, indicating late infection onset (>7-10 days).\n\nCONCLUSIONS AND RELEVANCESaliva-molecular testing is suitable in children aged 10 years and under, including infants aged <1 year, even bypassing RNA extraction methods. Importantly, the detected viral RNA levels were significantly above the infectivity threshold in several samples. Further investigation is required to understand how SARS-CoV-2 RNA levels correlate with viral transmission.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs saliva reverse transcription-quantitative polymerase chain reaction (RT-qPCR) testing (with and without RNA extraction) suitable to identify SARS-CoV-2 infected young children and can the cycle threshold (CT) be associated with infectivity in a heterogeneous population admitted to hospital for COVID-19-related and unrelated reasonsa\n\nFindingsIn this cross-sectional study of 85 children aged 10 years and under, RT-qPCR in saliva samples subjected or not to RNA extraction accurately detected SARS-CoV-2 RNA and infectious viruses could be recovered from CTs below 26.\n\nMeaningSaliva sampling coupled to RT-qPCR and specific antibody detection efficiently identifies infants and children infected with SARS-CoV-2. This approach is suitable for surveillance in kindergarten and school settings.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Marta Alenquer", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Tiago Milheiro Silva", - "author_inst": "Hospital Dona Estefania" - }, - { - "author_name": "Onome Akpogheneta", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Filipe Ferreira", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Silvia Vale-Costa", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Monica Medina-Lopes", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Frederico Batista", - "author_inst": "Hospital Prof Doutor Fernando Fonseca" - }, - { - "author_name": "Ana Margarida Garcia", - "author_inst": "Hospital Dona Estefania" - }, - { - "author_name": "Vasco M Barreto", - "author_inst": "CEDOC NOVA" - }, - { - "author_name": "Cathy Paulino", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Joao Costa", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Joao Sobral", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Maria Diniz-da-Costa", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Susana Ladeiro", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Jose Delgado Alves", - "author_inst": "CEDOC NOVA" - }, - { - "author_name": "Ricardo B Leite", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Jocelyne Demengeot", - "author_inst": "Instituto Gulbenkian de Ciencia" - }, - { - "author_name": "Maria Joao Rocha Brito", - "author_inst": "Hospital Dona Estefania" - }, - { - "author_name": "Maria Joao Amorim", - "author_inst": "Instituto Gulbenkian de Ciencia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.12.21261951", "rel_title": "Neutralization of VOCs including Delta one year post COVID-19 or vaccine", @@ -603410,6 +602098,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.12.21261943", + "rel_title": "The impact of school closures on adolescent health-related outcomes during the COVID-19 pandemic: A natural experiment in South Korea", + "rel_date": "2021-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261943", + "rel_abs": "A large number of countries implemented school closure as a response to the COVID-19 pandemic in 2020. As existing studies mostly rely on retrospective or pre/post comparisons that are prone to unmeasured confounding, the effect of school closure on adolescent health is poorly understood. The South Korean government implemented school closure to prevent the spread of COVID-19. A difference-in-differences comparing changes in health-related outcomes between provinces with differing degrees of school closure was performed. The main analysis group consists of middle school students of age 14 to 16 who were hit hardest where up to 73% of total schooling was taken online in Seoul (the physical attendance was reduced from 170 days to 45 days). For sensitivity analysis, a placebo group of high school students of age 19 who attended all school-days physically was included to detect any violation of our identification strategy. In the main analysis group of boys that experienced reduced physical school-days, both total and vigorous physical activity were reduced (-0.35 [-0.54 -0.17] days/week for vigorous physical activity and -0.38 [-0.61 -0.16] days/week for total physical activity) while such effect was absent in the placebo group of boys that actually did not experience school closure (-0.08 [-0.49 0.32] days/week for vigorous PA and -0.16 [-0.67 0.34] days/week for total PA). In girls, vigorous physical activity decreased (-0.22 [-0.40 -0.04] days/week) but the total physical activity was nearly constant (0.03 [-0.18 0.25] days/week). Other outcomes were largely unchanged.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hanbin Lee", + "author_inst": "Seoul National University" + }, + { + "author_name": "Buhm Han", + "author_inst": "Seoul National University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.11.21261883", "rel_title": "Severity of respiratory failure and computed chest tomography in acute COVID-19 correlates with pulmonary function and respiratory symptoms after infection with SARS-CoV-2: an observational longitudinal study over 12 months", @@ -604713,69 +603424,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.10.455872", - "rel_title": "N-dihydrogalactochitosan reduces mortality in a lethal mouse model of SARS-CoV-2", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455872", - "rel_abs": "The rapid emergence and global dissemination of SARS-CoV-2 that causes COVID-19 continues to cause an unprecedented global health burden resulting in nearly 7 million deaths. While multiple vaccine countermeasures have been approved for emergency use, additional treatments are still needed due to sluggish vaccine rollout, vaccine hesitancy, and inefficient vaccine-mediated protection. Immunoadjuvant compounds delivered intranasally can guide non-specific innate immune responses during the critical early stages of viral replication, reducing morbidity and mortality. N- dihydrogalactochitosan (GC) is a novel mucoadhesive immunostimulatory polymer of {beta}- 0-4-linked N-acetylglucosamine that is solubilized by the conjugation of galactose glycans with current applications as a cancer immunotherapeutic. We tested GC as a potential countermeasure for COVID-19. GC was well-tolerated and did not produce histopathologic lesions in the mouse lung. GC administered intranasally before and after SARS-CoV-2 exposure diminished morbidity and mortality in humanized ACE2 receptor expressing mice by up to 75% and reduced infectious virus levels in the upper airway. Fluorescent labeling of GC shows that it is confined to the lumen or superficial mucosa of the nasal cavity, without involvement of adjacent or deeper tissues. Our findings demonstrate a new application for soluble immunoadjuvants such as GC for preventing disease associated with SARS-CoV-2 and may be particularly attractive to persons who are needle-averse.\n\nIMPORTANCEThe ongoing COVID-19 pandemic necessitates new approaches to reduce disease caused by SARS-CoV-2. We tested the immunoadjuvant N-dihydrogalactochitosan (GC), used previously as an immunostimulant for tumor therapy and adjuvant for viral vaccines, as a potential COVID-19 countermeasure. When GC was administered before and after inoculation of a lethal dose of SARS-CoV-2 into the nose of humanized mice expressing an entry receptor for the virus, fewer mice showed weight loss and died compared to mice that received only the vehicle but no GC. GC-treated mice also had lower levels of infectious SARS-CoV-2 in their upper airway. These results suggest that GC may be a candidate to prevent or treat COVID-19.\n\nSingle Sentence SummaryThe immunoadjuvant N-dihydrogalactochitosan diminishes SARS-CoV-2 disease in humanized ACE2 mice, representing a new countermeasure against COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Christopher M Weiss", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Hongwei Liu", - "author_inst": "School of Veterinary Medicine, University of California" - }, - { - "author_name": "Erin E Ball", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Ashley R Hoover", - "author_inst": "University of Oklahoma" - }, - { - "author_name": "Talia S Wong", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Chun Fung Wong", - "author_inst": "Immunophotonics, Inc." - }, - { - "author_name": "Samuel Lam", - "author_inst": "Immunophotonics, Inc." - }, - { - "author_name": "Tomas Hode", - "author_inst": "Immunophotonics, Inc." - }, - { - "author_name": "Michael Kevin Keel", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Richard M Levenson", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Wei R Chen", - "author_inst": "University of Oklahoma" - }, - { - "author_name": "Lark L Coffey", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.11.455959", "rel_title": "Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization", @@ -605375,6 +604023,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.09.21261754", + "rel_title": "Use of health care services during the Covid-19 pandemic in Ethiopia: Evidence from a health facility survey", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261754", + "rel_abs": "IntroductionIn recent years Ethiopia has made enormous strides in enhancing access to health care, especially, maternal and child health care (MCH). With the onset and spread of Covid-19, the attention of the health care system has pivoted to handling the disease, potentially at the cost of other health care needs. This paper explores whether this shift has come at the cost of non-Covid related health care, especially the use of MCH services.\n\nMethodsGraphs, descriptive statistics and paired t-tests of significance are used to compare levels of inpatient and outpatient health care service utilization before and after the onset and spread of the virus. The analysis is based on a survey of 59 health centers and 29 public hospitals located in urban Ethiopia - the most acutely affected region of the country. Data on the use of health care services for a period of 24 months was gathered from the health management information systems (HMIS) of these facilities.\n\nResultsThere is a sharp reduction in the use of both inpatient (20-27%) and outpatient (27-34%) care, particularly in Addis Ababa, which has been most acutely affected by the virus. However, the decline does not come at the cost of MCH services. The use of several MCH components (skilled birth attendant deliveries, immunization, post-natal care) remains unaffected throughout the period while others (family planning services, ante-natal care) experience a decline (8-17%) in the immediate aftermath but recover soon after.\n\nConclusionConcerns about the crowding out of MCH services due to the focus on Covid 19 are unfounded. Pro-active measures taken by the government and health care facilities to ring-fence the use of essential health care services have mitigated service disruptions. The results underline the resilience and agility displayed by one of the worlds most resource-constrained health care systems.\n\nO_TEXTBOXSummary BoxO_ST_ABSWhat is already known?C_ST_ABSO_LISimulation studies suggest sharp increases in unwanted pregnancies, and in maternal and child mortality due to Covid related disruptions in the provision of mother and child health care services.\nC_LIO_LIEvidence on whether such service disruptions have indeed occurred is limited.\nC_LI\n\nWhat are the new findings?O_LIBased on retrospective health facility data collected from parts of Ethiopia that have been most acutely affected by Covid, we find that for most MCH services, disruption is temporary and rebounds to pre-covid levels within two months.\nC_LI\n\nWhat do the new findings imply?O_LIConcerns about the crowding out of MCH services due to the focus on Covid seem to be unfounded.\nC_LIO_LIPro-active measures taken by the government and health care facilities to adapt and to ring-fence the use of essential health care services have mitigated service disruptions.\nC_LIO_LIDespite resource-constraints it is possible to protect the provision of essential health care services and thereby hard-won gains in maternal and child health outcomes\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zemzem Shigute Shuka", + "author_inst": "Erasmus University Rotterdam and Addis Ababa University" + }, + { + "author_name": "Anagaw Derseh Mebratie", + "author_inst": "Addis Ababa University" + }, + { + "author_name": "Getnet Alemu", + "author_inst": "Addis Ababa University" + }, + { + "author_name": "Matthias Rieger", + "author_inst": "Erasmus University Rotterdam" + }, + { + "author_name": "Arjun Singh Bedi", + "author_inst": "Erasmus University Rotterdam" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.08.09.21261277", "rel_title": "Impacts of Regional Lockdown Policies on COVID-19 Transmission in India in 2020", @@ -606326,45 +605009,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.10.455702", - "rel_title": "Infectious SARS-CoV-2 is emitted in aerosols", - "rel_date": "2021-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455702", - "rel_abs": "Respiratory viruses such as SARS-CoV-2 are transmitted in respiratory droplets and aerosols, which are released during talking, breathing, coughing, and sneezing. Non-contact transmission of SARS-CoV-2 has been demonstrated, suggesting transmission in aerosols. Here we demonstrate that golden Syrian hamsters emit infectious SARS-CoV-2 in aerosols, prior to and concurrent with the onset of mild clinical signs of disease. The average emission rate is 25 infectious virions/hour on days 1 and 2 post-inoculation, with average viral RNA levels 200-fold higher than infectious virus in aerosols. Female hamsters have delayed kinetics of viral shedding in aerosols compared to male hamsters, with peak viral emission for females on dpi 2 and for males on dpi 1. The majority of virus is contained within aerosols <8 {micro}m in size. Thus, we provide direct evidence that, in hamsters, SARS-CoV-2 is an airborne virus.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Seth A. Hawks", - "author_inst": "Virginia Polytechnic Institute and State University" - }, - { - "author_name": "Aaron J. Prussin", - "author_inst": "Virginia Polytechnic Institute and State University" - }, - { - "author_name": "Sarah C. Kuchinsky", - "author_inst": "Virginia Polytechnic Institute and State University" - }, - { - "author_name": "Jin Pan", - "author_inst": "Virginia Polytechnic Institute and State University" - }, - { - "author_name": "Linsey C. Marr", - "author_inst": "Virginia Polytechnic Institute and State University" - }, - { - "author_name": "Nisha K. Duggal", - "author_inst": "Virginia Polytechnic Institute and State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.10.455799", "rel_title": "Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences", @@ -607205,6 +605849,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.06.21261689", + "rel_title": "Internet Use impact on Physical Health during COVID-19 pandemic in Bangladesh: A Web-based Cross-sectional study", + "rel_date": "2021-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261689", + "rel_abs": "BackgroundBangladesh ranked fifth largest internet user in Asia. Past studies on internet use have focused on its impact on mental health, with little known about its impact on the physical health of individuals during COVID-19 pandemic. Hence, this study examines the impact of Internet use frequency on physical health during the Covid-19 lockdown in Bangladesh.\n\nMethodsA web-based cross-sectional study on 3242 individuals aged 18 and above was conducted from 2nd August - 1st October 1, 2020, during the lockdown in Bangladesh. The survey covers demographics, Internet use frequency and physical health questions. Multiple linear regression analyses were used to examine the impact of internet use frequency on physical health.\n\nResultsThe result indicated that 72.5%, 69.9%, 65.1% and 55.3% reported headache, back pain, numbness of the fingers and neck pain, respectively. The multivariable analyses showed increased physical health impact among regular (coefficient {beta} =0.52, 95% confidence interval [CI]: 0.18-0.85, P=0.003), frequent ({beta} = 1.21, 95%CI: 0.88-1.54, P < .001) and intense ({beta} = 2.24, 95%CI: 1.91-2.57, P < .001) internet users. Other factors associated with physical health scores were gender, income (in Taka), occupation, regions, and working status.\n\nConclusionFrequent, intensive, and extensive use of the internet were strong predictors of increased physical health problems, and the study suggests the need for raising awareness of physical health problems triggered by high internet users among the high socioeconomic group in Bangladesh.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "TANVIR FITTIN ABIR", + "author_inst": "International University of Business Agriculture and Technology, Bangladesh" + }, + { + "author_name": "Uchechukwu Levu Osuagwu", + "author_inst": "Western Sydney University, Australia" + }, + { + "author_name": "Dewan Muhammad Nur -A Yazdani", + "author_inst": "International University of Business, Agriculture and Technology, Bangladesh" + }, + { + "author_name": "Abdullah Al Mamun Al Mamun", + "author_inst": "UCSI University, Kuala Lumpur 56000, Malaysia" + }, + { + "author_name": "Kaniz Kakon", + "author_inst": "International University of Business Agriculture and Technology, Bangladesh" + }, + { + "author_name": "Anas A. Salamah", + "author_inst": "Prince Sattam Bin Aziz University, Saudi Arabia" + }, + { + "author_name": "Noor Raihani Zainol", + "author_inst": "Universiti Malaysia Kelantan, Malaysia" + }, + { + "author_name": "Mansura Khanam", + "author_inst": "icddr,b Bangladesh" + }, + { + "author_name": "Kingsley Emwinyore Agho", + "author_inst": "Western Sydney University, Australia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.08.21261766", "rel_title": "Immunogenicity of BNT162b2 vaccine Against the Alpha and Delta Variants in Immunocompromised Patients", @@ -608412,53 +607107,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.03.454981", - "rel_title": "The emergence of highly fit SARS-CoV-2 variants accelerated by recombination", - "rel_date": "2021-08-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.03.454981", - "rel_abs": "The SARS-CoV-2 pandemic recently entered an alarming new phase with the emergence of the variants of concern (VOC) and understanding their biology is paramount to predicting future ones. Current efforts mainly focus on mutations in the spike glycoprotein (S), but changes in other regions of the viral proteome are likely key. We analyzed more than 900,000 SARS-CoV-2 genomes with a computational systems biology approach including a haplotype network and protein structural analyses to reveal lineage-defining mutations and their critical functional attributes. Our results indicate that increased transmission is promoted by epistasis, i.e., combinations of mutations in S and other viral proteins. Mutations in the non-S proteins involve immune-antagonism and replication performance, suggesting convergent evolution. Furthermore, adaptive mutations appear in geographically disparate locations, suggesting that either independent, repeat mutation events or recombination among different strains are generating VOC. We demonstrate that recombination is a stronger hypothesis, and may be accelerating the emergence of VOC by bringing together cooperative mutations. This emphasizes the importance of a global response to stop the COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Michael R Garvin", - "author_inst": "Oak Ridge National Laboratory, Computational Systems Biology, Biosciences; National Virtual Biotechnology Laboratory" - }, - { - "author_name": "Erica T Prates", - "author_inst": "Oak Ridge National Laboratory, Computational Systems Biology, Biosciences; National Virtual Biotechnology Laboratory" - }, - { - "author_name": "Jonathon Romero", - "author_inst": "The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville" - }, - { - "author_name": "Ashley Cliff", - "author_inst": "The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville" - }, - { - "author_name": "Joao Gabriel Felipe Machado Gazolla", - "author_inst": "Oak Ridge National Laboratory, Computational Systems Biology, Biosciences; National Virtual Biotechnology Laboratory" - }, - { - "author_name": "Monica Pickholz", - "author_inst": "Department of Physics, Faculty of Exact and Natural Sciences, University of Buenos Aires; Institute of Physics of Buenos Aires (IFBA), CONICET - University of B" - }, - { - "author_name": "Mirko Pavicic", - "author_inst": "Oak Ridge National Laboratory, Computational Systems Biology, Biosciences; National Virtual Biotechnology Laboratory" - }, - { - "author_name": "Daniel Jacobson", - "author_inst": "Oak Ridge National Laboratory, Computational Systems Biology, Biosciences; National Virtual Biotechnology Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.08.06.455494", "rel_title": "Broad-spectrum in vitro antiviral activity of ODBG-P-RVn: an orally-available, lipid-modified monophosphate prodrug of remdesivir parent nucleoside (GS-441524)", @@ -609327,6 +607975,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.08.06.455441", + "rel_title": "VPS29 exerts opposing effects on endocytic viral entry", + "rel_date": "2021-08-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455441", + "rel_abs": "Emerging zoonotic viral pathogens threaten global health and there is an urgent need to discover host and viral determinants influencing infection. We performed a loss-of-function genome-wide CRISPR screen in a human lung cell line using HCoV-OC43, a human betacoronavirus. One candidate gene, VPS29, was required for infection by HCoV-OC43, SARS-CoV-2, other endemic and pandemic threat coronaviruses as well as ebolavirus. However, VPS29 deficiency had no effect on certain other viruses that enter cells via endosomes and had an opposing, enhancing effect on influenza A virus infection. VPS29 deficiency caused changes endosome morphology, and acidity and attenuated the activity of endosomal proteases. These changes in endosome properties caused incoming coronavirus, but not influenza virus particles, to become entrapped therein. Overall, these data show how host regulation of endosome characteristics can influence viral susceptibility and identify a host pathway that could serve as a pharmaceutical target for intervention in zoonotic viral diseases.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Daniel Poston", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Yiska Weisblum", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Alvaro Hobbs", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Paul D Bieniasz", + "author_inst": "The Rockefeller University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.08.07.21261741", "rel_title": "SARS-CoV-2 Suppression and Early Closure of Bars and Restaurants : A Longitudinal Natural Experiment", @@ -610286,45 +608965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.08.05.21261565", - "rel_title": "COVID-19 mortality prediction model, 3C-M, built for use in resource limited settings - understanding the relevance of neutrophilic leukocytosis in predicting disease severity and mortality", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261565", - "rel_abs": "In this study, a combination of clinical and hematological information, collected on day of presentation to the hospital with pneumonia, was evaluated for its ability to predict severity and mortality outcomes in COVID-19. Ours is a retrospective, observational study of 203 hospitalized COVID-19 patients. All of them were confirmed RT-PCR positive cases. We used simple hematological parameters (total leukocyte count, absolute neutrophil count, absolute lymphocyte count, neutrophil to lymphocyte ration and platelet to lymphocyte ratio); and a severity classification of pneumonia (mild, moderate and severe) based on a single clinical parameter, the percentage saturation of oxygen at room air, to predict the outcome in these cases. The results show that a high absolute neutrophil count on day of onset of pneumonia symptoms correlated strongly with both severity and survival in COVID-19. In addition, it was the primary driver of an initial high neutrophil-to-lymphocyte ratio (NLR) observed in patients with severe disease. The effect of low lymphocyte count was not found to be very significant in our cohort. Multivariate logistic regression was done using Python 3.7 to assess whether these parameters can adequately predict survival. We found that clinical severity and a high neutrophil count on day of presentation of pneumonia symptoms could predict the outcome with 86% precision. This model is undergoing further evaluation at our centre for validation using data collected during the second wave of COVID-19. We present the relevance of an elevated neutrophil count in COVID-19 pneumonia and review the advances in research which focus on neutrophils as an important effector cell of COVID-19 inflammation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Niharika Agarwal", - "author_inst": "Lady Hardinge Medical College, Delhi, India" - }, - { - "author_name": "Devika Dua", - "author_inst": "Lady Hardinge Medical College" - }, - { - "author_name": "Ritika Sud", - "author_inst": "Lady Hardinge Medical College, Delhi, India" - }, - { - "author_name": "Madhur Yadav", - "author_inst": "Lady Hardinge Medical College, Delhi, India" - }, - { - "author_name": "Aparna Agarwal", - "author_inst": "Lady Hardinge Medical College, Delhi, India" - }, - { - "author_name": "Vijesh Vijayan", - "author_inst": "Lady Hardinge Medical Colege, Delhi, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21261660", "rel_title": "Rapid antigen testing for SARS-CoV-2 infection in a university setting in Ireland: learning from a 6-week pilot study.", @@ -611157,6 +609797,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.06.21261711", + "rel_title": "Preterm birth rates during the COVID-19 lockdown in Queensland Australia", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261711", + "rel_abs": "BackgroundPreventative strategies for preterm birth are lacking. Recent evidence proposed COVID-19 lockdowns may have contributed to changes in preterm birth. We aimed to determine the prevalence of preterm birth during the COVID-19 lockdown on the Sunshine Coast and in the state of Queensland, Australia.\n\nMethodsRetrospective cohort analysis of all births in Queensland including the Sunshine Coast University Hospital, during two epochs, April 1-May 31, 2020 (lockdown) and June 1-July 31, 2020 (post-lockdown), compared to antecedent calendar-matched periods in 2018-2019. Prevalence of preterm birth, stillbirth, and late terminations were examined.\n\nResultsThere were 64,989 births in Queensland from April to July 2018-2020. At the Sunshine Coast University Hospital, there was a significantly higher chance of birth at term during both lockdown (OR 1.81, 95% CI 1.17, 2.79; P=0.007) and post-lockdown (OR 2.01, 95% CI 1.27, 3.18; P=0.003). At the same centre, prevalence of preterm birth was 5.5% (30/547) during lockdown, compared to 9.1% (100/1095) in previous years, a 40.0% relative reduction (P=0.016). At this centre during lockdown, emergency caesareans concurrently decreased (P=0.034) and vacuum-assisted births increased (P=0.036). In Queensland overall, there was a nonsignificant decrease in the prevalence of preterm birth during lockdown.\n\nConclusionsThere is a link between lockdown and a reduction in the prevalence of preterm birth on the Sunshine Coast. The cause is speculative. Further research is needed to determine a causal link and assess if this can be translated into management which provides a sustained reduction in preterm birth and its associated morbidity and mortality.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Brittany Jasper", + "author_inst": "School of Medicine, Griffith University, Queensland, Australia; North West Anglia Healthcare NHS Trust, Cambridgeshire, United Kingdom; 3Department of Obstetric" + }, + { + "author_name": "Tereza Stillerova", + "author_inst": "School of Medicine, Griffith University, Queensland, Australia; 3Department of Obstetrics and Gynaecology, Sunshine Coast University Hospital, Queensland, Austr" + }, + { + "author_name": "Christopher Anstey", + "author_inst": "School of Medicine, Griffith University, Queensland, Australia; Faculty of Medicine, University of Queensland, Queensland, Australia" + }, + { + "author_name": "Edward Weaver", + "author_inst": "School of Medicine, Griffith University, Queensland, Australia; Department of Obstetrics and Gynaecology, Sunshine Coast University Hospital, Queensland, Austra" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.08.06.21261728", "rel_title": "Trends in accident-related admissions to pediatric intensive care units during the first COVID-19 lockdown in Germany", @@ -612376,53 +611047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.03.21261377", - "rel_title": "Building knowledge of university campus population dynamics to enhance near-to-source sewage surveillance for SARS-CoV-2 detection", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261377", - "rel_abs": "Wastewater surveillance has been widely implemented for monitoring of SARS-CoV-2 during the global COVID-19 pandemic, and near-to-source monitoring is of particular interest for outbreak management in discrete populations. However, variation in population size poses a challenge to the triggering of public health interventions using wastewater SARS-CoV-2 concentrations. This is especially important for near-to-source sites that are subject to significant daily variability in upstream populations. Focusing on a university campus in England, this study investigates methods to account for variation in upstream populations at a site with highly transient footfall and provides a better understanding of the impact of variable populations on the SARS-CoV-2 trends provided by wastewater-based epidemiology. The potential for complementary data to help direct response activities within the near-to-source population is also explored, and potential concerns arising due to the presence of heavily diluted samples during wet weather are addressed. Using wastewater biomarkers, it is demonstrated that population normalisation can reveal significant differences between days where SARS-CoV-2 concentrations are very similar. Confidence in the trends identified is strongest when samples are collected during dry weather periods; however, wet weather samples can still provide valuable information. It is also shown that building-level occupancy estimates based on complementary data aid identification of potential sources of SARS-CoV-2 and can enable targeted actions to be taken to identify and manage potential sources of pathogen transmission in localised communities.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Chris Sweetapple", - "author_inst": "University of Exeter" - }, - { - "author_name": "Peter Melville-Shreeve", - "author_inst": "University of Exeter" - }, - { - "author_name": "Albert Chen", - "author_inst": "University of Exeter" - }, - { - "author_name": "Jasmine M. S. Grimsley", - "author_inst": "Department of Health and Social Care" - }, - { - "author_name": "Joshua T. Bunce", - "author_inst": "Department of Health and Social Care" - }, - { - "author_name": "William Gaze", - "author_inst": "University of Exeter" - }, - { - "author_name": "Sean Fielding", - "author_inst": "University of Exeter" - }, - { - "author_name": "Matthew John Wade", - "author_inst": "Department of Health and Social Care" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.04.21261332", "rel_title": "Temporal considerations in the 2021 COVID-19 lockdown of Ho Chi Minh City", @@ -613003,6 +611627,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.01.21261309", + "rel_title": "Multiple-time measurements of multidimensional psychiatric states from immediately before the COVID-19 pandemic to one year later: A longitudinal online survey of the Japanese population", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.01.21261309", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has profoundly affected the mental health of both infected and uninfected people. Although most psychiatric disorders have highly overlapping genetic and pathogenic backgrounds, most studies investigating the impact of the pandemic have examined only single psychiatric disorders. It is necessary to examine longitudinal trajectories of factors that modulate psychiatric states across multiple dimensions. 2274 Japanese citizens participated in online surveys presented in December 2019 (before the pandemic), August 2020, Dec 2020, and April 2021. These surveys included nine questionnaires on psychiatric symptoms, such as depression and anxiety. Multi-dimensional psychiatric time series data were then decomposed into four principal components. We used generalized linear models to identify modulating factors for effects of the pandemic on these components. The four principal components can be interpreted as general psychiatric burden, social withdrawal, alcohol-related problems, and depression/anxiety. Principal components associated with general psychiatric burden and depression/anxiety peaked during the initial phase of the pandemic. They were further exacerbated by the economic burden of the pandemic. In contrast, principal components associated with social withdrawal showed a delayed peak, with human relationships as an important risk modulating factor. In addition, being elderly and female were risk factors shared across all components. Our results show that COVID-19 has imposed a large and varied burden on the Japanese population since the commencement of the pandemic. Although components related to the general psychiatric burden remained elevated, peak intensities differed between components related to depression/anxiety and those related to social anxiety. These results underline the importance of using flexible monitoring and mitigation strategies for mental problems, according to the phase of the pandemic.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Taiki Oka", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Takatomi Kubo", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Nao Kobayashi", + "author_inst": "KDDI CORPORATION" + }, + { + "author_name": "Fumiya Nakai", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Yuka Miyake", + "author_inst": "KDDI CORPORATION" + }, + { + "author_name": "Toshitaka Hamamura", + "author_inst": "Innovation center KDDI Research, Inc" + }, + { + "author_name": "Masaru Honjo", + "author_inst": "Innovation center KDDI Research, Inc" + }, + { + "author_name": "Hiroyuki Toda", + "author_inst": "National Defense Medical College" + }, + { + "author_name": "Shuken Boku", + "author_inst": "Kumamoto University Faculty of Life Sciences" + }, + { + "author_name": "Tetsufumi Kanazawa", + "author_inst": "Osaka Medical College" + }, + { + "author_name": "Masanori Nagamine", + "author_inst": "National Defense Medical College Research Institute" + }, + { + "author_name": "Aurelio Cortese", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Minoru Takebayashi", + "author_inst": "Kumamoto University Faculty of Life Sciences" + }, + { + "author_name": "Mitsuo Kawato", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Toshinori Chiba", + "author_inst": "Advanced Telecommunications Research Institute International" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.07.30.21261386", "rel_title": "Characterising COVID-19 empirical research production in Latin America and the Caribbean: a scoping review", @@ -614654,41 +613353,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.08.03.21261567", - "rel_title": "Challenges in Tracking the Risk of COVID-19 in Bangladesh: Evaluation of A Novel Method", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261567", - "rel_abs": "Identifying actual risk zones in a country where the overall test positive rate (TPR) is higher than 5% is crucial to contain the pandemic. However, TPR-based risk zoning methods are debatable since they do not consider the rate of infection in an area and thus, it has been observed to overestimate the risk. Similarly, the rate of infection in an area has been noticed to underestimate the risk of COVID-19 spreading for the zones with higher TPR. In this article, we discuss the shortcomings of currently available risk zoning methods that are followed in the lower-middle-income countries (LMIC), especially in Bangladesh. We then propose to determine a risk zone by combining the rate of infection with TPR and effective reproduction number, Rt in a distinct manner from existing methods. We evaluate the efficacy of the proposed method with respect to the mass-movement events and show its application to track the evolution of COVID-19 pandemic by identifying the risk zones over time. Demo website for the visualization of the analysis can be found at: http://erdos.dsm.fordham.edu:3000\n\nCCS CONCEPTSO_LIApplied computing [->] Health informatics.\nC_LI\n\nACM Reference FormatMd. Enamul Hoque, Md. Shariful Islam, Arnab Sen Sharma, Rashedul Islam, and Mohammad Ruhul Amin. 2021. Challenges in Tracking the Risk of COVID-19 in Bangladesh: Evaluation of A Novel Method. In Proceedings of August 15 (KDD Workshop on Data-driven Humanitarian Mapping, 27th ACM SIGKDD Conference). ACM, New York, NY, USA, 7 pages.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Enamul Hoque", - "author_inst": "Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh" - }, - { - "author_name": "Md Shariful Islam", - "author_inst": "Dapartment of Mathematics and Physics, North South University, Dhaka, Bangladesh" - }, - { - "author_name": "Arnab Sen Sharma", - "author_inst": "Department of CSE, Shahjalal University of Science and Technology, Sylhet, Bangladesh" - }, - { - "author_name": "Rashedul Islam", - "author_inst": "Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Mohammad Ruhul Amin", - "author_inst": "Department of Computer and Information Sciences, Fordham University, New York, New York, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.02.21261500", "rel_title": "Temporal Geospatial Analysis of COVID-19 Pre-infection Determinants of Risk in South Carolina", @@ -615273,6 +613937,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.03.21261545", + "rel_title": "Domestic and international mobility trends in the United Kingdom during the COVID-19 pandemic: An analysis of Facebook data", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261545", + "rel_abs": "Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which resulted in changes to mobility across different regions. An understanding of how these policies impacted travel patterns over time and at different spatial scales is important for designing effective strategies, future pandemic planning and in providing broader insights on the population geography of the country. Crowd level data on mobile phone usage can be used as a proxy for population mobility patterns and provide a way of quantifying in near-real time the impact of social distancing measures on changes in mobility. Here we explore patterns of change in densities, domestic and international flows and co-location of Facebook users in the UK from March 2020 to March 2021. We find substantial heterogeneities across time and region, with large changes observed compared to pre-pandemic patterns. The impacts of periods of lockdown on distances travelled and flow volumes are evident, with each showing variations, but some significant reductions in co-location rates. Clear differences in multiple metrics of mobility are seen in central London compared to the rest of the UK, with each of Scotland, Wales and Northern Ireland showing significant deviations from England at times. Moreover, the impacts of rapid changes in rules on international travel to and from the UK are seen in substantial fluctuations in traveller volumes by destination. While questions remain about the representativeness of the Facebook data, previous studies have shown strong correspondence with census-based data and alternative mobility measures, suggesting that findings here are valuable for guiding strategies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Harry E.R. Shepherd", + "author_inst": "University of Southampton" + }, + { + "author_name": "Florence S. Atherden", + "author_inst": "University of Southampton" + }, + { + "author_name": "Ho Man Theophilus Chan", + "author_inst": "University of Southampton" + }, + { + "author_name": "Alexandra Loveridge", + "author_inst": "University of Southampton" + }, + { + "author_name": "Andrew J Tatem", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.03.21261518", "rel_title": "Prospective cohort study of socioeconomic status and subsequent unemployment under COVID-19 in Japan", @@ -616448,73 +615147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.02.21261095", - "rel_title": "SARS-CoV-2-specific Humoral and Cell-mediated Immune Responses after Immunization with Inactivated COVID-19 Vaccine in Kidney Transplant Recipients (CVIM 1 Study)", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261095", - "rel_abs": "Immunogenicity following inactivated SARS-CoV-2 vaccination among solid organ transplant recipients has not been assessed. Seventy-five patients (37 kidney transplant [KT] recipients and 38 non-transplant controls) received two doses, at 4-week intervals, of an inactivated whole-virus SARS-CoV-2 vaccine. SARS-CoV-2-specific humoral (HMI) and cell-mediated immunity (CMI) were measured before, 4 weeks post-first dose, and 2 weeks post-second dose. The median age of KT recipients was 50 years (IQR, 42-54) and 89% were receiving calcineurin inhibitors/mycophenolate/corticosteroid regimens. The median time since transplant was 4.5 years (IQR, 2-9.5). Among 35 KT patients, anti-RBD IgG titer after vaccination was not significantly different to baseline, but was significantly lower than in controls (7.8 [95%CI 0.2-15.5] vs 2,691 [95%CI 1,581-3,802], p<0.001) as well as the percentage of surrogate virus neutralizing antibody inhibition (2 [95% CI -1-6] vs 71 [95%CI 61-81], p<0.001). However, the mean of SARS-CoV-2 mixed peptides-specific T-cell responses measured by enzyme-linked immunospot assays was significantly increased compared with baseline (66 [95%CI 36-99] vs. 34 [95%CI 19-50] T-cells/106 PBMCs, p=0.02) and comparable to that in controls. Our findings revealed weak HMI and marginal CMI responses in fully vaccinated KT recipients receiving inactivated SARS-CoV-2 vaccine. (Thai Clinical Trials Registry, TCTR20210226002).", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jackrapong Bruminhent", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Chavachol Sethaudom", - "author_inst": "Immunology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Pongsathon Chaumdee", - "author_inst": "4Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Sarinya Boongird", - "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Sasisopin Kiertiburanakul", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Kumthorn Malathum", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Arkom Nongnuch", - "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Angsana Phuphuakrat", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Sopon Jirasiritham", - "author_inst": "Division of Vascular and Transplant Surgery, Department of Surgery, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Chitimaporn Janphram", - "author_inst": "Somdech Phra Debaratana Medical Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Sansanee Thotsiri", - "author_inst": "Somdech Phra Debaratana Medical Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Supparat Upama", - "author_inst": "Samitivej Hospital Sukhumvit, Bangkok, Thailand" - }, - { - "author_name": "Montira Assanatham", - "author_inst": "Division of Nephrology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.02.21261479", "rel_title": "Tear antibodies to SARS-CoV-2: implications for transmission", @@ -617443,6 +616075,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.31.21261422", + "rel_title": "COVID-19 Mortality in Women and Men in Sub-Saharan Africa: A Cross Sectional Study", + "rel_date": "2021-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.31.21261422", + "rel_abs": "ObjectiveTo investigate differences of COVID-19 related mortality among women and men across sub-Saharan Africa (SSA) from the beginning of the pandemic.\n\nDesignA cross sectional study.\n\nSettingData from 20 member nations of the WHO African region until September 1, 2020.\n\nParticipants69,580 cases of COVID-19, stratified by sex (men, n=43071; women, n=26509) and age (0-39 years, n=41682; 40-59 years, n=20757; 60+ years, n=7141).\n\nMain outcome measuresWe computed the SSA- and country-specific case fatality rates (CFRs) and sex-specific CFR differences across various age groups, using a Bayesian approach.\n\nResultsA total of 1,656 (2.4% of total cases reported; 1656/69580) deaths were reported, with men accounting for 1168/1656 (70.5%) of total deaths. In SSA, women had a lower CFR than men (mean CFRdiff = -0.9%; 95% credible intervals -1.1% to -0.6%). The mean CFR estimates increased with age, with the sex-specific CFR differences being significant among those aged 40 or more (40-59 age-group: mean CFRdiff = -0.7%; 95% credible intervals -1.1% to -0.2%; 60+ age-group: mean CFRdiff = -3.9%; 95% credible intervals -5.3% to -2.4%). At the country level, seven of the twenty SSA countries reported significantly lower CFRs among women than men overall. Moreover, corresponding to the age-specific datasets, significantly lower CFRs in women than men were observed in the 60+ age-group in seven countries and 40-59 age-group in one country.\n\nConclusions>Sex and age are important predictors of COVID-19 mortality. Countries should prioritize the collection and use of sex-disaggregated data to understand the evolution of the pandemic. This is essential to design public health interventions and ensure that policies promote a gender sensitive public health response.\n\nSummary BoxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LILittle is known on the impact of COVID-19 among different sexes and age-groups in sub-Saharan Africa (SSA).\nC_LIO_LIThe availability of data on COVID-19 cases and deaths, disaggregated by both age and sex from the WHO African region has been scarce.\nC_LIO_LIIn most of the non-African countries, sex-specific COVID-19 severity and mortality were substantially worse for men than for women, during the first wave of the novel coronavirus (COVID-19) pandemic.\nC_LI\n\nWhat this study addsO_LITo the best of our knowledge, this is the largest study focussing on the COVID-19 related fatalities among men and women in SSA, and it confirmed that both sex and age are important predictors of COVID-19 mortality in SSA, similar to other regions.\nC_LIO_LIIn SSA, overall, men had a higher case fatality rate (CFR) than women. When disaggregated by age, this difference persisted only in individuals aged 40 or more. 7 among the 20 SSA countries included in this study also reported significantly higher CFRs in men than women for the age-aggregated dataset.\nC_LIO_LIPublic health prevention activities and responses should take into account gender differences in terms of disease severity and mortality, especially among men aged 40 or more in SSA.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jyoti Dalal", + "author_inst": "The GRAPH Network" + }, + { + "author_name": "Isotta Triulzi", + "author_inst": "Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy" + }, + { + "author_name": "Ananthu James", + "author_inst": "Indian Institute of Science, Bangalore" + }, + { + "author_name": "Benedict Nguimbis", + "author_inst": "Data analysis, The GRAPH Network (https://thegraphnetwork.org), Geneve, Switzerland" + }, + { + "author_name": "Gabriela Guizzo Dri", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Akarsh Venkatasubramanian", + "author_inst": "International Labour Organization, United Nations, Geneva, Switzerland" + }, + { + "author_name": "Noubi Tchoupopnou Royd Lucie", + "author_inst": "Health Systems Strengthening and Development Group Center, Yaounde, Cameroon" + }, + { + "author_name": "Sara Botero Mesa", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Claire Somerville", + "author_inst": "The Gender Centre, Graduate of Institute of International and Development Studies, Geneva, Switzerland" + }, + { + "author_name": "Giuseppe Turchetti", + "author_inst": "Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy" + }, + { + "author_name": "Beat Stoll", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Jessica Lee Abbate", + "author_inst": "UMI TransVIHMI (Institut de Recherche pour le Developpement, Institut National de la Sante et de la Recherche Medicale, Universite de Montpellier), Montpellier," + }, + { + "author_name": "Franck Mboussou", + "author_inst": "World Health Organization Regional Office for Africa, Brazzaville, Congo" + }, + { + "author_name": "Benido Impouma", + "author_inst": "World Health Organization Regional Office for Africa, Brazzaville, Congo" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" + }, + { + "author_name": "Flavio Codeco Coelho", + "author_inst": "School of Applied Mathematics, Getulio Vargas Foundation, Rio de Janeiro, Brazil" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.29.21261348", "rel_title": "Thrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2: a population-based cohort analysis", @@ -618462,45 +617173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.30.21261329", - "rel_title": "The association between statin and COVID-19 adverse outcomes: National COVID-19 cohort in South Korea", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261329", - "rel_abs": "BackgroundThere currently exists limited and conflicting clinical data on the use of statins amongst COVID-19 patients. Given the both paucity and lack of consensus among data on statins efficacy and safety amongst COVID-19 patients, the current guideline is to continue statin in COVID-19 patients, who have previously been treated with statins. The aim of this paper was to compare hospitalized patients with COVID-19 who did and did not receive statins, in terms of COVID-19 outcomes.\n\nMethodsWe conducted population-based retrospective study using South Koreas nationwide healthcare database as of May 15 2020. We identified 4,349 patients hospitalized with COVID-19 and aged 40 years or older. The cohort entry was defined as the date of hospitalization. Statin users were individuals with inpatient and outpatient prescription records of statins in the 240 days before cohort entry, and non-users were those without such records during this period. Our primary outcome was a composite endpoint of all-cause death, intensive care unit (ICU) admission, mechanical ventilation use and cardiovascular outcomes (myocardial infarction (MI), transient cerebral ischemic attacks (TIA) or stroke). We conducted inverse probability of treatment weighting (IPTW)-adjusted logistic regression analysis to estimate odds ratio (OR) and corresponding 95% confidence intervals (CI), to compare outcomes between statin users and non-users.\n\nFindings1,115 patients were statin users (mean age = 65.9 years; 60% female), and 3,234 were non-users (mean age = 58.3 years; 64% female). Statin use was not associated with increased risk of the primary outcome (IPTW OR 0.82; 95% CI: 0.60-1.11). Subgroup analysis showed a protective role of statins, for individuals with hypertension (IPTW OR 0.40; 95% CI: 0.23-0.69, p for interaction: 0.0087).\n\nInterpretationGiven that statins are not detrimental and that it may be beneficial amongst hypertensive patients and relatively cheap, we would encourage further investigation into statin for the prevention and treatment of COVID-19.\n\nFundingYGCs work was partially supported by 2020R1G1A1A01006229 awarded by the National Research Foundation of Korea.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere is limited and conflicting data reporting on statin use among COVID-19 patients, and its association with COVID-19 outcomes\n\nAdded value of this studyWe report no difference in COVID-19 outcomes between patients who used and did not use statins prior to COVID-19 diagnosis, except in hypertensive patients in which statins was shown to have a protective effect.\n\nImplications of all the available evidenceAs statins are not detrimental and relatively cheap, we encourage further investigation into statin for the prevention and treatment of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ronald Chow", - "author_inst": "Hanyang Impact Science Research Center, Seoul, South Korea" - }, - { - "author_name": "Jihui Lee", - "author_inst": "Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Hyerim Noh", - "author_inst": "Department of Statistics, Sookmyung Women's University, Seoul, South Korea" - }, - { - "author_name": "Jongseong Lee", - "author_inst": "School of Social Work, Columbia University, New York, NY, USA" - }, - { - "author_name": "Hyun Joon Shin", - "author_inst": "Division of Cardiology, Department of Medicine, Lemuel Shattuck Hospital, Massachusetts Department of Public Health, Jamaica Plains, MA, USA" - }, - { - "author_name": "Young-Geun Choi", - "author_inst": "Department of Statistics, Sookmyung Women's University, Seoul, South Korea" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.29.21261006", "rel_title": "Association of E484K and L452R spike protein mutations with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021", @@ -619369,6 +618041,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.28.21261261", + "rel_title": "Predictors of COVID-19 vaccination uptake and reasons for decline of vaccination: a systematic review", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261261", + "rel_abs": "BackgroundVarious COVID-19 vaccines with proven safety and effectiveness are available now but vaccine hesitancy remains a public threat. COVID-19 vaccines uptake appears to have an essential role in the successful control of the COVID-19 pandemic.\n\nObjectiveTo examine predictors of COVID-19 vaccination uptake and reasons for decline of vaccination.\n\nMethodsWe followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines for this systematic review. We searched Medline, PubMed, Web of Science, Scopus, ProQuest, CINAHL, and a pre-print service (medRxiv) from inception to July 12, 2021. We used the following key-words: vaccin*, COVID-19, and uptake. We included all types of studies (quantitative, qualitative, and mixed methods) reporting COVID-19 vaccination uptake. The review protocol was registered with PROSPERO (CRD42021267460).\n\nResultsTwelve studies met the inclusion and exclusion criteria. COVID-19 vaccination uptake ranged from 28.6% to 98% in the general population, while among healthcare workers ranged from 33.3% to 94.5%, and among patients ranged from 36% to 80%. The main predictors of COVID-19 vaccination uptake were male gender, white race, older age, higher socioeconomic status, higher self-perceived COVID-19 vulnerability, increased information about COVID-19 vaccines, and chronic illness. The most important reasons for decline of vaccination were concerns about the safety and effectiveness of vaccines, illness, medication, pregnancy, fertility, breastfeeding, religious reasons, ethical reasons, previous COVID-19 diagnosis, self-estimation that COVID-19 is not a severe disease, and limited knowledge about the vaccines.\n\nConclusionsSeveral factors affect COVID-19 vaccination uptake, while various reasons affect peoples decision to refuse to take a COVID-19 vaccine. These findings are essential to further enhance our understanding of COVID-19 vaccination uptake and design specific interventions. Given the high prevalence of COVID-19 vaccine hesitancy, our findings have major implications for the delivery of COVID-19 vaccination programmes in the public with special attention to people who are undecided or unlikely to take a COVID-19 vaccine.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Petros A Galanis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Irene Vraka", + "author_inst": "P & A Kyriakou Children's Hospital" + }, + { + "author_name": "Olga Siskou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Olympia Konstantakopoulou", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Aglaia Katsiroumpa", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Daphne Kaitelidou", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.27.21261163", "rel_title": "COVID-19 outcomes in hospitalized puerperal, pregnant, and neither pregnant nor puerperal women: a population study", @@ -620556,173 +619267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.07.27.21261150", - "rel_title": "Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261150", - "rel_abs": "Uruguay was able to control the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein we analyzed the country-wide genetic diversity of SARS-CoV-2 between November, 2020 and April, 2021. Our findings identified that the most prevalent viral variant during late 2020 was a B.1.1.28 sublineage carrying mutations Q675H+Q677H in the viral Spike, now designated as lineage P.6. This new lineage P.6 probably arose around November 2020, in Montevideo, Uruguays capital department and rapidly spread to other Uruguayan departments, with evidence of further local transmission clusters, also spread sporadically to the USA and Spain. The Q675H and Q677H mutations are in the proximity of the polybasic cleavage site at the S1/S2 boundary and also arose independently in many SARS-CoV-2 lineages circulating worldwide. Although the lineage P.6 was replaced by the Variant of Concern (VOC) P.1 as the predominant viral strain in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H+Q677H in VOCs should be of worldwide interest.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Natalia Rego", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Cecilia Salazar", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Mercedes Paz", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Alicia Costabile", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Alvaro Fajardo", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Ignacio Ferres", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Paula Perbolianachis", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Tamara Fernandez-Calero", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Veronica Noya", - "author_inst": "Sanatorio Americano" - }, - { - "author_name": "Rodrigo Arce", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Mailen Arleo", - "author_inst": "Sanatorio Americano" - }, - { - "author_name": "Tania Possi", - "author_inst": "Sanatorio Americano" - }, - { - "author_name": "Natalia Reyes", - "author_inst": "Sanatorio Americano" - }, - { - "author_name": "Maria Noel Bentancor", - "author_inst": "Sanatorio Americano" - }, - { - "author_name": "Andres Lizasoain", - "author_inst": "CENUR Litoral Norte, Universidad de la Republica, Salto, Uruguay" - }, - { - "author_name": "Viviana Bortagaray", - "author_inst": "CENUR Litoral Norte, Universidad de la Republica, Salto, Uruguay" - }, - { - "author_name": "Ana Moller", - "author_inst": "CENUR Litoral Norte, Universidad de la Republica, Salto, Uruguay" - }, - { - "author_name": "Odhille Chappos", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Nicolas Nin", - "author_inst": "Hospital Espanol, Uruguay" - }, - { - "author_name": "Javier Hurtado", - "author_inst": "Hospital Espanol, Uruguay" - }, - { - "author_name": "Melissa Duquia", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Belen Gonzalez", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Luciana Griffero", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Mauricio Mendez", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Maria Pia Techera", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Juan Zanetti", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay." - }, - { - "author_name": "Bernardina Rivera", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Matias Maidana", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Martina Alonso", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Cecilia Alonso", - "author_inst": "Centro Universitario Regional Este, Universidad de la Republica, Rocha, Uruguay" - }, - { - "author_name": "Julio Medina", - "author_inst": "Facultad de Medicina, Universidad de la Republica, Uruguay" - }, - { - "author_name": "Henry Albornoz", - "author_inst": "Facultad de Medicina, Universidad de la Republica, Uruguay" - }, - { - "author_name": "Rodney Colina", - "author_inst": "CENUR Litoral Norte, Universidad de la Republica, Salto, Uruguay" - }, - { - "author_name": "Gonzalo Bello", - "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil." - }, - { - "author_name": "Pilar Moreno", - "author_inst": "Universidad de la Republica. Institut Pasteur de Montevideo" - }, - { - "author_name": "Gonzalo Andres Moratorio", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Gregorio Iraola", - "author_inst": "Institut Pasteur de Montevideo" - }, - { - "author_name": "Lucia Spangenberg", - "author_inst": "Institut Pasteur de Montevideo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.29.21261317", "rel_title": "Correlation of SARS-CoV-2 Breakthrough Infections to Time-from-vaccine; Preliminary Study", @@ -621327,6 +619871,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.28.21261219", + "rel_title": "Effects of Various Policy Options on COVID-19 Cases in Nova Scotia including Vaccination Rollout Schedule: A Modelling Study", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261219", + "rel_abs": "BackgroundThe COVID-19 pandemic presents a significant challenge to minimize mortality and hospitalizations due to this disease. Vaccinations have begun to roll-out; however, restriction policies required during and after the rollout remain uncertain. A susceptible-exposed-infected-recovered (SEIR) model was developed for Nova Scotia, and it accounted for the provinces policy interventions, demographics, and vaccine rollout schedule.\n\nMethodsA modified SEIR model was developed to simulate the spread and outcomes from COVID-19 in Nova Scotia under different policy options. The model incorporated the age distribution and co-morbidity of the province. A system dynamics model was developed in Vensim. Several scenarios were run to determine the effects of various policy options and loosening of restrictions during and after the vaccine roll-out period.\n\nResultsWhen restrictions policy include moderate closure of businesses, restricting travel to Atlantic Canada, and the mandating of masks and physical distancing, the number of cumulative infections after 110 days was less than 120. However, if national travel was opened by July 5 2021 and there were no restrictions by September 2021, the number of active infections will peak at 6,114 by February 16 2022, and there will be a peak of 104 hospitalizations on February 16 2022. Immediate opening of travel and all restrictions on March 15, 2021 will result in 71,731 active infections by June 4 2021.\n\nDiscussionModerate restrictions will be required even after the population is fully vaccinated in order to avoid a large number of infections and hospitalizations because herd immunity is not reached due to children under 12 not being vaccinated, the efficacy of the vaccine, and the portion of the population that will choose not to be vaccinated.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Melissa Gillis", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Ahmed Saif", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Matthew Murphy", + "author_inst": "Nova Scotia Health" + }, + { + "author_name": "Noreen Kamal", + "author_inst": "Dalhousie University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.07.25.21261084", "rel_title": "Measuring odds of various COVID-19 infection prevention & control measures among the contacts traced during trace test and quarantine activities at district Quetta (An un-matched case control study).", @@ -622290,53 +620865,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.30.454063", - "rel_title": "A method for the generation of pseudotyped virus particles bearing SARS coronavirus spike protein in high yields", - "rel_date": "2021-07-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.30.454063", - "rel_abs": "The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has threatened human health and the global economy. Development of additional vaccines and therapeutics is urgently required, but such development with live virus must be conducted with biosafety level 3 confinement. Pseudotyped viruses have been widely adopted for studies of virus entry and pharmaceutical development to overcome this restriction. Here we describe a modified protocol to generate vesicular stomatitis virus (VSV) pseudotyped with SARS-CoV or SARS-CoV-2 Spike protein in high yield. We found that pseudovirions produced with the conventional transient expression system lacked coronavirus Spike protein at their surface as a result of inhibition of parental VSV infection by overexpression of this protein. Establishment of stable cell lines with an optimal expression level of coronavirus Spike protein allowed the efficient production of progeny pseudoviruses decorated with Spike protein. This improved VSV pseudovirus production method should facilitate studies of coronavirus entry and development of antiviral agents.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yoichiro Fujioka", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Sayaka Kashiwagi", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Aiko Yoshida", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Aya O. Satoh", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Mari Fujioka", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Maho Amano", - "author_inst": "Hokkaido University, Faculty of Medicine" - }, - { - "author_name": "Yohei Yamauchi", - "author_inst": "University of Bristol" - }, - { - "author_name": "Yusuke Ohba", - "author_inst": "Hokkaido University, Faculty of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.27.21261210", "rel_title": "Can Vaccine Prioritization Reduce Disparities in Covid-19 Burden for Historically Marginalized Populations?", @@ -623093,6 +621621,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.07.27.21261031", + "rel_title": "Prognostic accuracy of triage tools for adults with suspected COVID-19 in a pre-hospital setting: an observational cohort study", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261031", + "rel_abs": "Study ObjectiveTools proposed to triage patient acuity in COVID-19 infection have only been validated in hospital populations. We estimated the accuracy of five risk-stratification tools recommended to predict severe illness and compare accuracy to existing clinical decision-making in a pre-hospital setting.\n\nMethodsAn observational cohort study using linked ambulance service data for patients attended by EMS crews in the Yorkshire and Humber region of England between 18th March 2020 and 29th June 2020 was conducted to assess performance of the PRIEST tool, NEWS2, the WHO algorithm, CRB-65 and PMEWS in patients with suspected COVID-19 infection. The primary outcome was death or need for organ support.\n\nResultsOf 7549 patients in our cohort, 17.6% (95% CI:16.8% to 18.5%) experienced the primary outcome. The NEWS2, PMEWS, PRIEST tool and WHO algorithm identified patients at risk of adverse outcomes with a high sensitivity (>0.95) and specificity ranging from 0.3 (NEWS2) to 0.41 (PRIEST tool). The high sensitivity of NEWS2 and PMEWS was achieved by using lower thresholds than previously recommended. On index assessment, 65% of patients were transported to hospital and EMS decision to transfer patients achieved a sensitivity of 0.84 (95% CI 0.83 to 0.85) and specificity of 0.39 (95% CI 0.39 to 0.40).\n\nConclusionUse of NEWS2, PMEWS, PRIEST tool and WHO algorithm could improve sensitivity of EMS triage of patients with suspected COVID-19 infection. Use of the PRIEST tool would improve sensitivity of triage without increasing the number of patients conveyed to hospital.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Carl Marincowitz", + "author_inst": "(CURE), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Laura Sutton", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Tony Stone", + "author_inst": "CURE, Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Richard Pilbery", + "author_inst": "Yorkshire Ambulance Service NHS Trust" + }, + { + "author_name": "Richard Campbell", + "author_inst": "CURE, Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Ben Thomas", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Janette Turner", + "author_inst": "CURE, Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Peter Bath", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Fiona Bell", + "author_inst": "Yorkshire Ambulance Service NHS Trust" + }, + { + "author_name": "Katie Biggs", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Madina Hasan", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Frank Hopfgartner", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Suvodeep Mazumdar", + "author_inst": "Information School, University of Sheffield" + }, + { + "author_name": "Jennifer Petrie", + "author_inst": "Clinical Trials Research Unit (CTRU), Health Services Research School of Health and Related Research, University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "CURE, Health Services Research School of Health and Related Research, University of Sheffield" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.07.25.21261083", "rel_title": "Effectiveness of BNT162b2 and ChAdOx1 vaccines against symptomatic COVID-19 among Healthcare Workers in Kuwait: A retrospective cohort study", @@ -624256,141 +622859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.26.21261122", - "rel_title": "Immune responses to a single dose of the AZD1222/Covishield vaccine at 16 weeks in individuals in Sri Lanka", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261122", - "rel_abs": "IntroductionDue to limited access to vaccines, many countries have only administered a single dose of the AZD1222, while the dosage intervals have increased [≥] weeks. We sought to investigate the immunogenicity of a single dose of vaccine at [≥] 16 weeks.\n\nMethodsSARS-CoV-2 specific antibodies in 553 individuals and antibodies to the receptor binding domain (RBD) of the Wuhan virus (WT) and the variants of concern (VOCs), ACE2 receptor blocking antibodies, ex vivo and cultured IFN{gamma} T cell responses and B cell ELISpot responses were investigated in a sub-cohort.\n\nResultsThe seropositivity rates in those >70 years of age (93.7%) was not significantly different compared to other age groups (97.7 to 98.2, Pearson Chi-Square = 7.8, p-value = 0.05). The antibody titres (antibody index) significantly declined (p<0.0001) with increase in age. 18/69 (26.1%) of individuals did not have ACE2 receptor blocking antibodies, while responses to the RBD of WT (p=0.03), B.1.1.7 (p=0.04) and B.1.617.2 (p=0.02) were significantly lower in those who were >60 years. Ex vivo IFN {gamma} T cell ELISpot responses were seen in 10/66 (15.1%), while only a few expressed CD107a. However, >85% had a high frequency of cultured IFN{gamma} T cell ELISpot responses and B cell ELISpots.\n\nConclusionVirus specific antibodies were maintained at [≥] 16 weeks after receiving a single dose of AZD1222, although levels were lower to VOCs, especially in older individuals. A single dose induced a high frequency of memory T and B cell responses.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Chandima Jeewandara", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Dinuka Guruge", - "author_inst": "Colombo Municipal Council, Colombo" - }, - { - "author_name": "Pradeep Pushpakumara", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Achala Kamaladasa", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Inoka Aberathna", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Shyrar Tanussiya", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Banuri Gunasekera", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Ayesha Wijesinghe", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Osanda Dissanayaka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Heshan Kuruppu", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Thushali Ranasinghe", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Deshni Jayathilaka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Shashika Dayaratne", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Dinithi Ekanayaka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "MPDJ Jayamali", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Nayanathara Gamalath", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Anushika Mudunkotuwa", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Gayasha Somathilaka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Madushika Dissanayaka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Michael Harvie", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Thashmi Nimasha", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Deshan Madushanka", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Tibutius Jayadas", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - }, - { - "author_name": "Ruwan Wijayamuni", - "author_inst": "Colombo Municipal Council, Colombo" - }, - { - "author_name": "Lisa Schimanski", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" - }, - { - "author_name": "Tiong Tan", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford" - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Graham Ogg", - "author_inst": "MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford" - }, - { - "author_name": "Gathsaurie Neelika Malavige", - "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.07.28.21261159", "rel_title": "Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine", @@ -625351,6 +623819,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.15.21260606", + "rel_title": "The Costs and Benefits of Covid-19 Lockdowns in New Zealand", + "rel_date": "2021-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260606", + "rel_abs": "This paper considers the costs and benefits of New Zealands Covid-19 nation-wide lockdown strategy relative to pursuit of a mitigation strategy in March 2020. Using data available up to 28 June 2021, the estimated additional deaths from a mitigation strategy are 1,750 to 4,600, implying a Cost per Quality Adjusted Life Year saved by locking down in March 2020 of at least 13 times the generally employed threshold figure of $62,000 for health interventions in New Zealand; the lockdowns do not then seem to have been justified by reference to the standard benchmark. Using only data available to the New Zealand government in March 2020, the ratio is similar and therefore the same conclusion holds that the nation-wide lockdown strategy was not warranted. Looking forwards from 28 June 2021, if a new outbreak occurs that cannot be suppressed without a nation-wide lockdown, the death toll from adopting a mitigation strategy at this point would be even less than had it done so in March 2020, due to the vaccination campaign and because the period over which the virus would then inflict casualties would now be much less than the period from March 2020; this would favour a mitigation policy even more strongly than in March 2020. This approach of assessing the savings in quality adjusted life years and comparing them to a standard benchmark figure ensures that all quality adjusted life years saved by various health interventions are treated equally, which accords with the ethical principle of equity across people.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Martin Lally", + "author_inst": "Capital Financial Consultants Ltd" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.07.23.21261036", "rel_title": "Vaccines against Covid-19, venous thromboembolism, and thrombocytopenia. A population-based retrospective cohort study", @@ -626250,117 +624737,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.23.21261038", - "rel_title": "Epidemics of chikungunya, Zika, and COVID-19 reveal bias in case-based mapping", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261038", - "rel_abs": "Accurate tracing of epidemic spread over space enables effective control measures. We examined three metrics of infection and disease in a pediatric cohort (N {approx} 3,000) over two chikungunya and one Zika epidemic, and in a household cohort (N=1,793) over one COVID-19 epidemic in Managua, Nicaragua. We compared spatial incidence rates (cases/total population), infection risks (infections/total population), and disease risks (cases/infected population). We used generalized additive and mixed-effects models, Kulldorfs spatial scan statistic, and intracluster correlation coefficients. Across different analyses and all epidemics, incidence rates considerably underestimated infection and disease risks, producing large and spatially non-uniform biases distinct from biases due to incomplete case ascertainment. Infection and disease risks exhibited distinct spatial patterns, and incidence clusters inconsistently identified areas of either risk. While incidence rates are commonly used to infer infection and disease risk in a population, we find that this can induce substantial biases and adversely impact policies to control epidemics.\n\nArticle summary lineInferring measures of spatial risk from case-only data can substantially bias estimates, thereby weakening and potentially misdirecting measures needed to control an epidemic.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Fausto Andres Bustos Carrillo", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Brenda Lopez Mercado", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Jairo Carey Monterrey", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Damaris Collado", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Saira Saborio", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Tatiana Miranda", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Carlos Barilla", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Sergio Ojeda", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Nery Sanchez", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Miguel Plazaola", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Harold Suazo Laguna", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Douglas Elizondo", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Sonia Arguello", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Anna M. Gajewski", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Hannah E. Maier", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Krista Latta", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Bradley Carlson", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Josefina Coloma", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Leah Katzelnick", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Hugh Sturrock", - "author_inst": "Locational" - }, - { - "author_name": "Angel Balmaseda", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Guillermina Kuan", - "author_inst": "Sustainable Sciences Institute" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Eva Harris", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.24.21261046", "rel_title": "High throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.", @@ -627305,6 +625681,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.25.453717", + "rel_title": "ETAS(R)50 Attenuates SARS-CoV-2 Spike Protein-Induced IL-6 and IL-1\u03b2 Production by Suppressing p44/42 MAPK and Akt Phosphorylation in Murine Primary Macrophages", + "rel_date": "2021-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.25.453717", + "rel_abs": "Excessive host inflammation following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with severity and mortality in coronavirus disease 2019 (COVID-19). We recently reported that the SARS-CoV-2 spike protein S1 subunit (S1) induces pro-inflammatory responses by activating toll-like receptor 4 (TLR4) signaling in macrophages. ETAS(R)50, a standardized extract of Asparagus officinalis stem, is a unique functional food that elicits anti-photoaging effects by suppressing pro-inflammatory signaling in hydrogen peroxide- and ultraviolet B-exposed skin fibroblasts. To elucidate its potential in preventing excessive inflammation in COVID-19, we examined the effects of ETAS(R)50 on pro-inflammatory responses in S1-stimulated murine peritoneal exudate macrophages. Co-treatment of the cells with ETAS(R)50 significantly attenuated S1-induced secretion of interleukin (IL)-6 in a concentration-dependent manner without reducing cell viability. ETAS(R)50 also markedly suppressed the S1-induced transcription of IL-6 and IL-1{beta}. However, among the TLR4 signaling proteins, ETAS(R)50 did not affect the degradation of inhibitor {kappa}B, nuclear translocation of nuclear factor-{kappa}B p65 subunit, and phosphorylation of c-Jun N-terminal kinase p54 subunit after S1 exposure. In contrast, ETAS(R)50 significantly suppressed S1-induced phosphorylation of p44/42 mitogen-activated protein kinase (MAPK) and Akt. Attenuation of S1-induced transcription of IL-6 and IL-1{beta} by the MAPK kinase inhibitor U0126 was greater than that by the Akt inhibitor perifosine, and the effects were potentiated by simultaneous treatment with both inhibitors. These results suggest that ETAS(R)50 attenuates S1-induced IL-6 and IL-1{beta} production by suppressing p44/42 MAPK and Akt signaling in macrophages. Therefore, ETAS(R)50 may be beneficial in regulating excessive inflammation in patients with COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ken Shirato", + "author_inst": "Kyorin University" + }, + { + "author_name": "Jun Takanari", + "author_inst": "Amino Up Co., Ltd." + }, + { + "author_name": "Takako Kizaki", + "author_inst": "Kyorin University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.07.26.453840", "rel_title": "Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines", @@ -628488,137 +626891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.07.23.21260992", - "rel_title": "A cluster randomised trial of the impact of a policy of daily testing for contacts of COVID-19 cases on attendance and COVID-19 transmission in English secondary schools and colleges", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260992", - "rel_abs": "BackgroundSchool-based COVID-19 contacts in England are asked to self-isolate at home. However, this has led to large numbers of missed school days. Therefore, we trialled daily testing of contacts as an alternative, to investigate if it would affect transmission in schools.\n\nMethodsWe performed an open-label cluster randomised controlled trial in students and staff from secondary schools and further education colleges in England (ISRCTN18100261). Schools were randomised to self-isolation of COVID-19 contacts for 10 days (control) or to voluntary daily lateral flow device (LFD) testing for school contacts with LFD-negative contacts remaining at school (intervention). Household contacts were excluded from participation.\n\nCo-primary outcomes in all students and staff were symptomatic COVID-19, adjusted for community case rates, to estimate within-school transmission (non-inferiority margin: <50% relative increase), and COVID-19-related school absence. Analyses were performed on an intention to treat (ITT) basis using quasi-Poisson regression, also estimating complier average causal effects (CACE). Secondary outcomes included participation rates, PCR results in contacts and performance characteristics of LFDs vs. PCR.\n\nFindingsOf 99 control and 102 intervention schools, 76 and 86 actively participated (19-April-2021 to 27-June-2021); additional national data allowed most non-participating schools to be included in the co-primary outcomes. 2432/5763(42.4%) intervention arm contacts participated. There were 657 symptomatic PCR-confirmed infections during 7,782,537 days-at-risk (59.1/100k/week) and 740 during 8,379,749 days-at-risk (61.8/100k/week) in the control and intervention arms respectively (ITT adjusted incidence rate ratio, aIRR=0.96 [95%CI 0.75-1.22;p=0.72]) (CACE-aIRR=0.86 [0.55-1.34]). There were 55,718 COVID-related absences during 3,092,515 person-school-days (1.8%) and 48,609 during 3,305,403 person-school-days(1.5%) in the control and intervention arms (ITT-aIRR=0.80 [95%CI 0.53-1.21;p=0.29]) (CACE-aIRR 0.61 [0.30-1.23]). 14/886(1.6%) control contacts providing an asymptomatic PCR sample tested positive compared to 44/2981(1.5%) intervention contacts (adjusted odds ratio, aOR=0.73 [95%CI 0.33-1.61;p=0.44]). Rates of symptomatic infection in contacts were 44/4665(0.9%) and 79/5955(1.3%), respectively (aOR=1.21 [0.82-1.79;p=0.34]).\n\nInterpretationDaily contact testing of school-based contacts was non-inferior to self-isolation for control of COVID-19 transmission. COVID-19 rates in school-based contacts in both intervention and control groups were <2%. Daily contact testing is a safe alternative to home isolation following school-based exposures.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Bernadette C Young", - "author_inst": "University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Saroj Kendrick", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Chris White", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Sylvester Smith", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "George Beveridge", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Toby Nonnenmacher", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Fegor Ichofu", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Joseph Hillier", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Ian Diamond", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Emma Rourke", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Fiona Dawe", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ieuan Day", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Lisa Davies", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Paul Staite", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Andrea Lacey", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "James McCrae", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ffion Jones", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Joseph Kelly", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Urszula Bankiewicz", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Sarah Tunkel", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Richard Ovens", - "author_inst": "Deloitte MCS limited" - }, - { - "author_name": "David Chapman", - "author_inst": "Deloitte MCS limited" - }, - { - "author_name": "Peter Marks", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Nick Hicks", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Tom Fowler", - "author_inst": "Department of Health and Social Care, UK Government" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "Lucy Yardley", - "author_inst": "University of Bristol" - }, - { - "author_name": "Tim EA Peto", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.24.21261047", "rel_title": "Proxalutamide Improves Inflammatory, Immunologic, and Thrombogenic Markers in Mild-to-Moderate COVID-19 Males and Females: an Exploratory Analysis of a Randomized, Double-Blinded, Placebo-Controlled Trial Early Antiandrogen Therapy (EAT) with Proxalutamide (The EAT-Proxa Biochemical AndroCoV-Trial)", @@ -629291,6 +627563,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.22.21260972", + "rel_title": "The mystery of COVID-19 reinfections: A global systematic review and meta-analysis of 577 cases", + "rel_date": "2021-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260972", + "rel_abs": "BackgroundAs the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside reinfection and reactivation from previously recovered cases have been emerging. With newer waves and variants of COVID-19, we conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection.\n\nMethodsA comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. Quality assessment tool developed by the National Institute of Health (NIH) for assessment of case series was used. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with 95% confidence interval (CI).\n\nResultsEighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2{+/-}18.9 years with males accounting for 45.8% of the study population while 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6{+/-}48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%, respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Overall, comparable odds of symptomatic presentation and management were reported in the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with 565 patients fully recovering. Respiratory failure was the most common cause of death (7/10 deaths). Seventy-two studies were determined to be of good quality whilst nine studies were of fair quality.\n\nConclusionAs the first global-scale systematic review of its kind, our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities for devising an optimal strategy for controlling the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rubaid Azhar Dhillon", + "author_inst": "Medical College, Riphah International University, Rawalpindi, Pakistan" + }, + { + "author_name": "Mohammad Aadil Qamar", + "author_inst": "Ziauddin University, Karachi, Pakistan" + }, + { + "author_name": "Omar Irfan", + "author_inst": "Centre for Global Child Health, Hospital for Sick Children, Toronto, Canada" + }, + { + "author_name": "Jaleed Ahmed Gilani", + "author_inst": "Aga Khan University Hospital, Karachi, Pakistan" + }, + { + "author_name": "Usama Waqar", + "author_inst": "Medical College, Aga Khan University, Karachi, Pakistan" + }, + { + "author_name": "Mir Ibrahim Sajid", + "author_inst": "Aga Khan University, Karachi, Pakistan" + }, + { + "author_name": "Syed Faisal Mahmood", + "author_inst": "Section of Infectious Diseases, Aga Khan University, Karachi, Pakistan." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.22.21260755", "rel_title": "Dexamethasone 12 mg versus 6 mg for patients with COVID-19 and severe hypoxia: an international, randomized, blinded trial", @@ -631538,53 +629853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.07.22.21260760", - "rel_title": "The role of mouthwash sampling in SARS-CoV-2 diagnosis", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260760", - "rel_abs": "BackgroundThe current practice of COVID-19 diagnosis worldwide is the use of oro-nasopharyngeal (ONP) swabs. Our study aim was to explore mouthwash (MW) as an alternative diagnostic method, in light of the disadvantages of ONP swabs.\n\nMethodsCovid-19 outpatients molecular-confirmed by ONP-swab were repeatedly examined with ONP-swab and MW with normal-saline (0.9%). Other types of fluids were compared to normal-saline. The Cq values obtained with each method were compared.\n\nResultsAmong 137 pairs of ONP-swabs and MW samples, 84.6% (116/137) of ONP-swabs were positive by at least one of the genes (N, E, R). However MW detected 70.8% (97/137) of samples as positive, which means 83.6% (97/116) out of positive ONP-swabs, missing mainly Cq value>30. In both methods, the N gene was the most sensitive one. Therefore MW samples targeting N-gene, which was positive in 95/137 (69.3%), is comparable to ONP-swabs targeting E and R genes which gave equal results - 95/137 (69.3%) and 90/137 (65.7%) respectively.\n\nComparing saline MW to distilled-water gave equal results, while commercial mouth-rinsing solutions were less sensitive.\n\nConclusionsMW with normal-saline, especially when tested by N gene, can effectively detect COVID-19 patients. Furthermore, this method was not inferior when compared to R and E genes of ONP-swabs, which are common targets in many laboratories around the world.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Asaf Biber", - "author_inst": "The Center for Geographic Medicine and Tropical Diseases, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel" - }, - { - "author_name": "Dana Lev", - "author_inst": "The Center for Geographic Medicine and Tropical Diseases, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel." - }, - { - "author_name": "Yaniv Lustig", - "author_inst": "Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel." - }, - { - "author_name": "Geva Harmelin", - "author_inst": "Department of Emergency Medicine, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel." - }, - { - "author_name": "Amit Shaham", - "author_inst": "Department of Emergency Medicine, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel." - }, - { - "author_name": "Oran Erster", - "author_inst": "Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel." - }, - { - "author_name": "Eli Schwartz", - "author_inst": "The Center for Geographic Medicine and Tropical Diseases, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.22.21260854", "rel_title": "Air travel-related outbreak of multiple SARS-CoV-2 variants", @@ -632269,6 +630537,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.22.453309", + "rel_title": "A Highly Potent SARS-CoV-2 Blocking Lectin Protein", + "rel_date": "2021-07-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.22.453309", + "rel_abs": "COVID-19 pandemic effected more than 180 million people around the globe causing more than four million deaths as of July 2021. Sars-CoV-2, the new coronavirus, has been identified as the primary cause of the infection. The number of vaccinated people is increasing however prophylactic drugs are highly demanded to ensure a secure social contact. There have been a number of drug molecules repurposed to fight against Sars-CoV-2, however the proofs for the effectiveness of these drug candidates is limited. Here we demonstrated griffithsin (GRFT), a lectin protein, to block the entry of the Sars-CoV2 into the Vero6 cell lines and IFNAR-/-mouse models by attaching to spike protein of the Sars-CoV-2. Given the current mutation frequency of the Sars-CoV-2 we believe that GRFT protein-based drugs will have a high impact in preventing the transmission both on Wuhan strain as well as any other emerging variants including delta variant causing high speed spread of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Recep Erdem Ahan", + "author_inst": "Bilkent University UNAM" + }, + { + "author_name": "Alireza Hanifehnezhad", + "author_inst": "Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey" + }, + { + "author_name": "Ebru Sahin Kehribar", + "author_inst": "Bilkent University UNAM" + }, + { + "author_name": "Tuba Cigdem Oguzoglu", + "author_inst": "Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey" + }, + { + "author_name": "Katalin Foldes", + "author_inst": "Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey" + }, + { + "author_name": "Cemile Elif Ozcelik", + "author_inst": "Bilkent University UNAM" + }, + { + "author_name": "Nazlican Filazi", + "author_inst": "Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey" + }, + { + "author_name": "Sidika Oztop", + "author_inst": "Adana Dr. Turgut Noyan Medical and Research Center, Department of Immunology, Baskent University, Adana, Turkey" + }, + { + "author_name": "Sevgen Celik Onder", + "author_inst": "Faculty of Medicine, Department of Medical Pathology, Hacettepe University, Ankara, Turkey" + }, + { + "author_name": "Eray Ulas Bozkurt", + "author_inst": "UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey" + }, + { + "author_name": "Koray Ergunay", + "author_inst": "Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, Ankara, Turkey" + }, + { + "author_name": "Aykut Ozkul", + "author_inst": "Faculty of Veterinary Medicine, Department of Virology, Biotechnology Institute, Ankara University, Ankara, Turkey" + }, + { + "author_name": "Urartu Seker", + "author_inst": "Bilkent University UNAM" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.07.23.453470", "rel_title": "PDZ-containing proteins targeted by the ACE2 receptor", @@ -633440,57 +631775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.16.21260648", - "rel_title": "Surveillance of seasonal respiratory viruses among Chilean patients during the COVID-19 pandemic", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260648", - "rel_abs": "The StudySARS-CoV-2 has generated over 122 million cases worldwide. Non-pharmaceuticals interventions such as confinements and lockdowns started in Chile on March 18th 2020. In Europe, confinements and lockdowns have been accompanied by a decrease in the circulation of other respiratory viruses such as Influenza A virus(IAV), Influenza B virus(IBV) or respiratory syncytial virus(RSV) (1). Although changes in circulation patterns of respiratory viruses have been reported, limited information regarding the southern hemisphere is available where the SARS-CoV-2 pandemic merged with the winter season. We conducted viral surveillance of respiratory viruses and we evaluated their presence and establishing whether they were co-circulating with SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luis A. Alonso-Palomares", - "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Joaquin Caceres", - "author_inst": "Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA" - }, - { - "author_name": "Rodrigo Tapia", - "author_inst": "Laboratory of Emerging Viruses, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Paulina Aguilera-Cortes", - "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Santiago Valenzuela", - "author_inst": "Laboratory of Environmental Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Fernando Valiente-Echeverria", - "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Ricardo Soto-Rifo", - "author_inst": "Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Aldo Gaggero", - "author_inst": "Laboratory of Environmental Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - }, - { - "author_name": "Gonzalo P Barriga", - "author_inst": "Laboratory of Emerging Viruses, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.20.21260754", "rel_title": "Increase in ventilatory ratio indicates progressive alveolar damage and suggests poor prognosis in severe COVID-19: A single-center retrospective observational study.", @@ -634187,6 +632471,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.18.21259093", + "rel_title": "COVID-19 mortality across selected states in India: the role of age structure.", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21259093", + "rel_abs": "BackgroundMortality rates provide an opportunity to identify and act on the health system intervention for preventing deaths. Hence, it is essential to appreciate the influence of age structure while reporting mortality for a better summary of the magnitude of the epidemic.\n\nObjectivesWe described and compared the pattern of COVID-19 mortality standardized by age between selected states and India from January to November 2020.\n\nMethodsWe initially estimated the Indian population for 2020 using the decadal growth rate from the previous census (2011). This was followed by estimations of crude and age-adjusted mortality rate per million for India and the selected states. We used this information to perform indirect standardization and derive the age-standardized mortality rates for the states for comparison. In addition, we derived a ratio for age-standardized mortality to compare across age groups within the state. We extracted information regarding COVID-19 deaths from the Integrated Disease Surveillance Programme special surveillance portal up to November 16, 2020.\n\nResultsThe crude mortality rate of India stands at 88.9 per million population(118,883/1,337,328,910). Age-adjusted mortality rate (per million) was highest for Delhi (300.5) and lowest for Kerala (35.9).The age-standardized mortality rate (per million) for India is (<15 years=1.6, 15-29 years=6.3, 30-44 years=35.9, 45- 59 years=198.8, 60-74 years=571.2, [≥]75 years=931.6). The ratios for age-standardized mortality increase proportionately from 45-59 years age group across all the states.\n\nConclusionThere is high COVID-19 mortality not only among the elderly ages, but we also identified heavy impact of COVID-19 on the working population. Therefore, we recommend further evaluation of age-adjusted mortality for all States and inclusion of variables like gender, socio-economic status for standardization while identifying at-risk populations and implementing priority public health actions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mohamed Jainul Azarudeen", + "author_inst": "National Centre For Disease Control, New Delhi" + }, + { + "author_name": "Tanzin Dikid", + "author_inst": "NationalCentre For Disease Control" + }, + { + "author_name": "Karishma Kurup", + "author_inst": "South East Asia Field Epidemiology Network (Safetynet)" + }, + { + "author_name": "Khyati Aroskar", + "author_inst": "National Centre For Disease Control, New Delhi" + }, + { + "author_name": "Himanshu Chauhan", + "author_inst": "National Centre for Disease Control, New Delhi" + }, + { + "author_name": "Sudhir Kumar Jain", + "author_inst": "National Centre For Disease Control, New Delhi" + }, + { + "author_name": "Sujeet Singh", + "author_inst": "National Centre For Disease Control, New Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.18.21260555", "rel_title": "SARS-CoV-2 seroprevalence in the city of Hyderabad, India in early 2021", @@ -635642,101 +633969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260728", - "rel_title": "Antibody responses to BNT162b2 vaccination in Japan: Monitoring vaccine efficacy by measuring IgG antibodies against the receptor binding domain of SARS-CoV-2", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260728", - "rel_abs": "BACKGROUNDTo fight severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), mass vaccination has begun in many countries. To investigate the usefulness of a serological assay to predict vaccine efficacy, we analyzed the levels of IgG, IgM, and IgA against the receptor binding domain (RBD) of SARS-CoV-2 in the sera from BNT162b2 vaccinated individuals in Japan.\n\nMETHODSThis study included 219 individuals who received two doses of BNT162b2. The levels of IgG, IgM, and IgA against RBD were measured by enzyme-linked immunosorbent assay before and after the first and second vaccination, respectively. The relationship between antibody levels and several factors including age, gender, and hypertension were analyzed. Virus-neutralizing activity in sera was measured to determine the correlation with the levels of antibodies. A chemiluminescent enzyme immunoassay (CLEIA) method to measure IgG against RBD was developed and validated for the clinical setting.\n\nRESULTSThe levels of all antibody isotypes were increased after vaccination. Among them, RBD-IgG was dramatically increased after the second vaccination. The IgG levels in females were significantly higher than in males. There was a negative correlation between age and IgG levels in males. The IgG levels significantly correlated with the neutralizing activity. The CLEIA assay measuring IgG against RBD showed a reliable performance and a high correlation with neutralizing activity.\n\nCONCLUSIONSMonitoring of IgG against RBD is a powerful tool to predict the efficacy of SARS-CoV-2 vaccination and provides useful information in considering a personalized vaccination strategy for COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Hidetsugu Fujigaki", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Yasuko Yamamoto", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Takenao Koseki", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Sumi Banno", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Tatsuya Ando", - "author_inst": "Fujita Health University Hospital" - }, - { - "author_name": "Hiroyasu Ito", - "author_inst": "Fujita Health University Hospital" - }, - { - "author_name": "Takashi Fujita", - "author_inst": "Fujita Health University Hospital" - }, - { - "author_name": "Hiroyuki Naruse", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Tadayoshi Hata", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Saya Moriyama", - "author_inst": "National Institute of Infectious Diseases, Japan" - }, - { - "author_name": "Yoshimasa Takahashi", - "author_inst": "National Institute of Infectious Diseases, Japan" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases, Japan" - }, - { - "author_name": "Takahiro Murakami", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Yukihiro Yoshida", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Yo Yagura", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Takayoshi Oyamada", - "author_inst": "FUJIFILM Corporation" - }, - { - "author_name": "Masao Takemura", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Masashi Kondo", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Mitsunaga Iwata", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Kuniaki Saito", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.19.21260792", "rel_title": "Prevalence of SARS CoV-2 infection among Health Care Workers of a hybrid tertiary COVID 19 hospital in Kerala", @@ -636321,6 +634553,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.21.21260905", + "rel_title": "A Wastewater-based Epidemiology tool for COVID-19 Surveillance in Portugal", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260905", + "rel_abs": "Shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the feces and urine of infected patients and subsequent presence in wastewater has produced interest on the use of this matrix for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charite assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three COVID-19 reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. Sampling started late April 2020, during lockdown, and, for the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool for this virus, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Silvia Monteiro", + "author_inst": "Universidade Lisboa, Tecnico Lisbon" + }, + { + "author_name": "Daniela Rente", + "author_inst": "Instituto Superior Tecnico" + }, + { + "author_name": "Monica V. Cunha", + "author_inst": "Centre for Ecology, Evolution and Environmental Changes (cE3c)" + }, + { + "author_name": "Manuel Carmo Gomes", + "author_inst": "Faculdade Ciencias" + }, + { + "author_name": "Tiago Marques", + "author_inst": "Faculdade Ciencias" + }, + { + "author_name": "Artur Lourenco", + "author_inst": "Faculdade Ciencias" + }, + { + "author_name": "Eugenia Cardoso", + "author_inst": "Aguas do Tejo Atlantico" + }, + { + "author_name": "Pedro Alvaro", + "author_inst": "Aguas do Tejo Atlantico" + }, + { + "author_name": "Marco Silva", + "author_inst": "Aguas do Norte" + }, + { + "author_name": "Norberta Coelho", + "author_inst": "Aguas do Norte" + }, + { + "author_name": "Joao Vilaca", + "author_inst": "SIMDOURO" + }, + { + "author_name": "Fatima Meireles", + "author_inst": "SIMDOURO" + }, + { + "author_name": "Nuno Broco", + "author_inst": "AdP Valor" + }, + { + "author_name": "Marta Carvalho", + "author_inst": "AdP Valor" + }, + { + "author_name": "Ricardo Santos", + "author_inst": "Universidade Lisboa, Tecnico Lisbon" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260907", "rel_title": "Concentration of SARS-CoV-2 from large volumes of raw wastewater is enhanced with the inuvai R180 system", @@ -637320,45 +635627,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.17.21260690", - "rel_title": "Effects of COVID-19 2021 lockdown on the sleep quality and mental health of undergraduate medical and dental students of Pakistan: A cross-sectional study.", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.17.21260690", - "rel_abs": "Background and objectivesThe COVID-19 pandemic has been recognized as a cause of direct and indirect psychological consequences that impact mental health such as acute stress disorders, anxiety, irritability, poor concentration, and insomnia. This study was planned to evaluate the sleep quality and mental health of undergraduate students amidst the COVID-19 lockdown of 2021.\n\nMaterials and MethodsThis observational cross-sectional study was conducted in Lahore, Pakistan, where 261 undergraduate medical and dental students enrolled at a private medical and dental school were approached from March to May 2021. The Pittsburg Sleep Quality Index (PSQI) was used to identify the sleep quality along with the Generalized Anxiety Disorder Scale (GAD-7) to establish anxiety symptoms and the Physical Health Questionnaire (PHQ-9) for depression symptoms.\n\nResultsThe results show that 212 (81.2%) female and 49 (18.8%) male students participated in the study. Of the participants 75.1% experienced poor sleep quality, 90% had symptoms of depression, and 85.4% had symptoms of anxiety. The mean score on the PSQI scale was 8.59{+/-}4.10, on the GAD-7 scale was 11.36{+/-}5.94 and on the PHQ-9 scale was 13.70{+/-}6.81. Multiple regression analysis showed that anxiety symptoms ({beta} = 0.315, p = 0.000) and depression symptoms ({beta} = 0.398, p = 0.000) were significant predictors of sleep quality amongst the undergraduate medical and dental students.\n\nConclusionA high majority of the study participants are experiencing poor sleep quality along with suffering from depression and anxiety amidst the COVID-19 lockdown. It is concluded from the analysis that anxiety and depression symptoms are significant predictors of sleep quality. Relevant authorities need to set up systems that help undergraduate medical students in alleviating and coping with these symptoms midst the COVID-19 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Naveen Siddique Sheikh", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - }, - { - "author_name": "Aiza Anwar", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - }, - { - "author_name": "Iqra Pervaiz", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - }, - { - "author_name": "Zunaira Arshad", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - }, - { - "author_name": "Huma Saeed Khan", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - }, - { - "author_name": "Farida Hafeez", - "author_inst": "CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.18.21260733", "rel_title": "Spanish Version of the Attitude Towards COVID-19 Vaccines Scale: Reliability and Validity Assessment", @@ -637903,6 +636171,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.21260791", + "rel_title": "Role of Multi-resolution Vulnerability Indices in COVID-19 spread: A Case Study in India", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260791", + "rel_abs": "IntroductionThe outbreak of COVID-19 has differentially affected countries in the world, with health infrastructure and other related vulnerability indicators playing a role in determining the extent of the COVID-19 spread. Vulnerability of a geographical region/country to COVID-19 has been a topic of interest, particularly in low- and middle-income countries like India to assess the multi-factorial impact of COVID-19 on the incidence, prevalence or mortality data.\n\nDatasets and MethodsBased on publicly reported socio-economic, demographic, health-based and epidemiological data from national surveys in India, we compute contextual, COVID-19 Vulnerability Indices (cVIs) across multiple thematic resolutions for different geographical and spatial administrative regions. These multi-resolution cVIs were used in regression models to assess their impact on indicators of the spread of COVID-19 such as the average time-varying instantaneous reproduction number.\n\nResultsOur observational study was focused on 30 districts of the eastern Indian state of Odisha. It is an agrarian state, prone to natural disasters and one of the largest contributors of an unprotected migrant workforce. Our analyses identified housing and hygiene conditions, availability of health care and COVID preparedness as important spatial indicators.\n\nConclusionOdisha has demonstrated success in containing the COVID-19 infection to a reasonable level with proactive measures to contain the spread of the virus during the first wave. However, with the onset of the second wave of COVID, the virus has been making inroads into the hinterlands and peripheral districts of the state, burdening the already deficient public health system in these areas. The vulnerability index presented in this paper identified vulnerable districts in Odisha. While some of them may not have a large number of COVID-19 cases at a given point of time, they could experience repercussions of the pandemic. Improved understanding of the factors driving COVID-19 vulnerability will help policy makers prioritise resources and regions leading to more effective mitigation strategies for the COVID-19 pandemic and beyond.\n\nO_TEXTBOXWHAT IS ALREADY KNOWNMeasuring vulnerability to COVID-19 and other pandemics is a complex and layered subject. In Low-to-Middle-Income Country (LMIC) like India, complete reliance on incidence, prevalence or mortality data of the disease may not be the best measure since this data from the health system and DHS in public domain is limited.\n\nADDED VALUE OF THIS STUDYTo our knowledge, this is the first study at the district level concerning the COVID-19 situation in Odisha, characterized by a large tribal and migrant population. We defined vulnerability through relevant socio-economic domains that have an influence on mitigation strategies. Although we applied our methods to the districts of Odisha, we believe they can be used in other LMIC regions.\n\nIMPLICATIONS OF THE FINDINGSRegions with higher overall or theme-specific vulnerability index might experience potentially severe consequences of the COVID-19 outbreak demanding precise, dynamic and nimble policy decisions to prevent a potentially dire situation.\n\nC_TEXTBOX", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rupam Bhattacharyya", + "author_inst": "University of Michigan, Ann Arbor" + }, + { + "author_name": "Anik Burman", + "author_inst": "Indian Statistical Institute, Kolkata" + }, + { + "author_name": "Kalpana Singh", + "author_inst": "Public Health Foundation of India, New Delhi" + }, + { + "author_name": "Sayantan Banerjee", + "author_inst": "Indian Institute of Management Indore" + }, + { + "author_name": "Subha Maity", + "author_inst": "University of Michigan, Ann Arbor" + }, + { + "author_name": "Arnab Auddy", + "author_inst": "Columbia University, New York" + }, + { + "author_name": "Sarit Kumar Rout", + "author_inst": "Indian Institute of Public Health, Bhubaneswar" + }, + { + "author_name": "Supriya Lahoti", + "author_inst": "Public Health Foundation of India, New Delhi" + }, + { + "author_name": "Rajmohan Panda", + "author_inst": "Public Health Foundation of India, New Delhi" + }, + { + "author_name": "Veerabhadran Baladandayuthapani", + "author_inst": "University of Michigan, Ann Arbor" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.20.21260890", "rel_title": "Turnover of SARS-CoV-2 lineages shaped the pandemic and enabled the emergence of new variants in the state of Rio de Janeiro, Brazil", @@ -639054,97 +637377,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.07.21.453274", - "rel_title": "Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.21.453274", - "rel_abs": "SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Xuanting Wang", - "author_inst": "Columbia University" - }, - { - "author_name": "Carolina Q. Sacramento", - "author_inst": "FIOCRUZ" - }, - { - "author_name": "Steffen Jockusch", - "author_inst": "Columbia University" - }, - { - "author_name": "Ot\u00e1vio Augusto Chaves", - "author_inst": "Fiocruz" - }, - { - "author_name": "Chuanjuan Tao", - "author_inst": "Columbia University" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "FIOCRUZ" - }, - { - "author_name": "Minchen Chien", - "author_inst": "Columbia University" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Xiaoxu Li", - "author_inst": "Columbia University" - }, - { - "author_name": "Shiv Kumar", - "author_inst": "Columbia University" - }, - { - "author_name": "Wei Xie", - "author_inst": "Memorial Sloan-Kettering Cancer Center" - }, - { - "author_name": "Dinshaw J Patel", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Cindy Meyer", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Aitor Garzia", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Thomas Tuschl", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Patricia T Bozza", - "author_inst": "Lab Imunofarmacologia, Instituto Oswaldo Cruz, FIOCRUZ" - }, - { - "author_name": "James J Russo", - "author_inst": "Columbia University" - }, - { - "author_name": "Thiago Moreno L Souza", - "author_inst": "Fiocruz" - }, - { - "author_name": "Jingyue Ju", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.07.21.451321", "rel_title": "Unlike Chloroquine, mefloquine inhibits SARS-CoV-2 infection in physiologically relevant cells and does not induce viral variants.", @@ -639913,6 +638145,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.07.16.21260611", + "rel_title": "SARS-CoV-2 seroprevalence in Chattogram, Bangladesh before a National Lockdown, March-April 2021", + "rel_date": "2021-07-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260611", + "rel_abs": "In a representative serosurvey conducted March-June 2021, 64.1% (95%CrI 60.0- 68.1%) of Sitakunda subdistrict (Bangladesh) had anti-SARS-CoV-2 IgG antibodies after adjusting for age, sex, household clustering and test performance. Before the surge of Delta, most of the population had been infected despite low incidence of virologically-confirmed COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Taufiqur Rahman Bhuiyan", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Juan Dent Hulse", + "author_inst": "Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Sonia Hegde", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Marjahan Akhtar", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Taufiqul Islam", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Zahid Hasan Khan", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Ishtiakul Islam Khan", + "author_inst": "Bangladesh Institute of Tropical and Infectious Diseases" + }, + { + "author_name": "Shakeel Ahmed", + "author_inst": "Bangladesh Institute of Tropical and Infectious Diseases" + }, + { + "author_name": "Mamunur Rashid", + "author_inst": "Bangladesh Institute of Tropical and Infectious Diseases" + }, + { + "author_name": "Rumana Rashid", + "author_inst": "Bangladesh Institute of Tropical and Infectious Diseases" + }, + { + "author_name": "Tahmina Shirin", + "author_inst": "Institute of Epidemiology, Disease Control and Research (IEDCR)" + }, + { + "author_name": "Emily S Gurley", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Ashraful Islam Khan", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Andrew S Azman", + "author_inst": "Johns Hopkins University; University of Geneva" + }, + { + "author_name": "Firdausi Qadri", + "author_inst": "International Centre for Diarrhoeal Disease Research, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.16.21260651", "rel_title": "Evaluating discharges and readmissions using a COVID Virtual Ward model: a retrospective data study assessing patient outcomes and the likely staffing commitment", @@ -640836,101 +639143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.15.21260285", - "rel_title": "Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260285", - "rel_abs": "Unlike other respiratory viruses, SARS-CoV-2 disproportionately causes severe disease in older adults and only rarely in children. To investigate whether differences in the upper airway immune response could contribute to this disparity, we compared nasopharyngeal gene expression in 83 children (<19-years-old; 38 with SARS-CoV-2, 11 with other respiratory viruses, 34 with no virus) and 154 adults (>40-years-old; 45 with SARS-CoV-2, 28 with other respiratory viruses, 81 with no virus). Expression of interferon-stimulated genes (ISGs) was robustly activated in both children and adults with SARS-CoV-2 compared to the respective non-viral groups, with only relatively subtle distinctions. Children, however, demonstrated markedly greater upregulation of pathways related to B cell and T cell activation and proinflammatory cytokine signaling, including TNF, IFN{gamma}, IL-2 and IL-4 production. Cell type deconvolution confirmed greater recruitment of B cells, and to a lesser degree macrophages, to the upper airway of children. Only children exhibited a decrease in proportions of ciliated cells, the primary target of SARS-CoV-2, upon infection with the virus. These findings demonstrate that children elicit a more robust innate and adaptive immune response to SARS-CoV-2 infection in the upper airway that likely contributes to their protection from severe disease in the lower airway.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Eran Mick", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA; Division of Pulmonary and Critical Care Medicine, University of California, S" - }, - { - "author_name": "Alexandra Tsitsiklis", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA" - }, - { - "author_name": "Natasha Spottiswoode", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA" - }, - { - "author_name": "Saharai Caldera", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Paula Hayakawa Serpa", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Angela M Detweiler", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Norma Neff", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Angela Oliveira Pisco", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Lucy M Li", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Hanna Retallack", - "author_inst": "Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA" - }, - { - "author_name": "Kalani Ratnasiri", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Kayla M Williamson", - "author_inst": "Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Victoria Soesanto", - "author_inst": "Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Eric AF Sim\u00f5es", - "author_inst": "Department of Pediatrics, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Amy Kistler", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Brandie D Wagner", - "author_inst": "Department of Pediatrics, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA; Department of Biostatistics and Informatics, Colorado School" - }, - { - "author_name": "Joseph L DeRisi", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA" - }, - { - "author_name": "Lilliam Ambroggio", - "author_inst": "Department of Pediatrics, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA" - }, - { - "author_name": "Peter M Mourani", - "author_inst": "Department of Pediatrics, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA; Arkansas Children's Research Institute, Arkansas Children's " - }, - { - "author_name": "Charles Langelier", - "author_inst": "Division of Infectious Diseases, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.15.21260213", "rel_title": "Temporal Variations in Seroprevalence of SARS-CoV-2 Infections by Race and Ethnicity in Arkansas.", @@ -641811,6 +640023,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.16.21260638", + "rel_title": "Social determinants of health exacerbate disparities in COVID-19 illness severity and lasting symptom complaints", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260638", + "rel_abs": "BACKGROUNDIncreasing reports of long-term symptoms following COVID-19 infection, even among mild cases, necessitates systematic investigation into the prevalence and type of lasting illness. Notably, there is limited data regarding the influence of social determinants of health, like perceived discrimination and economic stress, which may exacerbate COVID-19 health risks. The primary goals of this study are to test the bearing of subjective experiences of discrimination, financial security, and quality of care on illness severity and lasting symptom complaints.\n\nMETHODS1,584 recovered COVID-19 patients that experienced mild to severe forms of the disease provided information about their illness, medical history, lasting symptoms, and psychosocial information. Prevalence data isolated differences in patients infected early versus late in the pandemic. Path analyses examined hypothesized associations between discrimination, illness severity, and lasting symptoms. Post hoc logistic regressions tested social determinants hypothesized to predict neurological, cognitive, or mood symptoms.\n\nRESULTS70.6% of patients reported presence of one or more lasting symptoms after recovery. Neural systems were especially impacted, and 19.4% and 25.1% of patients reported mood or cognitive/memory complaints, respectively. Path models demonstrated that frequency and stress about experiences of discrimination predicted increased illness severity and increased lasting symptom count, even when adjusting for sociodemographic factors and mental/physical health comorbidities. Notably, this effect was specific to stress related to discrimination, and did not extend to general stress levels. Further, perceived but not objective socioeconomic status (SES) was associated with increased lasting symptom complaints after recovery. Finally, associations between discrimination and illness differed with individual perceptions about quality of medical care.\n\nCONCLUSIONSLasting symptoms after recovery from COVID-19 are highly prevalent and neural systems are significantly impacted. Importantly, psychosocial factors (perceived discrimination and perceived SES) can exacerbate individual health risk. This study provides actionable directions for improved health outcomes by establishing that sociodemographic risk and medical care influence near and long-ranging health outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Moriah Thomason", + "author_inst": "New York University Langone" + }, + { + "author_name": "Cassandra L Hendrix", + "author_inst": "New York University Langone Health" + }, + { + "author_name": "Denise Werchan", + "author_inst": "New York University Langone Health" + }, + { + "author_name": "Natalie H Brito", + "author_inst": "New York University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260563", "rel_title": "SARS-CoV-2 infection in fully vaccinated individuals of old age strongly boosters the humoral immune response", @@ -642990,49 +641233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.452771", - "rel_title": "Comparison of Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.19.452771", - "rel_abs": "The increasing prevalence of SARS-CoV-2 variants has raised concerns regarding possible decreases in vaccine efficacy. Here, neutralizing antibody titers elicited by mRNA-based and an adenoviral vector-based vaccine against variant pseudotyped viruses were compared. BNT162b2 and mRNA-1273-elicited antibodies showed modest neutralization resistance against Beta, Delta, Delta plus and Lambda variants whereas Ad26.COV2.S-elicited antibodies from a significant fraction of vaccinated individuals were of low neutralizing titer (IC50 <50). The data underscore the importance of surveillance for breakthrough infections that result in severe COVID-19 and suggest the benefit of a second immunization following Ad26.COV2.S to increase protection against the variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Takuya Tada", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Hao Zhou", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Marie I Samanovic", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Belinda M Dcosta", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Amber Cornelius", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Nathaniel R Landau", - "author_inst": "NYU Grossman School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.19.452918", "rel_title": "Rosin Soap Exhibits Virucidal Activity", @@ -643721,6 +641921,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.16.21260079", + "rel_title": "Relative Ratios of Human Seasonal Coronavirus Antibodies Predict the Efficiency of Cross-Neutralization of SARS-CoV-2 Spike Binding to ACE2", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260079", + "rel_abs": "BackgroundAntibodies raised against human seasonal coronaviruses (sCoVs), which are responsible for the common cold, are known to cross-react with SARS-CoV-2 antigens. This prompts questions about their protective role against SARS-CoV-2 infections and COVID-19 severity. However, the relationship between sCoV exposure and SARS-CoV-2 correlates of protection are not clearly identified.\n\nMethodsWe performed a cross-sectional analysis of cross-reactivity and cross-neutralization to SARS-CoV-2 antigens (S-RBD, S-trimer, N) using pre-pandemic serum from four different groups: pediatrics and adolescents, persons 21 to 70 years of age, older than 70 years of age, and persons living with HCV or HIV.\n\nFindingsAntibody cross-reactivity to SARS-CoV-2 antigens varied between 1.6% and 15.3% depending on the cohort and the isotype-antigen pair analyzed. We also show a range of neutralizing activity (0-45%) in serum that interferes with SARS-CoV-2 spike attachment to ACE2. While the abundance of sCoV antibodies did not directly correlate with neutralization, we show that neutralizing activity is rather dependent on relative ratios of IgGs in sera directed to all four sCoV spike proteins. More specifically, we identified antibodies to NL63 and OC43 as being the most important predictors of neutralization.\n\nInterpretationOur data support that exposure to sCoVs triggers antibody responses that influence the efficiency of SARS-CoV-2 spike binding to ACE2, and may also impact COVID-19 disease severity through other latent variables.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSThere is a growing body of evidence showing that within the population there are varying levels of pre-existing immunity to SARS-CoV-2 infection and possibly COVID-19 disease severity. This immunity is believed to be attributable to prior infection by four prevalent seasonal coronaviruses (sCoVs) responsible for the common cold. Pre-existing immunity can be assessed in part by antibodies directed to sCoVs that also cross-react to SARS-CoV-2 antigens. The SARS-CoV-2 spike and, more specifically, the receptor binding domain are the primary targets for neutralizing antibodies. It is unclear if cross-reactive antibodies to SARS-CoV-2 are neutralizing and are also responsible for the broad spectrum of COVID-19 disease severity, from asymptomatic to critical, observed in the infected population.\n\nAdded-value of this studyHere we carried out a detailed analysis of sCoV prevalence in samples acquired before the pandemic from individuals of various age groups and in people living with HIV and HCV. We then analyzed the frequency of all the different types of antibodies that cross-react to three SARS-CoV-2 antigens. We found a high level of people with cross-reactive antibodies, surprisingly we also detected that some people have antibodies that block the SARS-CoV-2 spike from binding to its human receptor, ACE2. By using machine learning, we were able to accurate predict which individuals can neutralize SARS-CoV-2 spike-ACE2 interactions based on their relative ratios of antibodies against the four sCoVs.\n\nImplications of all the available evidenceWe demonstrate that it not absolute levels of sCoVs antibodies that are predictive of neutralization but the relative ratios to all four sCoVs, with NL63 being the most weighted for this prediction. Machine learning also highlighted the existence of latent variables that contribute to the neutralization and that may be related to the type of cellular immune response triggered by the infection to certain sCoVs. This study is one of the first to identify a functional relationship between prior-exposure to sCoV and the establishment of a certain degree of immunity to SARS-CoV-2 by way of a cross-reactive antibody response.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC=\"FIGDIR/small/21260079v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@e74392org.highwire.dtl.DTLVardef@1052bd5org.highwire.dtl.DTLVardef@80d88eorg.highwire.dtl.DTLVardef@10976cb_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yannick Galipeau", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Vinayakumar Siragam", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Genevieve Laroche", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Erika Marion", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Matthew Greig", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Michaeline McGuinty", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Ronald Booth", + "author_inst": "The Eastern Ontario Regional Laboratory Association" + }, + { + "author_name": "Yves Durocher", + "author_inst": "National Research Council of Canada" + }, + { + "author_name": "Miroslava Cuperlovic-Culf", + "author_inst": "National Research Council of Canada" + }, + { + "author_name": "Steffany L Bennett", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Angela M Crawley", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Patrick M. Giguere", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Curtis Cooper", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Marc-Andre Langlois", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21260361", "rel_title": "Global and regional prevalence and outcomes of COVID-19 in people living with HIV: A systematic review and meta-analysis", @@ -644916,45 +643187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.07.13.21259962", - "rel_title": "Monitoring of COVID-19 Pandemic-related Psychopathology using Machine Learning", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21259962", - "rel_abs": "The COVID-19 pandemic has been shown to have major impact on global mental health. We show that the developments in COVID-19 pandemic-related psychopathology can be meaningfully monitored using machine learning methods providing invaluable insights to psychiatric services and of the management of the psychological consequences of the COVID-19 pandemic. The COVID-19 pandemic-related psychopathology among patients with mental illness was found to covary with the pandemic pressure, however, was less pronounced during the second wave compared to the first wave of the pandemic - possibly due to habituation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kenneth C. Enevoldsen", - "author_inst": "Aarhus University" - }, - { - "author_name": "Andreas Danielsen", - "author_inst": "Aarhus University" - }, - { - "author_name": "Christopher Rohde", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Oskar Hougaard Jefsen", - "author_inst": "Aarhus University Hospital - Psychiatry" - }, - { - "author_name": "Kristoffer Nielbo", - "author_inst": "Aarhus University" - }, - { - "author_name": "Soren Dinesen Ostergaard", - "author_inst": "Department of Affective Disorders, Aarhus University Hospital, Aarhus, Denmark" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.13.21260417", "rel_title": "Clinical outcomes in vaccinated individuals hospitalized with Delta variant of SARS-CoV-2", @@ -645531,6 +643763,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.16.452441", + "rel_title": "A single de novo substitution in SARS-CoV-2 spike informs enhanced adherence to human ACE2.", + "rel_date": "2021-07-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452441", + "rel_abs": "SARS-CoV-2 initiates colonization of host cells by binding to cell membrane ACE2 receptor. This binding is mediated by the viral spike receptor binding domain (RBD). The COVID-19 pandemic has brought devastating consequences at a clinical, social and economical levels. Therefore, anticipation of potential novel SARS-causing species or SARS-CoV-2 variants with enhanced binding to ACE2 is key in the prevention of future threats to come. We have characterized a de novo single substitution, Q498Y, in SARS-CoV-2 RBD that confers stronger adherence to ACE2. While the SARS-CoV-2 {beta} variant, which includes three simultaneous amino acid replacements, induces a 4-fold stronger affinity, a single Q498Y substitution results in 2.5-fold tighter binding, compared to the Wuhan-Hu-1 SARS-CoV-2 2019 strain. Additionally, we crystallized RBDQ498Y complexed with ACE2 and provide here the structural basis for this enhanced affinity. These studies inform a rationale for prevention of potential SARS-causing viruses to come.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Elena Erausquin", + "author_inst": "Navarrabiomed" + }, + { + "author_name": "Jacinto Lopez-Sagaseta", + "author_inst": "Navarrabiomed" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.15.452504", "rel_title": "Neutralization of recombinant RBD-subunit vaccine ZF2001-elicited antisera to SARS-CoV-2 variants including Delta", @@ -646510,45 +644765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.07.14.452381", - "rel_title": "Single cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine", - "rel_date": "2021-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.14.452381", - "rel_abs": "mRNA based vaccines for SARS-CoV-2 have shown exceptional clinical efficacy providing robust protection against severe disease. However, our understanding of transcriptional and repertoire changes following full vaccination remains incomplete. We used single-cell RNA sequencing and functional assays to compare humoral and cellular responses to two doses of mRNA vaccine with responses observed in convalescent individuals with asymptomatic disease. Our analyses revealed enrichment of spike-specific B cells, activated CD4 T cells, and robust antigen-specific polyfunctional CD4 T cell responses in all vaccinees. On the other hand, CD8 T cell responses were both weak and variable. Interestingly, clonally expanded CD8 T cells were observed in every vaccinee, as observed following natural infection. TCR gene usage, however, was variable, reflecting the diversity of repertoires and MHC polymorphism in the human population. Natural infection induced expansion of larger CD8 T cell clones occupied distinct clusters, likely due to the recognition of a broader set of viral epitopes presented by the virus not seen in the mRNA vaccine. Our study highlights a coordinated adaptive immune response where early CD4 T cell responses facilitate the development of the B cell response and substantial expansion of effector CD8 T cells, together capable of contributing to future recall responses.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Suhas Sureshchandra", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Sloan A. Lewis", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Brianna Doratt", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Allen Jankeel", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Izabela Ibraim", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Ilhem Messaoudi", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.14.452401", "rel_title": "Improving comparability of studies using HCoV-OC43 as a surrogate for SARS-CoV-2", @@ -647257,6 +645473,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.15.452488", + "rel_title": "Monitoring the spread of SARS-CoV-2 variants in Moscow and the Moscow region using targeted high-throughput sequencing", + "rel_date": "2021-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.15.452488", + "rel_abs": "Since the outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 coronavirus, the international community has been concerned about the emergence of mutations that alter the biological properties of the pathogen, for example, increasing its infectivity or virulence. In particular, since the end of 2020, several variants of concern have been identified around the world, including variants \"alpha\" (B.1.1.7, \"British\"), \"beta\" (B.1.351, \"South African\"), \"gamma\" (P.1, \"Brazilian\") and \"delta\" (B.1.617.2, \"Indian\"). However, the existing mechanism for searching for important mutations and identifying strains may not be effective enough, since only a relatively small fraction of all identified pathogen samples can be examined for genetic changes by whole genome sequencing due to its high cost. In this study, we used the method of targeted high-throughput sequencing of the most significant regions of the gene encoding the S-glycoprotein of the SARS-CoV-2 virus, for which a primer panel was developed. Using this technique, we examined 579 random samples obtained from patients in Moscow and the Moscow region with coronavirus infection from February to June 2021. The study demonstrated the dynamics of the representation in the Moscow region of a number of SARS-CoV-2 strains and its most significant individual mutations in the period from February to June 2021. It was found that the strain B.1.617.2 began to spread rapidly in Moscow and the Moscow region in May, and in June it became dominant, partially displacing other varieties of the virus. The results obtained make it possible to accurately determine the belonging of the samples to the abovementioned and some other strains. The approach can be used to standardize the procedure for searching for new and existing epidemiologically significant mutations in certain regions of the SARS-CoV-2 genome, which allows studying a large number of samples in a short time and to get a more detailed picture of the epidemiological situation in the region.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.07.13.21260473", "rel_title": "ANALYSIS OF FOUR DIFFERENT TRANSPORT AND PRESERVATION MEDIUM KITS FOR SARS-COV-2 DIAGNOSIS FROM NASOPHARYNGEAL SWAB BY REAL-TIME PCR: ADAPTING TO THE CONSTANTLY INCREASING DEMAND OF SAMPLING PROCESSING AND STOCK-OUTS DURING THE PANDEMIC", @@ -648528,77 +646758,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.11.21260338", - "rel_title": "Vaccine serologic responses among transplant patients associate with COVID-19 infection and T peripheral helper cells", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260338", - "rel_abs": "BackgroundTherapeutically immunosuppressed transplant recipients exhibit attenuated responses to COVID-19 vaccines. To better understand the immune alterations that determined poor vaccine response, we correlated quantities of circulating T and B cell subsets at baseline with longitudinal serologic responses to SARS-CoV-2 mRNA vaccination in heart and lung transplant recipients.\n\nMethodsSamples at baseline and at approximately 8 and 30 days after each vaccine dose for 22 heart and lung transplant recipients with no history of COVID-19, four heart and lung transplant recipients with prior COVID-19 infection, and 12 healthy controls undergoing vaccination were analyzed. Anti-spike protein receptor binding domain (RBD) IgG and pseudovirus neutralization activity were measured. Proportions of B and T cell subsets at baseline were comprehensively quantitated.\n\nResultsAt 8-30 days post vaccination, healthy controls displayed robust anti-RBD IgG responses, whereas heart and lung transplant recipients showed minimally increased responses. A parallel absence of activity was observed in pseudovirus neutralization. In contrast, three of four (75%) transplant recipients with prior COVID-19 infection displayed robust responses at levels comparable to controls. Baseline levels of activated PD-1+ HLA-DR+ CXCR5- CD4+ T cells (also known as T peripheral helper [TPH] cells) and CD4+ T cells strongly predicted the ability to mount a response.\n\nConclusionsImmunosuppressed patients have defective vaccine responses but can be induced to generate neutralizing antibodies after SARS-CoV-2 infection. Strong correlations of vaccine responsiveness with baseline TPH and CD4+ T cell numbers highlights a role for T helper activity in B cell differentiation into antibody secreting cells during vaccine response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jacob E. Lemieux", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Amy Li", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Matteo Gentili", - "author_inst": "The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard" - }, - { - "author_name": "Cory A. Perugino", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Zoe F. Weiss", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kathryn Bowman", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Pierre Ankomah", - "author_inst": "The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard" - }, - { - "author_name": "Hang Liu", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Gregory D. Lewis", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Natasha Bitar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Taryn Lipiner", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Nir Hacohen", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Shiv S. Pillai", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital" - }, - { - "author_name": "Marcia B. Goldberg", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.14.21259081", "rel_title": "Use of 1-MNA to Improve Exercise Tolerance and Fatigue in Patients After COVID-19", @@ -649343,6 +647502,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.09.21260089", + "rel_title": "Comparison of immunogenicity between BNT162b2 and ChAdOx1 SARS-CoV-2 vaccines in a large haemodialysis population", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260089", + "rel_abs": "BackgroundLimited data exists on the immunogenicity of vector-based SARS-CoV-2 vaccines in patients with kidney disease. Given their use in over 180 countries, such data is of upmost importance to inform policy on optimal vaccination strategies. This study compares the immunogenicity of BNT162b2 with ChAdOx1 in patients receiving haemodialysis.\n\nMethods1021 patients were screened for spike protein antibodies (anti-S) following 2 doses of either BNT162b2 (n=523) or ChAdOx1 (n=498). 191 patients underwent assessment with T-cell ELISpot assays. 65 health care workers were used as a control group.\n\nResultsAnti-S was detected in 936 (91.2%) of patients post-vaccination. There was no difference in seroconversion rates between infection-naive patients who received BNT162b2, 248/281 (88.3%), compared with ChAdOx1, 227/272 (83.5%), p=0.11. Anti-S concentrations were higher following BNT162b, 462(152-1171) BAU/ml, compared with ChAdOx-1 79(20-213) BAU/ml, p<0.0001. Immunosuppression was associated with failure to seroconvert (p<0.0001); whilst being active on the transplant wait list was a predictor for seroconversion (p=0.02).\n\nOnly 73 (38.2%) of patients had detectable T-cell responses post-vaccination, with no proportional difference between infection-naive patients who received BNT162b2, 2/19 (10.5%), versus ChAdOx1, 15/75 (20.0%), p=0.34. There were no quantitative differences in T-cell responses in infection-naive patients, with a median 2(0-16) SFU/106 PBMCs and 10(4-28) SFU/106 PBMCs in those receiving BNT162b2 and ChAdOx1 respectively, p=0.35. These responses were significantly weaker compared with healthy controls.\n\nConclusionsEnhanced immunogenicity was seen with BNT162b2 compared with ChAdOx1, driven by superior humoral responses, with attenuated T-cell responses to both vaccines. Comparative data on clinical efficacy is now required.\n\nSignificance StatementLimited data exist on the immunogenicity of vector-based SARS-CoV-2 vaccines in patients with kidney disease. Given their use in over 180 countries worldwide, such data are of upmost importance to inform policy on optimal vaccination strategies. This study compares the immunogenicity of BNT162b2 (n=523) against the adenovirus vector vaccine, ChAdOx1 (n=498), in 1021 haemodialysis patients. In infection-naive patients, overall seroconversion rates were comparable, however, spike protein antibody concentrations were significantly higher following BNT162b2. No difference in T-cell responses was seen, however, all naive patients had weaker responses compared with healthy controls. Equivalent attenuated cellular responses to both vaccines, with greater humoral responses to BNT162b2, suggests BNT162b2 has superior immunogenicity in this patient population, with data on clinical efficacy required.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Candice L Clarke", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Martin", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Sarah Gleeson", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Tina Thomson", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Helena Edwards", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Paige Mortimer", + "author_inst": "Imperial College London" + }, + { + "author_name": "Stacey McIntyre", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jaid Deborah", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alison Cox", + "author_inst": "Northwest London Pathology NHS Trust" + }, + { + "author_name": "Graham Pickard", + "author_inst": "Northwest London Pathology NHS Trust" + }, + { + "author_name": "Liz Lightstone", + "author_inst": "Imperial College London" + }, + { + "author_name": "David Thomas", + "author_inst": "Imperial College London" + }, + { + "author_name": "Stephen P McAdoo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Peter Kelleher", + "author_inst": "Imperial College London, North West London Pathology NHS Trust" + }, + { + "author_name": "Maria Prendecki", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michelle Willicombe", + "author_inst": "Imperial College London" + }, + { + "author_name": "- OCTAVE Study Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.07.09.21260294", "rel_title": "Impacts of COVID-19 public measures on country-level trade flows: Global panel regression analysis", @@ -650386,53 +648628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.07.06.21260084", - "rel_title": "Mode of Presentation and Outcomes of COVID-19 Cases in a Tertiary Hospital in Nigeria", - "rel_date": "2021-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260084", - "rel_abs": "Coronavirus disease 2019 (COVID-19) has spread across the globe with its consequent human and economic challenges. To achieve effective control of the pandemic, efforts need to be holistic and global. Understanding patients demographics and clinical characteristics will assist in the control of the infection. However, there is a paucity of studies on the clinical presentation of COVID-19 patients from Nigeria and indeed Africa. Thus, this retrospective case series evaluated the medical records of COVID-19 patients admitted in a tertiary hospital in Nigeria. Patients demographics, and other clinical variables were assessed and presented. Data of 14 patients with complete records were included in the study. Most of the patients (78.6%) were males and the mean age of the study participants is 63.5 years (SD; 11.5). The commonest presenting symptoms were fever (93%), cough (71.4%), and dyspnoea (57.1%). At presentation, 13 patients had coexisting diseases while 8 (57.0%) patients had moderate disease and the remaining 6 (43.0%) had severe cases. After management, 1 patient died, two were referred and 11 recovered and were discharged alive. Thus, this study has identified advanced age, male gender, and comorbidity as increased risk factors for hospitalisation. The patient survival outcome in this study was also good.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yakubu Egigogo Raji", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria, Department of Medical Microbiology and Parasitology, College of Health Sci" - }, - { - "author_name": "Bala Waziri", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - }, - { - "author_name": "Sadiq Aliyu Hussaini", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - }, - { - "author_name": "Ahmad Idris Ja'agi", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - }, - { - "author_name": "Umar Isah Alhaji", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria;" - }, - { - "author_name": "Abdulmalik M Aliyu", - "author_inst": "Department of Radiology Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - }, - { - "author_name": "Abdullahi Muhammad", - "author_inst": "Department of Medicine Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - }, - { - "author_name": "Adama Saidu Garba", - "author_inst": "Family Medicine Department Ibrahim Badamasi Babangida Specialist Hospital Minna, Nigeria" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.09.21260253", "rel_title": "Transmission of SARS-CoV-2 into and within immigrant households. Nation-wide registry-study from Norway", @@ -650989,6 +649184,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.09.21260277", + "rel_title": "Predicted Norovirus Resurgence in 2021-2022 Due to the Relaxation of Nonpharmaceutical Interventions Associated with COVID-19 Restrictions in England: A Mathematical Modelling Study", + "rel_date": "2021-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260277", + "rel_abs": "BackgroundTo reduce the coronavirus disease burden in England, along with many other countries, the Government implemented a package of non-pharmaceutical interventions (NPIs) that have also impacted other transmissible infectious diseases such as norovirus. It is unclear what future norovirus disease incidence is likely to look like upon lifting these restrictions.\n\nMethodsHere we use a mathematical model of norovirus fitted to community incidence data in England to project forward expected incidence based on contact surveys that have been collected throughout 2020-2021.\n\nResultsWe report that susceptibility to norovirus infection has likely increased between March 2020 to mid-2021. Depending upon assumptions of future contact patterns incidence of norovirus that is similar to pre-pandemic levels or an increase beyond what has been previously reported is likely to occur once restrictions are lifted. Should adult contact patterns return to 80% of pre-pandemic levels the incidence of norovirus will be similar to previous years. If contact patterns return to pre-pandemic levels there is a potential for the expected annual incidence to be up to 2-fold larger than in a typical year. The age-specific incidence is similar across all ages.\n\nConclusionsContinued national surveillance for endemic diseases such as norovirus will be essential after NPIs are lifted to allow healthcare services to adequately prepare for a potential increase in cases and hospital pressures beyond what is typically experienced.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kathleen M O'Reilly", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Frank Sandmann", + "author_inst": "Public Health England" + }, + { + "author_name": "David Allen", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Amy Gimma", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Amy Douglas", + "author_inst": "Public Health England" + }, + { + "author_name": "Lesley Larkin", + "author_inst": "Public Health England" + }, + { + "author_name": "Kerry LM Wong", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Lisa Lindesmith", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Richard A Goldstein", + "author_inst": "University College London" + }, + { + "author_name": "Judith Breuer", + "author_inst": "University College London" + }, + { + "author_name": "W John Edmunds", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.10.21260304", "rel_title": "Analyzing the U.S. Post-marketing safety surveillance of COVID-19 vaccines", @@ -652148,45 +650414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.08.21260237", - "rel_title": "Confidence in government and rumors amongst international migrant workers involved in dormitory outbreaks of COVID-19: A cross-sectional survey", - "rel_date": "2021-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260237", - "rel_abs": "BackgroundIn the coronavirus disease (COVID-19) pandemic, confidence in the government and access to accurate information have been critical to the control of outbreaks. Although outbreaks have emerged amongst communities of international migrant workers worldwide, little is known about how they perceive the governments response or their exposure to rumors.\n\nMethodsBetween 22 June to 11 October 2020, we surveyed 1011 low-waged migrant workers involved in dormitory outbreaks within Singapore. Participants reported their confidence in the government; whether they had heard, shared, or believed widely-disseminated COVID-19 rumors; and their socio-demographics. Logistic regression models were fitted to identify factors associated with confidence and rumor exposure.\n\nResults1 in 2 participants (54.2%, 95% CI: 51.1-57.3%) reported that they believed at least one COVID-19 rumor. This incidence was higher than that observed in the general population for the host country (Singapore). Nonetheless, most participants (90.0%, 95% CI: 87.6-91.5%) reported being confident that the government could control the spread of COVID-19. Age was significantly associated with belief in rumors, while educational level was associated with confidence in government.\n\nConclusionsOur findings suggest that language and cultural differences may limit the access that migrant workers have to official COVID-19 updates. Correspondingly, public health agencies should use targeted messaging strategies to promote health knowledge within migrant worker communities.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Edina YQ Tan", - "author_inst": "Yale-NUS College" - }, - { - "author_name": "Dalia Albarazi", - "author_inst": "Yale-NUS College" - }, - { - "author_name": "Young Ern Saw", - "author_inst": "Yale-NUS College" - }, - { - "author_name": "P Buvanaswari", - "author_inst": "National University Health System" - }, - { - "author_name": "Kinjal Doshi", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Jean CJ Liu", - "author_inst": "Yale-NUS College" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.10.451880", "rel_title": "A mouse-adapted SARS-CoV-2 strain replicating in standard laboratory mice.", @@ -652867,6 +651094,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.09.451732", + "rel_title": "Reduced neutralization of SARS-CoV-2 B.1.617 variant by inactivated and RBD-subunit vaccine", + "rel_date": "2021-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.09.451732", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Spike protein that mediates coronavirus entry into host cells is a major target for COVID-19 vaccines and antibody therapeutics. However, multiple variants of SARS-CoV-2 have emerged, which may potentially compromise vaccine effectiveness. Using a pseudovirus-based assay, we evaluated SARS-CoV-2 cell entry mediated by the viral Spike B.1.617 and B.1.1.7 variants. We also compared the neutralization ability of monoclonal antibodies from convalescent sera and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine) and ZF2001 (RBD-subunit vaccine) against B.1.617 and B.1.1.7 variants. Our results showed that, compared to D614G and B.1.1.7 variants, B.1.617 shows enhanced viral entry and membrane fusion, as well as more resistant to antibody neutralization. These findings have important implications for understanding viral infectivity and for immunization policy against SARS-CoV-2 variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jie Hu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Xiao-yu Wei", + "author_inst": "Yong-Chuan Hospital of Chongqing Medical University" + }, + { + "author_name": "Jin Xiang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Pai Peng", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Feng-li Xu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kang Wu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Fei-yang Luo", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ai-shun Jin", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Liang Fang", + "author_inst": "Yong-Chuan Hospital of Chongqing Medical University" + }, + { + "author_name": "Bei-zhong Liu", + "author_inst": "Yong-Chuan Hospital of Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ailong Huang", + "author_inst": "Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.08.451696", "rel_title": "Therapeutic efficacy of CT-P59 against P.1 variant of SARS-CoV-2", @@ -653990,117 +652284,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.07.21260151", - "rel_title": "Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260151", - "rel_abs": "BackgroundWe aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave of the COVID-19 pandemic, explore risk factors associated with infection, and investigate the impact of antibody titres on assay sensitivity.\n\nMethodsHCWs at Sheffield Teaching Hospitals NHS Foundation Trust (STH) were prospectively enrolled and sampled at two time points. SARS-CoV-2 antibodies were tested using an in-house assay for IgG and IgA reactivity against Spike and Nucleoprotein (sensitivity 99{middle dot}47%, specificity 99{middle dot}56%). Data were analysed using three statistical models: a seroprevalence model, an antibody kinetics model, and a heterogeneous sensitivity model.\n\nFindingsAs of 12th June 2020, 24{middle dot}4% (n=311/1275) HCWs were seropositive. Of these, 39{middle dot}2% (n=122/311) were asymptomatic. The highest adjusted seroprevalence was measured in HCWs on the Acute Medical Unit (41{middle dot}1%, 95% CrI 30{middle dot}0-52{middle dot}9) and in Physiotherapists and Occupational Therapists (39{middle dot}2%, 95% CrI 24{middle dot}4-56{middle dot}5). Older age groups showed overall higher median antibody titres. Further modelling suggests that, for a serological assay with an overall sensitivity of 80%, antibody titres may be markedly affected by differences in age, with sensitivity estimates of 89% in those over 60 years but 61% in those [≤]30 years.\n\nInterpretationHCWs in acute medical units working closely with COVID-19 patients were at highest risk of infection, though whether these are infections acquired from patients or other staff is unknown. Current serological assays may underestimate seroprevalence in younger age groups if validated using sera from older and/or more symptomatic individuals.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for studies published up to March 6th 2021, using the terms \"COVID\", \"SARS-CoV-2\", \"seroprevalence\", and \"healthcare workers\", and in addition for articles of antibody titres in different age groups against coronaviruses using \"coronavirus\", \"SARS-CoV-2, \"antibody\", \"antibody tires\", \"COVID\" and \"age\". We included studies that used serology to estimate prevalence in healthcare workers. SARS-CoV-2 seroprevalence has been shown to be greater in healthcare workers working on acute medical units or within domestic services. Antibody levels against seasonal coronaviruses, SARS-CoV and SARS-CoV-2 were found to be higher in older adults, and patients who were hospitalised.\n\nAdded value of this studyIn this healthcare worker seroprevalence modelling study at a large NHS foundation trust, we confirm that those working on acute medical units, COVID-19 \"Red Zones\" and within domestic services are most likely to be seropositive. Furthermore, we show that physiotherapists and occupational therapists have an increased risk of COVID-19 infection. We also confirm that antibody titres are greater in older individuals, even in the context of non-hospitalised cases. Importantly, we demonstrate that this can result in age-specific sensitivity in serological assays, where lower antibody titres in younger individuals results in lower assay sensitivity.\n\nImplications of all the available evidenceThere are distinct occupational roles and locations in hospitals where the risk of COVID-19 infection to healthcare workers is greatest, and this knowledge should be used to prioritise infection prevention control and other measures to protect healthcare workers. Serological assays may have different sensitivity profiles across different age groups, especially if assay validation was undertaken using samples from older and/or hospitalised patients, who tend to have higher antibody titres. Future seroprevalence studies should consider adjusting for age-specific assay sensitivities to estimate true seroprevalence rates.\n\nAuthor Contributions\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@77acb4org.highwire.dtl.DTLVardef@eb9b35org.highwire.dtl.DTLVardef@1af298org.highwire.dtl.DTLVardef@12cf3e1org.highwire.dtl.DTLVardef@3f6476_HPS_FORMAT_FIGEXP M_TBL C_TBL", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Hayley Colton", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - }, - { - "author_name": "David Hodgson", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK" - }, - { - "author_name": "Hailey Hornsby", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Rebecca Brown", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Joanne Mckenzie", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Kirsty L Bradley", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Cameron James", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Benjamin B Lindsey", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - }, - { - "author_name": "Sarah Birch", - "author_inst": "Academic Directorate of Communicable Diseases and Specialised Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Louise Marsh", - "author_inst": "Academic Directorate of Communicable Diseases and Specialised Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Steven Wood", - "author_inst": "Department of Scientific Computing and Informatics, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Martin Bayley", - "author_inst": "Department of Scientific Computing and Informatics, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Gary Dickson", - "author_inst": "Department of Scientific Computing and Informatics, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "David C James", - "author_inst": "Department of Chemical and Biological Engineering, University of Sheffield, UK" - }, - { - "author_name": "Martin J.H. Nicklin", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Jon R Sayers", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK / The Florey Institute for Host-Pathogen Interactions, University of S" - }, - { - "author_name": "Domen Zafred", - "author_inst": "Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, UK" - }, - { - "author_name": "Sarah L Rowland-Jones", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - }, - { - "author_name": "Goura Kudesia", - "author_inst": "Department of Virology, Sheffield Teaching Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "-" - }, - { - "author_name": "Thomas C Darton", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - }, - { - "author_name": "Thushan I de Silva", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - }, - { - "author_name": "Paul J Collini", - "author_inst": "South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, UK / Department of Infection, Immunit" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.07.21260124", "rel_title": "BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in Systemic Lupus Erythematosus", @@ -654877,6 +653060,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.07.21260142", + "rel_title": "First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260142", + "rel_abs": "Contrary to the conventional genomic surveillance based on clinical samples (symptomatic patients), the wastewater-based genomic surveillance can identify all the variants shed by the infected individuals in the population, as it does also include RNA fragmented shredded by clinically escaped asymptomatic patients. We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/ Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis showed a total of 35 mutations in the spike protein across four samples categorized into 23 types. We noticed the presence of spike protein mutations linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not observed in the samples of Sep and Nov 2020 but appeared before the devastating second wave of COVID-19, which started in early April 2021 in India, caused rapid transmission and deaths all over India. We found the genetic traces of the B.1.617.2 in samples of early Feb 2021 i.e., more than a month before the first clinically confirmed case of the same variant in March 2021 in Ahmedabad, Gujarat. The present study tells about the circulating variants in Ahmedabad and suggests early prediction VOCs employing the wastewater genomic surveillance approach that must be exploited at a large scale for effective COVID-19 management.\n\nHighlightsO_LIWhole-genome sequencing of SARS-CoV-2 from the WW samples was carried out.\nC_LIO_LIVariant of Concern (VoC: VOC-21APR-02; B.1.617.2) were detected in WW samples.\nC_LIO_LIWBE may detect prevalent SARS-CoV-2 variants and monitor their cryptic transmission\nC_LIO_LIWW genomic surveillance can aid the decision-making system for public health policies.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Madhvi Joshi", + "author_inst": "Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India" + }, + { + "author_name": "Manish Kumar", + "author_inst": "IIT Gandhinagar" + }, + { + "author_name": "Vaibhav Srivastava", + "author_inst": "IIT Gandhinagar" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India" + }, + { + "author_name": "Dalipsingh Rathore", + "author_inst": "Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India" + }, + { + "author_name": "Ramesh Pandit", + "author_inst": "Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat 382 011, India" + }, + { + "author_name": "Chaitanya G Joshi", + "author_inst": "director.gbrc@gmail.com" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.08.21260182", "rel_title": "Impact of the national test strategy on the development of the Covid-19 pandemic in Denmark", @@ -655920,33 +654146,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.07.06.451357", - "rel_title": "SARS-CoV-2 genome sequencing with Oxford Nanopore Technology and Rapid PCR Barcoding in Bolivia", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451357", - "rel_abs": "SARS-CoV-2 genomic surveillance has Illumina technology as the golden standard. However, Oxford Nanopore Technology (ONT) provides significant improvements in accessibility, turnaround time and portability. Characteristics that gives developing countries the opportunity to perform genome surveillance. The most used protocol to sequence SARS-CoV-2 with ONT is an amplicon-sequencing protocol provided by the ARTIC Network which requires DNA ligation. Ligation reagents can be difficult to obtain in countries like Bolivia. Thus, here we provide an alternative for library preparation using the rapid PCR barcoding kit (ONT). We mapped more than 3.9 million sequence reads that allowed us to sequence twelve SARS-CoV-2 genomes from three different Bolivian cities. The average sequencing depth was 324X and the average genome length was 29527 bp. Thus, we could cover in average a 98,7% of the reference genome. The twelve genomes were successfully assigned to four different nextstrain clades (20A, 20B, 20E and 20G) and we could observe two main lineages of SARS-CoV-2 circulating in Bolivia. Therefore, this alternative library preparation for SARS-CoV-2 genome sequencing is effective to identify SARS-CoV-2 variants with high accuracy and without the need of DNA ligation. Hence, providing another tool to perform SARS-CoV-2 genome surveillance in developing countries.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Oscar M. Rollano-Penaloza", - "author_inst": "Lund University" - }, - { - "author_name": "Carmen Delgado", - "author_inst": "Hospital San Pedro Claver" - }, - { - "author_name": "Aneth Vasquez", - "author_inst": "Universidad Mayor de San Andres" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.07.06.451227", "rel_title": "T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations", @@ -656659,6 +654858,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259957", + "rel_title": "The rise and fall of an emerging SARS-CoV-2 variant with the spike protein mutation L452R", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259957", + "rel_abs": "Emerging SARS-CoV-2 variants may threaten global vaccination efforts and awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Orna Mor", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Michal Mandelboim", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Shay Fleishon", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Efrat Bucris", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Dana Bar-Ilan", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Michal Linial", + "author_inst": "Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel." + }, + { + "author_name": "Yaniv Lustig", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Ella Mendelson", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + }, + { + "author_name": "Neta S Zuckerman", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, 52621, Israel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21259946", "rel_title": "IFIH1 rs1990760 variants, systemic inflammation and outcome in critically-ill COVID-19 patients", @@ -657790,25 +656040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.04.21259205", - "rel_title": "Modelling, Simulations and Analysis of the First and Second COVID-19 Epidemics in Beijing", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259205", - "rel_abs": "BackgroundIn December 2019, a novel coronavirus-induced pneumonia (COVID-19) broke out in Wuhan, China. On 19 January and on 8 June 2020, there were two wave COVID-19 epidemics happened in Beijing. Modelling, simulations and analysis for the two wave epidemics are important issues.\n\nMethodsThis study introduces a symptomatic-asymptomatic-recoverer-death differential equation model (SARDDE). It presents the conditions of the asymptotical stability on the disease-free equilibrium of the SARDDE. It proposes the necessary conditions of disease spreading for the SARDDE. Based on the reported data of the first and the second COVID-19 epidemics in Beijing and numerical simulations, it determines the parameters of the SARDDE, respectively.\n\nResultsNumerical simulations of the SARDDE describe well the outcomes of the current symptomatic and asymptomatic individuals, the recovered symptomatic and asymptomatic individuals, and the died infected individuals, respectively. The numerical simulations obtain the following results.\n\nO_LIThe transmission rate of the symptomatic infections caused by the symptomatic individuals in the second Beijing epidemic is about two times higher than the one in the first Beijing epidemic.\nC_LIO_LIBoth the symptomatic and the asymptomatic individuals cause lesser asymptomatic spread than symptomatic spread.\nC_LIO_LIThe blocking rates of 89.32% and 97.48% (reaching the infection turning points) to the symptomatic infections cannot prevent the spreads of the first and the second COVID-19 epidemics in Beijing, respectively.\nC_LIO_LIThat on the day 28, the symptomatic infection blocking rates reached to 100% has made the second Beijing epidemics epidemic end on day 56.\nC_LIO_LIThat on the day 98, the symptomatic infection blocking rates reached to 100% has made the the first Beijing epidemics epidemic end on day 140.\nC_LIO_LIKeeping the blocking rates, the recovery rates and the death rates reaching the infection turning points would make the numbers of current hospitalized infected individuals reach, on day 140, 208958 individuals and 25017 individuals for the two Beijing epidemics, respectively.\nC_LI\n\nConclusionsVirtual simulations suggest that the strict prevention and control strategies implemented by Beijing government are effective and necessary; using the data from the beginning to the days after about two weeks after the turning points can estimate well and approximately the following outcomes of the two COVID-19 epidemics, respectively. To avoid multiple epidemic outbreaks, a recommendation is that the authorities need to have maintained the prevention and control measures implemented, at least, 7 days after reaching the turning point until new current infection cases disappear. It is expected that the research can provide better understanding, explaining, and dominating for epidemic spreads, prevention and control measures.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lequan Min", - "author_inst": "University of Science and Technology Beijing" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.05.21250138", "rel_title": "Peritraumatic Distress of COVID-19 on Physicians in Bangladesh: Implications and Policy Recommendations", @@ -658513,6 +656744,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.06.21260059", + "rel_title": "Initial SARS-CoV-2 vaccination response can predict booster response for BNT162b2 but not for AZD1222", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260059", + "rel_abs": "ObjectivesOur objective was to determine whether SARS-CoV-2 antibody levels after the first dose can predict the final antibody response and whether this is dependent on the vaccine type.\n\nMethods69 BNT162b2 (Pfizer/BioNTech) and 55 AZD1222 (AstraZeneca) vaccinees without previous infection or immunosuppressive medication were included. Anti-body levels were quantified 3 weeks after dose 1, in case of AZD1222 directly before boostering (11 weeks after dose 1) and 3 weeks after dose 2, with the Roche SARS-CoV-2 S total antibody assay.\n\nResultsPre-booster (BNT162b2: 80.6 [25.5-167.0] BAU/mL, AZD1222: 56.4 [36.4-104.8] BAU/mL, not significant) and post-booster levels (BNT162b2: 2,092.0 [1,216.3-4,431.8] BAU/mL, AZD1222: 957.0 [684.5-1,684.8] BAU/mL, p<0.0001) correlated well in BNT162b2 ({rho}=0.53) but not in AZD1222 recipients. Moreover, antibody levels after the first dose of BNT162b2 correlated inversely with age ({rho}=-0.33, P=0.013), whereas a positive correlation with age was observed after the second dose in AZD1222 recipients ({rho}=0.26, P=0.030).\n\nConclusionsIn conclusion, our data suggest that antibody levels quantified by the Roche Elecsys SARS-CoV-2 S assay before the booster shot could infer post-booster responses to BNT162b2, but not to AZ1222. In addition, we found a vaccine-dependent effect on antibody responses, suggesting a possible link between vaccine response and vector immunity.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Thomas Perkmann", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Nicole Perkmann-Nagele", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Patrick Mucher", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Astrid Radakovics", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Manuela Repl", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Thomas Koller", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Galateja Jordakieva", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Oswald F Wagner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Christoph J Binder", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Helmuth Haslacher", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21259654", "rel_title": "Development and Content Validation of the Symptoms Evolution of COVID-19: A Patient-Reported Electronic Daily Diary in Clinical and Real-World Studies", @@ -659560,69 +657846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.07.449660", - "rel_title": "Defining the Immune Responses for SARS-CoV-2-Human Macrophage Interactions", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.07.449660", - "rel_abs": "Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end organ malfunctions. All follow an abortive viral infection. To elucidate SARS-CoV-2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the SARS-CoV-2 receptor, the angiotensin-converting enzyme 2, paralleled monocyte-macrophage differentiation it failed to affect productive viral infection. In contrast, simple macrophage viral exposure led to robust pro-inflammatory cytokine and chemokine expression but attenuated type I interferon (IFN) activity. Both paralleled dysregulation of innate immune signaling pathways specifically those linked to IFN. We conclude that the SARS-CoV-2-infected host mounts a robust innate immune response characterized by a pro-inflammatory storm heralding consequent end-organ tissue damage.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Mai Abdelmoaty", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Pravin Yeapuri", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Jatin Machhi", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Katherine Olson", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Farah Shahjin", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "You Zhou", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Liang Jingjing", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Kabita Pandey", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Arpan Acharya", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Siddappa Byrareddy", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Lee Mosley", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Howard Gendelman", - "author_inst": "Nebraska Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.07.451505", "rel_title": "Immunogenicity of low dose prime-boost vaccination of mRNA vaccine CV07050101 in non-human primates", @@ -660639,6 +658862,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21257942", + "rel_title": "Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21257942", + "rel_abs": "Alpha (B.1.1.7) SARS-COV-2 variant was detected in September 2020 in minks and humans in Denmark and UK. This variant has several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The National Center for Disease Control (NCDC) announced on 24th February 2021 a 25% frequency of B.1.1.7 strain in Libya using a reverse-transcriptase quantitative PCR assay. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes its failure of amplification (SGTF). This deletion is not specific for B.1.1.7; but is also characteristic of two other SARS-COV-2 variants. This study aimed to estimate the frequency of B.1.1.7 and identify other variants circulating in Libya in February 2021. We performed whole genome sequencing of 67 positive SARS-COV-2 samples collected on 25th February 2021 in Libya which were also tested by RT-qPCR for SGTF. Our results showed that 55% of samples had mutations specific to B.1.525 strain and only [~]3% of samples belonged to B.1.1.7. These findings suggested that B.1.525 was spreading widely in Libya. The use of such RT-qPCR assay although useful to track some variants, it cannot discriminate between variants with H69-V70 deletion. RT-qPCR assays could be multiplexed to identify multiple variants and screen samples prior to sequencing. We emphasize on the need for providing whole-genome sequencing to the main COVID-19 diagnostic laboratories in Libya as well as establishing international collaboration for building capacity and advancing research in this time of the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Inas M Alhudiri", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Ahmad M Ramadan", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Khaled Ibrahim Ibrahim", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Mouna Eljilani", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Adel Abdalla Aboud", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Mohamed Ali Salem", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Hajer Mohamed Elgheriani", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Salah Edin El Meshri", + "author_inst": "Biotechnology Research Center" + }, + { + "author_name": "Adam Elzagheid", + "author_inst": "Biotechnology Research Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.05.21259547", "rel_title": "Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City", @@ -661398,57 +659672,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.01.21259828", - "rel_title": "Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259828", - "rel_abs": "Epidemics caused by microbial organisms are part of the natural phenomena of increasing biological complexity. The heterogeneity and constant variability of hosts, in terms of age, immunological status, family structure, lifestyle, work activities, social and leisure habits, daily division of time, and other demographic characteristics make it extremely difficult to predict the evolution of epidemics. Such prediction is, however, critical for implementing intervention measures in due time and with appropriate intensity. General conclusions should be precluded, given that local parameters dominate the flow of local epidemics. Membrane computing models allows us to reproduce the objects (viruses, hosts) and their interactions (stochastic but also with defined probabilities) with an unprecedented level of detail. Our LOIMOS model helps reproduce the demographics and social aspects of a hypothetical town of 10,320 inhabitants in an average European country where COVID-19 is imported from the outside. The above-mentioned characteristics of hosts and their lifestyle are minutely considered. The dynamics of the epidemics are reproduced and include the effects on viral transmission of innate and acquired immunity at various ages. The model predicts the consequences of delaying the adoption of non-pharmaceutical interventions (between 15 and 45 days after the first reported cases) and the effect of those interventions on infection and mortality rates (reducing transmission by 20%, 50%, and 80%) in immunological response groups. The lockdown for the elderly population as a single intervention appears to be effective. This modelling exercise exemplifies the application of membrane computing for designing appropriate interventions in epidemic situations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Fernando Baquero", - "author_inst": "Ramon y Cajal Institute for Biomedical Research" - }, - { - "author_name": "Marcelino Campos", - "author_inst": "Department of Microbiology, Ramon y Cajal University Hospital, IRYCIS, Madrid, Spain." - }, - { - "author_name": "Jose-Maria Sempere", - "author_inst": "Valencian Research Institute for Artificial Intelligence (VRAIN), Universitat Politecnica de Valencia, Valencia, Spain." - }, - { - "author_name": "Juan-Carlos Galan", - "author_inst": "Department of Microbiology, Ramon y Cajal University Hospital, IRYCIS, Madrid, Spain." - }, - { - "author_name": "Andres Moya", - "author_inst": "Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), Valencia, Spain" - }, - { - "author_name": "Carlos Llorens", - "author_inst": "Biotechvana, Parc Cientific, Universitat de Valencia" - }, - { - "author_name": "Cristina de-los-Angeles", - "author_inst": "Nursery Unit, Intensive Care Unit and Pain Therapy, Consortium University General Hospital, Valencia, Spain (CHGUV)" - }, - { - "author_name": "Fernando Baquero-Artigao", - "author_inst": "Department of Infectious Diseases and Tropical Pediatrics, La Paz University Hospital, Madrid, Spain" - }, - { - "author_name": "Rafael Canton", - "author_inst": "Department of Microbiology, Ramon y Cajal University Hospital, IRYCIS, Madrid, Spain." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.04.21259903", "rel_title": "Relating SARS-CoV-2 shedding rate in wastewater to daily positive tests data: A consistent model based approach", @@ -662213,6 +660436,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.01.21259132", + "rel_title": "A Cross Sectional Study To Assess The Attitude Regarding Online Lecture Among Nursing College Students After Impact of Covid-19 At Selected College of Nursing, Nadiad.", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259132", + "rel_abs": "BackgroundIn December 2019, a pathogenic human corona virus SARS- CoV-2, corona virus disease 2019 (COVID-19), was recognized and has caused serious illness and numerous deaths. The epidemics of COVID-19 have been recorded over 200 countries, territories, and areas with 2 878 196 confirmed cased and 198 668 death cases.\n\nAimsThe current study is to assess the attitude of nursing college students regarding online classes.\n\nObjective1. To determine the perceptions of students towards e-learning during the lock down. 2. To assess nursing students attitude towards the online lectures\n\nMethodologyO_ST_ABSSetting and DesignC_ST_ABSDescriptive cross sectional survey research design was used and not probability sampling methods was used to drawn samples through online Google form. The sample collected from nursing college students and study setting was Dinsha Patel College of nursing, Nadiad, Gujarat. There were total 20 attitude question with five point rating scale were used. Total sample were 136 nursing college students. Data has been collected online through Google form.\n\nStatistical Analysis usedDescriptive statistics applied where, data was analyzed by using SPSS software, and Frequency, percentage, tables etc were used to represent the statistical data.\n\nResultsOut of 136, 64(47.05%) were belong age 17-18 years, 115(84.56%) were female, 68(50%) were GNM students, 51(37.50%) B.Sc. nursing Students, 83(61.02%) were third year, 75(55.24%) were live urban, 61(44.86%) were rural area, 56(41.17%) were travel 21-30km, 40(29.41%) more than 30km, 65(47.79%) have above 15000 monthly family income 132(97.05%) were used mobile for online lecture 79(58.08%) were have average network.\n\nAttitude regarding Online Classes where 7 (5.14%) had Inadequate Attitude 86(63.25%) had Moderate Attitude, 43(31.61%) Had adequate Attitude.\n\nConclusionsRegarding the online lecture 63.25% nursing college students has moderate attitude and 31.61% had adequate attitude it means now days students are line online classes than physical mode due to various reasons such as, time consuming, reduce traveling, risk of accidents and corona, more time can spend with family etc", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "KAILASH NAGAR Sr.", + "author_inst": "DINSHA PATEL COLLEGE OF NURSING, NADIAD" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2021.07.01.21259884", "rel_title": "ANTI - SARS-CoV-2 ANTIBODY SCREENING IN HEALTH CARE WORKERS AND ITS CORRELATION WITH CLINICAL PRESENTATION", @@ -663272,45 +661514,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.30.21259758", - "rel_title": "Impact of regional heterogeneity on the severity of COVID-19", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259758", - "rel_abs": "BackgroundWe aimed to assess the impact of regional heterogeneity on the severity of COVID-19 in Japan.\n\nMethodsWe included 27,865 cases registered between January 2020 and February 2021 in the COVID-19 Registry of Japan to examine the relationship between the National Early Warning Score (NEWS) of COVID-19 patients on the day of admission and the prefecture where the patients live. A hierarchical Bayesian model was used to examine the random effect of each prefecture in addition to the patients backgrounds. In addition, we compared the results of two models; one model included the number of beds secured for COVID-19 patients in each prefecture as one of the fixed effects, and the other model did not.\n\nResultsThe results indicated that the prefecture had a substantial impact on the severity of COVID-19 on admission. Even when considering the effect of the number of beds separately, the heterogeneity caused by the random effect of each prefecture affected the severity of the case on admission.\n\nConclusionsOur analysis revealed a possible association between regional heterogeneity and increased/decreased risk of severe COVID-19 infection on admission. This heterogeneity was derived not only from the number of beds secured in each prefecture but also from other factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shinya Tsuzuki", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Yusuke Asai", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Nobuaki Matsunaga", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Haruhiko Ishioka", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Takayuki Akiyama", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Norio Ohmagari", - "author_inst": "National Center for Global Health and Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.30.21259794", "rel_title": "Examining the Relationship between COVID-19 Vaccinations and Reported Incidence", @@ -663991,6 +662194,57 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.07.03.450992", + "rel_title": "Increased Histone-DNA Complexes and Endothelial-Dependent Thrombin Generation in Severe COVID-19", + "rel_date": "2021-07-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.03.450992", + "rel_abs": "ObjectiveCoagulopathy in severe COVID-19 is common but poorly understood. The purpose of this study was to determine how SARS-CoV-2 infection impacts histone levels, fibrin structure, and endogenous thrombin potential in the presence and absence of endothelial cells.\n\nApproachWe studied individuals with SARS-CoV-2 infection and acute respiratory distress syndrome at the time of initiation of mechanical ventilation compared to healthy controls. Blood samples were assayed for levels of histone-DNA complexes. Confocal microscopy was used to evaluate fibrin structure in clots formed from recalcified plasma samples using fluorescently-labeled fibrinogen. Endogenous thrombin potential was measured by calibrated automated thrombin assays in the presence of tissue factor and phospholipid (PCPS) or cultured human endothelial cells.\n\nResultsCirculating nucleosomes were elevated in the plasma of COVID-19 patients relative to healthy controls (n=6, each group). COVID-19 patient plasma thrombin generation was also altered. Despite having an increased endogenous thrombin potential, patient plasma samples exhibited prolonged lag times and times to peak thrombin in the presence of added tissue factor and PCPS. Strikingly different results were observed when endothelial cells were used in place of tissue factor and PCPS. Control plasma samples did not generate measurable thrombin (lag time >60 min); in contrast, plasma samples from COVID-19+ patients generated thrombin (mean lag time [~]20 min). Consistent with the observed alterations in thrombin generation, clots from COVID-19 subjects exhibited a denser fibrin network, thinner fibers and lower fibrin resolvability.\n\nConclusionsElevated histones, aberrant fibrin formation, and increased endothelial-dependent thrombin generation in COVID-19 may contribute to coagulopathy.\n\nHIGHLIGHTSO_LIHistone-DNA complexes are significantly elevated in the plasma of patients with severe SARS-CoV-2 infection.\nC_LIO_LIMeasures of thrombin generation by calibrated automated thrombography and fibrin clots formed in situ are altered in severe COVID-19.\nC_LIO_LIPlasma from COVID-19 patients promotes thrombin generation on cultured endothelial cells in the absence of added tissue factor or phospholipids.\nC_LIO_LIThe additive effects of histones on thrombin generation and endothelial cell function may play a major role in the thrombotic complications observed in severe SARS-CoV-2 infection.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Beth A. Bouchard", + "author_inst": "University of Vermont" + }, + { + "author_name": "Christos Colovos", + "author_inst": "University of Vermont" + }, + { + "author_name": "Michael Lawson", + "author_inst": "University of Vermont" + }, + { + "author_name": "Adrian Sackhiem", + "author_inst": "University of Vermont" + }, + { + "author_name": "Kara J. Mould", + "author_inst": "National Jewish Health, Denver CO" + }, + { + "author_name": "William J. Janssen", + "author_inst": "National Jewish Health, Denver CO" + }, + { + "author_name": "Mitchell J. Cohen", + "author_inst": "University of Colorado School of Medicine" + }, + { + "author_name": "Devdoot Majumdar", + "author_inst": "University of Vermont" + }, + { + "author_name": "Kalev Freeman", + "author_inst": "University of Vermont" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.06.28.21259675", "rel_title": "COVID-19 vaccine hesitancy and refusal and associated factors in an adult population in Saskatchewan, Canada: Evidence from predictive modelling", @@ -664870,37 +663124,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.28.21259621", - "rel_title": "Facilitators and Barriers to Compliance with COVID-19 Guidelines: A Structural Topic Modelling Analysis of Free-Text Data from 17,500 UK Adults", - "rel_date": "2021-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259621", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, the UK government has implemented a series of guidelines, rules, and restrictions to change citizens behaviour to tackle the spread of the virus, such as the promotion of face-masks and the imposition of lockdown stay-at-home orders. The success of these measures requires active co-operation on the part of citizens, but compliance has not been complete. Detailed data is required on the factors aiding or hindering compliance with these measures.\n\nMethodsTo understand the facilitators and barriers to compliance with COVID-19 guidelines, we used structural topic modelling, a text mining technique, to extract themes from over 26,000 free-text survey responses from 17,500 UK adults, collected between 17 November and 23 December 2020.\n\nResultsThe main factors facilitating compliance were desires to reduce risk to ones self and ones family and friends and to, a lesser extent, the general public. Also of importance were a desire to return to normality, the availability of activities and technological means to contact family and friends, and the ability to work from home. Identified barriers were difficulties maintaining social distancing in public (due to the actions of other people or environmental constraints), the need to provide or receive support from family and friends, social isolation, missing loved one, and mental health impacts, perceiving the risks as low, social pressure to not comply, and difficulties understanding and keep abreast of changing rules. Several of the barriers and facilitators raised were related to participant characteristics. Notably, women were more likely to discuss needing to provide or receive mental health support from friends and family.\n\nConclusionThe results demonstrate an array of factors contribute to compliance with guidelines. Of particular policy importance, the results suggest that government communications that emphasizes the potential risks of COVID-19 and provides simple, consistent guidance on how to reduce the spread of the virus would improve compliance with preventive behaviours.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Liam Wright", - "author_inst": "University College London" - }, - { - "author_name": "Elise Paul", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.28.21258780", "rel_title": "Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections", @@ -665701,6 +663924,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.29.21259726", + "rel_title": "Prominent Spatiotemporal Waves of COVID-19 Incidence in the United States: Implications for Causality, Forecasting, and Control", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259726", + "rel_abs": "Better understanding of the spatiotemporal structure of the COVID-19 epidemic in the USA may help inform more effective prevention and control strategies. By analyzing daily COVID-19 case data in the United States, Mexico and Canada, we found four continental-scale epidemic wave patterns, including travelling waves, that spanned multiple state and even international boundaries. These major epidemic patterns co-varied strongly with continental-scale seasonal temperature change patterns. Geo-contiguous states shared similar timing and amplitude of epidemic wave patterns irrespective of similarities or differences in state government political party affiliations. These analyses provide evidence that seasonal factors, probably weather changes, have exerted major effects on local COVID-19 incidence rates. Seasonal wave patterns observed during the first year of the epidemic may become repeated in the subsequent years.\n\nOne Sentence SummaryThe COVID-19 epidemic in the United States has consisted of four continental-scale spatiotemporal waves of case incidence that have spanned multiple states and even international boundaries.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hawre Jalal", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kyueun Lee", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Donald S. Burke", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.29.21259625", "rel_title": "The Impact of Non-Pharmaceutical Interventions on the First COVID-19 Epidemic Wave in South Africa", @@ -666732,105 +664982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.23.21259402", - "rel_title": "Doctors and Nurses Social Media Ads Reduced Holiday Travel and COVID-19 infections: A cluster randomized controlled trial in 13 States", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259402", - "rel_abs": "During the COVID-19 epidemic, many health professionals started using mass communication on social media to relay critical information and persuade individuals to adopt preventative health behaviors. Our group of clinicians and nurses developed and recorded short video messages to encourage viewers to stay home for the Thanksgiving and Christmas Holidays. We then conducted a two-stage clustered randomized controlled trial in 820 counties (covering 13 States) in the United States of a large-scale Facebook ad campaign disseminating these messages. In the first level of randomization, we randomly divided the counties into two groups: high intensity and low intensity. In the second level, we randomly assigned zip codes to either treatment or control such that 75% of zip codes in high intensity counties received the treatment, while 25% of zip codes in low intensity counties received the treatment. In each treated zip code, we sent the ad to as many Facebook subscribers as possible (11,954,109 users received at least one ad at Thanksgiving and 23,302,290 users received at least one ad at Christmas). The first primary outcome was aggregate holiday travel, measured using mobile phone location data, available at the county level: we find that average distance travelled in high-intensity counties decreased by -0.993 percentage points (95% CI -1.616, -0.371, p-value 0.002) the three days before each holiday. The second primary outcome was COVID-19 infection at the zip-code level: COVID-19 infections recorded in the two-week period starting five days post-holiday declined by 3.5 percent (adjusted 95% CI [-6.2 percent, -0.7 percent], p-value 0.013) in intervention zip codes compared to control zip codes.\n\nOne sentence summaryIn a large scale clustered randomized controlled trial, short messages recorded by health professionals before the winter holidays in the United States and sent as ads to social media users led to a significant reduction in holiday travel, and to a decrease in subsequent COVID-19 infection at the population level.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Emily Breza", - "author_inst": "Harvard University, Department of Economics," - }, - { - "author_name": "Fatima Cody Stanford", - "author_inst": "Massachusetts General Hospital, Departments of Medicine and Pediatrics" - }, - { - "author_name": "Marcela Alsan", - "author_inst": "Harvard Kennedy School of Government" - }, - { - "author_name": "Burak Alsan", - "author_inst": "Online Care Group" - }, - { - "author_name": "Abhijit Banerjee", - "author_inst": "Massachusetts Institute of Technology, Department of Economics" - }, - { - "author_name": "Arun G Chandrasekhar", - "author_inst": "Stanford University, Department of Economics" - }, - { - "author_name": "Sarah Eichmeyer", - "author_inst": "Ludwig Maximilian University of Munich, Department of Economics" - }, - { - "author_name": "Traci Glushko", - "author_inst": "Bozeman Health Deaconess Hospital" - }, - { - "author_name": "Paul Goldsmith-Pinkham,", - "author_inst": "Yale University" - }, - { - "author_name": "Kelly Holland", - "author_inst": "Lynn Community Health Center" - }, - { - "author_name": "Emily Hoppe", - "author_inst": "Massachusetts General Hospital for Children, Department of Pediatrics" - }, - { - "author_name": "Mohit Karnani", - "author_inst": "Massachusetts Institute of Technology, Department of Economics" - }, - { - "author_name": "Sarah Liegl", - "author_inst": "St. Anthony North Family Medicine" - }, - { - "author_name": "Tristan Loisel", - "author_inst": "Paris School of Economics" - }, - { - "author_name": "Lucy Ogbu-Nwobodo", - "author_inst": "Massachusetts General Hospital, Department of Psychiatry" - }, - { - "author_name": "Benjamin Olken", - "author_inst": "Massachusetts Institute of Technology, Department of Economics" - }, - { - "author_name": "Carlos Torres", - "author_inst": "Massachusetts General Hospital for Children, Department of Pediatrics" - }, - { - "author_name": "Pierre-Luc Vautrey", - "author_inst": "Massachusetts Institute of Technology, Department of Economics" - }, - { - "author_name": "Erica T Warner", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Susan Wootton", - "author_inst": "McGovern Medical School at The University of Texas Health Science Center at Houston" - }, - { - "author_name": "Esther Duflo", - "author_inst": "Massachusetts Institute of Technology, Department of Economics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.06.23.21259415", "rel_title": "Use of recently vaccinated individuals to detect bias in test-negative case-control studies of COVID-19 vaccine effectiveness", @@ -667487,6 +665638,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.06.24.21255875", + "rel_title": "Genomic epidemiology of SARS-CoV-2 in Pakistan", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21255875", + "rel_abs": "Pakistan has been severely affected by the COVID-19 pandemic. To investigate the initial introductions and transmissions of the SARS-CoV-2 in the country, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected before June 1, 2020. We identified a total of 347 variants, 29 of which were over-represented in Pakistan. Meanwhile, we found over one thousand intra-host single-nucleotide variants. Several of them occurred concurrently, indicating possible interactions among them. Some of the hypermutable positions were not observed in the polymorphism data, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably contributed by a signature mutation of this cluster. Twenty-eight putative international introductions were identified, several of which were consistent with the epidemiological investigations. No progenies of any of these 150 viruses have been found outside of Pakistan, most likely due to the nonphmarcological intervention to control the virus. This study has inferred the introductions and transmissions of SARS-CoV-2 in Pakistan, which could provide a guidance for an effective strategy for disease control.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Shuhui Song", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Cuiping Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Lu Kang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Dongmei Tian", + "author_inst": "China National Center for Bioinformation" + }, + { + "author_name": "Nazish Badar", + "author_inst": "Pakistan National Institute of Health" + }, + { + "author_name": "Wentai Ma", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Shilei Zhao", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Xuan Jiang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Chun Wang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Yongqiao Sun", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Wenjie Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Meng Lei", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Shuangli Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Qiuhui Qi", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Aamer Ikram", + "author_inst": "Pakistan National Institute of Health" + }, + { + "author_name": "Muhammad Salman", + "author_inst": "Pakistan National Institute of Health" + }, + { + "author_name": "Massab Umair", + "author_inst": "Pakistan National Institute of Health" + }, + { + "author_name": "Huma Shireen", + "author_inst": "Quaid-i-Azam University" + }, + { + "author_name": "Fatima Batool", + "author_inst": "Quaid-i-Azam University" + }, + { + "author_name": "Bing Zhang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Hua Chen", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Yungui Yang", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Amir Ali Abbasi", + "author_inst": "Quaid-i-Azam University" + }, + { + "author_name": "Mingkun Li", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Yongbiao Xue", + "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation)" + }, + { + "author_name": "Yiming Bao", + "author_inst": "China National Center for Bioinformation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.23.21259020", "rel_title": "Low frequency of community-acquired bacterial co-infection in patients hospitalized for COVID-19 based on clinical, radiological and microbiological criteria; a retrospective cohort study.", @@ -668678,93 +666948,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.28.21259661", - "rel_title": "Proxalutamide (GT0918) Reduction of Mortality Rate in Hospitalized COVID-19 Patients Depends on Treatment Duration - an Exploratory Analysis of the Proxa-Rescue AndroCoV Trial", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259661", - "rel_abs": "IntroductionProxalutamide, a second-generation non-steroidal antiandrogen (NSAA), primarily developed for castration-resistant prostate cancer, demonstrated reduction in 28-day mortality rate of 77.7% in hospitalized COVID-19 patients in a double-blind, placebo-controlled, two-arm randomized clinical trial (RCT), through intention-to-treat (ITT) analysis. We observed a high 28-day mortality rate of patients that did not complete the 14-day treatment with proxalutamide, compared to the placebo arm. These differences may raise hypotheses to explain the wide differences between ITT and on-treatment (OT) analysis in terms of efficacy. Despite the inherent limitations of OT analysis, we aimed to respond to unanswered questions regarding the drug efficacy when the 14-day treatment with proxalutamide was complete, and secondarily understand the causality relationship between treatment interruption and mortality rate.\n\nMethodsThis is a post-hoc exploratory analysis of a double-blinded, randomized, placebo-controlled, prospective, multicentric, two-arm RCT of 300mg-daily 14-day proxalutamide therapy for hospitalized COVID-19 patients not requiring mechanical ventilation. OT population excluded patients that did not complete the full 14-day course of therapy or died from COVID-19 complications within 24 hours of randomization. The primary outcome was the 28-day COVID-19 mortality rate. Secondary outcomes included median hospital length, 14-day and 28-day alive hospital discharge rate and 28-day all-cause mortality rate of those who discontinued intervention.\n\nResultsIn total, 580 patients completed the 14-day treatment or died during treatment, including 288 patients in the proxalutamide arm and 292 patients in the placebo arm, with similar baseline characteristics between groups. The 28-day COVID-19 mortality rate was 4.2% in the proxalutamide group and 49.0% in the placebo group. The mortality risk ratio (RR) was 0.08 (95% CI, 0.05-0.15), with a number needed to treat (NNT) of 2.2 to prevent death. The median hospital length stay after randomization was 5 days (interquartile range [IQR] = 3 to 7.2 days) in the proxalutamide group and 9 days (IQR = 6 to 15 days) in the placebo group (p <0.001). The 28-day all-cause mortality rate of patients that received proxalutamide but interrupted treatment before 14 days was 79.3%, while those that received placebo and interrupted before 14 days was 52.8% (p = 0.054 between groups).\n\nConclusionThe reduction in 28-day all-cause mortality rate with 14-day proxalutamide treatment for hospitalized COVID-19 patients was more significant while on treatment adhesion (92%), compared to the reduction when all patients enrolled in the proxalutamide arm were considered (77.7%). However, the magnitude of statistical significance of the reduction in all-cause mortality and the NNT were similar between the OT and ITT analysis. The apparent high mortality risk rate with early interruption of proxalutamide treatments suggests that strategies for treatment compliance should be reinforced for future RCTs with proxalutamide. (NCT04728802)", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Ricardo A Zimerman", - "author_inst": "Hospital da Brigada Militar, Porto Alegre, Brazil" - }, - { - "author_name": "Daniel N Fonseca", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Michael N Correia", - "author_inst": "Hospital Regional Jose Mendes, Itacoatiara, Amazonas, Brazil" - }, - { - "author_name": "Renan N Barros", - "author_inst": "Hospital Municipal Jofre Cohen, Parintins, Amazonas, Brazil" - }, - { - "author_name": "Dirce C Onety", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Karla Cristina P Israel", - "author_inst": "Centro de Doencas Renais do Amazonas, Manaus, Brazil; Programa de Pos-Graduacao em Medicina Tropical - FMT/UEA, Manaus, Brazil" - }, - { - "author_name": "Emilyn O Guerreiro", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Jose Enrique M Medeiros", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Raquel N Nicolau", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Luiza Fernanda M Nicolau", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Patricia S da Silva", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Rafael X Cunha", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Maria Fernanda R Barroco", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Raysa WS Paulain", - "author_inst": "Hospital Municipal Jofre Cohen, Parintins, Amazonas, Brazil" - }, - { - "author_name": "Claudia E Thompson", - "author_inst": "Department of Pharmacosciences, Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Andy Goren", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA." - }, - { - "author_name": "Carlos Gustavo Wambier", - "author_inst": "Warren Alpert Medical School of Brown University" - }, - { - "author_name": "Flavio A Cadegiani", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA; Corpometria Institute, Brasilia, Brazil." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.02.450920", "rel_title": "Betacoronavirus-specific alternate splicing", @@ -669625,6 +667808,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.06.30.21259439", + "rel_title": "Efficacy, safety, and lot to lot immunogenicity of an inactivated SARS-CoV-2 vaccine (BBV152): a double-blind, randomised, controlled phase 3 trial", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259439", + "rel_abs": "BackgroundWe report the clinical efficacy against COVID-19 infection of BBV152, a whole-virion inactivated SARS-CoV-2 vaccine formulated with a Toll-like receptor 7/8 agonist molecule adsorbed to alum (Algel-IMDG).\n\nMethodsWe did a double-blind, randomised, multicentre, phase 3 clinical trial in 25 Indian hospitals to evaluate the efficacy, safety, and immunological lot consistency of BBV152. Healthy adults (age 18-98 years) randomised 1:1 using a computer-generated randomisation scheme received two intramuscular doses of vaccine or placebo administered four weeks apart. The primary outcome was laboratory-confirmed symptomatic COVID-19, occurring at least 14 days after the second dose. Secondary outcomes were efficacy in sub-groups for age (18-< 60 years and [≥] 60 years) and in participants with pre-existing stable medical conditions. We also evaluated safety, reactogenicity, and consistency of immune responses for three consecutive manufacturing lots.\n\nFindingsBetween November 16, 2020 and January 7, 2021 we recruited 25,798 participants who were randomised to BBV152 or placebo groups; 24,419 received two doses of BBV152 (n = 12,221) or placebo (n = 12,198). In a case-driven analysis, 130 cases of symptomatic COVID-19 were reported in 16,973 (0{middle dot}77%) participants with follow-up at least two weeks after the second vaccination; 24 occurred in the vaccine group and 106 in placebo recipients giving an overall vaccine efficacy of 77{middle dot}8% (95% CI: 65{middle dot}2-86{middle dot}4). Sixteen cases, one vaccinee and 15 placebo recipients, met the severe symptomatic COVID-19 case definition giving a vaccine efficacy of 93{middle dot}4% (57{middle dot}1-99{middle dot}8). Efficacy against asymptomatic COVID-19 was 63{middle dot}6% (29{middle dot}0-82{middle dot}4). BBV152 conferred 65{middle dot}2% (95% CI: 33{middle dot}1-83{middle dot}0) protection against the SARS-CoV-2 Variant of Concern, B.1.617.2 (Delta). BBV152 was well tolerated with no clinically or statistically significant differences in the distributions of solicited, unsolicited, or serious adverse events between vaccine and placebo groups. No cases of anaphylaxis or vaccine-related deaths were reported.\n\nInterpretationBBV152 was immunogenic and highly efficacious against symptomatic and asymptomatic COVID-19 variant associated disease, particularly against severe disease in adults. Vaccination was well tolerated with an overall incidence of adverse events observed over a median of 146 days that was lower than that observed with other COVID-19 vaccines.\n\nFundingThis work was supported and funded by Bharat Biotech International Limited and partly co-funded by the Indian Council of Medical Research.\n\nClinicaltrials.gov: NCT04641481", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Raches Ella MBBS, MS", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Siddharth Reddy MSc", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "William Blackwelder PhD", + "author_inst": "WB Statistical Consulting LLC" + }, + { + "author_name": "Varsha Potdar PhD", + "author_inst": "Indian Council of Medical Research-National Institute of Virology" + }, + { + "author_name": "Pragya Yadav PhD", + "author_inst": "Indian Council of Medical Research-National Institute of Virology" + }, + { + "author_name": "Vamshi Sarangi BSc", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Vinay Kumar Aileni PhD", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Suman Kanungo MD", + "author_inst": "Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases" + }, + { + "author_name": "Sanjay Rai MD", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Prabhakar Reddy MD", + "author_inst": "Nizams Institute of Medical Sciences" + }, + { + "author_name": "Savitha Verma MD", + "author_inst": "Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences" + }, + { + "author_name": "Chandramani Singh MD", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Sagar Redkar MD", + "author_inst": "Redkar Hospital" + }, + { + "author_name": "Satyajit Mohapatra MD", + "author_inst": "SRM Hospital and Research Centre" + }, + { + "author_name": "Anil Pandey MD", + "author_inst": "ESIC Medical College and Hospital" + }, + { + "author_name": "Pajanivel Ranganadin MD", + "author_inst": "Mahatma Gandhi Medical College" + }, + { + "author_name": "Raghavendra Gumashta MD", + "author_inst": "Peoples university" + }, + { + "author_name": "Manish Multani MD", + "author_inst": "Rahate Surgical Hospital" + }, + { + "author_name": "Shameem Mohammad MD", + "author_inst": "Aligarh Muslim University" + }, + { + "author_name": "Parul Bhatt MD", + "author_inst": "GMERS Medical College and Civil Hospital" + }, + { + "author_name": "Laxmi Kumari MD", + "author_inst": "Government Fever Hospital" + }, + { + "author_name": "Gajanan Sapkal PhD", + "author_inst": "Indian Council of Medical Research-National Institute of Virology-Pune" + }, + { + "author_name": "Nivedita Gupta MD", + "author_inst": "Indian Council of Medical Research" + }, + { + "author_name": "Priya Abraham PhD", + "author_inst": "Indian Council of Medical Research-National Institute of Virology-Pune" + }, + { + "author_name": "Samiran Panda MD", + "author_inst": "Indian Council of Medical Research" + }, + { + "author_name": "Sai Prasad MBA", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Balram Bhargava MD", + "author_inst": "Indian Council of Medical Research" + }, + { + "author_name": "Krishna Ella PhD", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Krishna Mohan Vadrevu PhD", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "- COVAXIN Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.28.21259639", "rel_title": "COVID-19 Has Long Term Effects on Chemosensory Functions", @@ -670928,65 +669246,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.06.23.21259400", - "rel_title": "Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record", - "rel_date": "2021-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259400", - "rel_abs": "BackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021.\n\nMethodsWe conducted a descriptive time series analysis utilising data from the Greater Manchester Care Record, which contains de-identified, primary care health records of 2.8 million patients. Counts of incident and all episodes of self-harm recorded between 1st January 2019 and 31st May 2021 were made for all patients, with stratification by sex, age group, ethnicity, and index of multiple deprivation (IMD) quintile and examination of overall differences by national and regional restriction phases.\n\nFindingsBetween 1st January 2019 and 31st May 2021, 33,444 episodes of self-harm by 13,148 individuals were recorded. Frequency ratios of incident and all episodes of self-harm were 0.59 (95% CI 0.51 to 0.69) and 0.69 (CI 0.63 to 0.75) respectively in April 2020 compared to February 2020. Between August 2020 and May 2021 frequency ratios were 0.92 (CI 0.88 to 0.96) for incident episodes and 0.86 (CI 0.84 to 0.88) for all episodes compared to the same months in 2019. Reductions were largest among men and people living in the most deprived neighbourhoods. An increase in all-episode self-harm (frequency ratio 1.09, CI 1.03 to 1.16) was observed for adolescents aged 10-17 between August 2020 and May 2021.\n\nInterpretationThe COVID-19 pandemic has had a sustained impact on help seeking for self-harm. Reductions in primary care recorded self-harm have implications for clinicians ability to assess the needs and risks of individuals. Some patients may be experiencing prolonged untreated deterioration in their mental health while other groups are presenting in higher numbers. Our findings have important implications for primary care and mental health services in manging ongoing demand.\n\nFundingUKRI COVID-19 Rapid Response Initiative (grant reference COV0499), University of Manchester Presidential Fellowship (SS), and NIHR Greater Manchester Patient Safety Translational Research Centre.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sarah Steeg", - "author_inst": "University of Manchester" - }, - { - "author_name": "Lana Bojani\u0107", - "author_inst": "University of Manchester" - }, - { - "author_name": "George Tilston", - "author_inst": "University of Manchester" - }, - { - "author_name": "Richard Williams", - "author_inst": "University of Manchester" - }, - { - "author_name": "David A Jenkins", - "author_inst": "University of Manchester" - }, - { - "author_name": "Matthew J Carr", - "author_inst": "University of Manchester" - }, - { - "author_name": "Niels Peek", - "author_inst": "University of Manchester" - }, - { - "author_name": "Darren M Ashcroft", - "author_inst": "University of Manchester" - }, - { - "author_name": "Nav Kapur", - "author_inst": "University of Manchester" - }, - { - "author_name": "Jennifer Voorhees", - "author_inst": "University of Manchester" - }, - { - "author_name": "Roger T Webb", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2021.06.28.21259576", "rel_title": "Immunogenicity of COVID-19 Vaccination in Immunocompromised Patients: An Observational, Prospective Cohort Study Interim Analysis", @@ -671663,6 +669922,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.29.450378", + "rel_title": "Comparative computational modeling of the bat and human immune response to viral infection with the Comparative Biology Immune Agent Based Model", + "rel_date": "2021-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.29.450378", + "rel_abs": "Given the impact of pandemics due to viruses of bat origin there is increasing interest in comparative investigation into the differences between bat and human immune responses. The practice of comparative biology can be enhanced by computational methods used for dynamic knowledge representation to visualize and interrogate the putative differences between the two systems. We present an agent-based model that encompasses and bridges the differences between bat and human responses to viral infection: the Comparative Biology Immune Agent-based Model, or CBIABM. The CBIABM examines differences in innate immune mechanisms between bats and humans, specifically regarding inflammasome activity and Type 1 Interferon dynamics, in terms of tolerance to viral infection. Simulation experiments with the CBIABM demonstrate the efficacy of bat-related features in conferring viral tolerance and also suggest a crucial role for endothelial inflammasome activity as a mechanism for bat systemic viral tolerance and affecting the severity of disease in human viral infections. We hope that this initial study will inspire additional comparative modeling projects to link, compare, and contrast immunological functions shared across different species, and in so doing, provide insight and aid in the preparation for future viral pandemics of zoonotic origin.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chase Cockrell", + "author_inst": "University of Vermont Larner College of Medicine" + }, + { + "author_name": "Gary An", + "author_inst": "University of Vermont Larner College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.29.450453", "rel_title": "Highly-Neutralizing COVID-19-Convalescent-Plasmas Potently Block SARS-CoV-2 Replication and Pneumonia in Syrian Hamsters.", @@ -672718,145 +671000,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.23.21259366", - "rel_title": "Japanese Project for Telepsychiatry Evaluation during COVID-19: Treatment Comparison Trial (J-PROTECT): Rationale, design, and methodology", - "rel_date": "2021-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259366", - "rel_abs": "IntroductionThe COVID-19 pandemic has had a profound impact on the mental health of people around the world. Anxiety related to infection, stress and stigma caused by the forced changes in daily life have reportedly increased the incidence and symptoms of depression, anxiety disorder and obsessive-compulsive disorder. Under such circumstances, telepsychiatry is gaining importance and attracting a great deal of attention. However, few large pragmatic clinical trials on the use of telepsychiatry targeting multiple psychiatric disorders have been conducted to date.\n\nMethodsThe targeted study cohort will consist of adults (>18 years) who meet the DSM-5 diagnostic criteria for either (1) depressive disorders, (2) anxiety disorders, or (3) obsessive-compulsive and related disorders. Patients will be assigned in a 1:1 ratio to either a \"telepsychiatry group\" (at least 50% of visits to be conducted using telemedicine, with at least one face-to-face treatment [FTF] every six months) or an \"FTF group\" (all visits to be conducted FTF, with no telemedicine). Both groups will receive the usual treatment covered by public medical insurance. The study will utilize a master protocol design in that there will be primary and secondary outcomes for the entire group regardless of diagnosis, as well as the outcomes for each individual disorder group.\n\nDiscussionThis study will be a non-inferiority trial to test that the treatment effect of telepsychiatry is not inferior to that of FTF alone. This study will provide useful insights into the effect of the COVID-19 pandemic on the practice of psychiatry.\n\nTrial RegistrationjRCT1030210037, Japan Registry of Clinical Trials (jRCT)", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Taishiro Kishimoto", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Shotaro Kinoshita", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Shogyoku Bun", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yasunori Sato", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Momoko Kitazawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Toshiaki Kikuchi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mitsuhiro Sado", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Akihiro Takamiya", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masaru Mimura", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Takashi Nakamae", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Yoshinari Abe", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Tetsufumi Kanazawa", - "author_inst": "Osaka Medical and Pharmaceutical University" - }, - { - "author_name": "Yasuo Kawabata", - "author_inst": "Osaka Medical and Pharmaceutical University" - }, - { - "author_name": "Hiroaki Tomita", - "author_inst": "Tohoku University Hospital" - }, - { - "author_name": "Koichi Abe", - "author_inst": "Tohoku University Hospital" - }, - { - "author_name": "Akitoyo Hishimoto", - "author_inst": "Yokohama City University Graduate School of Medicine" - }, - { - "author_name": "Takeshi Asami", - "author_inst": "Yokohama City University Graduate School of Medicine" - }, - { - "author_name": "Akira Suda", - "author_inst": "Yokohama City University Graduate School of Medicine" - }, - { - "author_name": "Yoshinori Watanabe", - "author_inst": "Himorogi Psychiatric Institute" - }, - { - "author_name": "Toru Amagai", - "author_inst": "Amagai Mental Clinic" - }, - { - "author_name": "Kei Sakuma", - "author_inst": "Asaka Hospital" - }, - { - "author_name": "Hisashi Kida", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Michitaka Funayama", - "author_inst": "Ashikaga Red Cross Hospital" - }, - { - "author_name": "Hiroshi Kimura", - "author_inst": "School of Medicine, International University of Health and Welfare" - }, - { - "author_name": "Aiko Sato", - "author_inst": "School of Medicine, International University of Health and Welfare" - }, - { - "author_name": "Shuichiro Fujiwara", - "author_inst": "Kanazawabunko Yell Clinic" - }, - { - "author_name": "Kiichiro Nagao", - "author_inst": "Neyagawa Sanatoriumu" - }, - { - "author_name": "Naoya Sugiyama", - "author_inst": "Numazu Chuo Hospital" - }, - { - "author_name": "Maki Takamiya", - "author_inst": "Takamiya Hospital" - }, - { - "author_name": "Hideyuki Kodama", - "author_inst": "Takamiya Hospital" - }, - { - "author_name": "Takaharu Azekawa", - "author_inst": "Shioiri Mental Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.06.24.21259505", "rel_title": "Assessment of COVID-19 vaccine hesitancy among Zimbabweans: A rapid national survey", @@ -673765,6 +671908,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.21.21259299", + "rel_title": "Meta-analytical evidence on mental disorder symptoms during the COVID-19 pandemic in Latin America", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259299", + "rel_abs": "ObjectiveThere is a lack of evidence related to the prevalence of mental disorder symptoms as well as their heterogeneities during the COVID-19 pandemic in Latin America, a continent across the equators. The current study aims to provide meta-analytical evidence on mental disorder symptoms during COVID-19 among frontline healthcare workers, general healthcare workers, the general population, and university students in Latin America.\n\nMethodsBibliographical databases, such as PubMed, Embase, Web of Sciences, PsycINFO, and medRxiv, were systematically searched to identify pertinent studies up to Februry 6, 2021. Two coders performed the screening using predefined eligibility criteria. Studies were assigned quality scores using the Mixed Methods Appraisal Tool. The double data extraction method was used to minimize data entry errors.\n\nResultsA total of 33 studies with 101,772 participants in Latin America were identified. The pooled prevalence of anxiety, depression, distress, and insomnia was 32%, 27%, 32%, and 35%, respectively. There was a higher prevalence of mental health symptoms in South America compared to Central America (33% vs. 27%, p <0.001). The pooled prevalence of mental health symptoms in the general population, general healthcare workers, frontline healthcare workers, and students in Latin America was 33%, 31%, 37%, and 36%, respectively.\n\nConclusionThe high yet heterogenous level of prevalence of mental disorder symptoms emphasizes the need for appropriate identification of psychological interventions in Latin America.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Stephen X. Zhang", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Kavita Batra", + "author_inst": "University of Nevada" + }, + { + "author_name": "Tao Liu", + "author_inst": "Southwest University" + }, + { + "author_name": "Rebecca Kechen Dong", + "author_inst": "University of South Australia" + }, + { + "author_name": "Wen Xu", + "author_inst": "University of Nottingham Ningbo China" + }, + { + "author_name": "Allen Yin", + "author_inst": "Southeast University" + }, + { + "author_name": "Andrew Delios", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Bryan Z. Chen", + "author_inst": "Crescent Valley High School" + }, + { + "author_name": "Richard Z. Chen", + "author_inst": "Crescent Valley High School" + }, + { + "author_name": "Saylor Miller", + "author_inst": "Oregon State University" + }, + { + "author_name": "Xue Wan", + "author_inst": "Tongji University" + }, + { + "author_name": "Jiyao Chen", + "author_inst": "Oregon State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.21.21259237", "rel_title": "Changes in mobility pre and post first SARS-CoV-2 vaccination: findings from a prospective community cohort study including GPS movement tracking in England and Wales (Virus Watch)", @@ -675336,61 +673542,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.25.449990", - "rel_title": "Effect of prophylactic use of intra-nasal oil formulations in the hamster model of Covid-19", - "rel_date": "2021-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.25.449990", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection initiates with viral entry in upper respiratory tract leading to coronavirus disease 2019 (Covid-19). Severe Covid-19 is characterized by pulmonary pathologies associated with respiratory failure. Thus, therapeutics aimed at inhibiting entry of the virus or its internalization in the upper respiratory tract, are of interest. Herein, we report the prophylactic application of two intra-nasal formulations provided by the National Medicinal Plant Board (NMPB), Anu oil and Til tailya in SARS-CoV2 infection hamster model. Prophylactic nasal instillation of these oil formulations exhibited reduced viral load in lungs, and resulted in reduced body weight loss and pneumonitis. In line with reduced viral load, histopathlogical analysis revealed a reduction in lung pathology in Anu oil group as compared to the control infected group. However, Til tailya group did not show a significant reduction in lung pathology. Furthermore, molecular analysis using mRNA expression profiling indicated reduced expression of pro-inflammatory cytokines genes, including Th1 and Th17 cytokines for both the intra-nasal formulations as a result of decreased viral load. Together, the prophylactic intra-nasal application of Annu oil seems to be useful in limiting both the viral load and disease severity disease in SARS-CoV2 infection in hamster model.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zaigham Abbas Rizvi", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Manas Ranjan Tripathy", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Nishant Sharma", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Sandeep Goswami", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "N Srikanth", - "author_inst": "Central Council for Ayurvedic Sciences, New Delhi" - }, - { - "author_name": "JLN Shastry", - "author_inst": "National Medicinal Plants Board, Ministry of AYUSH, New Delhi" - }, - { - "author_name": "Shailendra Mani", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Milan Surjit", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Amit Awasthi", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Madhu Dikshit", - "author_inst": "Translational Health Science and Technology Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.28.449914", "rel_title": "Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants", @@ -676375,6 +674526,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.06.20.21259177", + "rel_title": "The evaluation of factors affecting antibody response after administration of the BNT162b2 vaccine: A prospective study in Japan", + "rel_date": "2021-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21259177", + "rel_abs": "The aim of this study was to evaluate the antibody reaction after administration of the BNT162b2 vaccine, and to reveal the factors that affect antibody production. This prospective study was carried out in the Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital, in Tokyo, Japan, from April 15, 2021 to June 09, 2021. All our hospitals workers who were administered the BNT162b2 vaccine as part of a routine program were included in this study.\n\nWe calculated the anti-SARS-CoV-2 spike-specific antibody titter 1) before vaccination, 2) seven to twenty days after the first vaccination, and 3) seven to twenty days after the second vaccination.\n\nThe low-antibody titer group (LABG) was defined as the group having less than 25 percentiles of antibody titer. Univariate and Multivariate logistic regression analysis were performed to ascertain the effects of factors on the likelihood of LABG. 374 participants were eventually included in our study, and they were divided into 94 LABG and 280 non-LABG. All samples showed significant antibody elevation in the second antibody test, with a mean value of 3476 U/mL. When comparing the LABG and non-LABG groups, the median age, blood sugar, and HbA1c were significantly higher in the LABG group. The rates of participants with low BMI (<18.5) and high BMI (>30) were significantly higher in the LABG group. The proportion of chronic lung disease, hypertension, diabetes, dyslipidemia, autoimmune disease, and cancer were significantly higher in the LABG group. Although there was no significant difference confirmed with respect to the exercise hours per day, the proportion of participants that did not perform outdoor activities was significantly higher in the LABG group. The time interval between the second vaccination and the second antibody test, and between the first and the second vaccination was significantly longer in the non-LABG group.\n\nOur logistic regression analysis revealed that the age, obesity, hypertension, diabetes, dyslipidemia, antihypertensive drug, antilipid drug, {gamma}-GT, BS, HbA1c, and lack of outdoor activity were significant suppressors of antibody reaction, whereas maintaining the appropriate time interval between the first and the second vaccination could promote a significant antibody response. In the multivariate logistic regression analysis, age, obesity, and lack of outdoor activities were significant suppressors of antibody reaction, whereas the length of days from the first to the second vaccination promoted a significant antibody response.\n\nOur single-center study demonstrates that age, obesity, and lack of outdoor activities were significant suppressors of antibody response, whereas maintaining the appropriate time interval between the first and the second vaccination could promote a significant antibody response. Evidence from multi-center studies is needed to develop further vaccination strategies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Toshiya Mitsunaga", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + }, + { + "author_name": "Yuhei Ohtaki", + "author_inst": "Jikei university school of medicine" + }, + { + "author_name": "Yutaka Seki", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + }, + { + "author_name": "Masakata Yoshioka", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + }, + { + "author_name": "Hiroshi Mori", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + }, + { + "author_name": "Midori Suzuka", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + }, + { + "author_name": "Syunsuke Mashiko", + "author_inst": "Jikei university school of medicine" + }, + { + "author_name": "Satoshi Takeda", + "author_inst": "Jikei university school of medicine" + }, + { + "author_name": "Kunihiro Mashiko", + "author_inst": "Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.20.21259167", "rel_title": "Effectiveness of Face Masks in Blocking the Transmission of SARS-CoV-2: a Preliminary Evaluation of Masks Used by SARS-CoV-2-Infected Individuals", @@ -677594,37 +675796,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.20.21259216", - "rel_title": "Impact of COVID-19 on deaths from respiratory diseases: Panel Data evidence from Chile.", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21259216", - "rel_abs": "The COVID-19 pandemic has left other pathologies commonly present in the population in a secondary context. Therefore, it is necessary to study the evolution of these diseases in the presence or absence of COVID-19.\n\nObjectivesThe present study had the following objectives: 1. To evaluate the relationship between the COVID-19 epidemic and the possible decrease in deaths from respiratory diseases in Chile. 2 Study the relationship between meteorological variables and severity of COVID-19 with respect to deaths from respiratory diseases from January 2018 to February 2021.\n\nMethodsThe variable number of deaths due to respiratory diseases in Chile was analyzed considering the monthly records of meteorological variables (temperature, precipitation and humidity) in each Region of Chile and severity of COVID-19, to evaluate the mortality trend before and after the pandemic. For this, different Non-Observable Heterogeneity Models for Panel Data were used\n\nResultsOur findings show that among the variables that affect the mortality rate from respiratory diseases, there are the number of deaths from COVID-19 that has a negative effect, the number of patients with COVID-19 in intensive care unit (ICU) that has a positive effect and the minimum temperature with a negative effect. These results are supported by the application of the panel regression with one-way random-effects models.\n\nConclusionThis study revealed that there is an unexpected reduction in deaths from respiratory diseases in Chile in the post-pandemic period. Therefore, it can be concluded that this variable decreased with the appearance of the COVID-19 pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Claudia Barria Sandoval", - "author_inst": "Universidad de las Americas" - }, - { - "author_name": "Angie Mendez", - "author_inst": "Universidad de Concepcion" - }, - { - "author_name": "Guillermo Ferreia", - "author_inst": "Universidad de Concepcion" - }, - { - "author_name": "Maria Cecilia Toffoletto", - "author_inst": "Universidad de las Americas" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.22.21258971", "rel_title": "Temporal Analysis of Social Determinants Associated with COVID-19 Mortality", @@ -678241,6 +676412,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.23.21259176", + "rel_title": "Averting an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a university residence hall through wastewater surveillance", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259176", + "rel_abs": "A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by RT-qPCR in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore Swab approach, SARS-CoV-2 was detected in wastewater samples on just two days after passive samplers were activated. These samples were also positive for the B.1.1.7 (Alpha) Variant of Concern (VOC) by RT-qPCR. The positive result triggered a public health case finding response including a mobile testing unit deployed to the residence hall the following day with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of B.1.1.7 variant COVID-19. These individuals were re-located to a separate quarantine facility averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the B.1.1.7 VOC of SARS-CoV-2 in individuals from a non-clinical setting.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Ryland Corchis-Scott", + "author_inst": "University of Windsor" + }, + { + "author_name": "Qiudi Geng", + "author_inst": "University of Windsor" + }, + { + "author_name": "Rajesh Seth", + "author_inst": "University of Windsor" + }, + { + "author_name": "Rajan Ray", + "author_inst": "University of Windsor" + }, + { + "author_name": "Mohsan Beg", + "author_inst": "University of Windsor" + }, + { + "author_name": "Nihar Biswas", + "author_inst": "University of Windsor" + }, + { + "author_name": "Lynn Charron", + "author_inst": "University of Windsor" + }, + { + "author_name": "Kenneth G. Drouillard", + "author_inst": "University of Windsor" + }, + { + "author_name": "Ramsey D'Souza", + "author_inst": "Windsor-Essex County Health Unit" + }, + { + "author_name": "Daniel D. Heath", + "author_inst": "University of Windsor" + }, + { + "author_name": "Chris Houser", + "author_inst": "University of Windsor" + }, + { + "author_name": "Felicia Lawal", + "author_inst": "Windsor-Essex County Health Unit" + }, + { + "author_name": "James McGinlay", + "author_inst": "University of Windsor" + }, + { + "author_name": "Sherri Lynne Menard", + "author_inst": "University of Windsor" + }, + { + "author_name": "Lisa A. Porter", + "author_inst": "University of Windsor" + }, + { + "author_name": "Diane Rawlings", + "author_inst": "University of Windsor" + }, + { + "author_name": "Yufeng Tong", + "author_inst": "University of Windsor" + }, + { + "author_name": "Matthew L Scholl", + "author_inst": "University of Windsor" + }, + { + "author_name": "K. W. Michael Siu", + "author_inst": "University of Windsor" + }, + { + "author_name": "Christopher G. Weisener", + "author_inst": "University of Windsor" + }, + { + "author_name": "Steven W. Wilhelm", + "author_inst": "The University of Tennessee" + }, + { + "author_name": "R. Michael L. McKay", + "author_inst": "University of Windsor" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.24.21259283", "rel_title": "Diet quality and risk and severity of COVID-19: a prospective cohort study", @@ -679148,149 +677422,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.24.21259277", - "rel_title": "Risk factors for long COVID: analyses of 10 longitudinal studies and electronic health records in the UK", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259277", - "rel_abs": "BackgroundThe impact of long COVID is considerable, but risk factors are poorly characterised. We analysed symptom duration and risk factor from 10 longitudinal study (LS) samples and electronic healthcare records (EHR).\n\nMethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 participants in the UK LS, and 3,327 adults with COVID-19, were assigned a long COVID code from 1,199,812 individuals in primary care EHR. Outcomes for LS included symptom duration lasting 4+ weeks (long COVID) and 12+ weeks. Association with of age, sex, ethnicity, socioeconomic factors, smoking, general and mental health, overweight/obesity, diabetes, hypertension, hypercholesterolaemia, and asthma was assessed.\n\nResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%).\n\nConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Ellen J. Thompson", - "author_inst": "King's College London" - }, - { - "author_name": "Dylan M. Williams", - "author_inst": "University College London" - }, - { - "author_name": "Alex J. Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ruth E. Mitchell", - "author_inst": "University of Bristol" - }, - { - "author_name": "Claire L. Niedzwiedz", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Tiffany C. Yang", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Charlotte Huggins", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Alex S. F. Kwong", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard Silverwood", - "author_inst": "University College London" - }, - { - "author_name": "Giorgio Di Gessa", - "author_inst": "University College London" - }, - { - "author_name": "Ruth C. E. Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Kate Northstone", - "author_inst": "University of Bristol" - }, - { - "author_name": "Bo Hou", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Michael J. Green", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Brian Dodgeon", - "author_inst": "University College London" - }, - { - "author_name": "Katie J. Doores", - "author_inst": "King's College London" - }, - { - "author_name": "Emma Duncan", - "author_inst": "King's College London" - }, - { - "author_name": "Frances M. K. Williams", - "author_inst": "King's College London" - }, - { - "author_name": "- OpenSAFELY Collaborative", - "author_inst": "" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "David J. Porteous", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Rosemary R. C. McEachan", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "University College London" - }, - { - "author_name": "George B. Ploubidis", - "author_inst": "University College London" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Kate Tilling", - "author_inst": "University of Bristol" - }, - { - "author_name": "Christopher T. Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nicholas J. Timpson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "University College London" - }, - { - "author_name": "Claire J. Steves", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.24.449840", "rel_title": "Phylogenetic network analysis revealed the recombinant origin of the SARS-CoV-2 VOC202012/01 (B.1.1.7) variant first discovered in U.K.", @@ -679827,6 +677958,273 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.21.21257822", + "rel_title": "Identification of driver genes for severe forms of COVID-19 in a deeply phenotyped young patient cohort", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21257822", + "rel_abs": "The etiopathogenesis of severe COVID-19 remains unknown. Indeed given major confounding factors (age and co-morbidities), true drivers of this condition have remained elusive. Here, we employ an unprecedented multi-omics analysis, combined with artificial intelligence, in a young patient cohort where major co-morbidities have been excluded at the onset. Here, we established a three-tier cohort of individuals younger than 50 years without major comorbidities. These included 47 \"critical\" (in the ICU under mechanical ventilation) and 25 \"non-critical\" (in a noncritical care ward) COVID-19 patients as well as 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cells proteomics, cytokine profiling and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing and structural causal modeling led to key findings. Critical patients were characterized by exacerbated inflammation, perturbed lymphoid/myeloid compartments, coagulation and viral cell biology. Within a unique gene signature that differentiated critical from noncritical patients, several driver genes promoted severe COVID-19 among which the upregulated metalloprotease ADAM9 was key. This gene signature was replicated in an independent cohort of 81 critical and 73 recovered COVID-19 patients, as were ADAM9 transcripts, soluble form and proteolytic activity. Ex vivo ADAM9 inhibition affected SARS-CoV-2 uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, COVID-19 cohort, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. The key driver, ADAM9, interfered with SARS-CoV-2 biology. A repositioning strategy for anti-ADAM9 therapeutic is feasible.\n\nOne sentence summaryEtiopathogenesis of severe COVID19 in a young patient population devoid of comorbidities.", + "rel_num_authors": 63, + "rel_authors": [ + { + "author_name": "Raphael Carapito", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Richard Li", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Julie Helms", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Christine Carapito", + "author_inst": "Laboratoire de Spectrometrie de Masse BioOrganique, Universite de Strasbourg, CNRS, IPHC, UMR 7178 ; 67000, Strasbourg, France. Federation Hospitalo-Universitai" + }, + { + "author_name": "Sharvari Gujja", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Veronique Rolli", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Raony Guimaraes", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Jose Malagon-Lopez", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Perrine Spinnhirny", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Razieh Mohseninia", + "author_inst": "Center for Quantum Information Science and Technology, University of Southern California; Los Angeles, 90089-0484 CA, USA." + }, + { + "author_name": "Aurelie Hirschler", + "author_inst": "Laboratoire de Spectrometrie de Masse BioOrganique, Universite de Strasbourg, CNRS, IPHC, UMR 7178 ; 67000, Strasbourg, France. Federation Hospitalo-Universitai" + }, + { + "author_name": "Leslie Muller", + "author_inst": "Laboratoire de Spectrometrie de Masse BioOrganique, Universite de Strasbourg, CNRS, IPHC, UMR 7178 ; 67000, Strasbourg, France. Federation Hospitalo-Universitai" + }, + { + "author_name": "Paul Bastard", + "author_inst": "St Giles laboratory of human genetics of infectious diseases, Rockefeller Branch, The Rockefeller University; New York, NY 10065, USA. Laboratory of human genet" + }, + { + "author_name": "Adrian Gervais", + "author_inst": "Laboratory of human genetics of infectious diseases, Necker Branch, INSERM, Necker Hospital for Sick Children; 75015 Paris, France. University of Paris, Imagine" + }, + { + "author_name": "Qian Zhang", + "author_inst": "St Giles laboratory of human genetics of infectious diseases, Rockefeller Branch, The Rockefeller University; New York, NY 10065, USA. Laboratory of human genet" + }, + { + "author_name": "Francois Danion", + "author_inst": "Department of Infectious and Tropical Diseases, Hopitaux Universitaires de Strasbourg ; 67091 Strasbourg, France. Federation Hospitalo-Universitaire (FHU) OMICA" + }, + { + "author_name": "Yvon Ruch", + "author_inst": "Department of Infectious and Tropical Diseases, Hopitaux Universitaires de Strasbourg ; 67091 Strasbourg, France. Federation Hospitalo-Universitaire (FHU) OMICA" + }, + { + "author_name": "Maleka Schenck-Dhif", + "author_inst": "Service de Medecine Intensive-Reanimation, Hopital de Hautepierre, Hopitaux Universitaires de Strasbourg ; Avenue Moliere, 67200 Strasbourg, France. Federation " + }, + { + "author_name": "Olivier Collange", + "author_inst": "Service d'Anesthesie-Reanimation et Medecine Peri-Operatoire, Nouvel Hopital Civil, Hopitaux Universitaires de Strasbourg ; Strasbourg, France. Federation Hospi" + }, + { + "author_name": "Thien-Nga Chamaraux-Tran", + "author_inst": "Service d'Anesthesie-Reanimation et Medecine Peri-Operatoire, Hopital de Hautepierre, Hopitaux Universitaires de Strasbourg ; 67200 Strasbourg Cedex, France. Fe" + }, + { + "author_name": "Anne Molitor", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Angelique Pichot", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Alice Bernard", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Ouria Tahar", + "author_inst": "Service d'Immunologie Biologique, Plateau Technique de Biologie, Pole de Biologie, Nouvel Hopital Civil ; 67091 Strasbourg, France. Federation Hospitalo-Univers" + }, + { + "author_name": "Sabrina Bibi-Triki", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Haiguo Wu", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Nicodeme Paul", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Sylvain Mayeur", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Annabel Larnicol", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Geraldine Laumond", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Julia Frappier", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Sylvie Schmidt", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Antoine Hanauer", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Cecile Macquin", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Tristan Stemmelen", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Michael Simons", + "author_inst": "Yale Cardiovascular Research Center, Departments of Medicine and Cell Biology, Yale University School of Medicine; New Haven, CT 06511, USA." + }, + { + "author_name": "Xavier Mariette", + "author_inst": "Department of Rheumatology, Hopital Bicetre, Assistance Publique-Hopitaux de Paris; 94270 Paris, France. Universite Paris-Saclay, INSERM UMR_S 1184 ; 94270 Le K" + }, + { + "author_name": "Olivier Hermine", + "author_inst": "Department of Hematology, Hopital Necker, Assistance Publique - Hopitaux de Paris ; 75015 Paris, France. University of Paris, Imagine Institute ; 75015 Paris, F" + }, + { + "author_name": "Samira Fafi-Kremer", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Bernard Goichot", + "author_inst": "Service de Medecine Interne, Endocrinologie et Nutrition, Hopital de Hautepierre, Hopitaux Universitaires de Strasbourg ; 67200 Strasbourg, France. Federation H" + }, + { + "author_name": "Bernard Drenou", + "author_inst": "Departement Hematologie, Groupe Hospitalier de la region Mulhouse Sud Alsace ; 68100 Mulhouse, France." + }, + { + "author_name": "Khaldoun Kuteifan", + "author_inst": "Service de Reanimation Medicale, Groupe Hospitalier de la region Mulhouse Sud Alsace ; 68100 Mulhouse, France." + }, + { + "author_name": "Julien Pottecher", + "author_inst": "Service d'Anesthesie-Reanimation et Medecine Peri-Operatoire, Hopital de Hautepierre, Hopitaux Universitaires de Strasbourg ; 67200 Strasbourg Cedex, France. Fe" + }, + { + "author_name": "Paul-Michel Mertes", + "author_inst": "Service d'Anesthesie-Reanimation et Medecine Peri-Operatoire, Nouvel Hopital Civil, Hopitaux Universitaires de Strasbourg ; Strasbourg, France. Federation Hospi" + }, + { + "author_name": "Shweta Kailasan", + "author_inst": "Integrated BioTherapeutics, Inc.; Rockville, MD 20850, USA." + }, + { + "author_name": "Javad Aman", + "author_inst": "Integrated BioTherapeutics, Inc.; Rockville, MD 20850, USA." + }, + { + "author_name": "Elisa Pin", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab; Stockholm, SE-171 21, Sweden." + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab; Stockholm, SE-171 21, Sweden." + }, + { + "author_name": "Anne Thomas", + "author_inst": "Plateforme Auragen ; 69003 Lyon, France." + }, + { + "author_name": "Alain Viari", + "author_inst": "Plateforme Auragen ; 69003 Lyon, France." + }, + { + "author_name": "Damien Sanlaville", + "author_inst": "Plateforme Auragen ; 69003 Lyon, France." + }, + { + "author_name": "Francis Schneider", + "author_inst": "Service de Medecine Intensive-Reanimation, Hopital de Hautepierre, Hopitaux Universitaires de Strasbourg ; Avenue Moliere, 67200 Strasbourg, France. Federation " + }, + { + "author_name": "Jean Sibilia", + "author_inst": "Service de Rhumatologie, Centre National de Reference des Maladies Auto-immunes Systemiques Rares Est Sud-Ouest, Hopitaux Universitaires de Strasbourg ; 67200 S" + }, + { + "author_name": "Pierre-Louis Tharaux", + "author_inst": "INSERM (Institut de la Sante et de la Recherche Medicale), Universite de Paris, Paris Cardiovascular Center-PARCC ; 75015 Paris, France." + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "St Giles laboratory of human genetics of infectious diseases, Rockefeller Branch, The Rockefeller University; New York, NY 10065, USA. Laboratory of human genet" + }, + { + "author_name": "Yves Hansmann", + "author_inst": "Department of Infectious and Tropical Diseases, Hopitaux Universitaires de Strasbourg ; 67091 Strasbourg, France. Federation Hospitalo-Universitaire (FHU) OMICA" + }, + { + "author_name": "Daniel Lidar", + "author_inst": "Center for Quantum Information Science and Technology, University of Southern California; Los Angeles, 90089-0484 CA, USA. Department of Electrical and Computer" + }, + { + "author_name": "Mirjana Radosavljevic", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Jeffrey R Gulcher", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA." + }, + { + "author_name": "Ferhat Meziani", + "author_inst": "Service de Medecine Intensive-Reanimation, Nouvel Hopital Civil, Hopitaux Universitaires de Strasbourg ; 67091 Strasbourg, France. Federation Hospitalo-Universi" + }, + { + "author_name": "Christiane Moog", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + }, + { + "author_name": "Thomas W Chittenden", + "author_inst": "Genuity AI Research Institute, Genuity Science ; Boston, MA 02114, USA. Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School; B" + }, + { + "author_name": "Seiamak Bahram", + "author_inst": "Laboratoire d'ImmunoRhumatologie Moleculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculte de Medecine, Institut Thematique Interdisciplinaire (ITI) de Medeci" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.22.21259302", "rel_title": "Association between SARS-Cov-2 infection during pregnancy and adverse pregnancy outcomes: a re-analysis of data from Wei et al. (2021).", @@ -680730,33 +679128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.16.21259046", - "rel_title": "Delay of molecular SARS-CoV-2 testing and turnaround time in Mexico and Colombia", - "rel_date": "2021-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21259046", - "rel_abs": "ObjectiveTo quantify the delay in SARS-CoV-2 real time polymerase chain reaction (RT-PCR) testing and test result reporting in Mexico and Colombia, and to assess the relation between margination status and these delays.\n\nMethodsWe quantified time in days from symptom onset until testing (latency one) and delay in test results report (latency two) using freely available country-wide open data from Mexico and Colombia. Directed acyclic graphs were built to determine which associations were appropriate to assess. Stratification by margination status, state and hospitalization status was used to determine corresponding associations.\n\nResultsIn almost all the study period latency two was longer than latency one. Median latency one was 3 (IQR 0-6) days and latency two 7 (IQR 4-11) days in Colombia, while in Mexico they were 3 (IQR 1-5) days and 4 (IQR 3-6) days. In Colombia, worse margination status prolonged latency two. In Mexico, a lower number and percentage of point-of-care (POC) tests in areas with worse margination.\n\nConclusionPOC tests must be used as a widespread means to reduce latency two, and until then should be prioritized in areas with longer latency two. An unequal distribution of this resource should be avoided.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Isaac N\u00fa\u00f1ez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Pablo F. Belaunzar\u00e1n-Zamudio", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Yanink Caro-Vega", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.21.449211", "rel_title": "Anti-prothrombin autoantibodies enriched after infection with SARS-CoV-2 and influenced by strength of antibody response against SARS-CoV-2 proteins", @@ -681517,6 +679888,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.19.21259172", + "rel_title": "Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia", + "rel_date": "2021-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21259172", + "rel_abs": "Sequencing of SARS-CoV-2 provides essential information into viral evolution, transmission, and epidemiology. Short-read next-generation sequencing platforms are currently the gold-standard approaches characterized by the highest accuracy. Meanwhile, Oxford Nanopores long-read sequencing devices show great promise, offering comparable accuracy, fast turnaround time, and reduced cost. In this study, we performed whole-genome sequencing and molecular-genetic characterization of SARS-CoV-2 from clinical specimens using an amplicon-based nanopore sequencing approach. Lineage and phylogenetic analysis identified the most prevalent lineages at different time points (B.1.1.163, B.1.1.208, B.1.1, and since March 2021 - B.1.1.7). In addition, we evaluated the possible effect of identified mutations on the efficacy of recommended primers and probes used for PCR detection of SARS-CoV-2. In summary, a high-quality SARS-CoV-2 genome can be acquired by nanopore sequencing and it can serve as an efficient and affordable alternative to short-read next-generation sequencing and be used for epidemiologic surveillance and molecular-genetic analyses of the virus.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Diana Avetyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia and Institute of Biomedicine and Pharmacy, Russian-Armenian Universit" + }, + { + "author_name": "Siras Hakobyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia; Institute of Biomedicine and Pharmacy, Russian-Armenian University," + }, + { + "author_name": "Maria Nikoghosyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia; Institute of Biomedicine and Pharmacy, Russian-Armenian University," + }, + { + "author_name": "Gisane Khachatryan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia and Institute of Biomedicine and Pharmacy, Russian-Armenian Universit" + }, + { + "author_name": "Tamara Sirunyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia and Institute of Biomedicine and Pharmacy, Russian-Armenian Universit" + }, + { + "author_name": "Nelli Muradyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Roksana Zakharyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia and Institute of Biomedicine and Pharmacy, Russian-Armenian Universit" + }, + { + "author_name": "Andranik Chavushyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Hovsep Ghazaryan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Ani Melkonyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Ani Stepanyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Varduhi Hayrapetyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Sofi Atshemyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia" + }, + { + "author_name": "Gevorg Martirosyan", + "author_inst": "Davidyants Laboratories, 0054, Yerevan, Armenia" + }, + { + "author_name": "Gayane Melik-Andreasyan", + "author_inst": "National Center of Disease Control and Prevention, Ministry of Health RA, 0025, Yerevan, Armenia" + }, + { + "author_name": "Shushan Sargsyan", + "author_inst": "National Center of Disease Control and Prevention, Ministry of Health RA, 0025, Yerevan, Armenia" + }, + { + "author_name": "Armine Ghazazyan", + "author_inst": "National Center of Disease Control and Prevention, Ministry of Health RA, 0025, Yerevan, Armenia" + }, + { + "author_name": "Naira Aleksanyan", + "author_inst": "National Center of Disease Control and Prevention, Ministry of Health RA, 0025, Yerevan, Armenia" + }, + { + "author_name": "Lilit Nersisyan", + "author_inst": "SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden" + }, + { + "author_name": "Arsen Arakelyan", + "author_inst": "Laboratory of Human Genomics, Institute of Molecular Biology NASRA, 0014, Yerevan, Armenia; Institute of Biomedicine and Pharmacy, Russian-Armenian University," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.23.449594", "rel_title": "SARS-CoV-2 neutralising antibodies in Dogs and Cats in the United Kingdom", @@ -682536,45 +681002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.15.21258983", - "rel_title": "Prior sleep-wake behavior predicts mental health resilience among adults in the United States during the COVID-19 pandemic", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258983", - "rel_abs": "Rigorous nonpharmaceutical interventions (e.g., stay-at-home orders, remote-work directives) were implemented in early 2020 for coronavirus disease 2019 (COVID-19) pandemic containment in the U.S. During this time, increased sleep duration and delayed sleep timing were reported through surveys (Leone et al., 2021) and wearable data (Rezaei and Grandner, 2021), as were elevated adverse mental health symptom (Czeisler et al., 2020). Inter-relationships between sleep and mental health have not been examined using longitudinal objective sleep-wake data, during these abruptly imposed lifestyle changes.\n\nWe examined objective sleep-wake data and surveyed mental health data collected among 4,912 U.S. adult users of a validated sleep wearable (WHOOP, Boston, Massachusetts) before and during the COVID-19 pandemic. Comparing the pre-pandemic (January 1 to March 12, 2020) and acute pandemic-onset intervals (March 13 to April 12, 2020), participants exhibited increased mean sleep duration (0.25h [95% CI = 0.237-0.270]), later sleep onset (18m [17.378-20.045]) and offset (36m [35.111-38.106]), and increased consistency of sleep timing (3.51 [3.295-3.728] out of 100); all P < 0.0001. Generally, participants with persistent sleep deficiency and low sleep consistency had higher odds of symptoms of anxiety or depression, burnout, and new or increased substance use during the pandemic. Decreases in sleep duration (adjusted odds ratio [aOR] = 1.30, 95% CI = 1.03-1.65, P = 0.025) and sleep consistency (2.05 [1.17-3.67], P = 0.009) were associated with increased anxiety and depression symptoms during the pandemic. We suggest that sleep duration and consistency may be important predictors of risk of adverse mental health outcomes during a pandemic.\n\nM.J. Leone, M. Sigman, D.A. Golombek. Effects of lockdown on human sleep and chronotype during the COVID-19 pandemic. Curr Biol 30(16), R930-R931 (2020).\n\nN. Rezaei N, M.A. Grandner. Changes in sleep duration, timing, and variability during the COVID-19 pandemic: Large-scale Fitbit data from 6 major US cities. Sleep Health 10.1016/j.sleh.2021.02.008. (2021).\n\nM.E. Czeisler, R.I. Lane, E. Petrosky, et al., Mental Health, Substance Use, and Suicidal Ideation During the COVID-19 Pandemic - United States, June 24-30, 2020. MMWR Morb Mortal Wkly Rep 69(32), 1049-1057 (2020).\n\nSignificance StatementThe coronavirus disease 2019 (COVID-19) pandemic has had profound effects on health, including increased sleep duration and worsened mental health. We examined associations between (1) objective sleep-wake data before and during the COVID-19 pandemic and (2) adverse mental health symptoms and substance use among users of a validated sleep wearable. We found that, in general, participants with persistent sleep deficiency and low sleep consistency had higher odds of symptoms of anxiety or depression, new or increased substance use, and burnout. Our findings suggest that sleep of sufficient duration and consistent timing are associated with mental health resilience, exemplified in this case by the impact of the pandemic and related abrupt lifestyle changes on adverse mental health symptoms.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mark \u00c9 Czeisler", - "author_inst": "Monash University" - }, - { - "author_name": "Emily R Capodilupo", - "author_inst": "WHOOP Inc." - }, - { - "author_name": "Matthew D Weaver", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Charles A Czeisler", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Mark E Howard", - "author_inst": "Austin Health" - }, - { - "author_name": "Shantha MW Rajaratnam", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.15.21258969", "rel_title": "Modeling the waves of Covid-19", @@ -682951,6 +681378,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.06.18.21258798", + "rel_title": "Impact of vaccination in reducing Hospital expenses, Mortality and Average length of stay among COVID 19 patients. A retrospective cohort study from India", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258798", + "rel_abs": "Background & AimWHO listed vaccine hesitancy among the top 10 global threats to health and there are very few reports highlighting vaccine benefits against COVID-19. The aim of this study was to study the impact of vaccination on reducing the average length of stay (ALOS), intensive care unit (ICU) requirement, mortality and cost of the treatment among COVID-19 patients.\n\nMethodsIn this retrospective cohort study all the patients above 45 years who underwent treatment for COVID-19 were included. The data of patients treated pan India during the period March & April 2021 with the diagnosis of COVID-19, under health insurance cover, were extracted to study parameters like the ALOS, mortality, ICU requirement, total hospital expenses incurred and the vaccination status.\n\nResultsAmong 3820 patients with COVID-19, 3301 (86.4%) were unvaccinated while 519 (13.6%) were vaccinated. Among the unvaccinated the mean (s.d) ALOS was 7 days. Fourteen days after second dose of vaccination this was significantly less (p=0.01) at 4.9. The mean total hospital expense among the unvaccinated was Rs. 277850. Fourteen days after second dose of vaccination this was further less (p=0.001) at Rs. 217850. Among the unvaccinated population 291/3301 (8.8%) required ICU and this was significantly less (p=0.03) at 31/519 (6%) among the vaccinated. Among those who received two doses of vaccination it was further less at 1/33 (3%). The mortality among unvaccinated patients was 16/3301 (0.5%) while there was no mortality among the vaccinated. Among those who received two doses of vaccination there was a 66% relative risk reduction in ICU stay and 81% relative risk reduction in mortality.\n\nConclusionsThere was a significant reduction in ALOS, ICU requirement, mortality & treatment cost in patients who had completed two doses of vaccination. These findings may be used in motivating public and promoting vaccination drive.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Madhumathi Ramakrishnan", + "author_inst": "Star Health & Allied Insurance, Chennai" + }, + { + "author_name": "Prakash Subbarayan", + "author_inst": "Star Health & Allied Insurance Co Ltd, Chennai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.17.21258371", "rel_title": "ADESSO detects SARS-CoV-2 and its variants: extensive clinical validation of an optimised CRISPR-Cas13-based COVID-19 test", @@ -683650,25 +682100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.16.21259061", - "rel_title": "State of Emergency and Human Mobility during the COVID-19 Pandemic", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21259061", - "rel_abs": "BackgroundTo help control the spread of the coronavirus disease 2019 (COVID-19), the Japanese government declared a state of emergency (SoE) four times. However, these were less stringent than other nations. It has not been assessed whether soft containment policies were sufficiently effective in promoting social distancing or reducing human contact.\n\nMethodsUtilising the Google mobility index to assess social distancing behaviour in all Japanese prefectures between 15 February 2020 and 21 September 2021, mobility changes were assessed by an interrupted time-series analysis after adjusting for seasonality and various prefecture-specific fixed-effects and distinguishing potential heterogeneity across multiple SoEs and time passed after the declaration.\n\nResultsThe mobility index for retail and recreation showed an immediate decline after the declaration of the SoE by 7.94 percent-points (95%CI: -8.77 to -7.12) and a further decline after the initial period (beta: -1.27 95%CI: -1.43 to -1.11), but gradually increased by 0.03 percent-points (95%CI: 0.02 - 0.03). This trend was similar for mobilities in other places. Among the four SoEs, the overall declines in human mobility outside the home in the third and fourth SoE were the least significant, suggesting that people were less compliant with social distancing measures during these periods.\n\nConclusionAlthough less stringent government responses to the pandemic may help promote social distancing by controlling human mobilities outside the home, their effectiveness may decrease if these interventions are repeated and enforced for extended periods, distorting ones health belief by heuristics biases. By combining these with other measures (i.e. risk-communication strategies), even mild containment and closure policies can be effective in curbing the spread of the virus.\n\nWhat is already known?O_LIHuman mobility, in terms of tracing social distancing and human contact in places such as shops, restaurants, and workplaces, was reported to be a useful indicator for predicting COVID-19 outbreaks.\nC_LIO_LIContainment and closure policies, such as country lockdowns and a State of Emergency (SoE) declarations, effectively reduce human mobility.\nC_LI\n\nWhat are the new findings?O_LIThis study first evaluated if longer and repeated SoEs were effective to reduce human mobility.\nC_LIO_LIThe findings from this study suggests that although less stringent government responses to the pandemic may help promote social distancing by controlling human mobilities outside the home, their effectiveness decreases if these interventions are repeated and enforced for extended periods.\nC_LI\n\nWhat do the new findings imply?O_LIWhile less stringent government responses to the pandemic are effective in promoting social distancing by controlling human mobilities outside the home, their effectiveness may decrease if similar interventions are repeated for extended periods of time.\nC_LIO_LIHowever, by combining these with other measures such as risk-communication strategies, even less costly interventions such as mild containment and closure policies can be effective in curbing the spread of the COVID-19 virus.\nC_LI\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIt has been shown that human mobility, in terms of tracing social distancing and human contact in places such as shops, restaurants, and workplaces, was reported to be a useful indicator for predicting COVID-19 outbreaks. Also, previous studies have shown that containment and closure policies, such as country lockdowns and a State of Emergency (SoE) declarations, effectively reduce human mobility. However, it is not explicitly known whether longer and repeated alerts requesting citizens to avoid nonessential activities with risk communication strategies are equally effective.\n\nAdded-value of this studyThis study first evaluated if longer and repeated SoEs were effective to reduce human mobility, suggesting three main findings. First, individuals engage in social distancing behaviours during the initial periods of the SoE but become less compliant as time passes. Second, when mobility changes during each SoE were distinguished, overall declines in mobilities outside the home and increases in stay-at-home time were less obvious during the succeeding SoEs. Third, under the stringent government responses to the pandemic and decline in mobilities, the consumption level--especially for activities outside the home-- sharply declined, suggesting that strong public interventions may worsen the economy.\n\nImplications of all the available evidenceWhile less stringent government responses to the pandemic are effective in promoting social distancing by controlling human mobilities outside the home, their effectiveness may decrease if similar interventions are repeated for extended periods of time. However, by combining these with other measures such as risk-communication strategies, even less costly interventions such as mild containment and closure policies can be effective in curbing the spread of the COVID-19 virus.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Shohei Okamoto", - "author_inst": "Tokyo Metropolitan Institute of Gerontology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.16.21258673", "rel_title": "Antibody neutralization to SARS-CoV-2 and variants after one year in Wuhan", @@ -684369,6 +682800,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.17.21257667", + "rel_title": "\"It's hard to keep a distance when you're with someone you really care about\" -a qualitative study of adolescents' pandemic-related health literacy and how Covid-19 affects their lives", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21257667", + "rel_abs": "PurposeThe aim of this study was to explore how adolescents accessed, understood, appraised, and applied information on pandemic preventive measures, how their lives were impacted by long-lasting regulations and how they described their quality of life.\n\nMethodsA qualitative design with focus group interviews was used to elaborate on the quantitative survey results obtained and analyzed in a previous survey study from the first phase of the Covid-19 pandemic. Five focus groups with seventeen adolescents were conducted digitally during the second pandemic phase in November and December 2020. The interview data were analyzed with directed content analysis.\n\nResultsThe adolescents reported using traditional media and official websites as sources for Covid-19 information. They engaged in preventive behavior, and washing hands and keeping a distance from strangers had become a habit. However, not being physically close to friends felt strange and unpleasant. The measure most frequently discussed was limiting social contact, which was a constant struggle. No one disputed the authorities guidelines and rules, but the social restrictions caused boredom and despair, particularly due to interrupted schooling and missed opportunities to engage in life events, and freely socialize with friends.\n\nConclusionThe adolescents gave an overall impression of being health literate, which corresponds well with the results from our previous survey study. Their descriptions of how they translated protective measures into their everyday lives demonstrate that they took responsibility and accepted personal costs for the collective good. However, life with social restrictions decreased their quality of life.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kirsti Riiser", + "author_inst": "OsloMet - Oslo Metropolitan University" + }, + { + "author_name": "Kare Ronn Richardsen", + "author_inst": "OsloMet - Oslo Metropolitan University" + }, + { + "author_name": "Kristin Haraldstad", + "author_inst": "University of Agder" + }, + { + "author_name": "Solvi Helseth", + "author_inst": "OsloMet - Oslo Metropolitan University" + }, + { + "author_name": "Astrid Torbjornsen", + "author_inst": "OsloMet - Oslo Metropolitan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.17.21258914", "rel_title": "Public health relevant consequences of the COVID-19 pandemic on malaria in sub-Saharan Africa: A scoping review", @@ -685516,49 +683982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.20.21258392", - "rel_title": "Excellent negative predictive value (99.8%) of two rapid molecular COVID-19 tests compared to conventional RT-PCR for SARS-CoV-2 (COVID-19) in 2,011 tests performed in a single centre.", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21258392", - "rel_abs": "Conventional Reverse Transcription Polymerase Chain Reaction (RT-PCR) remains the gold standard for testing SARS-CoV-2. Since their availability, two rapid molecular COVID-19 tests were performed in parallel with RT-PCR in all urgent and emergency admissions, as the negative predictive value was not yet ascertained. In this study, we present the data of 2,011 test results using either ID Now COVID-19 (Abbott) (Abbott ID NOW) or Xpert Xpress SARS-CoV-2 (Cepheid) (GeneXpert) tests comparing to conventional RT-PCR results. The negative predictive value is 99.8%(3 false negatives out of 1,964 tests) using a cut-off CT value of 40. Using a cut-off of RT-PCR CT value of 30 (predicting infectivity), the negative predictive value is reduced to 99.9% (1 out of 1,964 tests). With these results, we feel confident to recommend the immediate use of the rapid PCR tests alone and to use conventional RT-PCR for confirmation testing after.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kin Wah Leong", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Tong Lif Law", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Aswan bin Salleh Saiful", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Chung Chueng Kang", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Yen Yen Woo", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Ting Soo Chow", - "author_inst": "Gleneagles Hospital Penang" - }, - { - "author_name": "Zi Ling Yong", - "author_inst": "Gleneagles Hospital Penang" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.19.21259125", "rel_title": "Plasma gradient of soluble urokinase-type plasminogen activator receptor is linked to pathogenic plasma proteome and immune transcriptome and stratifies outcomes in severe COVID-19", @@ -686602,6 +685025,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.17.21259100", + "rel_title": "COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya", + "rel_date": "2021-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259100", + "rel_abs": "Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya ([~]75% June 1st) have implications for a fourth wave and future control strategies.\n\nOne Sentence SummaryCOVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Samuel P C Brand", + "author_inst": "University of Warwick" + }, + { + "author_name": "John Ojal", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Rabia Aziza", + "author_inst": "University of Warwick" + }, + { + "author_name": "Vincent Were", + "author_inst": "Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" + }, + { + "author_name": "Emelda Okiro", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Ivy Kombe", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Caroline Mburu", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Morris Ogero", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Ambrose Agweyu", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "George M Warimwe", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "James Nyagwange", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Henry Karanja", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "John Gitonga", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Daisy Mugo", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Sophie Uyoga", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Ifedayo M O Adetifa", + "author_inst": "Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "J Anthony G Scott", + "author_inst": "Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Edward Otieno", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Nickson Murunga", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Mark Otiende", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Lynette I Ochola-Oyier", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Charles N Agoti", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "George Githinji", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Kadondi Kasera", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Patrick Amoth", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Mercy Mwangangi", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Rashid Aman", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Wangari Ng'ang'a", + "author_inst": "Presidential Policy & Strategy Unit, The Presidency, Government of Kenya" + }, + { + "author_name": "Benjamin Tsofa", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Philip Bejon", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Matt J Keeling", + "author_inst": "University of Warwick" + }, + { + "author_name": "D James Nokes", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + }, + { + "author_name": "Edwine Barasa", + "author_inst": "Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.16.21259052", "rel_title": "Rapid spread of the SARS-CoV-2 \u03b4 variant in the area of Paris (France) in June 2021", @@ -687581,37 +686151,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.11.21258747", - "rel_title": "Correlation between Pregnancy Status and Severe Corona-Virus Disease Characterized by Cytokine Storm: Systematic Review and Meta-Analysis", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258747", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SAR2-COV-2) that identified first in Wuhan, China, in December 2019, rapidly spreading to the rest of the globe, becoming a pandemic. Some studies have eluded to an association between pregnancy status and severe COVID-19 cytokine storm, some, in contrast, have demonstrated such. The aim of the current study was to find the relationship between pregnancy status and clinical COVID-19 severity characterized by cytokine storm through a systematic review and meta-analysis approach.\n\nMethodsWe searched Google Scholar, PubMed, Scopus, Web of Science, and Embase databases to identify clinical studies suitable for inclusion in this meta-analysis. Studies reporting pregnancy status and comparing the COVID-19 severity cytokine storm outcome were included. The COVID-19 severity characterized by cytokine storm was described using parameters such as; Intensive Care Unit Admission, Invasive Mechanical Ventilation, Mechanical Ventilation, Hospital Admission, Pro and Inflammatory cytokine levels, consolidation on chest CT scan, pulmonary infiltration, extreme fevers as characteristic of cytokine storm, syndromic severity, higher neutrophil count indicative of cytokine storm and severe COVI-19 presentation.\n\nResultsA total of 17 articles detailing 840332 COVID-19 women were included. Our meta-analysis revealed a relationship between positive pregnancy status and severe COVID-19 cytokine storm case (random effect model, OR=2.47; 95% CI: 1.63-3.73; P < 0.0001), with a cumulative incidence of 6432 (14.1%) among the pregnant women with COVID-19 and 24352 (3.1%) among the non-pregnant women with COVI-19. Further to this, we found that the sub-analysis between Single Centre and Multiple Centre studies demonstrated seemingly the same as heterogeneity (I2 = 72 and (I2 = 98), respectively. Sensitivity analysis on each sub-group revealed that pregnancy was significantly related to severe COVID-19 with cytokine storm from single Centre studies, (fixed effect model, OR= 3.97; 95% CI: 2.26-6.95; P< 0.00001) with very low heterogeneity (I2 = 2 %; P = 0.42).\n\nConclusionBeing pregnant is clearly associated with experiencing a severe COVID-19 characterized by a cytokine storm. The SARS-COV-2 epidemic should serve as an impetus for pregnant women diagnosed with COVID-19, and map out salient risk factors associated with its severity. The trial is registered with the International Prospective Register of Systematic Reviews (PROSPERO) CRD42021242011.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Muthuka J Kyalo", - "author_inst": "Jomo Kenyatta University of Agriculture & Technology/Kenya Medical Training College" - }, - { - "author_name": "Michael Kiptoo", - "author_inst": "Kenya Medical Training College" - }, - { - "author_name": "Kelly Oluoch", - "author_inst": "Kenya Medical Training College" - }, - { - "author_name": "Everlyn Nyamai", - "author_inst": "Kenya Medical Training College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.06.14.21258910", "rel_title": "A Multi-center, Prospective, Observational-cohort controlled study of Clinical Outcomes following COVID-19 Convalescent plasma therapy in hospitalized COVID-19 patients", @@ -688400,6 +686939,153 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.06.18.448958", + "rel_title": "Structure and computation-guided design of a mutation-integrated trimeric RBD candidate vaccine with broad neutralization against SARS-CoV-2", + "rel_date": "2021-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.18.448958", + "rel_abs": "The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 is an attractive target for COVID-19 vaccine developments, which naturally exists in a trimeric form. Here, guided by structural and computational analyses, we present a mutation-integrated trimeric form of RBD (mutI tri-RBD) as a broadly protective vaccine candidate, in which three RBDs were individually grafted from three different circulating SARS-CoV-2 strains including the prototype, Beta (B.1.351) and Kappa (B.1.617). The three RBDs were then connected end-to-end and co-assembled to possibly mimic the native trimeric arrangements in the natural S protein trimer. The recombinant expression of the mutI tri-RBD, as well as the homo-tri-RBD where the three RBDs were all truncated from the prototype strain, by mammalian cell exhibited correct folding, strong bio-activities, and high stability. The immunization of both the mutI tri-RBD and homo-tri-RBD plus aluminum adjuvant induced high levels of specific IgG and neutralizing antibodies against the SARS-CoV-2 prototype strain in mice. Notably, regarding to the \"immune-escape\" Beta (B.1.351) variant, mutI tri-RBD elicited significantly higher neutralizing antibody titers than homo-tri-RBD. Furthermore, due to harboring the immune-resistant mutations as well as the evolutionarily convergent hotspots, the designed mutI tri-RBD also induced strong broadly neutralizing activities against various SARS-CoV-2 variants, especially the variants partially resistant to homo-tri-RBD. Homo-tri-RBD has been approved by the China National Medical Products Administration to enter clinical trial (No. NCT04869592), and the superior broad neutralization performances against SARS-CoV-2 support the mutI tri-RBD as a more promising vaccine candidate for further clinical developments.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Yu Liang", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Jing Zhang", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Run Yu Yuan", + "author_inst": "Guangdong Provincial Institute of Public Health" + }, + { + "author_name": "Mei Yu Wang", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Peng He", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Ji Guo Su", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Zi Bo Han", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Yu Qin Jin", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Jun Wei Hou", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Hao Zhang", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Xue Feng Zhang", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Shuai Shao", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Ya Nan Hou", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Zhao Ming Liu", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Li Fang Du", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Fu Jie Shen", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Wei Min Zhou", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Fang Tang", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Ze Hua Lei", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Shuo Liu", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Wei Zhen", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Jin Juan Wu", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Xiang Zheng", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Ning Liu", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Shi Chen", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Zhi Jing Ma", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Fan Zheng", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Si Yu Ren", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Zhong Yu Hu", + "author_inst": "National Vaccine and Serum Institute" + }, + { + "author_name": "Gui Zhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Wei Jin Huang", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Chang Wen Ke", + "author_inst": "Guangdong Provincial Institute of Public Health" + }, + { + "author_name": "Qi Ming Li", + "author_inst": "National Vaccine and Serum Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.15.21259002", "rel_title": "A cross-sectional study of the relationship between exercise, physical activity, and health-related quality of life among Japanese workers during the COVID-19 pandemic", @@ -689203,77 +687889,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.17.448814", - "rel_title": "Western diet increases COVID-19 disease severity in the Syrian hamster", - "rel_date": "2021-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448814", - "rel_abs": "Pre-existing comorbidities such as obesity or metabolic diseases can adversely affect the clinical outcome of COVID-19. Chronic metabolic disorders are globally on the rise and often a consequence of an unhealthy diet, referred to as a Western Diet. For the first time in the Syrian hamster model, we demonstrate the detrimental impact of a continuous high-fat high-sugar diet on COVID-19 outcome. We observed increased weight loss and lung pathology, such as exudate, vasculitis, hemorrhage, fibrin, and edema, delayed viral clearance and functional lung recovery, and prolonged viral shedding. This was accompanied by an increased trend of systemic IL-10 and IL-6, as well as a dysregulated serum lipid response dominated by polyunsaturated fatty acid-containing phosphatidylethanolamine, recapitulating cytokine and lipid responses associated with severe human COVID-19. Our data support the hamster model for testing restrictive or targeted diets and immunomodulatory therapies to mediate the adverse effects of metabolic disease on COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Julia R Port", - "author_inst": "NIH" - }, - { - "author_name": "Danielle R Adney", - "author_inst": "NIH" - }, - { - "author_name": "Benjamin Schwarz", - "author_inst": "NIH" - }, - { - "author_name": "Jonathan Schulz", - "author_inst": "NIH" - }, - { - "author_name": "Daniel E Sturdevant", - "author_inst": "NIH" - }, - { - "author_name": "Brian J Smith", - "author_inst": "NIH" - }, - { - "author_name": "Victoria Avanzato", - "author_inst": "NIH" - }, - { - "author_name": "Myndi G Holbrook", - "author_inst": "NIH" - }, - { - "author_name": "Jyothi Purushotham", - "author_inst": "NIH" - }, - { - "author_name": "Kaitlin A Stromberg", - "author_inst": "NIH" - }, - { - "author_name": "Ian Leighton", - "author_inst": "NIH" - }, - { - "author_name": "Catharine Bosio", - "author_inst": "Rocky Mountain Laboratories" - }, - { - "author_name": "Carl Shaia", - "author_inst": "NIH" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.17.448882", "rel_title": "Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins", @@ -690310,6 +688925,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.10.21258715", + "rel_title": "Role of Hemogram-Derived Ratios and Systemic-Immune Inflammation Index in Prediction of COVID-19 Progression in Egyptian Patients", + "rel_date": "2021-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258715", + "rel_abs": "BackgroundEarly detection of COVID-19 patients with potentially severe disease is crucial for predicting the diseases course and prioritizing medical resources, lowering overall disease mortality.\n\nObjectivesTo explore the role of hemogram-derived ratios and systemic-immune inflammation index (SII), in addition to C-reactive protein (CRP), in predicting COVID-19 severity and prognosis.\n\nMethodsIn this retrospective study, data were collected from the medical records of 425 COVID-19 patients. Neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and SII, together with the CRP, were investigated and compared.\n\nResultsNLR, PLR, SII, and CRP increased significantly in severe cases and with ICU admission (p [≤] 0.001). But, in non-survivors only NLR and CRP were significantly elevated (p < 0.05). By interpreting area under the receiver operating characteristic curve (ROC-AUC), CRP and NLR were better predictors of disease severity (AUC: 0.7 for both), the need for ICU admission (AUC: 0.763 and 0.727, respectively) and in-hospital mortality (AUC: 0.812 and 0.75, respectively). SII was significantly associated with the risk of severe disease development (odds ratio (OR): 3.143; 95% confidence interval (CI): 1.101-8.976); CRP (OR: 2.902; CI95%: 1.342-6.273) and NLR (OR: 2.662; CI95%, 1.072-6.611) were significantly associated with ICU admission risk; and only CRP was significantly associated with in-hospital mortality risk (OR: 3.988; CI95%: 1.460-10.892).\n\nConclusionsValues of CRP, SII, and NLR at the time of hospital admission could be independent prognostic biomarkers to predict COVID-19 progression. The integration of CRP, SII, and NLR into prognostic nomograms may lead to improved prediction.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sara I. Taha", + "author_inst": "Department of Clinical Pathology/ Immunology, Faculty of Medicine, Ain Shams University, Cairo, Egypt" + }, + { + "author_name": "Sara F. Samaan", + "author_inst": "Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Shereen A. Baioumy", + "author_inst": "Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt." + }, + { + "author_name": "Aalaa K. Shata", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Ain Shams university, Cairo, Egypt." + }, + { + "author_name": "Mariam K. Youssef", + "author_inst": "Department of Clinical Pathology/ Hematology, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.11.21258741", "rel_title": "Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies", @@ -691925,93 +690575,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.06.12.21258813", - "rel_title": "The 5-months impact of tozinameran (BNT162b2) mRNA vaccine on kidney transplant and chronic dialysis patients", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.12.21258813", - "rel_abs": "BackgroundDetermining the humoral immunogenicity of tozinameran (BNT162b2) vaccine in patients requiring chronic renal replacement therapy, and its impact on COVID-19 morbidity several months after vaccination, will guide risk assessment and subsequent changes in vaccination policy.\n\nMethodsIn a prospective post-vaccination cohort study with up to 5 months follow-up we studied outpatient dialysis and kidney transplant patients and respective healthcare teams. Outcomes were anti S1/S2 antibody response to vaccine or infection and infection rate during followup.\n\nResults175 dialysis patients (40% women, 65{+/-}15 years), 252 kidney transplant patients (33% women, 54{+/-}14 years) and 71 controls (65% women, 44{+/-}14 years) were followed. Three months or longer after vaccination we detected anti S1/S2 IgG antibodies in 80% of dialysis patients, 44% of transplant recipients and 100% of controls, whereas respective rates after infection were 94%, 75% and 100%. Predictors of non-response were older age, diabetes, history of cancer, lower lymphocyte count and lower vitamin-D levels. Factors associated with lower titers in dialysis patients were modality (hemodialysis vs peritoneal) and high serum ferritin levels. In transplant patients, hypertension and higher calcineurin or mTOR inhibitor drug levels were linked with diminished antibody response. Vaccination associated with fewer subsequent infections (HR=0.23, p<0.05). Moreover, higher antibody titers associated with fewer events, HR 0.41 for each unit increased in log10titer (p<0.05).\n\nConclusionsDialysis patients, and more so kidney transplant recipients, mounted reduced antibody response to COVID-19 mRNA vaccination, and lesser humoral response associated with more infections. Measures to identify and protect non-responsive patients are urgently required.\n\nSignificanceReports on the humoral immunogenicity of SARS-CoV-2 mRNA vaccines in patients with end stage renal disease are scarce, and association with subsequent COVID-19 morbidity is unknown. In this cohort study that included 175 patients treated with dialysis, 252 kidney transplant recipients and 71 control volunteers, the proportion achieving an antibody response was time- and group-dependent, reaching 80%, 44% and 100% at 3 months post prime inoculation. Personal history of vaccination, positive antibody responses and antibody titers associated with significantly lower risk of COVID-19 infection. Thus, in patients with end stage renal disease, SARS-CoV-2 antibody testing may be warranted after vaccination, to identify non-responders at higher risk for disease.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Iddo Z. Ben-Dov", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Yonatan Oster", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Keren Tzukert", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Talia Alster", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Raneem Bader", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Ruth Israeli", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Haya Asayag", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Michal Aharon", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Ido Burstein", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Hadas Pri-Chen", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Ashraf Imam", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Roy Abel", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Irit Mor-Yosef Levi", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Abed Khalaileh", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Esther Oiknine-Djian", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Aharon Bloch", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Dana G. Wolf", - "author_inst": "Hadassah Medical Center" - }, - { - "author_name": "Michal Dranitzki Elhalel", - "author_inst": "Hadassah Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.06.14.447967", "rel_title": "Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation", @@ -692671,6 +691234,85 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.06.13.21258862", + "rel_title": "Similar Rates of AKI during the First Two Waves of COVID-19 in Northern Italy: a single-center study", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258862", + "rel_abs": "IntroductionTwo waves of COVID-19 cases have overwhelmed most European countries during 2020. It is unclear if the incidence of acute kidney injury (AKI) has changed during the COVID-19 outbreaks. This study aims to evaluate the differences in incidence, risk factors and outcome of AKI in patients with SARS-CoV-2 infection during the first and second wave of COVID-19.\n\nMethodWe reviewed the health medical records of 792 consecutive patients with COVID-19 hospitalized at the University Hospital of Modena, Italy, from February 25 to December 14, 2020.\n\nResultsAKI was diagnosed in 122 (15.4%) patients. Incidence of AKI remained steady rate during wave-1 (15.9%) and wave-2 (14.7%) (P=0.89). AKI patients were older (P=<0.001) and had a more severe respiratory impairment (PO2/FO2) (P=[≤]0.001) than their non-AKI counterparts. AKI led to a longer hospital stay (P=0.001), complicated with a higher rate of ICU admission. COVID-19-related AKI was associate with 59.7% of deaths during wave-1 and 70.6% during wave-2. At the end of the period of observation, 24% (wave-1) and 46.7% (wave-2) of survivors were discharged with a not fully recovered kidney function. Risk factors for AKI in patients with COVID-19 were diuretics (HR=5.3; 95%CI, 1.2-23.3; P=0.025) and cardiovascular disease (HR, 2.23; 95%CI, 1.05-5.1; P=0.036).\n\nConclusionThe incidence of AKI (about 15%) remained unchanged during 2020, regardless of the trend of COVID-19. AKI occurred in patients with severe COVID-19 symptoms and was associated with a higher incidence of deaths than non-AKI patients. The risk factors of COVID-19-related AKI were diuretic therapy and cardiovascular disease.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Gaetano Alfano", + "author_inst": "Policlinico of Modena" + }, + { + "author_name": "Silvia Giovanella", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Francesco Fontana", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Jovana Milic", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Giulia Ligabue", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Francesco Giaroni", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Giacomo Mori", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Riccardo Magistroni", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Erica Franceschini", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Andrea Bedini", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Giacomo Cuomo", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Margherita DiGaetano", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Marianna Meschiari", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Cristina Mussini", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Gianni Cappelli", + "author_inst": "University Hospital of Modena" + }, + { + "author_name": "Giovanni Guaraldi", + "author_inst": "University Hospital of Modena" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.06.14.21258113", "rel_title": "Humoral Response to BNT162b2 mRNA Covid19 Vaccine in Peritoneal and Hemodialysis Patients: a Comparative Study", @@ -693426,29 +692068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.13.21258844", - "rel_title": "Hospital saturation and risk of death without receiving mechanical ventilation in hospitalized COVID-19 patients: a city-wide analysis", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258844", - "rel_abs": "BackgroundPneumonia is the hallmark of severe COVID-19, with supplemental oxygen requirement being the main indication for hospitalization. Refractory hypoxemia in these patients requires invasive mechanical ventilation (IMV) otherwise, death is imminent. In places with a high disease burden, availability of critical care experts, beds, or resources is challenged and many patients could die without receiving them.\n\nMethodsWe performed a retrospective cohort study using open databases from Mexico City about suspected or confirmed COVID-19 patients, health system saturation, and deaths between May 8th, 2020, and January 5th, 2021. After building a directed acyclic graph, we performed a binary logistic regression to identify the association between proposed causal variables and dying without receiving IMV (the outcome).\n\nResultsWe included 33 805 hospitalized patients with suspected or confirmed COVID-19, of which 19 820 (58.6%) did not require IMV and survived, 5416 (16.1%) required and received IMV, and 8569 (25.3%) required IMV but died without receiving it. Saturation of IMV-capable beds did not increase the odds of the outcome (odds ratio 1.07, 95% confidence interval 0.94-1.22 of 90%vs50% occupancy), while general bed saturation (2, 1.86-2.14 of 90%vs50% occupancy) and IMV-capable to general bed ratio (1.64, 1.52-1.77 for a ratio of 2vs0.5) did. Private healthcare decreased the odds of the outcome (0.12, 0.08-0.17) and dyspnea increased them (1.33, 1.19-1.9).\n\nConclusionsIn Mexico City, increased general hospital bed saturation and IMV-capable to general bed ratio were associated with a higher risk of dying without receiving IMV. Private healthcare was the most protective factor.\n\nKey messagesO_LIHospital saturation has been a central feature of public health messaging, but it is not known how outcomes relate to hospital saturation or capacity.\nC_LIO_LIIn Mexico City, 90% of COVID-19 patients requiring mechanical ventilation died but less than half received it.\nC_LIO_LIHigher general bed saturation and an increased ratio of IMV-capable beds to general beds increased the probability of dying without being intubated while receiving private healthcare decreased this probability.\nC_LIO_LIHaving available beds to intubate patients is possible thanks to the conversion of general beds, however, still yields suboptimal critical care.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Isaac N\u00fa\u00f1ez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Adrian Soto-Mota", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.11.21258661", "rel_title": "Grouping theory of epidemiology", @@ -693828,6 +692447,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.13.21258845", + "rel_title": "Importance of adequate COVID-19 case definitions in the SARS-CoV-2 pandemic", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258845", + "rel_abs": "BackgroundEpidemiologic case definitions serve a myriad of purposes during a pandemic, including contact tracing and monitoring disease trends. It is unknown how any COVID-19 case definition fares against the current gold standard of molecular or antigen tests.\n\nMethodsWe calculated the diagnostic properties of five COVID-19 definitions (three of the Mexican government and two of the WHO) using open data of suspected COVID-19 cases in Mexico City from March 24th 2020 until January 31st 2021.\n\nResultsAll 1,632,420 people included in the analysis met the WHO suspected case definition (sensitivity 100%, specificity 0%). The WHO probable case definition was met by 1.4%, while the first and second Mexican suspected case had sensitivities of 61 and 62% and specificities of 58 and 62%, respectively. Confirmed case by epidemiological contact had a low sensitivity (33%) but slightly higher specificity (77%).\n\nConclusionsCase definitions should maximize sensitivity, especially in a high-transmission area such as Mexico City. The WHO suspected case definition has the potential for detecting most symptomatic cases. We underline the need for routine evaluation of case definitions as new evidence arises to maximize their usefulness.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.12.21258810", "rel_title": "Antibody Responses to SARS-CoV-2 after Infection or Vaccination in Children and Young Adults with Inflammatory Bowel Disease", @@ -694770,61 +693403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.11.21258756", - "rel_title": "A pan-European study of SARS-CoV-2 variants in wastewater under the EU Sewage Sentinel System", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258756", - "rel_abs": "Wastewater based surveillance employing qPCR has already shown its utility for monitoring SARS-CoV-2 at community level, and consequently the European Commission has recommended the implementation of an EU Sewage Sentinel System. However, using sequencing for the determination of genomic variants in wastewater is not fully established yet. Therefore, we focused on the sequencing analysis of SARS-CoV-2 RNA in wastewater samples collected across 20 European countries including 54 municipalities. Our results provide unprecedented insight into the abundance and the profile of the mutations associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2, which were present in various wastewater samples. This study shows that integrating genomic and wastewater-based epidemiology (WBE) can support the identification of variants circulating in a city at community level.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shelesh Agrawal", - "author_inst": "Technical University of Darmstadt" - }, - { - "author_name": "Laura Orschler", - "author_inst": "Technical University of Darmstadt" - }, - { - "author_name": "Selina Schubert", - "author_inst": "Technical University of Darmstadt" - }, - { - "author_name": "Kira Zachmann", - "author_inst": "Technical University of Darmstadt" - }, - { - "author_name": "Leo Heijnen", - "author_inst": "KWR, Water Research Institute" - }, - { - "author_name": "Simona Tavazzi", - "author_inst": "European Commission, Joint Research Centre" - }, - { - "author_name": "Bernd Manfred Gawlik", - "author_inst": "European Commission, Joint Research Centre" - }, - { - "author_name": "Miranda de Graaf", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Gertjan Medema", - "author_inst": "KWR Water Research Institute" - }, - { - "author_name": "Susanne Lackner", - "author_inst": "Technical University of Darmstadt" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.11.21258575", "rel_title": "Support needs and barriers to accessing support: Baseline results of a mixed-methods national survey of people bereaved during the COVID-19 pandemic", @@ -695653,6 +694231,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.07.21258488", + "rel_title": "Risk factors for hospitalization, disease severity and mortality in children and adolescents with COVID-19: Results from a nationwide German registry", + "rel_date": "2021-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258488", + "rel_abs": "ObjectiveTo characterize the clinical features of children and adolescents hospitalized with SARS-CoV-2 infections and to explore predictors for disease severity.\n\nDesignNationwide prospective observational cohort study.\n\nSettingData collected from 169 out of 351 childrens hospitals in Germany between March 18, 2020 and April 30, 2021 and comparison with the Statutory Notification System.\n\nParticipants1,501 children and adolescents up to 19 years of age with laboratory confirmed SARS-CoV-2 infections who were admitted to childrens hospitals and subsequently reported to the COVID-19 registry of the German Pediatric Infectious Disease Society (DGPI).\n\nMain outcome measuresAdmission to intensive care, in-hospital.\n\nResultsAs compared to the information in the statutory notification system, up to 30% of all children and adolescents hospitalized in Germany during the study period were reported to the DGPI registry. Median age was three years (IQR, 0-12), with 36% of reported cases being infants. Although roughly half of patients in the registry were not admitted to the hospital due to their SARS-CoV-2 infection, 72% showed infection-related symptoms during hospitalization. Preexisting comorbidities were present in 28%, most commonly respiratory disorders, followed by neurological, neuromuscular, and cardiovascular diseases. Median length of hospitalization was five days (IQR 3-10). Only 20% of patients received a SARS-CoV-2-related therapy. Infants were less likely to require therapy as compared to older children. Overall, 111 children and adolescents were admitted to intensive care units (ICU). In a fully adjusted model, patient age, trisomy 21, coinfections and primary immunodeficiencies (PID) were significantly associated with intensive care treatment. In a bivariate analysis, pulmonary hypertension, cyanotic heart disease, status post (s/p) cardiac surgery, fatty liver disease, epilepsy and neuromuscular impairment were statistically significant risk factors for ICU admission.\n\nConclusionOverall, a small proportion of children and adolescents was hospitalized in Germany during the first year of the pandemic. The majority of patients within our registry was not admitted due to COVID-19 suggesting an overestimation of the disease burden even in hospitalized children. Nevertheless, a large proportion of children and adolescents with confirmed COVID-19 reported in Germany could be captured. This allowed for detailed assessment of overall disease severity and underlying risk factors in our cohort. The main risk factors for COVID-19 disease associated intensive care treatment were older patient age, trisomy 21, PIDs and coinfection at the time of hospitalization.\n\nTrial registrationRegistry of hospitalized pediatric patients with SARS-CoV-2 infection (COVID-19), DRKS00021506", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jakob Peter Armann", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Maren Doenhardt", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Markus Hufnagel", + "author_inst": "Division of Pediatric Infectious Diseases and Rheumatology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Medical Faculty, Univer" + }, + { + "author_name": "Nathalie Diffloth", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Felix Reichert", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Walter Haas", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Julia Schilling", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Sebastian Haller", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Johannes Huebner", + "author_inst": "Division of Pediatric Infectious Diseases, Hauner Childrens Hospital, Ludwig-Maximilians- Universitaet Muenchen, Munich, Germany" + }, + { + "author_name": "Arne Simon", + "author_inst": "Pediatric Oncology and Hematology, Children's Hospital Medical Center. University Clinics, Saarland, Germany" + }, + { + "author_name": "Dominik T Schneider", + "author_inst": "Clinic of Pediatrics, Municipal Hospital Dortmund, Dortmund, Germany" + }, + { + "author_name": "Juergen Brunner", + "author_inst": "Department of Pediatrics, Medical University Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Andreas Trotter", + "author_inst": "Childrens Hospital and Center for Perinatal Medicine, Teaching Hospital of the University of Freiburg, Singen, Germany" + }, + { + "author_name": "Martin Roessler", + "author_inst": "Center for Evidence-based Healthcare, Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Jochen Schmitt", + "author_inst": "Center for Evidence-based Healthcare, Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + }, + { + "author_name": "Reinhard Berner", + "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.10.21258721", "rel_title": "Early Prediction of In-Hospital Death of COVID-19 Patients: A Machine-Learning Model Based on Age, Blood Analyses, and Chest X-Ray Score", @@ -696592,53 +695249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.07.21258522", - "rel_title": "SARS-CoV-2 in wastewater from Mexico City used for irrigation in the Mezquital Valley: quantification and modelling of geographic dispersion", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258522", - "rel_abs": "Quantification of SARS-CoV-2 in urban wastewaters has emerged as a cheap, efficient strategy to follow trends of active COVID-19 cases in populations. Moreover, mathematical models have been developed that allow prediction of active cases following the temporal patterns of viral loads in wastewaters. In Mexico, no systematic efforts have been reported in the use of this strategies. In this work, we quantified SARS-CoV-2 in rivers and irrigation canals in the Mezquital Valley, Hidalgo, an agricultural region where wastewater from Mexico City is distributed and used for irrigation. Using quantitative RT-PCR, we detected the virus in 6 out of 8 water samples from rivers, and 5 out of 8 water samples from irrigation canals. Notably, samples showed a general consistent trend of having the highest viral loads in the sites closer to Mexico City, indicating that this is the main source that contributes to detection. Using the data for SARS-CoV-2 concentration in the river samples, we generated a simplified transport model that describes the spatial patterns of dispersion of virus in the river. We suggest that this model can be extrapolated to other wastewater systems that require knowledge of spatial patterns of viral dispersion at a geographic scale. Our work highlights the need for improved practices and policies related to the use of wastewater for irrigation in Mexico and other countries.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yaxk'in Coronado", - "author_inst": "Conacyt - Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarrollo" - }, - { - "author_name": "Roberto Navarro", - "author_inst": "Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarrollo" - }, - { - "author_name": "Carlos Mosqueda", - "author_inst": "Instituto Tecnologico de Celaya" - }, - { - "author_name": "Valeria Valenzuela", - "author_inst": "Universidad Tecnologica de Queretaro" - }, - { - "author_name": "Juan Pablo Perez", - "author_inst": "Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarollo" - }, - { - "author_name": "Victor Gonzalez-Mendoza", - "author_inst": "Conacyt - Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarrollo" - }, - { - "author_name": "Mayra De la Torre", - "author_inst": "Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarollo" - }, - { - "author_name": "Jorge Rocha", - "author_inst": "Conacyt - Unidad Regional Hidalgo, Centro de Investigacion en Alimentacion y Desarrollo" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.09.21258234", "rel_title": "Personal space Increases during the COVID-19 Pandemic in Response to Real and Virtual Humans", @@ -697315,6 +695925,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.08.21258546", + "rel_title": "Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258546", + "rel_abs": "BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies.\n\nMethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates.\n\nResultsPrevalence of disruption varied across studies; between 6.4% (TwinsUK) and 31.8 % (Understanding Society) of study participants reported any disruption. Females (Odd Ratio (OR): 1.27 [95%CI: 1.15,1.40]; I2=53%), older persons (e.g. OR: 1.39 [1.13,1.72]; I2=77% for 65-75y vs 45-54y), and Ethnic minorities (excluding White minorities) (OR: 1.19 [1.05,1.35]; I2=0% vs White) were more likely to report healthcare disruptions. Those in a more disadvantaged social class (e.g. OR: 1.17 [1.08, 1.27]; I2=0% for manual/routine vs managerial/professional) were also more likely to report healthcare disruptions, but no clear differences were observed by education levels.\n\nConclusionThe COVID-19 pandemic has led to unequal healthcare disruptions, which, if unaddressed, could contribute to the maintenance or widening of existing health inequalities.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jane Maddock", + "author_inst": "University College London" + }, + { + "author_name": "Sam Parsons", + "author_inst": "University College London" + }, + { + "author_name": "Giorgio Di Gessa", + "author_inst": "University College London" + }, + { + "author_name": "Michael J Green", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "King's College London" + }, + { + "author_name": "Anna J Stevenson", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Alex S.F. Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Eoin McElroy", + "author_inst": "University of Leicester" + }, + { + "author_name": "Gillian Santorelli", + "author_inst": "Bradford Institute for Health Research" + }, + { + "author_name": "Richard J Silverwood", + "author_inst": "University College London" + }, + { + "author_name": "Gabriella Captur", + "author_inst": "University College London" + }, + { + "author_name": "Nish Chaturvedi", + "author_inst": "University College London" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "University College London" + }, + { + "author_name": "Praveetha Patalay", + "author_inst": "University College London" + }, + { + "author_name": "George B Ploubidis", + "author_inst": "University College London" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.06.08.21258565", "rel_title": "MicroRNA-based regulation of genomics and transcriptomics of inflammatory cytokines in COVID-19", @@ -698542,25 +697235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.06.07.21258451", - "rel_title": "Modelling the effect of an improved trace and isolate system in the wake of a highly transmissible Covid-19 variant with potential vaccine escape", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258451", - "rel_abs": "ObjectiveHow helpful would a properly functioning find, test, trace, isolate and support (FTTIS) system be now in the UK with new Covid-19 infections at a low level and half the adult population immunised but with a highly transmissible variant becoming predominant?\n\nDesigna dynamic causal model of Covid-19 supplied with the latest available empirical data is used to assess the impact of a new highly transmissible variant.\n\nSettingthe United Kingdom.\n\nParticipantsa population based study.\n\nInterventionsscenarios are used to explore a Covid-19 transmission rate 50% more and twice the current rate with or without a more effective FTTIS system.\n\nMain outcome measuresincidence, death rate and reproductive ratio\n\nResultsa small short third wave of infections occurs which does not occur if FTTIS effectiveness is improved from 25% to 30%.\n\nConclusiona modest improvement in FTTIS would prevent a third wave caused by a highly transmissible virus.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Cam Bowie", - "author_inst": "Retired" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.06.08.21258444", "rel_title": "Does reactogenicity after a second injection of the BNT162b2 vaccine predict spike IgG antibody levels in healthy Japanese subjects?", @@ -699085,6 +697759,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.07.21258230", + "rel_title": "A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: from theory to practice", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258230", + "rel_abs": "BackgroundCOVID-19 vaccine coverage in the Latinx community depends on delivery systems that overcome barriers such as institutional distrust, misinformation, and access to care. We hypothesized that a community-centered vaccination strategy that included mobilization, vaccination, and \"activation\" components could successfully reach an underserved Latinx population, utilizing its social networks to boost vaccination coverage.\n\nMethods and FindingsOur community-academic-public health partnership, \"Unidos en Salud,\" utilized a theory-informed approach to design our \"Motivate, Vaccinate, and Activate\" COVID-19 vaccination strategy. Our strategys design was guided by the PRECEDE Model and sought to address and overcome predisposing, enabling, and reinforcing barriers to COVID-19 vaccination faced by Latinx individuals in San Francisco. We evaluated our prototype outdoor, \"neighborhood\" vaccination program located in a central commercial and transport hub in the Mission District in San Francisco, using the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework during a 16-week period from February 1, 2021 to May 19, 2021. Programmatic data, city-wide COVID-19 surveillance data, and a survey conducted between May 2, 2021 and May 19, 2021 among 997 vaccinated clients [≥]16 years old were used in the evaluation.\n\nThere were 20,792 COVID-19 vaccinations administered at the neighborhood site during the 16-week evaluation period. Vaccine recipients had a median age of 43 (IQR 32-56) years, 53.9% were male and 70.5% were Latinx, 14.1% white, 7.7% Asian, 2.4% Black, and 5.3% other. Latinx vaccinated clients were substantially more likely than non-Latinx clients to have an annual household income of less than $50,000 a year (76.1% vs. 33.5%), be a first-generation immigrant (60.2% vs. 30.1%), not have health insurance (47.3% vs. 16.0%), and not have access to primary care provider (62.4% vs. 36.2%). The most frequently reported reasons for choosing vaccination at the site were its neighborhood location (28.6%), easy and convenient scheduling (26.9%) and recommendation by someone they trusted (18.1%); approximately 99% reported having an overall positive experience, regardless of ethnicity. Notably, 58.3% of clients reported that they were able to get vaccinated earlier because of the neighborhood vaccination site, 98.4% of clients completed both vaccine doses, and 90.7% said that they were more likely to recommend COVID-19 vaccination to family and friends after their experience; these findings did not substantially differ according to ethnicity. There were 40.3% of vaccinated clients who said they still knew at least one unvaccinated person (64.6% knew [≥]3). Among clients who received both vaccine doses (n=729), 91.0% said that after their vaccination experience, they had personally reached out to at least one unvaccinated person they knew (61.6% reached out to [≥]3) to recommend getting vaccinated; 83.0% of clients reported that one or more friends, and/or family members got vaccinated as a result of their outreach, including 18.9% who reported 6 or more persons got vaccinated as a result of their influence.\n\nConclusionsA multi-component, \"Motivate, Vaccinate, and Activate\" community-based strategy addressing barriers to COVID-19 vaccination for the Latinx population reached the intended population, and vaccinated individuals served as ambassadors to recruit other friends and family members to get vaccinated.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Carina Marquez", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Andrew D. Kerkhoff", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Jamie Naso", + "author_inst": "Unidos en Salud, San Francisco, CA, USA" + }, + { + "author_name": "Maria G. Contreras", + "author_inst": "Unidos en Salud, San Francisco, CA, USA" + }, + { + "author_name": "Edgar Castellanos", + "author_inst": "Unidos en Salud, San Francisco, CA, USA" + }, + { + "author_name": "Susana Rojas", + "author_inst": "The San Francisco Latino Task Force on COVID-19, San Francisco, CA, USA" + }, + { + "author_name": "James Peng", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Luis Rubio", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Diane Jones", + "author_inst": "Unidos en Salud, San Francisco, CA, USA" + }, + { + "author_name": "Jon Jacobo", + "author_inst": "The San Francisco Latino Task Force on COVID-19, San Francisco, CA, USA" + }, + { + "author_name": "Susy Rojas", + "author_inst": "The San Francisco Latino Task Force on COVID-19, San Francisco, CA, USA" + }, + { + "author_name": "Rafael Gonzalez", + "author_inst": "San Francisco Department of Public Health, San Francisco, California, USA" + }, + { + "author_name": "Jonathan D. Fuchs", + "author_inst": "San Francisco Department of Public Health, San Francisco, California, USA" + }, + { + "author_name": "Douglas Black", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Salustiano Ribeiro", + "author_inst": "Bay Area Phlebotomy and Laboratory Services (BayPLS), San Francisco, CA, USA" + }, + { + "author_name": "Jen Nossokoff", + "author_inst": "Bay Area Phlebotomy and Laboratory Services (BayPLS), San Francisco, CA, USA" + }, + { + "author_name": "Valerie Tulier-Laiwa", + "author_inst": "The San Francisco Latino Task Force on COVID-19, San Francisco, CA, USA" + }, + { + "author_name": "Jacqueline Martinez", + "author_inst": "Unidos en Salud, San Francisco, CA, USA" + }, + { + "author_name": "Gabriel Chamie", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + }, + { + "author_name": "Genay Pilarowski", + "author_inst": "Department of Pathology, Stanford University, Stanford, California, USA" + }, + { + "author_name": "Joseph DeRisi", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, California, USA" + }, + { + "author_name": "Maya Petersen", + "author_inst": "Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA" + }, + { + "author_name": "Diane V. Havlir", + "author_inst": "Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.09.21258602", "rel_title": "Relevance of prediction scores derived from the SARS-CoV-2 first wave, in the UK COVID-19 second wave, for early discharge, severity and mortality: a PREDICT COVID UK prospective observational cohort study", @@ -700336,113 +699117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.06.08.21258366", - "rel_title": "Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 nai\u0308ve residents of nursing homes", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258366", - "rel_abs": "BackgroundResidents of nursing homes (NH) are at high risk of COVID-19 related morbidity and death and may respond poorly to vaccination because of old age and frequent comorbidities.\n\nMethodsForty residents and forty staff members either naive or previously infected with SARS-CoV-2 were recruited in two NH in Belgium before immunization with two doses of 30{micro}g BNT162b2 mRNA vaccine at day 0 and day 21. Binding antibodies (Ab) to SARS-CoV-2 receptor binding domain (RBD), spike domains S1 and S2, RBD Ab avidity, and neutralizing Ab against SARS-CoV-2 wild type and B.1.351 variant were assessed at days 0, 21, 28, and 49.\n\nResultsSARS-CoV-2 naive residents had lower Ab responses to BNT162b2 mRNA vaccination than naive staff. These poor responses involved lower levels of IgG to all domains of the vaccine antigen, lower avidity of RBD IgG, and lower levels of Ab neutralizing the vaccine strain. No naive resident had detectable neutralizing Ab to the B.1.351 variant. High and comparable Ab responses were observed in residents and staff previously infected with SARS-CoV-2. Clustering analysis revealed that poor vaccine responders not only included naive residents but also naive staff, emphasizing the heterogeneity of responses to mRNA vaccination in the general population.\n\nConclusionsThe poor Ab responses to mRNA vaccination observed in infection naive residents and in some naive staff members of NH suggest suboptimal protection against breakthrough infection, especially with variants of concern. Adapted vaccination regimens may be needed to provide optimal protection against COVID-19 to vulnerable populations.\n\nSummaryPoor antibody responses to COVID-19 mRNA vaccination were observed in SARS-CoV-2 infection naive residents and some naive staff members of nursing homes. This suggests suboptimal protection against breakthrough infection, especially with variants of concern, and the need for adapted vaccination regimens.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Pieter Pannus", - "author_inst": "SD Epidemiology and Public Health, Sciensano, Anderlecht, Belgium" - }, - { - "author_name": "Kristof Y Neven", - "author_inst": "SD Epidemiology and Public Health, Sciensano, Anderlecht, Belgium" - }, - { - "author_name": "St\u00e9phane De Craeye", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Sara Vande Kerckhove", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Daphn\u00e9e Georges", - "author_inst": "Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Universit\u00e9 libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Johan Michiels", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Antoine Francotte", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Marc Van Den Bulcke", - "author_inst": "SD Epidemiology and Public Health, Sciensano, Anderlecht, Belgium" - }, - { - "author_name": "Maan Zrein", - "author_inst": "InfYnity Biomarkers, Lyon, France" - }, - { - "author_name": "Steven Van Gucht", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Marie-No\u00eblle Schmickler", - "author_inst": "Mensura EDPB, Occupational Health Service, Antwerp, Belgium" - }, - { - "author_name": "Mathieu Verbrugghe", - "author_inst": "Mensura EDPB, Occupational Health Service, Antwerp, Belgium" - }, - { - "author_name": "Andr\u00e9 Matagne", - "author_inst": "Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Universit\u00e9 libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Isabelle Thomas", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Katelijne Dierick", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Joshua Alex Weiner", - "author_inst": "Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA" - }, - { - "author_name": "Stanislas Goriely", - "author_inst": "Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Universit\u00e9 libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Maria E Goossens", - "author_inst": "SD Epidemiology and Public Health, Sciensano, Anderlecht, Belgium" - }, - { - "author_name": "Kevin K. Ari\u00ebn", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, An" - }, - { - "author_name": "Isabelle Desombere", - "author_inst": "SD Infectious Diseases in Humans, Sciensano, Ukkel, Belgium" - }, - { - "author_name": "Arnaud Marchant", - "author_inst": "Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Universit\u00e9 libre de Bruxelles (ULB), Gosselies, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.07.21258520", "rel_title": "Post-Acute COVID Syndrome, the Aftermath of Mild to Severe COVID-19 in Brazilian Patients", @@ -701171,6 +699845,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.09.447662", + "rel_title": "Intranasal administration of a monoclonal neutralizing antibody protects mice against SARS-CoV-2 infection", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447662", + "rel_abs": "Despite recent availability of vaccines against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), there is an urgent need for specific anti-SARS-CoV-2 drugs. Monoclonal neutralizing antibodies are an important drug class in the global fight against the SARS-CoV-2 pandemic due to their ability to convey immediate protection and their potential to be used as both, prophylactic and therapeutic drugs. Clinically used neutralizing antibodies against respiratory viruses are currently injected intravenously, which can lead to suboptimal pulmonary bioavailability and thus to a lower effectiveness.\n\nHere we describe DZIF-10c, a fully human monoclonal neutralizing antibody that binds the receptor-binding domain of SARS-CoV-2 spike protein. DZIF-10c displays an exceptionally high neutralizing potency against SARS-CoV-2 and retains activity against the variants of concern B.1.1.7 and B.1.351. Importantly, not only systemic but also intranasal application of DZIF-10c abolished presence of infectious particles in the lungs of SARS-CoV-2 infected mice and mitigated lung pathology. Along with a favorable pharmacokinetic profile, these results highlight DZIF-10c as a novel human SARS-CoV-2 neutralizing antibody with high in vitro and in vivo antiviral potency. The successful intranasal application of DZIF-10c paves the way for clinical trials investigating topical delivery of anti-SARS-CoV-2 antibodies.\n\nSignificance StatementMonoclonal neutralizing antibodies are important in the global fight against the SARS-CoV-2 pandemic due to their ability to convey immediate protection. However, their intravenous application might lead to suboptimal bioavailability in the lung. We here precisely characterize a new monoclonal neutralizing antibody (DZIF-10c) that binds to the receptor binding domain of the spike protein of SARS-CoV-2. DZIF-10c neutralizes SARS-CoV-2 with exceptionally high potency and maintains activity against circulating variants of concern. The antibody has a favorable pharmacokinetic profile and protects mice from SARS-CoV-2 infection. Importantly, we show that intranasal administration of DZIF-10c generates protective efficacy. These results not only identify DZIF-10c as a novel highly potent neutralizing antibody, but further pave the way for a topical application of anti-SARS-CoV-2 antibodies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Sandro Halwe", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Alexandra Kupke", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Kanika Vanshylla", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Falk Liberta", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Henning Gruell", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Matthias Zehner", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Cornelius Rohde", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Verena Kraehling", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Michelle Gellhorn-Serra", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Christoph Kreer", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Michael Kluever", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Lucie Sauerhering", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Joerg Schmidt", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Zheng Cai", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Fei Han", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "David Young", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Guangwei Yang", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Marek Widera", + "author_inst": "Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main" + }, + { + "author_name": "Manuel Koch", + "author_inst": "Center for Molecular Medicine Cologne (CMMC), University of Cologne" + }, + { + "author_name": "Anke Werner", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Lennart Kaemper", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Nico Becker", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Michael S Marlow", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Markus Eickmann", + "author_inst": "Institute of Virology, Philipps University Marburg" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main" + }, + { + "author_name": "Felix Schiele", + "author_inst": "Biotherapeutics Discovery, Boehringer Ingelheim" + }, + { + "author_name": "Florian Klein", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne" + }, + { + "author_name": "Stephan Becker", + "author_inst": "Institute of Virology, Philipps University Marburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.09.447760", "rel_title": "Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection", @@ -702326,61 +701127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.06.07.21258375", - "rel_title": "Seroprevalence of SARS-CoV-2 Antibodies Among Rural Healthcare Workers", - "rel_date": "2021-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258375", - "rel_abs": "The objective of this longitudinal cohort study was to determine the seroprevalence of antibodies to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in healthcare workers employed at healthcare clinics in three rural counties in eastern South Dakota and western Minnesota from May 13, 2020 through December 22, 2020. Three blood draws were performed at five clinical sites and tested for the presence of antibodies against the SARS-CoV-2 virus. Serum samples were tested for the presence of antibodies using a fluorescent microsphere immunoassay (FMIA), neutralization of SARS-CoV-2 Spike-pseudotyped particles (SARS-CoV-2pp) assay, and serum virus neutralization (SVN) assay. The seroprevalence was determined to be 1/336 (0.29%) for samples collected from 5/13/20-7/13/20, 5/260 (1.92%) for samples collected from 8/13/20-9/25/20, and 35/235 (14.89%) for samples collected from 10/16/20-12/22/20. Eight of the 35 (22.8%) seropositive individuals identified in the final draw did not report a previous diagnosis with COVID-19. There was a high correlation (>90%) among the FMIA and virus neutralization assays. Each clinical sites seroprevalence was higher than the cumulative incidence for the general public in each respective county as reported by state public health agencies. As of December 2020, there was a high percentage (85%) of seronegative individuals in the study population.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jordan Z Neises", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Hossain Md Saddam", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Rifat Sultana", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Kevin N Wanniarachchi", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Jared W Wollman", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Eric Nelson", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Bonny L Specker", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Adam D Hoppe", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Steven R Lawson", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Natalie W Thiex", - "author_inst": "South Dakota State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.08.21258531", "rel_title": "The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies", @@ -703165,6 +701911,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.30.21257913", + "rel_title": "Highly sensitive scent-detection of COVID-19 patients in vivo by trained dogs", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21257913", + "rel_abs": "Timely and accurate diagnostics are essential to fight the COVID-19 pandemic, but no test satisfies both conditions. Dogs can scent-identify the unique odors of the volatile organic compounds generated during infection by interrogating specimens or, ideally, the body of a patient. After training 6 dogs to detect SARS-CoV-2 in human respiratory secretions (in vitro scent-detection), we retrained 5 of them to diagnose the infection by scenting the patient directly (in vivo scent-detection). Then, efficacy trials were designed to compare the diagnostic performance of the dogs against that of the rRT-PCR in 848 human subjects: 269 hospitalized patients (COVID-19 prevalence 30.1%), 259 hospital staff (prevalence 2.7%), and 320 government employees (prevalence 1.25%). The limit of detection in vitro was lower than 10-12 copies ssRNA/mL. In vivo, all dogs detected 92 COVID-19 patients present among the 848 study subjects. Detection was immediate, and independent of prevalence, time post-exposure, or presence of symptoms, with 95.2% accuracy and high sensitivity (95.9%; 95% C.I. 93.6-97.4), specificity (95.1%; 94.4-95.8), positive predictive value (69.7%; 65.9-73.2), and negative predictive value (99.5%; 99.2-99.7). To determine real-life performance, we waited 75 days to carry out an effectiveness assay among the riders of the Metro System of Medellin, deploying the human-canine teams without previous training or announcement. Three dogs (one of each breed) scent-interrogated 550 citizens who volunteered for simultaneous canine and rRT-PCR testing. Negative predictive value remained at 99.0% (95% C.I. 98.3-99.4), but positive predictive value dropped to 28.2% (95% C.I. 21.1-36.7). Canine scent-detection in vivo is a highly accurate screening test for COVID-19, and it detects more than 99% of infected individuals independently of the key variables. However, real-life conditions increased substantially the number of false positives, indicating the necessity of training a threshold for the limit of detection to discriminate environmental odoriferous contamination from infection.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Omar Vesga", + "author_inst": "Hospital Universitario San Vicente Fundacion and GRIPE, University of Antioquia" + }, + { + "author_name": "Maria Agudelo", + "author_inst": "Hospital Universitario San Vicente Fundacion and GRIPE, University of Antioquia" + }, + { + "author_name": "Andres F Valencia-Jaramillo", + "author_inst": "GRIPE, University of Antioquia and Colina K-9" + }, + { + "author_name": "Alejandro Mira-Montoya", + "author_inst": "GRIPE, University of Antioquia" + }, + { + "author_name": "Ivan Felipe Ossa-Ospina", + "author_inst": "GRIPE, University of Antioquia" + }, + { + "author_name": "Esteban Ocampo", + "author_inst": "Colina K-9" + }, + { + "author_name": "Karl Ciuoderis", + "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin" + }, + { + "author_name": "Laura Perez", + "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin" + }, + { + "author_name": "Andres Cardona", + "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin" + }, + { + "author_name": "Yudy Aguilar", + "author_inst": "GRIPE, University of Antioquia" + }, + { + "author_name": "Yuli Agudelo", + "author_inst": "Hospital Universitario San Vicente Fundacion" + }, + { + "author_name": "Juan Pablo Hernandez-Ortiz", + "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin" + }, + { + "author_name": "Jorge E Osorio", + "author_inst": "Department of Pathobiology, School of Veterinary Medicine, University of Wisconsin, Madison, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.04.21258343", "rel_title": "The efficacy and safety of monoclonal antibody treatments against COVID-19: A systematic review and meta-analysis of randomized clinical trials", @@ -704220,37 +703033,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.06.06.21258272", - "rel_title": "Long-COVID following mild SARS CoV-2 infection: characteristic T cell alterations and response to antihistamines", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258272", - "rel_abs": "BackgroundLong-COVID is characterised by the emergence of multiple debilitating symptoms following SARS CoV2 infection. Its aetiology is unclear, and it often follows a mild acute illness. Anecdotal reports of gradual clinical responses to histamine receptor antagonists (HRA) suggest a histamine-dependent mechanism distinct from anaphylaxis. Histamine is a paracrine regulator of T-cells: although T-cell perturbations are reported in acute COVID-19, the T-cell landscape in recovered patients and its relationship to long-COVID remains under-explored.\n\nObjectiveTo survey T-cell populations in patients recovered from mild COVID-19, comparing those with long-COVID and asymptomatic individuals, and to analyse these data in light of symptoms and response to HRA.\n\nDesignProspective observational cohort study.\n\nSettingSingle-site outpatient clinic\n\nParticipants65 (87 to 408 days post mild COVID-19). None had sought treatment for acute COVID-19. 16 recovered uneventfully (asymptomatic group), 49 presented with long-COVID (symptomatic group), of whom 25 received HRA.\n\nMeasurementsStructured long-COVID symptom questionnaire; quantification of T-cell subsets using a standard diagnostic assay.\n\nResultsHRA significantly reduced mean symptom burden. T-cell profiles distinguished asymptomatic and long-COVID groups, but did not predict response to HRA. Long-COVID patients had reduced CD4+ and CD8+ effector memory (EM) cells and increased PD-1 expression on central memory (CM) cells. Asymptomatic controls had reduced CD8+ EM cells and increased CD28 expression on CM cells.\n\nConclusionHRA reduce long-COVID symptoms. T-cell perturbations persist for up to 400 days following mild acute COVID-19 irrespective of long-COVID symptoms.\n\nLimitationsPreliminary, single health system study.\n\nPrimary Funding SourcePhilanthropic donations from The Dominvs Group and Sir Peter Wood", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paul Glynne", - "author_inst": "The Physicians' Clinic, University College London Hospitals" - }, - { - "author_name": "Natasha Tahmasebi", - "author_inst": "Kings College London Medical School" - }, - { - "author_name": "Vanya A Gant", - "author_inst": "University College London Hospitals" - }, - { - "author_name": "Rajeev Gupta", - "author_inst": "UCL Cancer Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.03.21258312", "rel_title": "Outcomes of SARS-CoV-2 Infection in Patients with Chronic Liver Disease and Cirrhosis: a N3C Study", @@ -704883,6 +703665,101 @@ "type": "contradictory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.06.07.447286", + "rel_title": "Dual roles of a novel oncolytic viral vector-based SARS-CoV-2 vaccine: preventing COVID-19 and treating tumor progression", + "rel_date": "2021-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.447286", + "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cancer patients are usually immunocompromised and thus are particularly susceptible to SARS-CoV-2 infection resulting in COVID-19. Although many vaccines against COVID-19 are being preclinically or clinically tested or approved, none have yet been specifically developed for cancer patients or reported as having potential dual functions to prevent COVID-19 and treat cancer. Here, we confirmed that COVID-19 patients with cancer have low levels of antibodies against the spike (S) protein, a viral surface protein mediating the entry of SARS-CoV-2 into host cells, compared with COVID-19 patients without cancer. We developed an oncolytic herpes simplex virus-1 vector-based vaccine named oncolytic virus (OV)-spike. OV-spike induced abundant anti-S protein neutralization antibodies in both tumor-free and tumor-bearing mice, which inhibit infection of VSV-SARS-CoV-2 and wild-type (WT) live SARS-CoV-2 as well as the B.1.1.7 variant in vitro. In the tumor-bearing mice, OV-spike also inhibited tumor growth, leading to better survival in multiple preclinical tumor models than the untreated control. Furthermore, OV-spike induced anti-tumor immune response and SARS-CoV-2-specific T cell response without causing serious adverse events. Thus, OV-spike is a promising vaccine candidate for both preventing COVID-19 and enhancing the anti-tumor response.\n\nOne Sentence SummaryA herpes oncolytic viral vector-based vaccine is a promising vaccine with dual roles in preventing COVID-19 and treating tumor progression", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Michael A. Caligiuri", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Jianhua Yu", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Yaping Sun", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Wenjuan Dong", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Lei Tian", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Youliang Rao", + "author_inst": "Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Califo" + }, + { + "author_name": "Chao Qin", + "author_inst": "Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Califo" + }, + { + "author_name": "Sierra A. Jaramillo", + "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA" + }, + { + "author_name": "Erik W. Settles", + "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA" + }, + { + "author_name": "Shoubao Ma", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Jianying Zhang", + "author_inst": "Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Kang Yu", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Bo Xu", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Jiazhuo Yan", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Rui Ma", + "author_inst": "Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Zhuo Li", + "author_inst": "Department of Molecular and Cellular Biology, Electron Microscopy Core Facility, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Sanjeet S. Dadwal", + "author_inst": "Division of Infectious Diseases, City of Hope National Medical Center, Los Angeles, CA 91010, USA" + }, + { + "author_name": "Bridget M. Barker", + "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA" + }, + { + "author_name": "Paul S. Keim", + "author_inst": "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA" + }, + { + "author_name": "Pinghui Feng", + "author_inst": "Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Califo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.07.447351", "rel_title": "Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways", @@ -705910,33 +704787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.06.02.21258217", - "rel_title": "Tracking deaths can provide an indicator of latent COVID19 cases", - "rel_date": "2021-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258217", - "rel_abs": "BackgroundWith countries across the world facing repeated epidemic waves, it becomes critical to monitor, mitigate and prevent subsequent waves. Common indicators like active case numbers can flatter to deceive in the presence of systemic inefficiencies like insufficient testing or contact tracing. Test positivity rates are sensitive to testing strategies and cannot estimate the extent of undetected cases. Reproductive numbers estimated from logarithms of new incidences are inaccurate in dynamic scenarios and not sensitive enough to capture changes in efficiencies. Systemic fatigue results in lower testing, inefficient tracing and quarantining thereby precipitating the onset of the epidemic wave.\n\nMethodsWe propose a novel indicator for detecting the slippage of test-trace efficiency based on the numbers of deaths/hospitalizations resulting from known and hitherto unknown infections. This can also be used to forecast an epidemic wave that is advanced or exacerbated due to drop in efficiency.\n\nResultsUsing a modified SEIRD epidemic simulator we show that (i) Ratio of deaths/hospitalizations from an undetected infection to total deaths converges to a measure of systemic test-trace inefficiency. (ii) This index forecasts the slippage in efficiency earlier than other known metrics. (iii) Mitigation triggered by this index helps reduce peak active caseload and eventual deaths.\n\nConclusionsDeaths/hospitalizations accurately track the systemic inefficiencies and detect latent cases. Based on these results we make a strong case that administrations use this metric in the ensemble of indicators. Further hospitals may need to be mandated to distinctly register deaths/hospitalizations due to previously undetected infections.\n\nKey MessagesO_LIDeaths or Hospitalizations are unmissable events in an epidemic and this paper proposes a metric Dratio based on these numbers to monitor the inefficiencies in test-track-trace performance.\nC_LIO_LIThe ratio of deaths(or hospitalizations) resulting from undetected infections to total deaths (or hospitalizations) detect the onset of laxity in regulations earlier than other conventional metrics like daily increase in active cases, daily deaths or even reproductive number estimates.\nC_LIO_LIMitigation by tracking the Dratio reduces or truncates the epidemic wave intensity or delays it sufficiently.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yashaswini Mandayam Rangayyan", - "author_inst": "Indian Institute of Technology, Hyderabad" - }, - { - "author_name": "Sriram Kidambi", - "author_inst": "University of Texas at Dallas" - }, - { - "author_name": "Mohan Raghavan", - "author_inst": "Indian Institute of Technology Hyderabad" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.02.21258221", "rel_title": "Classifying Texas counties using ARIMA Models on COVID-19 daily confirmed cases: the impact of political affiliation and face covering orders", @@ -706477,6 +705327,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2021.06.03.21258302", + "rel_title": "Comparative Household Secondary Attack Rates associated with B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants", + "rel_date": "2021-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258302", + "rel_abs": "BackgroundThe emergence of SARS-CoV-2 variants associated with increased transmissibility are driving a 3rd global surge in COVID-19 incidence. There are currently few reliable estimates for the P.1 and B.1.351 lineages. We sought to compare the secondary attack rates of SARS-COV-2 mutations and variants in Canadas largest province of Ontario, using a previously validated household-based approach.\n\nMethodsWe identified individuals with confirmed SARS-CoV-2 infection in Ontarios provincial reportable disease surveillance system. Cases were grouped into households based on reported residential address. Index cases had the earliest of symptom onset in the household. Household secondary attack rate was defined as the percentage of household contacts identified as secondary cases within 1-14 days after the index case.\n\nResultsWe identified 26,888 index household cases during the study period. Among these, 7,555 (28%) were wild-type, 17,058 (63%) were B.1.1.7, 1674 (6%) were B.1.351 or P.1, and 601 (2%) were non-VOC mutants (Table 1). The secondary attack rates, according to index case variant were as follows: 20.2% (wild-type), 25.1% (B.1.1.7), 27.2% (B.1.351 or P.1), and 23.3% (non-VOC mutants). In adjusted analyses, we found that B.1.1.7, B.1.351, and P.1 index cases had the highest transmissibility (presumptive B.1.1.7 ORadjusted=1.49, 95%CI 1.36, 1.64; presumptive B.1.351 or P.1 ORadjusted=1.60, 95%CI 1.37, 1.87).\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1f1a4e9org.highwire.dtl.DTLVardef@181f042org.highwire.dtl.DTLVardef@1c483fborg.highwire.dtl.DTLVardef@b4fba0org.highwire.dtl.DTLVardef@1f3d626_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSecondary attack rates of persons infected with SARS-CoV-2, March 1 to April 17.\n\nC_TABLECAPTION C_TBL DiscussionSubstantially higher transmissibility associated with variants will make control of SARS-CoV-2 more difficult, reinforcing the urgent need to increase vaccination rates globally.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kevin A Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Semra Tibebu", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Sunnybrook Hospital" + }, + { + "author_name": "Kevin L Schwartz", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Michael Whelan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.27.21257726", "rel_title": "High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with Next Generation Sequencing", @@ -707392,41 +706281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.01.21258186", - "rel_title": "Formation of oxidized gases and secondary organic aerosol from a commercial oxidant-generating electronic air cleaner", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258186", - "rel_abs": "Airborne virus transmission during the COVID-19 pandemic increased the demand for indoor air cleaners. While some commercial electronic air cleaners could be effective in reducing primary pollutants and inactivating bioaerosol, studies on the formation of secondary products from oxidation chemistry during their use are limited. Here, we measured oxygenated volatile organic compounds (OVOCs) and the chemical composition of particles generated from a hydroxyl radical generator in an office. During operation, enhancements in OVOCs, especially low-molecular-weight organic and inorganic acids, were detected. Rapid increases in particle number and volume concentrations were observed, corresponding to the formation of highly-oxidized secondary organic aerosol (SOA) (O:C [~]1.3). The organic mass spectra showed an enhanced signal at m/z 44 (CO2+) and the aerosol evolved with a slope of [~] -1 in the Van Krevelen diagram. These results suggest that organic acids generated during VOC oxidation contributed to particle nucleation and SOA formation. Nitrate, sulfate, and chloride also increased during the oxidation without a corresponding increase in ammonium, suggesting organic nitrate, organic sulfate, and organic chloride formation. As secondary species are reported to have detrimental health effects, further studies are needed to evaluate potential OVOCs and SOA formation from electronic air cleaners in different indoor environments.\n\nSynopsisWe observed formation of oxygenated volatile organic compounds and secondary organic aerosol from an electronic air cleaner.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Taekyu Joo", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Jean C Rivera-Rios", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Daniel Alvarado-Velez", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Sabrina Westgate", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Nga Lee Ng", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.04.21258316", "rel_title": "A Prospective Observational Study to Investigate Performance of a Chest X-ray Artificial Intelligence Diagnostic Support Tool Across 12 U.S. Hospitals", @@ -708151,6 +707005,73 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.06.02.21257981", + "rel_title": "COVID-19 Sniffer Dog experimental training: which protocol and which implications for reliable identification?", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21257981", + "rel_abs": "The introduction of trained sniffer dogs for COVID-19 disease detection could be an opportunity, as previously described for other diseases. Dogs could be trained to detect volatile organic compounds (VOCs), the whiff of COVDI-19 disease. Dogs involved in the study were three one male and two females from different breeds, Black German Shepherd, German Shepherd and Dutch Shepherd. The training was performed using sweat samples from COVID-19 positive apteints and from covid-19 free patients admitted at the University Hospital Campus Bio-medico of Rome. Gauze with sweat were collected in glass jar with metal top and put in metal boxes used for dog training. The dog training protocol was performed in two phase: the olfactory conditioning and the olfactory discrimintaion research. The training palnning was focused on the switch moment for the sniffer dog, the moment when the dog was able to identify VOCs specific for COVID-19 disease. At this time the dog was able to identify VOCs specific for COVID-19 disease with significant reliability, in terms of number of correct versus uncorrect (p<0.0001) reporting. In conclusion, this protocol could provide a useful tool for sniffer dogs training and their introduction in mass screening context, cheaper and faster than a conventional testing method.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Silvia Angeletti", + "author_inst": "University Campus Bio-Medico of Rome" + }, + { + "author_name": "Francesco Travaglino", + "author_inst": "Campus Biomedico Roma" + }, + { + "author_name": "Silvia Spoto", + "author_inst": "Campus Biomedico, Roma Italia" + }, + { + "author_name": "Maria Chiara Pascarella", + "author_inst": "Campus Biomedico Roma, Italy" + }, + { + "author_name": "Giorgia Mansi", + "author_inst": "Universita Campus Biomedico" + }, + { + "author_name": "Marina De Cesaris", + "author_inst": "Universita Campus Biomedico" + }, + { + "author_name": "Silvia Sartea", + "author_inst": "University Campus Bio-Medico of Rome" + }, + { + "author_name": "Marta Giovanetti", + "author_inst": "Oswaldo Cruz Institute" + }, + { + "author_name": "Marta Fogolari", + "author_inst": "University Campus Bio-Medico of Rome" + }, + { + "author_name": "Davide Plescia", + "author_inst": "K9 Unit SecurityDogs, NGS Private Security Company." + }, + { + "author_name": "Massimiliano Macera", + "author_inst": "K9 Unit SecurityDogs, NGS Private Security Company." + }, + { + "author_name": "Raffaele Antonelli Incalzi", + "author_inst": "University Campus Bio-Medico of Rome" + }, + { + "author_name": "Massimo Ciccozzi", + "author_inst": "University Campus Bio-Medico of Rome" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.06.02.21257804", "rel_title": "Impaired Humoral Immunity to SARS-CoV-2 Vaccination in Non-Hodgkin Lymphoma and CLL Patients", @@ -709410,53 +708331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.28.21258025", - "rel_title": "SARS-CoV-2 specific memory B-cells from individuals with diverse disease severities recognize SARS-CoV-2 variants of concern.", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258025", - "rel_abs": "In this investigation we examined the magnitude, breadth, and durability of SARS-CoV-2 specific antibodies in two distinct B-cell compartments: long-lived plasma cell-derived antibodies in the plasma, and peripheral memory B-cells along with their associated antibody profiles elicited after in vitro stimulation. We found that magnitude varied amongst individuals, but was the highest in hospitalized subjects. Variants of concern (VoC) -RBD-reactive antibodies were found in the plasma of 72% of samples in this investigation, and VoC-RBD-reactive memory B-cells were found in all but 1 subject at a single time-point. This finding, that VoC-RBD-reactive MBCs are present in the peripheral blood of all subjects including those that experienced asymptomatic or mild disease, provides a reason for optimism regarding the capacity of vaccination, prior infection, and/or both, to limit disease severity and transmission of variants of concern as they continue to arise and circulate.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zoe L Lyski", - "author_inst": "Oregon Health and Science University, Department of Molecular Microbiology and Immunology" - }, - { - "author_name": "Amanda E Brunton", - "author_inst": "Oregon Health and Science University, OHSU-PSU school of public health" - }, - { - "author_name": "Mathew I Strnad", - "author_inst": "Oregon Health and Science University, OHSU-PSU school of public health" - }, - { - "author_name": "Peter E Sullivan", - "author_inst": "Oregon Health and Science University, OHSU-PSU school of public health" - }, - { - "author_name": "Sarah A.R. Siegel", - "author_inst": "Oregon Health and Science University, OHSU-PSU school of public health" - }, - { - "author_name": "Fikadu G Tafesse", - "author_inst": "Oregon Health & Science University, Department of Molecular Microbiology and Immunology" - }, - { - "author_name": "Mark K Slifka", - "author_inst": "Oregon Health and Science University, Division of Neuroscience, Oregon National Primate Research Center" - }, - { - "author_name": "William B Messer", - "author_inst": "Oregon Health and Science University, Molecular Microbiology and Immunology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.05.31.21258129", "rel_title": "Physical integrity of medical exam gloves with repeated applications of disinfecting agents: evidence for extended use", @@ -710313,6 +709187,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.31.21256946", + "rel_title": "Confirmed COVID-19 cases per economic activity during Autumn wave in Belgium", + "rel_date": "2021-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21256946", + "rel_abs": "ObjectiveTo assess the COVID-19 incidence per economic activity during the Autumn wave 2020 in Belgium.\n\nMethodsThe 14-day incidence of confirmed COVID-19 cases per NACE-BEL code is described in the periods immediately preceding the Belgian more strict measures of October 19, 2020, and is evaluated longitudinally by a Gaussian-Gaussian modelling two-stage approach. Additionally, the number of high-risk contacts in working segments and regions is described.\n\nResultsThe peak of COVID-19 14-day incidence in most NACE-BEL sectors is reached in the period October 20-November 2, 2020 and was considerably higher than average in human health activities, residential care activities, fitness facilities, human resource provision, hairdressing and other beauty treatment and some public service activities. Human health activities, residential care activities, food and beverage service activities, hotels, arts, food retail activities, and human resources provision have high pre-lockdown incidences. The frequency of index cases that report more than two high risk contacts is increasing over time in all sectors.\n\nConclusionDespite the restrictive protocols present in many sectors before the Autumn wave, employees in activities where close contact with others is high, show increased risk of COVID-19 infection. Especially sports activities are among the highest risk activities. Finally, the increasing amount of high-risk contacts by COVID-19 confirmed cases is compatible with the decreasing motivation over time to adhere to the measures.\n\nKey Messages\n\nWhat is already known about this subject?Certain occupational sectors, such as human health and care, food and beverage, cultural and sport activities, have been related to a high risk of SARS-CoV-2 infection at the workplace.\n\nWhat are the new findings?COVID-19 confirmed cases of employees are linked with the main economic activity of their employer. The effect of opening of sectors, potentially under restrictive protocols, is evaluated. Despite the restrictive protocols present in many sectors, employees in activities where close and/or prolonged contact with others is high exhibit increased risk of COVID-19 infection, even higher than the high-risk sector of human health and care. Full restriction of these sectors decreases adequately the COVID-19 incidences, even in those sectors with physical contacts that remain open, for example human health, care and food shops. Finally, the increasing amount of high-risk contacts by COVID-19 confirmed cases might be related to decreasing motivation over time to adhere to the measures.\n\nHow might this impact on policy or clinical practice in the foreseeable future?These insights offer guidance to policy makers on which economic activity to restrict or subject to stricter protocols to better control the COVID-19 pandemic whilst keeping the work floor as safe as possible.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Johan Verbeeck", + "author_inst": "UHasselt" + }, + { + "author_name": "Lieve Vanersmissen", + "author_inst": "IDEWE" + }, + { + "author_name": "Jannes Peeters", + "author_inst": "UHasselt" + }, + { + "author_name": "Sofieke Klamer", + "author_inst": "Sciensano" + }, + { + "author_name": "Sharon Hancart", + "author_inst": "Sciensano" + }, + { + "author_name": "Tinne Lernout", + "author_inst": "Sciensano" + }, + { + "author_name": "Mathias Dewatripont", + "author_inst": "ULB" + }, + { + "author_name": "Lode Godderis", + "author_inst": "UZLeuven" + }, + { + "author_name": "Geert Molenberghs", + "author_inst": "Universiteit Hasselt and KU Leuven" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.05.29.21258055", "rel_title": "The impact of three progressively introduced interventions on second wave daily COVID-19 case numbers in Melbourne, Australia", @@ -711336,117 +710261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.05.26.21256092", - "rel_title": "Cross-reactive antibodies after SARS-CoV-2 infection and vaccination", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21256092", - "rel_abs": "Current SARS-CoV-2 vaccines are losing efficacy against emerging variants and may not protect against future novel coronavirus outbreaks, emphasizing the need for more broadly protective vaccines. To inform the development of a pan-coronavirus vaccine, we investigated the presence and specificity of cross-reactive antibodies against the spike (S) proteins of human coronaviruses (hCoV) after SARS-CoV-2 infection and vaccination. We found an 11 to 123-fold increase in antibodies binding to SARS-CoV and MERS-CoV as well as a 2 to 4-fold difference in antibodies binding to seasonal hCoVs in COVID-19 convalescent sera compared to pre-pandemic healthy donors, with the S2 subdomain of the S protein being the main target for cross-reactivity. In addition, we detected cross-reactive antibodies to all hCoV S proteins after SARS-CoV-2 S protein immunization in macaques, with higher responses for hCoV more closely related to SARS-CoV-2. These findings support the feasibility of and provide guidance for development of a pan-coronavirus vaccine.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Marloes Grobben", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Karlijn van der Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Philip J.M. Brouwer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Mitch Brinkkemper", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Pauline Maisonnasse", - "author_inst": "CEA" - }, - { - "author_name": "Nathalie Dereuddre-Bosquet", - "author_inst": "CEA" - }, - { - "author_name": "Judith A. Burger", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Meliawati Poniman", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Melissa Oomen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "RIVM" - }, - { - "author_name": "Tom P.L. Bijl", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Hugo D.G. van Willigen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Elke Wynberg", - "author_inst": "GGD" - }, - { - "author_name": "Bas J. Verkaik", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Orlane J.A. Figaroa", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Peter J. de Vries", - "author_inst": "Tergooi Hospital" - }, - { - "author_name": "Tessel M. Boertien", - "author_inst": "Tergooi Hospital" - }, - { - "author_name": "Roger Le Grand", - "author_inst": "CEA" - }, - { - "author_name": "Menno D. de Jong", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Maria Prins", - "author_inst": "GGD" - }, - { - "author_name": "Amy W. Chung", - "author_inst": "Peter Doherty Institute" - }, - { - "author_name": "Godelieve J. de Bree", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Rogier W. Sanders", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "Amsterdam UMC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.26.21257063", "rel_title": "Evaluation of the INDICAID COVID-19 Rapid Antigen Test in symptomatic populations and asymptomatic community testing", @@ -711975,6 +710789,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.05.31.21257367", + "rel_title": "A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21257367", + "rel_abs": "The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94% and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Serafeim C. Chaintoutis", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Taxiarchis Chassalevris", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "George Tsiolas", + "author_inst": "Centre of Research and Technology Hellas" + }, + { + "author_name": "Sofia Balaska", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Ioannis Vlatakis", + "author_inst": "EnzyQuest PC" + }, + { + "author_name": "Evangelia Mouchtaropoulou", + "author_inst": "Centre of Research and Technology Hellas" + }, + { + "author_name": "Victoria I. Siarkou", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Areti Tychala", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Dimitris Koutsioulis", + "author_inst": "EnzyQuest PC" + }, + { + "author_name": "Lemonia Skoura", + "author_inst": "Aristotle University of Thessaloniki" + }, + { + "author_name": "Anagnostis Argiriou", + "author_inst": "Centre of Research and Technology Hellas" + }, + { + "author_name": "Chrysostomos I. Dovas", + "author_inst": "Aristotle University of Thessaloniki" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.31.21257841", "rel_title": "Aerosol SARS-CoV-2 in hospitals and long-term care homes during the COVID-19 pandemic.", @@ -713114,45 +711991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.05.30.21258068", - "rel_title": "COVID-19 Associated Mucormycosis: Scoping Review Protocol", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21258068", - "rel_abs": "Background and ObjectiveMucormycosis, a serious and rare fungal infection, has occurred concurrently in COVID-19 patients globally. Mucormycosis is associated with a high risk of all-cause mortality, with mortality depending on body site infected, fungus type, and the patients overall condition. This deadly fungal infection is quite difficult and expensive to treat. Therefore, this scoping review aims to map all the empirical evidence on the COVID-19 associated mucormycosis with a special focus on clinical presentation, treatment, and patient outcomes.\n\nMethodsThe proposed scoping review will be developed by adhering to the JBI methodology for scoping reviews and will be reported as per the Preferred Reporting Items for Systematic Reviews and Meta-analyses for Scoping Reviews (PRISMA-ScR). A detailed search strategy has already been utilized to locate both published and unpublished studies. Literature search was carried out in three phases. PubMed, Scopus, Cochrane, Google scholar was searched. We will include all those studies which are presenting mucormycosis cases in COVID-19 positive patients. Data will be extracted in a pre-designed data extraction sheet and risk of bias will be assessed using JBI critical appraisal tool. The primary outcome will be to summarize the clinical presentation, treatment, and patient outcomes in COVID-19 associated mucormycosis. Data will be presented in tabular form.\n\nOSF registration numberosf.io/438sm", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Salman Hussain", - "author_inst": "Masaryk University" - }, - { - "author_name": "Harveen Baxi", - "author_inst": "Independent Researcher, New Delhi, India" - }, - { - "author_name": "Abanoub Riad", - "author_inst": "Masaryk University" - }, - { - "author_name": "Jitka Kulgarova", - "author_inst": "Masaryk University" - }, - { - "author_name": "Radim Licenik", - "author_inst": "Masaryk University" - }, - { - "author_name": "Miloslav Klugar", - "author_inst": "Masaryk University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.29.21257760", "rel_title": "Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec", @@ -713761,6 +712599,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.06.01.446181", + "rel_title": "Characterization of SARS2 Nsp15 Nuclease Activity Reveals it's Mad About U", + "rel_date": "2021-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446181", + "rel_abs": "Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3 of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3 of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA and will aid in the development of new anti-viral therapeutics.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Meredith N Frazier", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Lucas B Dillard", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Juno M Krahn", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Lalith Perera", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Jason G Williams", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Isha M Wilson", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Zachary D. Stewart", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Monica C Pillon", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Leesa J Deterding", + "author_inst": "NIEHS/NIH" + }, + { + "author_name": "Mario J. Borgnia", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Robin E Stanley", + "author_inst": "NIEHS/NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.06.01.446491", "rel_title": "SARS coronavirus vaccines protect against different coronaviruses", @@ -714532,81 +713429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.23.21257668", - "rel_title": "Antigenic minimalism of SARS-CoV-2 is linked to surges in COVID-19 community transmission and vaccine breakthrough infections", - "rel_date": "2021-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.23.21257668", - "rel_abs": "The raging COVID-19 pandemic in India and reports of \"vaccine breakthrough infections\" globally have raised alarm mandating the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed 1.57 million SARS-CoV-2 genomes from 187 countries/territories and performed whole-genome viral sequencing from 53 COVID-19 patients, including 20 vaccine breakthrough infections. We identified 89 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a three-month window. Deletions in the Spike protein N-terminal domain (NTD) are highly enriched for these surge-associated mutations (Odds Ratio = 41.8, 95% CI: 6.36-1758, p-value = 7.7e-05). In the recent COVID-19 surge in India, an NTD deletion ({Delta}F157/R158) increased over 10-fold in prevalence from February 2021 (1.1%) to April 2021 (15%). During the recent surge in Chile, an NTD deletion ({Delta}246-253) increased rapidly over 30-fold in prevalence from January 2021 (0.86%) to April 2021 (33%). Strikingly, these simultaneously emerging deletions associated with surges in different parts of the world both occur at an antigenic supersite that is targeted by neutralizing antibodies. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences and identified deletions within this NTD antigenic supersite in a patient with vaccine breakthrough infection ({Delta}156-164) and other deletions from unvaccinated severe COVID-19 patients that could represent emerging deletion-prone regions. Overall, the expanding repertoire of Spike protein deletions throughout the pandemic and their association with case surges and vaccine breakthrough infections point to antigenic minimalism as an emerging evolutionary strategy for SARS-CoV-2 to evade immune responses. This study highlights the urgent need to sequence SARS-CoV-2 genomes at a larger scale globally and to mandate a public health policy for transparent reporting of relevant clinical annotations (e.g. vaccination status) in order to aid the development of comprehensive therapeutic strategies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "AJ Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Praveen Anand", - "author_inst": "nference Labs" - }, - { - "author_name": "Patrick Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Pritha Ghosh", - "author_inst": "nference Labs" - }, - { - "author_name": "Rohit Suratekar", - "author_inst": "nference Labs" - }, - { - "author_name": "Abhishek Siroha", - "author_inst": "nference Labs" - }, - { - "author_name": "Dibyendu Roy Chowdhury", - "author_inst": "nference" - }, - { - "author_name": "John C OHoro", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Joseph D Yao", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Bobbi S Pritt", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew Norgan", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Ryan T Hurt", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John D Halamka", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.31.446476", "rel_title": "COVID-19 Mortality is Associated with Impaired Innate Immunity in Pre-existing Health Conditions", @@ -715222,6 +714044,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.05.28.21257973", + "rel_title": "CoMix: Changes in social contacts as measured by the contact survey during the 1 COVID-19 pandemic in England between March 2020 and March 2021", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21257973", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, the UK government imposed public health policies in England to reduce social contacts in hopes of curbing virus transmission. We measured contact patterns weekly from March 2020 to March 2021 to estimate the impact of these policies, covering three national lockdowns interspersed by periods of lower restrictions.\n\nMethodsData were collected using online surveys of representative samples of the UK population by age and gender. We calculated the mean daily contacts reported using a (clustered) bootstrap and fitted a censored negative binomial model to estimate age-stratified contact matrices and estimate proportional changes to the basic reproduction number under controlled conditions using the change in contacts as a scaling factor.\n\nResultsThe survey recorded 101,350 observations from 19,914 participants who reported 466,710 contacts over 53 weeks. Contact patterns changed over time and by participants age, personal risk factors, and perception of risk. The mean of reported contacts among adults have reduced compared to previous surveys with adults aged 18 to 59 reporting a mean of 2.39 (95% CI 2.20 - 2.60) contacts to 4.93 (95% CI 4.65 - 5.19) contacts, and the mean contacts for school-age children was 3.07 (95% CI 2.89 - 3.27) to 15.11 (95% CI 13.87 - 16.41). The use of face coverings outside the home has remained high since the government mandated use in some settings in July 2020.\n\nConclusionsThe CoMix survey provides a unique longitudinal data set for a full year since the first lockdown for use in statistical analyses and mathematical modelling of COVID-19 and other diseases. Recorded contacts reduced dramatically compared to pre-pandemic levels, with changes correlated to government interventions throughout the pandemic. Despite easing of restrictions in the summer of 2020, mean reported contacts only returned to about half of that observed pre-pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Amy Gimma", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "James D Munday", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kerry LM Wong", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Kevin van Zandvoort", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kiesha Prem", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "- CMMID COVID 1-9 Working Group", + "author_inst": "" + }, + { + "author_name": "Pietra Klepac", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "G James Rubin", + "author_inst": "Department of Psychological Medicine, King's College London" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "W. John Edmunds", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.27.21257937", "rel_title": "Modeling the impact of COVID-19 vaccination in Lebanon: A call to speed-up vaccine roll out", @@ -716177,65 +715062,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.27.21257813", - "rel_title": "Increased prevalence and clinical impact of hypocalcaemia in severe COVID-19 distinguishes it from other forms of infective pneumonia", - "rel_date": "2021-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257813", - "rel_abs": "BackgroundHypocalcaemia has been reported in the context of acute COVID-19, where it has been associated with an increased risk of hospitalisation and disease severity. Calcium is an important intracellular messenger that controls diverse cellular processes. Two other clinically important coronaviruses, SARS-CoV-1 and Middle East respiratory syndrome (MERS)-CoV, can use calcium ions to enter and replicate within host cells. Calcium may therefore be important in the pathophysiology of COVID-19 infection. We sought to investigate whether calcium derangement was a specific feature of COVID-19 that distinguishes it from other infective pneumonias, and its association with disease severity.\n\nMethodsWe conducted a single centre retrospective study of albumin-corrected serum calcium on adult patients with COVID-19 who presented between March 1st and May 16th 2020. The primary outcome was maximal level of care based on the World Health Organization Clinical Progression Scale for COVID-19. Cases with community acquired pneumonia (CAP) and viral pneumonia (VP) were identified through a clinical database over three intervals (January to February 2018, January to February 2019 and September to December 2019).\n\nResultsWe analysed data from 506 patients with COVID-19, 95 patients with CAP and 152 patients with VP. Hypocalcaemia (serum calcium <2.2mmol/L) was a specific and common clinical finding in patients with COVID-19 that was not present in other respiratory infections. Calcium levels were significantly lower in those with severe disease. Ordinal regression of risk estimates for categorised care levels showed that baseline hypocalcaemia was incrementally associated with odds ratio of 2.33 for higher level of care, superior to other variables that have previously been shown to predict worse COVID-19 outcome. Serial calcium levels showed improvement by day 7-9 of admission, only in in survivors of COVID-19.\n\nConclusionHypocalcaemia may independently predict not only more severe but more progressive disease and warrants detailed prognostic investigation. The fact that decreased serum calcium is observed at the time of clinical presentation in COVID-19, but not other infective pneumonias, suggests that its early derangement is pathophysiological and may influence the deleterious evolution of this disease. If calcium is ultimately shown to be critical to the entry and replication of SARS-CoV-2 in host cells, unravelling how this mechanism could be therapeutically targeted deserves more intensive examination.\n\nTrial registration HRA20/HRA/2344.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Meera Mehta", - "author_inst": "West Hertfordshire Hospital NHS Trust" - }, - { - "author_name": "Hakim Ghani", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Felix Chua", - "author_inst": "Royal Brompton and Harefield NHS Foundation" - }, - { - "author_name": "Adrian Draper", - "author_inst": "St. George's Hospital, London" - }, - { - "author_name": "Sam Calmonson", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Meghna Prabhakar", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Rijul Shah", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Alessio Navarra", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Tejal Vaghela", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Andrew Barlow", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Rama Vancheeswaran", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.05.28.21254613", "rel_title": "Antibody Response to CoronaVac Vaccine in Indonesian COVID-19 Survivor", @@ -716896,6 +715722,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.26.21257844", + "rel_title": "The real-life impact of vaccination on COVID-19 mortality in Europe and Israel", + "rel_date": "2021-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257844", + "rel_abs": "OBJECTIVESThis study aimed at estimating the real-life impact of vaccination on COVID-19 mortality, with adjustment for SARS-CoV-2 variants spread and other factors across Europe and Israel.\n\nMETHODSTime series analysis of daily number of COVID-19 deaths was performed using non-linear Poisson mixed regression models. Variants frequency, demographic, climate, health and mobility characteristics of thirty-two countries were considered as potentially relevant adjustment factors between January 2020 and April 2021.\n\nRESULTSThe analysis revealed that vaccination efficacy in terms of protection against deaths was equal to 72%, with a lower reduction of number of deaths for B.1.1.7 versus non-B.1.1.7 variants (70% and 78%, respectively). Other factors significantly related to mortality were arrivals at airports, mobility change from the pre-pandemic level and temperature.\n\nCONCLUSIONSOur study confirms a strong effectiveness of COVID-19 vaccination based on real-life public data, although lower than expected from clinical trials. This suggests the absence of indirect protection for non-vaccinated individuals. Results also show that vaccination effectiveness against mortality associated with the B.1.1.7 variant is slightly lower compared with other variants. Lastly, this analysis confirms the role of mobility reduction, within and between countries, as an effective way to reduce COVID-19 mortality and suggests the possibility of seasonal variations in COVID-19 incidence.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Katarzyna Jablonska", + "author_inst": "Creativ-Ceutical" + }, + { + "author_name": "Samuel Aballea", + "author_inst": "Creativ-Ceutical" + }, + { + "author_name": "Mondher Toumi", + "author_inst": "Aix Marseille University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.27.446089", "rel_title": "SARS-CoV-2 spike glycoprotein-reactive T cells can be readily expanded from COVID-19 vaccinated donors", @@ -717923,20 +716776,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.27.446014", - "rel_title": "The legacy of maternal SARS-CoV-2 infection on the immunology of the neonate", - "rel_date": "2021-05-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.27.446014", - "rel_abs": "Despite extensive and ongoing studies of SARS-CoV-2 and evidence that pregnant women are at increased risk of severe COVID-19, the effect of maternal infection on the developing infant remains unclear. To determine the potential impact of exposure to SARS-CoV-2 in utero on the neonate, we have assessed the immunological status of infants born to mothers with confirmed SARS-CoV-2 infection during gestation. No evidence of vertical transmission of SARS-CoV-2 was observed, but transfer of maternal SARS-CoV-2 specific IgG to infants was apparent, although to a lesser extent in cases of active or recent maternal infection. Infants born to mothers with recent/ongoing infection had elevated circulating pro-inflammatory cytokines and enhanced percentages of innate immune cells compared to that seen in infants born to uninfected mothers. In tandem, higher frequencies of FOXP3+ regulatory T cells and circulating IL-10 demonstrated a further nuance to the neonatal effector response. Interestingly, cytokine functionality was enhanced in infants born to mothers exposed to SARS-CoV-2 at any time during pregnancy. This indicates that maternal SARS-CoV-2 infection influences in utero priming of the fetal immune system.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.27.21257938", "rel_title": "Non-pharmaceutical interventions and the emergence of pathogen variants", @@ -718513,6 +717352,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.25.21257783", + "rel_title": "Development and performance of a population-based risk stratification model for COVID-19", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257783", + "rel_abs": "The shortage of recently approved vaccines against the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has highlighted the need for evidence-based tools to prioritize healthcare resources for people at higher risk of severe coronavirus disease 2019 (COVID-19). Current evidence indicates that age is far from accurate in identifying the risk of severe illness; furthermore, the count of individual risk factors has limited applicability to population-based \"stratify-and-shield\" strategies. We developed a COVID-19 risk stratification system that allows allocating people into four mutually-exclusive risk categories based on multivariate models for hospital admissions, transfer to intensive care unit (ICU), and mortality among the general population. The model was developed using clinical, hospital, and epidemiological data from the entire population of Catalonia (North-East Spain; 7.5 million people) and validated using an independent dataset of 218,329 individuals with PCR-confirmed COVID-19, who were infected after developing the model. This showed high discrimination capacity, with an area under the curve of the receiving operating characteristics of 0.85 (95% CI 0.85 - 0.85) for hospital admissions, 0.86 (0.86 - 0.97) for ICU transfers, and 0.96 (0.96 - 0.96) for deaths. Our results provide clinicians and policymakers with an evidence-based tool for prioritizing COVID-19 healthcare resources other population groups aside from those with higher exposure to SARS-CoV-2 and frontline workers.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Emili Vela", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Sistema de Salut de Catalunya. Catalan Health Service, Barcelona, Spain" + }, + { + "author_name": "Gerard Carot-Sans", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Catalan Health Service. Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Montse Cl\u00e8ries", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Catalan Health Service, Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "David Monterde", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Sistema de Salut de Catalunya, Barcelona, Spain. Catalan Institute of Health, Barcelona, S" + }, + { + "author_name": "X\u00e8nia Acebes", + "author_inst": "Servei Catal\u00e0 de la salut, Barcelona, Spain" + }, + { + "author_name": "Adri\u00e0 Comella", + "author_inst": "Servei Catal\u00e0 de la Salut, Barcelona, Spain" + }, + { + "author_name": "Lu\u00eds Garc\u00eda Eroles", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Catalan Health Service. Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Marc Coca", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Catalan Health Service. Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Dami\u00e0 Valero-Bover", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Catalan Health Service. Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Jordi Piera-Jim\u00e9nez", + "author_inst": "Digitalization for the Sustainability of the Healthcare System (DS3), Sistema de Salut de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Pol P\u00e9rez Sust", + "author_inst": "Servei Catal\u00e0 de la Salut, Barcelona, Spain" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.27.445958", "rel_title": "A new method to study genome mutations using the information entropy", @@ -719728,137 +718626,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.22.21257633", - "rel_title": "Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257633", - "rel_abs": "The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Harald S. Vohringer", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC" - }, - { - "author_name": "Theo Sanderson", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK" - }, - { - "author_name": "Matthew Sinnott", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Nicola De Maio", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK" - }, - { - "author_name": "Thuy Nguyen", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Richard Goater", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Frank Schwach", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE" - }, - { - "author_name": "Ian Harrison", - "author_inst": "Public Health England PHE" - }, - { - "author_name": "Joel Hellewell", - "author_inst": "London School of Hygiene & Tropical Medicine, London, UK" - }, - { - "author_name": "Cristina Ariani", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Sonia Goncalves", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "David Jackson", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Ian Johnston", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Alexander W. Jung", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK" - }, - { - "author_name": "Callum Saint", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "John Sillitoe", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Maria Suciu", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Nick Goldman", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK" - }, - { - "author_name": "Jasmina Panovska-Griffiths", - "author_inst": "Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK" - }, - { - "author_name": "- The Wellcome Sanger Institute Covid-19 Surveillance Team", - "author_inst": "" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium", - "author_inst": "" - }, - { - "author_name": "Ewan Birney", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK" - }, - { - "author_name": "Erik Volz", - "author_inst": "Imperial College, London, UK" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine, London, UK" - }, - { - "author_name": "Dominic Kwiatkowski", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Meera Chand", - "author_inst": "Public Health England PHE" - }, - { - "author_name": "Inigo Martincorena", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Jeffrey C. Barrett", - "author_inst": "Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Moritz Gerstung", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.24.21257707", "rel_title": "Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?", @@ -720751,6 +719518,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.26.445880", + "rel_title": "Evidence of neutralizing antibodies against SARS-CoV-2 in domestic cats living with owners with a history of COVID-19 in Lima, Peru", + "rel_date": "2021-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.26.445880", + "rel_abs": "SARS-CoV-2 can infect a variety of wild and domestic animals worldwide. Of these, domestic cats are highly susceptible species and potential viral reservoirs. As such, it is important to investigate disease exposure in areas with active community transmission and high disease prevalence. In this report we demonstrate the presence of serum neutralizing antibodies against the receptor binding-domain (RBD) of the SARS-CoV-2 in cats whose owners had been infected with SARS-CoV-2 in Lima, Peru, using a commercial competitive ELISA SARS-CoV-2 Surrogate Virus Neutralization Test. Out of 41 samples, 17.1% (7/41) and 31.7% (13/41) were positive, using the cut-off inhibition value of 30% and 20%, respectively. Not all cats living in a single house had detectable neutralizing antibodies showing that heterogenous exposure and immune among cohabiting animals. This is the first report of SARS-COV-2 exposure of domestic cats in Lima, Peru. Further studies are required to ascertain the prevalence of SARS-COV-2 exposure among domestic cats of Lima, Peru.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Luis M. Jara", + "author_inst": "Facultad de Medicina Veterinaria, Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Cusi Ferradas", + "author_inst": "Unidad de Investigacion en Enfermedades Emergentes y Cambio Climatico (Emerge), Facultad de Salud Publica y Administracion" + }, + { + "author_name": "Francesca Schiaffino", + "author_inst": "Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Camila Sanchez-Carrion", + "author_inst": "Clinica Veterinaria Gatuario" + }, + { + "author_name": "Ana Martinez", + "author_inst": "Clinica Veterinaria Los Dominicos" + }, + { + "author_name": "Alexandra Ulloa", + "author_inst": "Clinica Veterinaria Gatuario" + }, + { + "author_name": "Gisela Isasi-Rivas", + "author_inst": "Farmacologicos Veterinarios (FARVET)" + }, + { + "author_name": "Angela Montalvan", + "author_inst": "Farmacologicos Veterinarios (FARVET)" + }, + { + "author_name": "Luis Guevara Sarmiento", + "author_inst": "Farmacologicos Veterinarios (FARVET)" + }, + { + "author_name": "Manolo Clemente Fernandez Diaz", + "author_inst": "Farmacologicos Veterinarios (FARVET)" + }, + { + "author_name": "Mirko Zimic", + "author_inst": "Laboratorio de Bioinformatica, Biologia Molecular y Desarrollos Tecnologicos" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.26.445787", "rel_title": "SARS-CoV-2 Nsp14 activates NF-\u03baB signaling and induces IL-8 upregulation", @@ -721518,101 +720344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.23.21257670", - "rel_title": "Association of Intravenous Bamlanivimab Use with Reduced Hospitalization, Intensive Care Unit Admission, and Mortality in Patients with Mild to Moderate COVID-19", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.23.21257670", - "rel_abs": "BackgroundClinical data to support the use of bamlanivimab for the treatment of outpatients with mild to moderate coronavirus disease-19 (COVID-19) is needed.\n\nMethods2,335 patients who received single-dose bamlanivimab infusion between November 12, 2020 to February 17, 2021 were compared with a propensity-matched control of 2,335 untreated patients with mild to moderate COVID-19 at Mayo Clinic facilities across 4 states. The primary outcome was the rate of hospitalization at days 14, 21 and 28.\n\nResultsThe median age of the population was 63; 47.3% of the bamlanivimab-treated cohort were [≥]65 years; 49.3% were female. High-risk characteristics included hypertension (54.2%), body mass index [≥]35 (32.4%), diabetes mellitus (26.5%), chronic lung disease (25.1%), malignancy (16.6%), and renal disease (14.5%). Patients who received bamlanivimab had lower all-cause hospitalization rates at days 14 (1.5% vs 3.5%; Odds Ratio [OR], 0.38), 21 (1.9% vs 3.9%; OR, 0.46), and 28 (2.5% vs 3.9%; OR, 0.61). Secondary exploratory outcomes included lower intensive care unit admission rates at days 14 (0.14% vs 1%; OR, 0.12), 21 (0.25% vs 1%; OR: 0.24) and 28 (0.56% vs 1.1%; OR: 0.52), and lower all-cause mortality at days 14 (0% vs 0.33%), 21 (0.05% vs 0.4%; OR,0.08) and 28 (0.11% vs 0.44%; OR, 0.01). Adverse events were uncommon with bamlanivimab, occurring in 19/2355, most commonly fever (n=6), nausea (n=5), and lightheadedness (n=3).\n\nConclusionsAmong high-risk patients with mild to moderate COVID-19, treatment with bamlanivimab was associated with a statistically significant lower rate of hospitalization compared with usual care.\n\nFundingMayo Clinic.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ravindra Ganesh", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nFerence" - }, - { - "author_name": "John C O'Horo", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Lori L Arndt", - "author_inst": "Mayo Clinic Health Systems" - }, - { - "author_name": "Richard Arndt", - "author_inst": "Mayo Clinic Health Systems" - }, - { - "author_name": "Sarah J Bell", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Dennis M Bierle", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Molly Destro Borgen", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Sara N Hanson", - "author_inst": "Mayo Clinic Health Systems" - }, - { - "author_name": "Alexander Heyliger", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Jennifer J Larsen", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Patrick J Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Robert Orenstein", - "author_inst": "Mayo Clinic Arizona" - }, - { - "author_name": "Arjun Puranik", - "author_inst": "nFerence" - }, - { - "author_name": "Leigh L Speicher", - "author_inst": "Mayo Clinic Florida" - }, - { - "author_name": "Sidna M Tulledge-Scheitel", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Aiveliagaram J Venkatakrishnan", - "author_inst": "Nference" - }, - { - "author_name": "Caroline G Wilker", - "author_inst": "Mayo Clinic Health Systems" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Raymund R Razonable", - "author_inst": "Mayo Clinic Rochester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.21.21257624", "rel_title": "Monoclonal Antibody Treatment, Prophylaxis and Vaccines Combined to Reduce SARS CoV-2 Spread", @@ -722169,6 +720900,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.05.25.21257644", + "rel_title": "Engagement with daily testing instead of self-isolating in contacts of confirmed cases of SARS-CoV-2: A qualitative analysis", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257644", + "rel_abs": "IntroductionIn December 2020 and January 2021 Public Health England (PHE) with NHS Test and Trace conducted a study to explore the feasibility and acceptability of daily testing as an alternative to self-isolation following close contact with a confirmed COVID-19 case. This qualitative paper aims to identify factors influencing uptake among those offered daily testing, and the subsequent impact on behaviour.\n\nMethodsWe conducted in-depth interviews with 52 participants who had taken part in the feasibility study. Participants were asked about their experiences of daily testing or self-isolating, their reasons for choosing to test or isolate, and their behaviour during the study period. Data were analysed using inductive thematic analysis.\n\nResultsResults are presented under two main headings: 1) factors influencing acceptance of testing and 2) impact of test results. Participants appeared highly motivated to engage in behaviours that would protect others from the virus. Factors influencing the decision to accept testing included 1) needing to avoid self-isolation 2) concerns about test sensitivity and 3) perceived benefits of detecting infection. Participants who were taking tests reported:1) positive consequences following confirmation of COVID status 2) engaging in essential activities 3) uncertainty and 4) self-isolating whilst testing.\n\nConclusionsThis study has identified a range of factors that appear to influence the decision to engage in daily testing or to self-isolate following close contact with a positive case, many of which could be addressed by clear communications. Covid-19 infection rates and government restrictions influenced experiences, and so further research is needed to explore perceptions of daily testing and behaviour following close contact with a positive case among a wider range of individuals, in the context of lower rates of COVID-19, few government restrictions on general population behaviour and more widespread testing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex F Martin", + "author_inst": "King's College London" + }, + { + "author_name": "Nicola K Love", + "author_inst": "Public Health England" + }, + { + "author_name": "Derren Ready", + "author_inst": "Public Health England" + }, + { + "author_name": "Isabel Oliver", + "author_inst": "Public Health England" + }, + { + "author_name": "Richard Amlot", + "author_inst": "Public Health England" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Bristol" + }, + { + "author_name": "James K Rubin", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.25.21257370", "rel_title": "SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from functional annotations of SNPs, MNPs and InDels", @@ -723392,77 +722170,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.20.21257343", - "rel_title": "Attitudes Toward The COVID-19 Vaccine Among North Carolina Participants In The COVID-19 Community Research Partnership", - "rel_date": "2021-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257343", - "rel_abs": "Willingness to receive the newly developed Coronavirus Disease-2019 (COVID-19) vaccines is highly variable. To assess the receptiveness of a select sample of North Carolinians to COVID-19 vaccination, a brief survey was conducted among participants in the COVID-19 Community Research Partnership (CCRP) affiliated with five medical centers in North Carolina. A total of 20,232 CCRP participants completed a multiple choice, mini survey electronically between December 17, 2020 and January 13, 2021. Of the 20,232 survey respondents, 15,422 (76.2%) were receptive to vaccination. Vaccine receptiveness increased incrementally with age with those >70 years being the most willing to be vaccinated compared to all other age groups. Respondents with no previous COVID-19 diagnosis were more likely to accept the vaccine compared to those that have a previous COVID-19 diagnosis (76.6% vs 60.9%). Comparative analysis of gender, race/ethnicity, and residence locale revealed that women, African Americans, and suburban participants were less willing to get a COVID-19 vaccine. There was no difference in vaccine intent based on healthcare worker status. Of those unwilling to get the vaccine, 82% indicated that the reason was uncertainty about the safety and efficacy of the vaccine.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Chukwunyelu Enwezor", - "author_inst": "Wake Forest Baptist Medical Center" - }, - { - "author_name": "James E. Peacock Jr.", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Sharon L Edelstein", - "author_inst": "Biostatistics Center, George Washington University Milken School of Public Health, Washington, DC" - }, - { - "author_name": "Amy N Hinkelman", - "author_inst": "Campbell University NC" - }, - { - "author_name": "Austin L Seals", - "author_inst": "Department of Internal Medicine, Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC, 275157" - }, - { - "author_name": "Thomas F Wierzba", - "author_inst": "Department of Internal Medicine, Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC, 275157" - }, - { - "author_name": "Iqra Munawar", - "author_inst": "Department of Internal Medicine, Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC, 275157" - }, - { - "author_name": "Michael S Runyon", - "author_inst": "Atrium Health, Charlotte, NC, 28204" - }, - { - "author_name": "Patrick D Magurie", - "author_inst": "New Hanover Regional Medical Center, Wilmington, NC, 28401" - }, - { - "author_name": "William H Lagarde", - "author_inst": "Wake Med Health and Hospitals, Raleigh, NC, 27610" - }, - { - "author_name": "Michael A Gibbs", - "author_inst": "Atrium Health, Charlotte, NC, 28204" - }, - { - "author_name": "Thomas R Gallaher", - "author_inst": "Vidant Health, Greenville, NC, 27834" - }, - { - "author_name": "John W Sanders", - "author_inst": "Department of Internal Medicine, Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC, 275157" - }, - { - "author_name": "david herrington", - "author_inst": "wake forest university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.22.21257658", "rel_title": "Effectiveness of COVID-19 vaccines against the B.1.617.2 variant", @@ -724259,6 +722966,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.23.445305", + "rel_title": "Dimerization of SARS-CoV-2 nucleocapsid protein affects sensitivity of ELISA based diagnostics of COVID-19", + "rel_date": "2021-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.23.445305", + "rel_abs": "Diagnostics has played a significant role in effective management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nucleocapsid protein (N protein) is the primary antigen of the virus for development of sensitive diagnostic assays. Thus far, limited knowledge exists about the antigenic properties of the N protein. In this paper, we demonstrate the significant impact of dimerization of SARS-CoV-2 nucleocapsid protein on sensitivity of enzyme-linked immunosorbent assay (ELISA) based diagnostics of COVID-19. The expressed purified protein from E.coli consists of two forms, dimeric and monomeric forms, which have been further characterized by biophysical and immunological means. Indirect ELISA indicated elevated susceptibility of the dimeric form of the nucleocapsid protein for identification of protein-specific monoclonal antibody as compared to the monomeric form of the protein. These findings have also been confirmed with the modelled structure of monomeric and dimeric nucleocapsid protein via HHPred software and its solvent accessible surface area, which indicates higher stability and antigenicity of the dimeric type as compared to the monomeric form. It is evident that use of the dimeric form will increase the sensitivity of the current nucleocapsid dependent ELISA for rapid COVID-19 diagnostic. Further, the results indicate that monitoring and maintaining of the monomerdimer composition is critical for accurate and robust diagnostics.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC=\"FIGDIR/small/445305v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@16bf153org.highwire.dtl.DTLVardef@1b0be6corg.highwire.dtl.DTLVardef@a5b3aeorg.highwire.dtl.DTLVardef@b784a3_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Wajihul Hasan Khan", + "author_inst": "Indian Institute of Technology" + }, + { + "author_name": "Nida Khan", + "author_inst": "Indian Institute of Technology, Delhi" + }, + { + "author_name": "Avinash Mishra", + "author_inst": "Indian Institute of Technology, New Delhi, India" + }, + { + "author_name": "Surbhi Gupta", + "author_inst": "Indian Institute of Technology, New Delhi, India" + }, + { + "author_name": "Vikrant Bansode", + "author_inst": "Indian Institute of Technology, New Delhi, India" + }, + { + "author_name": "Deepa Mehta", + "author_inst": "National Chemical Laboratory, Pune, India" + }, + { + "author_name": "Rahul Bhambure", + "author_inst": "National Chemical Laboratory, Pune, India" + }, + { + "author_name": "Anurag S. Rathore", + "author_inst": "Indian Institute of Technology, Delhi-110016" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.05.24.445335", "rel_title": "SARS-CoV-2 spike protein unlikely to bind to integrins via the Arg-Gly-Asp (RGD) motif of the Receptor Binding Domain: evidence from structural analysis and microscale accelerated molecular dynamics", @@ -725322,41 +724076,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.20.21257518", - "rel_title": "Predictors of SARS CoV-2 Infection Among Healthcare Workers: The Impact of Community-Hospital Gradient", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257518", - "rel_abs": "AimWe aimed to detect the risk factors for SARS-CoV-2 infection among healthcare workers (HCWs) in 2020, before vaccination era.\n\nMethodsWe surveyed the SARS-CoV-2 infection among the HCWs in a hospital by screening of antibody levels and detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) between May 2020 to December 2020. Occupational and non-occupational potential predictors of disease were surveyed for the HCWs included in this study.\n\nResultsAmong 1925 personnel in the hospital, 1732 were included to the study with the response rate of 90%. Overall seroprevalence was 15% at the end of 2020, before vaccinations started. In multivariate analysis, being janitorial staff (OR:2.24, CI:1.21-4.14, p=0.011), being medical secretary (OR: 4.17, CI: 2.12-8.18, p<0.001), having at least one household member with COVID-19 diagnosis (OR:8.98, CI: 6.64-12.15, p<0.001) and number of household members >3 (OR:1.67, CI:1.26-2.22, p<0.001) were found to be significantly associated with SARS-CoV-2 infection.\n\nConclusionBy the end of 2020, just before the era of vaccination and variants, seroprevalence was 15% among HCWs. Medical secretary and janitorial staff were under increased risk of SARS-CoV-2 infection. Community-hospital gradient can explain the mode of transmission for infection among HCWs. In the setting of this study, community measures were less strict, whereas hospital infection control was adequate and provided necessary personal protective equipment. Increasing risk in larger households and households with diagnosed COVID-19 patient indicates community acquired transmission of the infection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Fatihan Pinarlik", - "author_inst": "Koc University School of Medicine" - }, - { - "author_name": "Zeliha Akbulut", - "author_inst": "Koc University Hospital" - }, - { - "author_name": "Mahir Kapmaz", - "author_inst": "Koc University Hospital" - }, - { - "author_name": "Suda Tekin", - "author_inst": "Koc University Hospital" - }, - { - "author_name": "Onder Ergonul", - "author_inst": "Koc University Isbank Center for Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.18.21257396", "rel_title": "A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program", @@ -726253,6 +724972,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.21.20248630", + "rel_title": "A Deep Recurrent Reinforced Learning model to compare the efficacy of targeted local vs. national measures on the spread of COVID-19 in the UK", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.20248630", + "rel_abs": "ObjectivesWe have developed a deep learning model that provides predictions of the COVID-19 related number of cases and mortality in the upcoming 5 weeks and simulates the effect of policy changes targeting COVID-19 spread.\n\nMethodsWe developed a Deep Recurrent Reinforced Learning (DRRL) based model. The data used to train the DRRL model was based on various available datasets that have the potential to influence the trend in the number of COVID-19 cases and mortality. Analyses were performed based on the simulation of policy changes targeting COVID-19 spread, and the geographical representation of these effects.\n\nResultsModel predictions of the number of cases and mortality of COVID-19 in the upcoming 5 weeks closely matched the actual values. Local lockdown with social distancing (LD_SD) was found to be ineffective compared to national lockdown. The ranking of effectiveness of supplementary measures for LD_SD were found to be consistent across national hotspots and local areas. Measure effectiveness were ranked from most effective to least effective: 1) full lockdown; 2) LD_SD with international travel -50%; 3) LD_SD with 100% quarantine; 4) LD_SD with closing school -50%; 5) LD_SD with closing pubs -50%. There were negligible differences observed between LD_SD, LD_SD with -50% food & Accommodation and LD_SD with -50% Retail.\n\nConclusionsThe second national lockdown should be followed by measures which are more effective than LD_SD alone. Our model suggests the importance of restrictions on international travel and travel quarantines, thus suggesting that follow-up policies should consist of the combination of LD_SD and a reduction in the number of open airports within close proximity of the hotspot regions. Stricter measures should be placed in terms travel quarantine to increase the impact of this measure. It is also recommended that restrictions should be placed on the number of schools and pubs open.\n\nO_TEXTBOXStrengths and limitations of this study\n\n- The proposed Deep Recurrent Reinforced Learning (DRRL)-based model takes into account of both relationships of variables across local authorities and across time, using ideas from reinforcement learning to improve predictions.\n- Whilst, predicting the geographical trend in COVID-19 cases based on the simulation of different measures in the UK at both the national and local levels in the UK has proved challenging, this study has provided a methodology by which useful predictions and simulations can be obtained.\n- The Office for National Statistics only released data on UK international travel up to March 2019 at the time of this study, and therefore this study used the amount of UK tourists in Spain as a reference variable for understanding the effect of international travel on COVID-19 spread.\n\n\nC_TEXTBOX", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Tim Dong", + "author_inst": "University of Bristol" + }, + { + "author_name": "umberto benedetto", + "author_inst": "University of Bristol" + }, + { + "author_name": "Shubhra Sinha", + "author_inst": "university of bristol" + }, + { + "author_name": "Arnaldo Dimagli", + "author_inst": "university of bristol" + }, + { + "author_name": "Massimo Caputo", + "author_inst": "university of bristol" + }, + { + "author_name": "Gianni D Angelini", + "author_inst": "university of bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.20.21257181", "rel_title": "Clinical and experimental factors that affect the reported performance characteristics of rapid testing for SARS-CoV-2", @@ -727492,101 +726250,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.19.21257472", - "rel_title": "Effectiveness of the CoronaVac vaccine in the elderly population during a P.1 variant-associated epidemic of COVID-19 in Brazil: A test-negative case-control study", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257472", - "rel_abs": "ObjectiveTo estimate the effectiveness of the inactivated whole-virus vaccine, CoronaVac, against symptomatic COVID-19 in the elderly population of Sao Paulo State, Brazil during widespread circulation of the Gamma variant.\n\nDesignTest negative case-control study.\n\nSettingHealth-care facilities in Sao Paulo State, Brazil.\n\nParticipants43,774 adults aged 70 years or older who were residents of Sao Paulo State and underwent SARS-CoV-2 RT-PCR testing from January 17 to April 29, 2021. 26,433 cases with symptomatic COVID-19 and 17,622 symptomatic, test negative controls were selected into 7,950 matched pairs, according to age, sex, self-reported race, municipality of residence, prior COVID-19 status and date of RT-PCR testing.\n\nInterventionVaccination with a two-dose regimen of CoronaVac.\n\nMain outcome measuresRT-PCR confirmed symptomatic COVID-19 and COVID-19 associated hospitalizations and deaths.\n\nResultsAdjusted vaccine effectiveness against symptomatic COVID-19 was 18.2% (95% CI, 0.0 to 33.2) in the period 0-13 days after the second dose and 41.6% (95% CI, 26.9 to 53.3) in the period [≥]14 days after the second dose. Adjusted vaccine effectiveness against hospitalisations was 59.0% (95% CI, 44.2 to 69.8) and against deaths was 71.4% (95% CI, 53.7 to 82.3) in the period [≥]14 days after the second dose. Vaccine effectiveness [≥]14 days after the second dose declined with increasing age for the three outcomes, and among individuals aged 70-74 years it was 61.8% (95% CI, 34.8 to 77.7) against symptomatic disease, 80.1% (95% CI, 55.7 to 91.0) against hospitalisations and 86.0% (95% CI, 50.4 to 96.1) against deaths.\n\nConclusionsVaccination with CoronaVac was associated with a reduction in symptomatic COVID-19, hospitalisations and deaths in adults aged 70 years or older in a setting with extensive Gamma variant transmission. However, significant protection was not observed until completion of the two-dose regimen, and vaccine effectiveness declined with increasing age amongst this elderly population.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSRandomised controlled trials (RCT) have yielded varying estimates (51 to 84%) for the effectiveness of the inactivated whole-virus vaccine, CoronaVac, against symptomatic COVID-19.\n\nCurrent evidence is limited on whether CoronaVac is effective against severe disease or death caused by the SARS-CoV-2 variant of concern, Gamma, or in the setting of extensive Gamma variant circulation.\n\nMore evidence is needed for the real-world effectiveness of CoronaVac and other inactivated vaccines among elderly individuals, a population that was underrepresented in RCTs of these vaccines.\n\nWhat this study addsA two-dose regimen of CoronaVac provides significant protection against symptomatic COVID-19, hospitalisations and deaths among adults [≥]70 years of age in the setting of widespread Gamma variant transmission.\n\nSignificant protection did not occur until [≥]14 days after administration of the second dose of CoronaVac.\n\nThe effectiveness of CoronaVac declines with increasing age in the elderly population.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Otavio T. Ranzani", - "author_inst": "Barcelona Institute for Global Health, ISGlobal, Spain. Pulmonary Division, Heart Institute (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Unive" - }, - { - "author_name": "Matt Hitchings", - "author_inst": "Department of Biology, University of Florida, Gainesville, FL, USA. Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA" - }, - { - "author_name": "Murilo Dorion Neto", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA" - }, - { - "author_name": "Tatiana Lang D'Agostini", - "author_inst": "Disease Control Coordination of the Sao Paulo State Department of Health, Sao Paulo, Brazil" - }, - { - "author_name": "Regiane Cardoso de Paula", - "author_inst": "Disease Control Coordination of the Sao Paulo State Department of Health, Sao Paulo, Brazil" - }, - { - "author_name": "Olivia Ferreira Pereira de Paula", - "author_inst": "Disease Control Coordination of the Sao Paulo State Department of Health, Sao Paulo, Brazil" - }, - { - "author_name": "Edlaine Faria de Moura Villela", - "author_inst": "Disease Control Coordination of the Sao Paulo State Department of Health, Sao Paulo, Brazil" - }, - { - "author_name": "Mario Sergio Scaramuzzini Torres", - "author_inst": "Municipal Health Secretary of Manaus, Brazil, AM, Brazil" - }, - { - "author_name": "Silvano Barbosa de Oliveira", - "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil 9-Universidade de Brasilia, Brasilia, DF, Brazil" - }, - { - "author_name": "Wade L Schulz", - "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Maria Almiron", - "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil" - }, - { - "author_name": "Rodrigo Said", - "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil" - }, - { - "author_name": "Roberto Dias de Oliveira", - "author_inst": "State University of Mato Grosso do Sul - UEMS, Dourados, MS, Brazil" - }, - { - "author_name": "Patricia Vieira da Silva", - "author_inst": "Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil" - }, - { - "author_name": "Wildo Navegantes de Araujo", - "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil 9-Universidade de Brasilia, Brasilia, DF, Brazil. National Institute for Science and Technology for Healt" - }, - { - "author_name": "Jean Carlo Gorinchteyn", - "author_inst": "Health Secretariat of the State of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "Department of Biology, University of Florida, Gainesville, FL, USA. Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA" - }, - { - "author_name": "Albert Ko", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, BA" - }, - { - "author_name": "Julio Croda", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. Universidade Federal de Mato Grosso do Sul - UFMS, Campo Gra" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.20.21257523", "rel_title": "Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in Asymptomatic and Symptomatic populations at an Institution of Higher Education", @@ -728211,6 +726874,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.05.19.21257237", + "rel_title": "SARS-CoV-2 infection of BNT162b2(mRNA)-vaccinated individuals is not restricted to variants of concern or high-risk exposure environments", + "rel_date": "2021-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257237", + "rel_abs": "The emergence of SARS-CoV-2 variants of concern (VOC) has raised questions regarding the extent of protection of currently implemented vaccines. Ten \"vaccination breakthrough\" infections were identified in Alachua County, Florida, among individuals fully vaccinated with the BNT162b2 mRNA vaccine as a result of social or household transmission. Eight individuals presented mild symptoms in the absence of infection with other common respiratory viruses, confirmed using viral genetic sequencing. SARS-CoV-2 genomes were successfully generated for five of the vaccine breakthroughs and 399 individuals in the surrounding area and were included for reference-based phylogenetic investigation. These five individuals were characterized by infection with both VOCs and low-frequency variants present within the surrounding population. Mutations, in the Spike glycoprotein, were consistent with their respective circulating lineages. However, we detected an additional mutation in Spikes N-terminal domain of a B.1.1.7 strain, present at low-frequency ([~]1%) in the unvaccinated population, potentially affecting proteins stability and functionality. The findings highlight the critical need for continued testing and monitoring of infection among individuals regardless of vaccination status.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Brittany Rife Magalis", + "author_inst": "University of Florida" + }, + { + "author_name": "Carla Mavian", + "author_inst": "University of Florida" + }, + { + "author_name": "Massimiliano Tagliamonte", + "author_inst": "University of Florida" + }, + { + "author_name": "Shannan Rich", + "author_inst": "University of Florida" + }, + { + "author_name": "Melanie Cash", + "author_inst": "University of Florida" + }, + { + "author_name": "Alberto Riva", + "author_inst": "University of Florida" + }, + { + "author_name": "Julia C Loeb", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael Norris", + "author_inst": "University of Florida" + }, + { + "author_name": "David Moraga Amador", + "author_inst": "University of Florida" + }, + { + "author_name": "Yanping Zhang", + "author_inst": "University of Florida" + }, + { + "author_name": "Jerne Shapiro", + "author_inst": "University of Florida" + }, + { + "author_name": "Petr Starostik", + "author_inst": "University of Florida" + }, + { + "author_name": "Simone Marini", + "author_inst": "University of Florida" + }, + { + "author_name": "Paul Myers", + "author_inst": "Florida Department of Health" + }, + { + "author_name": "David A Ostrov", + "author_inst": "University of Florida" + }, + { + "author_name": "John A Lednicky", + "author_inst": "University of Florida" + }, + { + "author_name": "John Glenn Morris Jr.", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael Lauzardo", + "author_inst": "University of Florida" + }, + { + "author_name": "Marco Salemi", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.20.21257490", "rel_title": "Metformin Is Associated with Favorable Outcomes in Patients with COVID-19 and Type 2 Diabetes Mellitus", @@ -729126,65 +727880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.14.21254691", - "rel_title": "Spectrum of neurological manifestations and systematic evaluation of cerebrospinal fluid for SARS-CoV2 in patients admitted to hospital during the COVID-19 epidemic in South Africa", - "rel_date": "2021-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21254691", - "rel_abs": "Neurological manifestations of COVID-19 are increasingly described in the literature. There is uncertainty whether these occur due to direct neuroinvasion of the virus, para-infectious immunopathology, as result of systemic complications of disease such as hypercoagulability or due to a combination of these mechanisms. Here we describe clinical and radiological manifestations in a sequential cohort of patients presenting to a district hospital in South Africa with neurological symptoms with and without confirmed COVID-19 during the first peak of the epidemic. In these patients, where symptoms suggestive of meningitis and encephalitis were most common, thorough assessment of presence in CSF via PCR for SARS-CoV2 did not explain neurological presentations, notwithstanding very high rates of COVID-19 admissions. Although an understanding of potential neurotropic mechanisms remains an important area of research, these results provide rationale for greater focus towards the understanding of para-immune pathogenic processes and the contribution of systemic coagulopathy and their interaction with pre-existing risk factors in order to better manage neurological disease in the context of COVID-19. These results also inform the clinician that consideration of an alternative diagnosis and treatment for neurological presentations in this context is crucial, even in the patient with a confirmed diagnosis COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Angharad G Davis", - "author_inst": "University of Cape Town. The Francis Crick Institute. University College London" - }, - { - "author_name": "Marise Bremer", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Georgia Schafer", - "author_inst": "University of Cape Town. International Centre for Genetic Engineering and Biotechnology (ICGEB)" - }, - { - "author_name": "Luke Dixon", - "author_inst": "Imperial College NHS Healthcare Trust" - }, - { - "author_name": "Fatima Abrahams", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rene Goliath", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Mpumi Maxebengula", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alize Proust", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anesh Chavda", - "author_inst": "West Middlesex University Hospital and Chelsea and Westminster Hospital" - }, - { - "author_name": "John Black", - "author_inst": "University of Cape Town 8. Walter Sisulu University" - }, - { - "author_name": "Robert J Wilkinson", - "author_inst": "University of Cape Town. Francis Crick Institute. University College London. Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.05.18.21257416", "rel_title": "Integrating health behavior theories to predict COVID-19 vaccine acceptance: differences between medical students and nursing students in Israel", @@ -729897,6 +728592,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.19.21257452", + "rel_title": "SARS-CoV-2 screening prevalence in educational staff in Berlin, Germany, June-December 2020", + "rel_date": "2021-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257452", + "rel_abs": "SARS-CoV-2 infections in childcare and school settings potentially bear occupational risks to educational staff. We analyzed data derived from voluntary, PCR-based screening of childcare educators and teachers attending five testing sites in Berlin, Germany, between June and December 2020.\n\nWithin seven months, 17,491 tests were performed (4,458 educators, 13,033 teachers). Participants were largely female (72.9%), and median age was 41 years. Overall, SARS-CoV-2 infection prevalence was 1.2% (95%CI, 1.1-1.4%). Prevalence in educational staff largely resembled community incidence until the start of the second pandemic wave in mid-September 2020, when an unsteady prevalence plateau was reached. Then, infection prevalence in teachers (1.2% [95%CI, 0.8-1.8%]) did not significantly differ from the population prevalence (0.9% [0.6-1.4%]) but it was increased in educators (2.6% [1.6-4.0%]; aOR, 1.6 [1.3-2.0]). Irrespective of occupation, those that reported contact to a confirmed SARS-CoV-2 case outside of work had increased risk of infection (aOR, 3.0 [95%CI, 1.5-5.5]). In a step-wise backwards selection, the best set of associated factors with SARS-CoV-2 infection involved age, occupation, and calendar week.\n\nThese results are in line with findings that teachers do not bear an increased risk of SARS-CoV-2 infection, while childcare educators do. Infection control and prevention measures need to be strengthened in child care settings to further reduce respective occupational hazards. At the same time, the private environment appears to be the main source of SARS-CoV-2 infection for educational staff.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sophia Kindzierski", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Welmoed van Loon", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Johanna Theuring", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Franziska Hommes", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Eberhard Thombansen", + "author_inst": "Vivantes" + }, + { + "author_name": "Malik Boettcher", + "author_inst": "Gemeinschaftskrankenhaus Havelhoehe" + }, + { + "author_name": "Harald Matthes", + "author_inst": "Gemeinschaftskrankenhaus Havelhoehe" + }, + { + "author_name": "Heike Roessig", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "David Weiger", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Christof Wiesmann", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Tobias Kurth", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Kirchberger Valerie", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Joachim Seybold", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Frank P Mockenhaupt", + "author_inst": "Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Maximilian Gertler", + "author_inst": "Charite Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.19.444881", "rel_title": "Single-dose AAV-based vaccine induces a high level of neutralizing antibodies and provides long-term protection against SARS-CoV-2 in rhesus macaques", @@ -731148,65 +729918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.18.21257371", - "rel_title": "Cancer and the risk of COVID-19 diagnosis, hospitalisation, and death: a population-based multi-state cohort study including 4,618,377 adults in Catalonia, Spain", - "rel_date": "2021-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257371", - "rel_abs": "ObjectivesTo investigate the associations between cancer and risk of outpatient COVID-19 diagnosis, hospitalisation, and COVID-19-related death, overall and by years since cancer diagnosis (<1-year, 1-5-years, >5-years), sex, age, and cancer type.\n\nDesignPopulation-based cohort study\n\nSettingPrimary care electronic health records including [~]80% of the population in Catalonia, Spain, linked to hospital and mortality records between 1 March and 6 May 2020.\n\nParticipantsIndividuals aged [≥]18 years with at least one year of prior medical history available from the general population. Cancer was defined as any prior diagnosis of a primary invasive malignancy excluding non-melanoma skin cancer.\n\nMain outcome measuresCause-specific hazard ratios (aHR) with 95% confidence intervals for each outcome. Estimates were adjusted by age, sex, deprivation, smoking status, and comorbidities.\n\nResultsWe included 4,618,377 adults, of which 260,667 (5.6%) had a history of cancer. Patients with cancer were older and had more comorbidities than cancer-free patients. A total of 98,951 individuals (5.5% with cancer) were diagnosed and 6,355 (16.4% with cancer) were directly hospitalised (no prior diagnosis) with COVID-19. Of those diagnosed, 6,851 were subsequently hospitalised (10.7% with cancer) and 3,227 died without being hospitalised (18.5% with cancer). Among those hospitalised, 1,963 (22.5% with cancer) died. Cancer was associated with an increased risk of COVID-19 diagnosis (aHR: 1.08; 95% confidence interval [1.05-1.11]); direct COVID-19 hospitalisation (1.33 [1.24-1.43]); and death following a COVID-19 hospitalisation (1.12 [1.01-1.25]). These associations were stronger for patients recently diagnosed with cancer, aged <70 years, and with haematological cancers.\n\nConclusionsPatients recently diagnosed with cancer, aged <70 years, or with haematological cancers are a high-risk population for COVID-19 diagnosis and severity. These patients should be prioritised in COVID-19 vaccination campaigns and continued non-pharmaceutical interventions.\n\nWhat is already known on this subjectO_LIPrior studies addressing the relationship between cancer and COVID-19 infection and adverse outcomes have found conflicting results\nC_LIO_LIThe majority of these studies had small sample sizes, were not population-based (i.e. restricted to hospitalised patients), thus increasing the risks of selection and collider bias.\nC_LIO_LIIn addition, they used different definitions for cancer (i.e. some included only patients with active cancer, while others focused on specific cancer types, etc.), which limits the comparability of their findings, and only a few analysed the effect of cancer across different patient subgroups.\nC_LI\n\nWhat this study addsO_LIWe conducted a population-based cohort study to analyse the associations between having a prior diagnosis of cancer and the risks of COVID-19 diagnosis, hospitalisation and COVID-19-related deaths from 1 March to 6 May 2020.\nC_LIO_LIIn a population of 4,618,377 adults, we found that cancer was associated with an increased risk of COVID-19 diagnosis (aHR: 1.08; 95% confidence interval [1.05-1.11]); direct COVID-19 hospitalisation (1.33 [1.24-1.43]); and death following a COVID-19 hospitalisation (1.12 [1.01-1.25]).\nC_LIO_LIThese risks were higher for patients recently diagnosed with cancer (within the last year), younger than 70 years, or with haematological cancers. We also found a particularly high risk of COVID-19 hospitalisation and death among patients with lung and bladder cancer.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Elena Roel", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Andrea Pistillo", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Martina Recalde", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Sergio Fernandez-Bertolin", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Maria Aragon", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Isabelle Soerjomataram", - "author_inst": "International Agency for Research on Cancer (IARC-WHO)" - }, - { - "author_name": "Mazda Jenab", - "author_inst": "International Agency for Research on Cancer (IARC-WHO)" - }, - { - "author_name": "Diana Puente", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford" - }, - { - "author_name": "Edward Burn", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford" - }, - { - "author_name": "Talita Duarte-Salles", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.18.444723", "rel_title": "The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A", @@ -731871,6 +730582,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.19.21257447", + "rel_title": "Analysis of the Second COVID-19 Wave in India Using a Birth-Death Model", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257447", + "rel_abs": "India is witnessing the second wave of the COVID-19 disease from the first half of February 2021. The method in [5] is applied here to analyze the second wave in India. We start with fitting a birth-death model to the active and total cases data for the period from 13th to 28th February 2021. This initial dataset is expanded step by step by adding the two future weeks data to it until 14th May 2021. This resulted in six models in total. The efficacy of each model is tested in terms of predictions made for the next two weeks. The infectivity rates are found to be ever-increasing in the case of the five initial models. The infectivity rate for the sixth model, which is based on the data from 13th February to 14th May 2021, shows a decreasing nature with an increase in time. This indicates a decline in the second wave, which may start from 4th June 2021 according to the fitted parameters.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Narayanan C Viswanath", + "author_inst": "Government Engineering College, Thrissur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.18.444690", "rel_title": "Garcinia kola and garcinoic acid suppress SARS-CoV-2 spike glycoprotein S1-induced hyper-inflammation in human PBMCs through inhibition of NF-\u03baB activation", @@ -734478,49 +733208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.14.21257250", - "rel_title": "The specter of Manaus: the risks of a rapid return to pre-pandemic conditions after COVID-19 vaccine rollout", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257250", - "rel_abs": "The development and deployment of several SARS-CoV-2 vaccines in a little over a year is an unprecedented achievement of modern medicine. The high levels of efficacy against transmission for some of these vaccines makes it feasible to use them to suppress SARS-CoV-2 altogether in regions with high vaccine acceptance. However, viral variants with reduced susceptibility to vaccinal and natural immunity threaten the utility of vaccines, particularly in scenarios where a return to pre-pandemic conditions occurs before the suppression of SARS-CoV-2 transmission. In this work we model the situation in the United States at present, to demonstrate how the P.1 variant of SARS-CoV-2 can cause a rebound wave of COVID-19 in a matter of months, similar to what happened in Manaus at the beginning of this year. A high burden of morbidity (and likely mortality) remains possible, even if the vaccine is partially effective against new variants and widely accepted. Our modeling suggests that variants that are already present within the population may be capable of quickly defeating the vaccines as a public health intervention, a fatal flaw in strategies that emphasize rapid reopening before achieving control of SARS-CoV-2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Debra Van Egeren", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Madison Stoddard", - "author_inst": "Fractal Therapeutics" - }, - { - "author_name": "Alexander Novokhodko", - "author_inst": "University of Washington" - }, - { - "author_name": "Michael Rogers", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Diane Joseph-McCarthy", - "author_inst": "Boston University" - }, - { - "author_name": "Bruce Zetter", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Arijit Chakravarty", - "author_inst": "Fractal Therapeutics" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.13.21257152", "rel_title": "Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection", @@ -735201,6 +733888,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.16.21257297", + "rel_title": "The effect of smaller classes on infection-related school absence: Evidence from the Project STAR randomized controlled trial", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.16.21257297", + "rel_abs": "In an effort to reduce viral transmission, many schools are planning to reduce class size if they have not reduced it already. Yet the effect of class size on transmission is unknown. To determine whether smaller classes reduce school absence, especially when community disease prevalence is high, we merge data from the Project STAR randomized class size trial with influenza and pneumonia data from the 122 Cities Mortality Reporting System on deaths from pneumonia and influenza.\n\nProject STAR was a block-randomized trial that followed 10,816 Tennessee schoolchildren from kindergarten in 1985-86 through third grade in 1988-89. Children were assigned at random to small classes (13 to 17 students), regular-sized classes (22 to 26 students), and regular-sized class with a teachers aide.\n\nMixed effects regression showed that small classes reduced absence, but not necessarily by reducing infection. In particular, small classes reduced absence by 0.43 days/year (95% CI -0.06 to -0.80, p<0.05), but had no significant interaction with pneumonia and influenza mortality (95% CI -0.27 to +0.30, p>0.90). Small classes, by themselves, may not suffice to reduce the spread of viruses.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Paul T von Hippel", + "author_inst": "University of Texas, Austin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.05.13.21257140", "rel_title": "Drug Repositioning by Merging Active Subnetworks Validated in Cancer and COVID-19", @@ -736284,105 +734990,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.18.444675", - "rel_title": "Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents", - "rel_date": "2021-05-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444675", - "rel_abs": "Spike (S) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical determinants of the infectivity and antigenicity of the virus. Several mutations in the spike protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, spike proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa (29.065%) had the highest percentage of unique S proteins. Notably, only North America had 87% (14046) of the total (16143) specific S proteins available in the NCBI database(across all continents). Based on the amino acid frequency distributions in the S protein variants from all the continents, the phylogenetic relationship implies that unique S proteins from North America were significantly different from those of the other five continents. Overtime, the unique variants originating from North America are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. Hence it is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sk. Sarif Hassan", - "author_inst": "Pingla Thana Mahavidyalaya" - }, - { - "author_name": "Kenneth Lundstrom", - "author_inst": "PanTherapeutics" - }, - { - "author_name": "Pabitra Pal Choudhury", - "author_inst": "Indian Statistical Institute, Kolkata" - }, - { - "author_name": "Giorgio Palu", - "author_inst": "University of Padova" - }, - { - "author_name": "Bruce Uhal", - "author_inst": "Michigan State University" - }, - { - "author_name": "Ramesh Kandimalla", - "author_inst": "CSIR-Indian Institute of Chemical Technology" - }, - { - "author_name": "Murat Seyran", - "author_inst": "none" - }, - { - "author_name": "Amos Lal", - "author_inst": "Mayo Clinic, USA" - }, - { - "author_name": "Samendra P Sherchan", - "author_inst": "Department of Environmental Health Sciences, Tulane University" - }, - { - "author_name": "Gajendra Kumar Azad", - "author_inst": "Patna University" - }, - { - "author_name": "Alaa A. A. Aljabali", - "author_inst": "Yarmouk University" - }, - { - "author_name": "Adam Brufsky", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Angel Serrano-Aroca", - "author_inst": "Universidad Catolica de Valencia San Vicente Martir" - }, - { - "author_name": "Parise Adadi", - "author_inst": "University of Otago" - }, - { - "author_name": "Tarek Mohamed Abd El-Aziz", - "author_inst": "Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA" - }, - { - "author_name": "Elrashdy M. Redwan", - "author_inst": "King Abdulaziz University" - }, - { - "author_name": "Kazuo Takayama", - "author_inst": "Kyoto University" - }, - { - "author_name": "D Barh", - "author_inst": "IIOAB" - }, - { - "author_name": "Nima Rezaei", - "author_inst": "Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Murtaza Tambuwala", - "author_inst": "Ulster University" - }, - { - "author_name": "Vladimir N Uversky", - "author_inst": "University of South Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.05.18.21256128", "rel_title": "Phylogenomics and population genomics of SARS-CoV-2 in Mexico reveals variants of interest (VOI) and a mutation in the Nucleocapsid protein associated with symptomatic versus asymptomatic carriers", @@ -737003,6 +735610,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.14.21257248", + "rel_title": "Interim Report of a Phase 2 Randomized Trial of a Plant-Produced Virus-Like Particle Vaccine for Covid-19 in Healthy Adults Aged 18-64 and Older Adults Aged 65 and Older", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257248", + "rel_abs": "The rapid spread of SARS-CoV-2 continues to impact humanity on a global scale with rising total morbidity and mortality. Despite the development of several effective vaccines, new products are needed to supply ongoing demand and the needs of specific populations. We report herein a pre-specified interim analysis of the phase 2 portion of an ongoing Phase 2/3, randomized, placebo-controlled trial of a coronavirus virus-like particle (CoVLP) vaccine candidate produced in plants that displays the SARS-CoV-2 spike glycoprotein adjuvanted with AS03 (NCT04636697). A total of 753 subjects were recruited between 25 November 2020 and 24 March 2021 into three groups: Healthy Adults (18-64 years: N=306), Older Adults ([≥] 65 years: N=282) and Adults with Comorbidities ([≥]18 years: N=165) and randomized 5:1 to receive two intramuscular doses of either vaccine CoVLP (3.75 g/dose + AS03) or placebo 21 days apart. This report presents safety, tolerability and immunogenicity data collected up to 21 days after the second dose. The immune outcomes presented include neutralizing antibody (NAb) titres and cellular (IFN-{gamma} and IL-4 ELISpot) responses. In this study, CoVLP+AS03 was well-tolerated and adverse events (AE) after each dose were generally mild to moderate and transient. Solicited AEs in Older Adults and Adults with Comorbidities were generally less frequent than in Healthy Adults. CoVLP+AS03 induced seroconversion in >35% of subjects in each group after the first dose and in [~]98% of subjects 21 days after the second dose. In all treatment groups, NAb levels were [~]10-fold higher than those in a panel of convalescent sera. A significant minority ([~]20%) of subjects had evidence of a pre-existing IFN-{gamma} response to the S protein and almost all subjects in all groups (>88%) had detectable cellular responses (IFN-{gamma}, IL-4 or both) at 21 days after the second dose. A Th1-biased response was most evident after the first dose and was still present after dose two. These data demonstrated that CoVLP+AS03 will likely be well-tolerated and highly immunogenic in adults [≥]18 years of age with and without comorbidities.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Philipe Gobeil", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "St\u00e9phane Pillet", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Iohann Boulay", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Annie S\u00e9guin", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Alexander Makarkov", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Gretchen Heizer", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Kapil Bhutada", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Asif Mahmood", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Nathalie Charland", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Sonia Tr\u00e9panier", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Karen Hager", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Julia Jiang-Wright", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Judith Atkins", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Matthew P Cheng", + "author_inst": "Research Institute of the McGill University Health Centre,\t1001 Decarie St, Montreal, QC H4A 3J1" + }, + { + "author_name": "Donald C Vinh", + "author_inst": "Research Institute of the McGill University Health Centre, 1001 Decarie St, Montreal, QC, H4A 3J1" + }, + { + "author_name": "Philippe Boutet", + "author_inst": "GlaxoSmithKline Biologicals SA (Vaccines), Avenue Fleming 20, 1300 Wavre, Belgium" + }, + { + "author_name": "Fran\u00e7ois P Roman", + "author_inst": "GlaxoSmithKline Biologicals SA (Vaccines), Avenue Fleming 20, 1300 Wavre, Belgium" + }, + { + "author_name": "Robbert Van Der Most", + "author_inst": "GlaxoSmithKline Biologicals SA (Vaccines), rue de l'Institut 89, 1330 Rixensart, Belgium" + }, + { + "author_name": "Maria Angeles Ceregido", + "author_inst": "GlaxoSmithKline Biologicals SA (Vaccines), Avenue Fleming 20, 1300 Wavre, Belgium" + }, + { + "author_name": "Marc Dionne", + "author_inst": "CHU de Qu\u00e9bec-Universit\u00e9 Laval, 2400 d-Estimauville, Quebec City, QC G1E 7G9" + }, + { + "author_name": "Guy Tellier", + "author_inst": "Manna Research (Mirabel), 101-13714 du Cur\u00e9-Labelle Mirabel Qu\u00e9bec J7J 2K8" + }, + { + "author_name": "Jean-S\u00e9bastien Gauthier", + "author_inst": "Q&T Research Sherbrooke Inc., 2185 King Street West, Suite 101, Sherbrooke, Qu\u00e9bec J1J 2G2" + }, + { + "author_name": "Brandon Essink", + "author_inst": "Meridian Clinical Research, LLC, 3319 North 107 Street, Omaha, NE 68134" + }, + { + "author_name": "Michael Libman", + "author_inst": "Research Institute of the McGill University Health Centre, 1001 Decarie St, Montreal, QC H4A 3J1" + }, + { + "author_name": "Jason Haffizulla", + "author_inst": "Precision Clinical Research, LLC, 8399 West Oakland Park Blvd, Suite B & C, Sunrise, FL 33351" + }, + { + "author_name": "Andr\u00e9 Fr\u00e9chette", + "author_inst": "Diex Research Quebec Inc., 205 rue Montmagny, Suite 103, Quebec City, Quebec G1N 4V3" + }, + { + "author_name": "Marc-Andr\u00e9 D'Aoust", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Nathalie Landry", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9" + }, + { + "author_name": "Brian J Ward", + "author_inst": "Medicago Inc., 1020 route de l'\u00c9glise office 600, Quebec, QC, Canada, G1V 3V9 and Research Institute of the McGill University Health Centre, 1001 Decarie St, Mo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.11.21257052", "rel_title": "Dear Watch, Should I Get a COVID-19 Test? Designing deployable machine learning for wearables", @@ -737970,53 +736708,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.05.12.21257130", - "rel_title": "The SARS-CoV-2 B.1.351/V2 variant is outgrowing the B.1.1.7/V1 variant in French regions in April 2021", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257130", - "rel_abs": "SARS-CoV-2 variants threaten our ability to control COVID-19 epidemics. We analyzed 36,590 variant-specific RT-PCR tests performed on samples collected between April 12 and May 7, 2021 in France to compare variant spread. Contrarily to January to March 2021, we found that the V2 variant had a significant transmission advantage over V1 in some regions (15.1 to 16.1% in Ile-de-France and 16.1 to 18.8% in Hauts-de-France). This shift in transmission advantage is consistent with the immune evasion abilities of V2 and the high levels of immunization in these regions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Benedicte Roquebert", - "author_inst": "Laboratoire Cerba, France" - }, - { - "author_name": "Sabine Trombert-Paolantoni", - "author_inst": "Laboratoire Cerba, France" - }, - { - "author_name": "Stephanie Haim-Boukobza", - "author_inst": "Laboratoire Cerba, France" - }, - { - "author_name": "Emmanuel Lecorche", - "author_inst": "Laboratoire Cerba, France" - }, - { - "author_name": "Laura Verdurme", - "author_inst": "Laboratoire Cerba, France" - }, - { - "author_name": "Vincent Foulonge", - "author_inst": "CHU de Montpellier, Montpellier" - }, - { - "author_name": "Mircea T. Sofonea", - "author_inst": "MIVEGEC, University of Montpellier, CNRS, IRD" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "MIVEGEC, CNRS, IRD, University of Montpellier" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.17.21257223", "rel_title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", @@ -738901,6 +737592,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.05.12.21257133", + "rel_title": "Effect of polymerized type I collagen in hyperinflammation of adult outpatients with symptomatic COVID-19: a double blind, randomised, placebo-controlled clinical trial.", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257133", + "rel_abs": "BACKGROUNDCurrently, therapeutic options for ambulatory COVID-19 patients are limited.\n\nOBJECTIVETo evaluate the safety, efficacy and effect of the intramuscular administration of polymerized type I collagen (PTIC) on hyperinflammation, oxygen saturation and symptom improvement in adult outpatients with symptomatic COVID-19.\n\nDESIGNDouble-blind, randomised, placebo-controlled clinical trial of PTIC vs placebo.\n\nSETTINGSingle Third-level hospital in Mexico City (Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran)\n\nPARTICIPANTSEighty-nine adult participants with a confirmed COVID-19 diagnosis and symptom onset within the 7 days preceding recruitment were included from August 31, 2020 to November 7, 2020 and followed for 12 weeks. Final date of follow-up was February 4, 2021.\n\nINTERVENTIONSPatients were randomly assigned to receive either 1.5 ml of PTIC intramuscularly every 12 h for 3 days and then every 24 h for 4 days (n=45), or matching placebo (n=44).\n\nMAIN OUTCOMES AND MEASURESThe primary outcome was a mean reduction of at least 50% in the level of IP-10 compared to baseline. The secondary outcomes were mean oxygen saturation [≥]92% while breathing ambient air and duration of symptoms.\n\nRESULTSOf 89 patients who were randomised, 87 (97.8%) were included in an intention-to-treat analysis; 37 (41.6%) were male and mean age was 48.5{+/-}14.0 years. The IP-10 levels decreased 75% in the PTIC group and 40% in the placebo group vs baseline. The comparison between treatment vs placebo was also statistically significant (P=0.0047). The IL-8 (44%, P=0.045), M-CSF (25%, P=0.041) and IL-1Ra (36%, P=0.05) levels were also decreased in the PTIC group vs baseline. Mean oxygen saturation [≥]92% was achieved by 40/44 (90%), 41/42 (98%) and 40/40 (100%) of participants that received PTIC at 8, 15 and 97 days of follow-up vs 29/43 (67%), 31/39 (80%) and 33/37 (89%) of patients treated with placebo (P=0.001). The unadjusted accelerated failure time model showed that patients treated with PTIC achieved the primary outcome 2.70-fold faster (P<0.0001) than placebo. In terms of risk, the group of patients treated with PTIC had a 63% lower risk of having a mean oxygen saturation <92% vs placebo (P<0.0001). Symptom duration in patients treated with PTIC was reduced by 6.1{+/-}3.2 days vs placebo. No differences in adverse effects were observed between the groups at 8, 15 and 97 days of follow-up.\n\nCONCLUSIONSIn this study, treatment with PTIC down-regulated IP-10, IL-8, M-CSF and IL-Ra levels, which could explain the PTIC effect on the higher proportion of patients with mean oxygen saturation readings [≥]92% and a shorter duration of symptoms as compared to patients treated with placebo. Although results are encouraging, larger randomised trials are needed.\n\nTRIAL REGISTRATIONClinicalTrials.gov Identifier: NCT04517162", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Silvia Mendez-Flores", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Angel Alexis Priego-Ranero", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Daniel Azamar-Llamas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Hector Olvera-Prado", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Kenia Illian Rivas-Redondo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Eric Ochoa-Hein", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Andric C Perez-Ortiz", + "author_inst": "Universidad Panamericana" + }, + { + "author_name": "Estefano Rojas-Castaneda", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Said Urbina-Teran", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Luis Septien-Stute", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Thierry Hernandez-Gilsoul", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Adrian Andres Aguilar-Morgan", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Dheni Aide Fernandez-Camargo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Elizabeth Olivares-Martinez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Diego Francisco Hernandez-Ramirez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Gonzalo Torres-Villalobos", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Janette Furuzawa-Carballeda", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.17.443632", "rel_title": "\"How do we do this at a distance?!\" A descriptive study of remote undergraduate research programs during COVID-19", @@ -740223,89 +738997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.05.12.21257102", - "rel_title": "Spike-antibody responses following first and second doses of ChAdOx1 and BNT162b2 vaccines by age, gender, and clinical factors - a prospective community cohort study (Virus Watch)", - "rel_date": "2021-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257102", - "rel_abs": "BackgroundVaccination constitutes the best long-term solution against Coronavirus Disease 2019 (COVID-19). Real-world immunogenicity data are sparse, particularly for ChAdOx1 and in populations with chronic conditions; and given the UKs extended dosing interval, it is also important to understand antibody responses in SARS-CoV-2-naive individuals following a single dose.\n\nMethodsAdults aged [≥]18 years from households enrolled in Virus Watch, a prospective community cohort study in England and Wales, provided capillary blood samples and self-reported vaccination status. Primary outcome variables were quantitative Spike total antibody levels (U/ml) and seropositivity to Spike ([≥]0.8 U/ml), as per Roches Elecsys Anti-SARS-CoV-2 S assay. Samples seropositive for Nucleocapsid, and samples taken prior to vaccination, were excluded. Outcomes were analysed by days since vaccination, vaccine type (BNT162b2 and ChAdOx1), and a range of self-reported demographic and clinical factors.\n\nResults8,517 vaccinated participants (median age 65 years [IQR: 58, 71]), contributed 13,232 samples (8,115 following ChAdOx1, 5,008 following BNT162b2). Seropositivity to Spike was 96.42% (95%CI 96, 96.79) at 28-34 days following a single dose, reaching 99.08% (97.8, 99.62) at 7-14 days after a second dose. Seropositivity rates, and Spike-antibody levels rose more quickly following the first dose of BNT162b2, however, were equivalent for both vaccines by 4 and 8 weeks, respectively. There was evidence of lower S-antibody levels with increasing age (p=0.0001). In partially vaccinated 65-79 year-olds, lower S-antibody levels were observed in men (25.9 vs 42.3 U/ml, p<0.0001), those with a chronic condition (33.0 vs 41.2 U/ml, p<0.0001), diabetes (22.32 vs 36.01 U/ml, p<0.0001), cardiovascular disease (32.1 vs 36.7 U/ml, p=0.0002), or history of cancer (30.1 vs 35.7 U/ml, p=0.0001), particularly those with haematological rather than solid organ cancer (7.48 vs 31.68 U/ml, p<0.0001), and those currently on immunosuppressive therapy (21.7 vs 35.6 U/ml, p<0.0001). Following a second dose, high S-antibody titres ([≥]250U/ml) were observed for nearly all individuals.\n\nInterpretationA single dose of either BNT162b2 or ChAdOx1 leads to high Spike seropositivity rates in SARS-CoV-2-naive individuals. However, observed disparities in antibody levels after the first dose by vaccine type, age, and comorbidities highlight the importance of ongoing non-pharmaceutical preventative measures such as social distancing, for partially vaccinated adults, particularly those who are older and more clinically vulnerable.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Madhumita Shrotri", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - }, - { - "author_name": "Cyril Geismar", - "author_inst": "University College London" - }, - { - "author_name": "Vincent Nguyen", - "author_inst": "University College London" - }, - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Isobel Braithwaite", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Edward Byrne", - "author_inst": "University College London" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "University College London" - }, - { - "author_name": "Jana Kovar", - "author_inst": "University College London" - }, - { - "author_name": "Annalan M D Navaratnam", - "author_inst": "University College London" - }, - { - "author_name": "Parth Patel", - "author_inst": "University College London" - }, - { - "author_name": "Anna Aryee", - "author_inst": "University College London" - }, - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Anne M Johnson", - "author_inst": "University College London" - }, - { - "author_name": "Alison Rodger", - "author_inst": "University College London" - }, - { - "author_name": "Andrew C Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.12.21257079", "rel_title": "Computational modelling of COVID-19: A study of compliance and superspreaders", @@ -741122,6 +739813,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.11.21257048", + "rel_title": "Impact of the COVID-19 pandemic on the provision of routine childhood immunizations in Ontario, Canada", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257048", + "rel_abs": "BackgroundThe COVID-19 pandemic has a worldwide impact on all health services, including childhood immunizations. In Canada, there is limited data to quantify and characterize this issue.\n\nMethodsWe conducted a descriptive, cross-sectional study by distributing online surveys to physicians across Ontario. The survey included three sections: provider characteristics, impact of COVID-19 on professional practice, and impact of COVID-19 on routine childhood immunization services. Multivariable logistic regression identified factors associated with modification of immunization services.\n\nResultsA total of 475 respondents answered the survey from May 27th to July 3rd 2020, including 189 family physicians and 286 pediatricians. The median proportion of in-person visits reported by physicians before the pandemic was 99% and dropped to 18% during the first wave of the pandemic in Ontario. In total, 175 (44.6%) of the 392 respondents who usually provide vaccination to children acknowledged a negative impact caused by the pandemic on their immunization services, ranging from temporary closure of their practice (n=18; 4.6%) to postponement of vaccines in certain age groups (n=103; 26.3%). Pediatricians were more likely to experience a negative impact on their immunization services compared to family physicians (adjusted odds ratio [aOR]=2.64, 95% CI: 1.48-4.68), as well as early career physicians compared to their more senior colleagues (aOR=2.69, 95% CI: 1.30-5.56), whereas physicians from suburban settings were less impacted than physicians from urban settings (aOR=0.62, 95% CI: 0.39-0.99). The most frequently identified barriers to immunizations during the pandemic were parental concerns around COVID-19 (n=305; 77.8%), lack of personal protective equipment (PPE; n=123; 31.3%) and healthcare workers concerns of contracting COVID-19 (n=105; 26.8%).\n\nConclusionsCOVID-19 has caused substantial modifications to pediatric immunization services across Ontario. Strategies to mitigate barriers to immunizations during the pandemic need to be implemented in order to avoid immunity gaps that could lead to an increase in vaccine preventable diseases.\n\nHIGHLIGHTSO_LIWe have conducted a descriptive, cross-sectional study by distributing online surveys to pediatricians and family physicians across Ontario to assess the impact of the COVID-19 pandemic on their immunization practices.\nC_LIO_LIThe COVID-19 pandemic has caused a substantial decrease in in-person visits and a related disruption to routine childhood immunization services during the first wave of the pandemic.\nC_LIO_LIThe main barriers to immunizations during the pandemic included parents and healthcare providers concerns of contracting COVID-19, and lack of appropriate personal protective equipment (PPE).\nC_LIO_LISolutions to maintain childhood immunizations during the pandemic included assistance in providing PPE to clinical practices, dedicated centers for vaccination, and parental education.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pierre-Philippe Pich\u00e9-Renaud", + "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children" + }, + { + "author_name": "Catherine Ji", + "author_inst": "Toronto Western Family Health Team, University Health Network" + }, + { + "author_name": "Daniel S. Farrar", + "author_inst": "Centre for Global Child Health, The Hospital for Sick Children" + }, + { + "author_name": "Jeremy N. Friedman", + "author_inst": "Division of Pediatric Medicine, The Hospital for Sick Children" + }, + { + "author_name": "Michelle Science", + "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children" + }, + { + "author_name": "Ian Kitai", + "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children" + }, + { + "author_name": "Sharon Burey", + "author_inst": "Pediatricians Alliance of Ontario" + }, + { + "author_name": "Mark Feldman", + "author_inst": "Department of Pediatrics, Faculty of Medicine, University of Toronto" + }, + { + "author_name": "Shaun K. Morris", + "author_inst": "Division of Infectious Diseases, The Hospital for Sick Children" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.11.21257057", "rel_title": "Family responsibilities and mental health of kindergarten educators during the first COVID-19 pandemic lockdown in Ontario, Canada", @@ -742157,53 +740899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.09.21256911", - "rel_title": "Post-acute COVID-19 syndrome and its prolonged effects: An updated systematic review", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.09.21256911", - "rel_abs": "ObjectiveThis systematic review aimed at estimating the demographics, clinical characteristics, and prevalence of post-acute COVID-19 symptoms in view of published literature that studied prolonged clinical manifestations after recovery from acute COVID-19 infection.\n\nMethodsAfter protocol setting, relevant articles were searched on various databases including PubMed, Medline, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, and Web of Sciences using MeSH keywords. The data regarding demographic, clinical characteristics, and prevalence of each persisting symptom were carefully studied and tabulated. Data analysis was carried out using Statistical Package for Social Sciences (SPSS) version 26.\n\nResultsOut of the 153 articles reviewed, 21 articles qualified for the final analysis. The most common persistent clinical manifestations were fatigue (54.11%), dyspnea (24.38%), alopecia (23.21%), hyperhidrosis (23.6%), insomnia (25.98%), anxiety (17.29%), and arthralgia (16.35%). In addition to these symptoms, new onset hypertension, diabetes, neuropsychiatric disorders, and bladder incontinence were also reported.\n\nConclusionClinical features of post-acute COVID-19 infection can manifest even after 60 days of initial infection. Constitutional symptoms include fatigue, dyspnea, anosmia, and insomnia were the most commonly reported in literature. Multidisciplinary care along with regular follow-up must be a provided to such patients. Curation and modification of guidelines is required for the assessment of discharged hospitalized patients for better management of their post-acute COVID-19 syndrome.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jahanzeb Malik", - "author_inst": "Rawalpindi Institute of Cardiology" - }, - { - "author_name": "Syed Muhammad Jawad Zaidi", - "author_inst": "Rawalpindi Medical University" - }, - { - "author_name": "Uzma Ishaq", - "author_inst": "Foundation University Medical College" - }, - { - "author_name": "Muhammad Ali", - "author_inst": "Rawalpindi Institute of Cardiology" - }, - { - "author_name": "Abdul Sattar Rana", - "author_inst": "Rawalpindi Institute of Cardiology" - }, - { - "author_name": "Raafe Iqbal", - "author_inst": "POF Hospital Wah Cantt." - }, - { - "author_name": "Ali Umer Waqar", - "author_inst": "Shifa International Hospital" - }, - { - "author_name": "Muhammad Kashif", - "author_inst": "Rawalpindi Institute of Cardiology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.13.21257129", "rel_title": "Immune Responses to COVID-19 mRNA Vaccines in Patients with Solid Tumors on Active, Immunosuppressive Cancer Therapy", @@ -742916,6 +741611,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.05.13.21256973", + "rel_title": "A Randomized Placebo-Controlled Trial of Sarilumab in Hospitalized Patients with Covid-19", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21256973", + "rel_abs": "BACKGROUNDSarilumab (anti-interleukin-6 receptor- monoclonal antibody) may attenuate the inflammatory response in Covid-19.\n\nMETHODSWe performed an adaptive, phase 2/3, randomized, double-blind, placebo-controlled trial of intravenous sarilumab 200 mg or 400 mg in adults hospitalized with Covid-19. The phase 3 primary analysis population (cohort 1) was patients with critical Covid-19 receiving mechanical ventilation (MV) randomized to sarilumab 400 mg or placebo. The primary end point for phase 3 was the proportion of patients with [≥]1-point improvement in clinical status from baseline to day 22.\n\nRESULTSFour-hundred fifty-seven (457) and 1365 patients were randomized and treated in phases 2 and 3, respectively. Among phase 3 critical patients receiving MV (n=289; 34.3% on corticosteroids), the proportion with [≥]1-point improvement in clinical status (alive not receiving MV) at day 22 was 43.2% in sarilumab 400 mg and 35.5% in placebo (risk difference [RD] +7.5%; 95% confidence interval [CI], -7.4 to 21.3; P=0.3261), representing a relative risk improvement of 21.7%. Day 29 all-cause mortality was 36.4% in sarilumab 400 mg versus 41.9% in placebo (RD -5.5%; 95% CI, -20.2 to 8.7; relative risk reduction 13.3%). In post hoc analyses pooling phase 2 and 3 critical patients receiving MV, the hazard ratio (HR) for death in sarilumab 400 mg compared with placebo was 0.76 (95% CI, 0.51 to 1.13) overall, improving to 0.49 (95% CI, 0.25 to 0.94) in patients receiving corticosteroids at baseline.\n\nCONCLUSIONIn hospitalized patients with Covid-19 receiving MV, numerical benefits with sarilumab did not achieve statistical significance, but benefit may be greater in patients receiving corticosteroids. A larger study is required to confirm this observed numerical benefit.\n\n(ClinicalTrials.gov number, NCT04315298)", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Sumathi Sivapalasingam", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "David Lederer", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Rafia Bhore", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Negin Hajizadeh", + "author_inst": "Northwell Health" + }, + { + "author_name": "Gerard Criner", + "author_inst": "Lewis Katz School of Medicine at Temple University" + }, + { + "author_name": "Romana Hosain", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Adnan Mahmood", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Angeliki Giannelou", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Selin Somersan-Karakaya", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Meagan O'Brien", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Anita Boyapati", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Janie Parrino", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Bret Musser", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Emily Labriola-Tompkins", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Divya Ramesh", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Lisa Purcell", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Daya Gulabani", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Wendy Kampman", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Alpana Waldron", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Michelle Ng Gong", + "author_inst": "Montefiore - Moses" + }, + { + "author_name": "Suraj Saggar", + "author_inst": "Holy Name Medical Center" + }, + { + "author_name": "Steven Sperber", + "author_inst": "Hackensack Meridian School of Medicine and Hackensack University Medical Center" + }, + { + "author_name": "Vidya Menon", + "author_inst": "NYC Health + Hospitals/Lincoln" + }, + { + "author_name": "David Stein", + "author_inst": "Jacobi Medical Center" + }, + { + "author_name": "Magdalena Sobieszczyk", + "author_inst": "Columbia University" + }, + { + "author_name": "William Park", + "author_inst": "Pulmonary and Sleep Disorder Clinic" + }, + { + "author_name": "Judith Aberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Samuel Brown", + "author_inst": "Intermountain Medical Center and University of Utah" + }, + { + "author_name": "Jack Kosmicki", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Julie Horowitz", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Manuel Ferreira", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Aris Baras", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Bari Kowal", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "A. Thomas DiCioccio", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Bolanle Akinlade", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Michael Nivens", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Ned Braunstein", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Gary Herman", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "George Yancopoulos", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "David Weinreich", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "- Sarilumab-COVID-19 Study Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.12.21256956", "rel_title": "Systematic Testing for SARS-CoV-2 Infection Among Essential Workers in Montreal, Canada: A Prospective Observational and Cost Assessment Study", @@ -744783,53 +743657,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.13.443734", - "rel_title": "CV2CoV, an enhanced mRNA-based SARS-CoV-2 vaccine candidate, supports higher protein expression and improved immunogenicity in rats", - "rel_date": "2021-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.13.443734", - "rel_abs": "More than two years after the emergence of SARS-CoV-2, 33 COVID-19 vaccines, based on different platforms, have been approved in 197 countries. Novel variants that are less efficiently neutralised by antibodies raised against ancestral SARS-CoV-2 are circulating, highlighting the need to adapt vaccination strategies. Here, we compare the immunogenicity of a first-generation mRNA vaccine candidate, CVnCoV, with a second-generation mRNA vaccine candidate, CV2CoV, in rats. Higher levels of spike (S) protein expression were observed in cell culture with CV2CoV mRNA than with CVnCoV mRNA. Vaccination with CV2CoV also induced higher titres of virus neutralising antibodies with accelerated kinetics in rats compared with CVnCoV. Significant cross-neutralization of the SARS-CoV-2 variants, Alpha (B.1.1.7), Beta (B.1.351), and the mink variant (B1.1.298) that were circulating at the time in early 2021 was also demonstrated. In addition, CV2CoV induced higher levels of antibodies at lower doses than CVnCoV, suggesting that dose-sparing could be possible with the next generation SARS-CoV-2 vaccine which could improve worldwide vaccine supply.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nicole Roth", - "author_inst": "CureVac AG" - }, - { - "author_name": "Jacob Schoen", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut" - }, - { - "author_name": "Moritz Thran", - "author_inst": "CureVac AG" - }, - { - "author_name": "Andreas Thess", - "author_inst": "CureVac AG" - }, - { - "author_name": "Stefan O. Mueller", - "author_inst": "CureVac AG" - }, - { - "author_name": "Benjamin Petsch", - "author_inst": "CureVac AG" - }, - { - "author_name": "Susanne Rauch", - "author_inst": "CureVac AG" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.12.443948", "rel_title": "Plasmacytoid dendritic cells produce type I interferon and reduce viral replication in airway epithelial cells after SARS-CoV-2 infection", @@ -745402,6 +744229,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.07.21256803", + "rel_title": "Neutralizing response against E484K variant after original SARS-CoV-2 infection", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256803", + "rel_abs": "Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants, which are spreading in the United Kingdom (UK) and elsewhere, have been found in infected individuals in Japan. The virus mutates, to facilitate its life in the host, during the process of repeated proliferation in the body of the host, including humans. In other words, it is natural that a human-compatible mutant strain always predominates in infection and proliferation. As a result, the viral mutants acquire strong proliferative potential in the host and are highly pathogenic. The number of people infected with the mutated SARS-CoV-2 variant E484K, which is different from the SARS-CoV-2 variants that are spreading in the UK, South Africa, and Brazil, is increasing in Tokyo. It has been pointed out that the effects of immunity and vaccines may be reduced against the Tokyo-type SARS-CoV-2 variant E484K. We have investigated the neutralization response to various mutations in the spike glycoprotein using the serum of people already infected with the original SARS-CoV-2. The results showed that SARS-CoV-2 variants with Y543F or N501Y mutations in the spike glycoprotein affect the neutralization reaction. However, single E484K mutations within the spiked glycoprotein of the Tokyo-type SARS-CoV-2 variant are unlikely to have a significant effect on the affinity of the host antibody for the virus.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Takuma Hayashi", + "author_inst": "National Hospital Organization Kyoto Medical Center" + }, + { + "author_name": "Nobuo Yaegashi", + "author_inst": "Tohoku University Graduate School of Medicine" + }, + { + "author_name": "Ikuo Konishi", + "author_inst": "Kyoto University / National Hospital Organization Kyoto Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.07.21256860", "rel_title": "SIR-based model with multiple imperfect vaccines.", @@ -746649,45 +745503,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.12.443357", - "rel_title": "First description of two immune escape indian B.1.1.420 and B.1.617.1 SARS-CoV2 variants in France", - "rel_date": "2021-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.12.443357", - "rel_abs": "Following the outbreak of the SARS-CoV2 virus worldwide in 2019, the rapid widespread overtime of variants suggests today an undergoing positive selection of variants which could potentially provide advantageous genetic property of the virus. Numerous variants have already been described across different countries including N501Y, E484K or L452R mutations on gene coding to spike protein. Most recently, 2 new Indian variants with N440K and E484Q and L452R mutations associated with impaired antibody response and immune reactions were identified in India. The potential consequences of emerging variants are increased transmissibility, increased pathogenicity and the ability to escape natural or vaccine-induced immunity.\n\nWe described for the first time in France both variants: the N440K immune escape variant within a new strain detected in France in a couple of patients who did not have any history of travel abroad and the new E484Q and L452R Indian variant from a patient travelling from Indian to Marseille to embark on a ship as a crew member.\n\nSuch study of the circulating viral strains and their variants within the increasing number of infected people worldwide will provide further insights into the viral dissemination. Hence, real time close monitoring variant could help the scientific community to prevent fast-spreading and raise alarms towards potentially harmful variants.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vincent Garcia", - "author_inst": "Laboratoire ALPHABIO" - }, - { - "author_name": "Veronique Vig", - "author_inst": "ARS PACA (Agence Regionale de Sante)" - }, - { - "author_name": "Laurent Peillard", - "author_inst": "ARS PACA (Agence Regionale de Sante)" - }, - { - "author_name": "Alaa Ramdani", - "author_inst": "ARS PACA (Agence Regionale de Sante)" - }, - { - "author_name": "Sofiane Mohamed", - "author_inst": "ABL, Marseille" - }, - { - "author_name": "Philippe Halfon", - "author_inst": "Laboratoire Alphabio" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.05.11.443686", "rel_title": "Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations", @@ -747652,6 +746467,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.07.21249238", + "rel_title": "multiSero: open multiplex-ELISA platform for analyzing antibody responses to SARS-CoV-2 infection", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21249238", + "rel_abs": "Serology has provided valuable diagnostic and epidemiological data on antibody responses to SARS-CoV-2 in diverse patient cohorts. Deployment of high content, multiplex serology platforms across the world, including in low and medium income countries, can accelerate longitudinal epidemiological surveys. Here we report multiSero, an open platform to enable multiplex serology with up to 48 antigens in a 96-well format. The platform consists of three components: ELISA-array of printed proteins, a commercial or home-built plate reader, and modular python software for automated analysis (pysero). We validate the platform by comparing antibody titers against the SARS-CoV-2 Spike, receptor binding domain (RBD), and nucleocapsid (N) in 114 sera from COVID-19 positive individuals and 87 pre-pandemic COVID-19 negative sera. We report data with both a commercial plate reader and an inexpensive, open plate reader (nautilus). Receiver operating characteristic (ROC) analysis of classification with single antigens shows that Spike and RBD classify positive and negative sera with the highest sensitivity at a given specificity. The platform distinguished positive sera from negative sera when the reactivity of the sera was equivalent to the binding of 1 ng mL-1 RBD-specific monoclonal antibody. We developed normalization and classification methods to pool antibody responses from multiple antigens and multiple experiments. Our results demonstrate a performant and accessible pipeline for multiplexed ELISA ready for multiple applications, including serosurveillance, identification of viral proteins that elicit antibody responses, differential diagnosis of circulating pathogens, and immune responses to vaccines.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Janie R Byrum", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Eric Waltari", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Owen Janson", + "author_inst": "EPPIcenter Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA" + }, + { + "author_name": "Syuan-Ming Guo", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Jenny Folkesson", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Bryant B Chhun", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Joanna Vinden", + "author_inst": "EPPIcenter Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA; D" + }, + { + "author_name": "Ivan E Ivanov", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Marcus L Forst", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA; Department of Applied Physics, 348 Via Pueblo Mall, Stanford University, Stanford, CA 94" + }, + { + "author_name": "Hongquan Li", + "author_inst": "Department of Electrical Engineering, Stanford University, Stanford, CA" + }, + { + "author_name": "Adam G Larson", + "author_inst": "Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Wesley Wu", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Cristina M Tato", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Krista M McCutcheon", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA; Immune-Onc Therapeutics, Inc, 795 San Antonio Road, Palo Alto, CA 94303" + }, + { + "author_name": "Michael J Peluso", + "author_inst": "Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA" + }, + { + "author_name": "Timothy J Henrich", + "author_inst": "Division of Experimental Medicine, University of California San Francisco, San Francisco, California, USA" + }, + { + "author_name": "Steven G Deeks", + "author_inst": "Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, California, USA" + }, + { + "author_name": "Manu Prakash", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA; Department of Computer Science, Stanford University, Stanford, CA" + }, + { + "author_name": "Bryan Greenhouse", + "author_inst": "EPPIcenter Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA; C" + }, + { + "author_name": "John E Pak", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + }, + { + "author_name": "Shalin B Mehta", + "author_inst": "Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.07.21256844", "rel_title": "Resuming In-Person Classes under COVID-19: Evaluating Assigned Seating Protocols in Limiting Contacts at Postsecondary Institutions", @@ -749363,49 +748277,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.11.21257042", - "rel_title": "COVID-19 Pandemic and Academic Speculation of Medical Students of Bangladesh: A Cross-sectional, Comparative Study", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257042", - "rel_abs": "BackgroundCOVID-19 pandemic has caused unprecedented disruptions worldwide including education system. While the necessary focus has been on patient care andwellbeing of healthcare professionals, the impacts on medical students need to be discussed.\n\nMethodsThis cross-sectional comparative study was conducted to evaluate the academic speculation of medical students studying in government and non-government institute during COVID-19 pandemic. A structured questionnaire survey linked in the google form was used as study instrument and was distributed among study population through email, messenger, whatsapp and other social media. Total 1020 students were participated in the study\n\nResultsIn this research, 441 (43.24%) and 579 (56.77%) students were from government and non-government medical colleges respectively. Opinion of both group was almost similar regarding disruption of medical education, loss of clinical skills and competency, future career plan, and stress and anxiety but significant differences were observed between both group regarding issue of financial burden, meaningful learning opportunities, fear of getting infected and maintenance of social distancing in hostel.\n\nConclusionThe study revealed similar kind of viewpoint about disruption of education, loss of clinical skill and competency, changing aspects of future career plan and increased level of stress and anxiety among medical students of government and non-government institutes of Bangladesh but different speculations were found regarding issue of financial burden, meaningful learning opportunities, fear of getting infected and possibility of maintenance of social distancing in hostel.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fatema Johora", - "author_inst": "Army Medical College Bogura, Bangladesh" - }, - { - "author_name": "Asma Akter Abbasy", - "author_inst": "Brahmanbaria Medical College" - }, - { - "author_name": "Fatiha Tasmin Jeenia", - "author_inst": "Chattagram International Medical College" - }, - { - "author_name": "Mithun Chandro Bhowmik", - "author_inst": "Rangpur Medical College" - }, - { - "author_name": "Priyanka Moitra Moitra", - "author_inst": "Colonel Malek Medical College, Manikganj" - }, - { - "author_name": "Sabiha Mahboob", - "author_inst": "CMH Bogura" - }, - { - "author_name": "Jannatul Ferdoush", - "author_inst": "BGC Trust Medical College, Chattogram" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.05.11.21256876", "rel_title": "The Impact of Control and Mitigation Strategies during the Second Wave of COVID-19 Infections in Spain and Italy", @@ -750134,6 +749005,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.07.21256539", + "rel_title": "Immune profile of children with post-acute sequelae of SARS-CoV-2 infection (Long Covid)", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256539", + "rel_abs": "There is increasing reporting by patients organization and researchers of long covid (or post-acute sequelae of SARS-CoV-2 - PASC), characterized by symptoms such as fatigue, dyspnea, chest pain, cognitive and sleeping disturbances, arthralgia and decline in quality of life. Immune system dysregulation with a hyperinflammatory state, direct viral toxicity, endothelial damage and microvascular injury have been proposed as pathologenic mechanisms. Recently, cohorts of children with PASC have been reported in Italy, Sweden and Russia. However, immunological studies of children with PASC have never been performed.\n\nIn this study, we documented significant immunologic differences between children that completely recovered from acute infection and those with PASC, providing the first objective laboratory sign of the existence of PASC in children.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabriele Di Sante", + "author_inst": "Fondazione Policlinico Universitario A.Gemelli, Rome, Italy" + }, + { + "author_name": "Danilo Buonsenso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Cristina De Rose", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Piero Valentini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Francesco Ria", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Maurizio Sanguinetti", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Michela Sali", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.07.21256841", "rel_title": "Results of an Academic Dialysis Program-Wide SARS-CoV-2 Vaccination Effort", @@ -751309,161 +750223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.07.21256725", - "rel_title": "Seroprevalence of SARS-CoV-2 antibodies in social housing areas in Denmark", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256725", - "rel_abs": "BackgroundCOVID-19 is suggested to be more prevalent among ethnic minorities and individuals with low socioeconomic status. We aimed to investigate the prevalence of SARS-CoV-2 antibodies during the COVID-19 pandemic among citizens 15 years or older in Denmark living in social housing (SH) areas.\n\nMethodsAs part of \"Testing Denmark\", a nationwide sero-epidemiological surveillance survey, we conducted a study between January 8th and January 31st, 2021 with recruitment in 13 selected SH areas in Denmark. Participants were offered a point-of-care rapid SARS-CoV-2 IgM and IgG antibody test and a questionnaire concerning previous testing (viral throat- and nasopharyngeal swab or antibody test), test results for COVID-19, demographics, household characteristics, employment, risk factors for SARS-CoV-2 infection and history of symptoms associated with COVID-19. Data on seroprevalence from Danish blood donors in same period using a total Ig ELISA assay were used as a proxy for the general Danish population.\n\nFindingsOf the 13,279 included participants, 2,296 (17.3%) were seropositive (mean age 46.6 (SD 16.4) years, 54.2% female), which was 3 times higher than in the general Danish population (mean age 41.7 (SD 14.1) years, 48.5% female) in the same period (5.8%, risk ratios (RR) 2.96, 95% CI 2.78-3.16, p>0.001). Seropositivity was higher among males than females (RR 1.1, 95% CI 1.05-1.22%, p=0.001) and increased with age, with an OR seropositivity of 1.03 for each 10-year increase in age (95% CI 1.00-1.06, p=0.031). Close contact with COVID-19-infected individuals was associated with a higher risk of infection, especially among members of the same households (OR 5.0, 95% CI 4.1-6.2 p<0,001). Adjusted for age, gender and region living at least 4 people in a household significantly increased the OR of seropositivity (OR 1.3, 95% CI 1.1-1.6, p=0.02) as did living in a multi-generational household (OR 1.3 per generation, 95% CI 1.1-1.5, p=0.007). Only 1.6% of participants reported not following any of the national COVID-19 recommendations. Anosmia (RR 3.2 95% CI 2.8-3.7, p<0.001) and ageusia (RR 3.3, 95% CI 2.9-3.8, p<0.001) were strongest associated with seropositivity.\n\nInterpretationDanish citizens living in SH areas of low socioeconomic status had a three times higher SARS-CoV-2 seroprevalence compared to the general Danish population. The seroprevalence was significantly higher in males and increased with age. Living in multiple generations or more than four persons in a household was an independent risk factor for being seropositive. Results of this study can be used for future consideration of the need for preventive measures in the populations living in SH areas.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Kamille Fogh", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Alexandra RR Eriksen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Rasmus B Hasselbalch", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Emilie Sofie Kristensen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Henning Bundgaard", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Susanne D Nielsen", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Charlotte S Joergensen", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Bibi FSS Scharff", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Christian Erikstrup", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Susanne G Saekmose", - "author_inst": "Department of Clinical Immunology, Zealand University Hospital, Koege, Denmark" - }, - { - "author_name": "Dorte K Holm", - "author_inst": "Department of Clinical Immunology, Odense University Hospital, Odense, Denmark" - }, - { - "author_name": "Bitten Aagaard", - "author_inst": "Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark" - }, - { - "author_name": "Jakob B Norsk", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Pernill B Nielsen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Jonas H Kristensen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - }, - { - "author_name": "Lars Oestergaard", - "author_inst": "Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Svend Ellermann-Eriksen", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Berit Andersen", - "author_inst": "University Research Clinic for Cancer Screening, Randers Regional Hospital, Randers, Denmark" - }, - { - "author_name": "Henrik Nielsen", - "author_inst": "Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark" - }, - { - "author_name": "Isik S Johansen", - "author_inst": "Department of Infectious Diseases, Odense University Hospital, Odense, Denmark" - }, - { - "author_name": "Lothar Wiese", - "author_inst": "Department of Infectious Diseases, Zealand University Hospital, Roskilde, Denmark" - }, - { - "author_name": "Lone Simonsen", - "author_inst": "Department of Science and Environment, University of Roskilde, Denmark" - }, - { - "author_name": "Thea R Fischer", - "author_inst": "Department of Clinical Research, North Zealand Hospital, Hilleroed, Denmark" - }, - { - "author_name": "Fredrik Folke", - "author_inst": "Copenhagen Emergency Medical Services, Copenhagen, Denmark" - }, - { - "author_name": "Freddy Lippert", - "author_inst": "Copenhagen Emergency Medical Services, Copenhagen, Denmark" - }, - { - "author_name": "Sisse R Ostrowski", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Steen Ethelberg", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Anders Koch", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Denmark and Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Anne-Marie Vangsted", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Tyra Grove Krause", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Anders Formsgaard", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Claus Nielsen", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Henrik Ullum", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Robert Skov", - "author_inst": "Statens Serum Institut, Copenhagen Denmark" - }, - { - "author_name": "Kasper Iversen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark and Department of Emergency Medicine, Copenhagen University Hospital, Her" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.10.21256951", "rel_title": "The impact of COVID-19 pandemic on the provision of ambulatory care for patients with chronic neurological diseases in Japan: evaluation of an administrative claims database", @@ -752204,6 +750963,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.10.443474", + "rel_title": "Binding of SARS-CoV-2 fusion peptide to host membranes", + "rel_date": "2021-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.10.443474", + "rel_abs": "During infection the SARS-CoV-2 virus fuses its viral envelope with cellular membranes of its human host. Initial contact with the host cell and membrane fusion are both mediated by the viral spike (S) protein. Proteolytic cleavage of S at the S2' site exposes its 40 amino acid long fusion peptide (FP). Binding of the FP to the host membrane anchors the S2 domain of S in both the viral and the host membrane. The reorganization of S2 then pulls the two membranes together. Here we use molecular dynamics (MD) simulations to study the two core functions of the SARS-CoV-2 FP: to attach quickly to cellular membranes and to form an anchor strong enough to withstand the mechanical force during membrane fusion. In eight 10 s-long MD simulations of FP in proximity to endosomal and plasma membranes, we find that FP binds spontaneously to the membranes and that binding proceeds predominantly by insertion of two short amphipathic helices into the membrane interface. Connected via a flexible linker, the two helices can bind the membrane independently, yet binding of one promotes the binding of the other by tethering it close to the target membrane. By simulating mechanical pulling forces acting on the C-terminus of the FP we then show that the bound FP can bear forces up to 250 pN before detaching from the membrane. This detachment force is more than ten-fold higher than an estimate of the force required to pull host and viral membranes together for fusion. We identify a fully conserved disulfide bridge in the FP as a major factor for the high mechanical stability of the FP membrane anchor. We conclude, first, that the sequential binding of two short amphipathic helices allows the SARS-CoV-2 FP to insert quickly into the target membrane, before the virion is swept away after shedding the S1 domain connecting it to the host cell receptor. Second, we conclude that the double attachment and the conserved disulfide bridge establish the strong anchoring required for subsequent membrane fusion. Multiple distinct membrane-anchoring elements ensure high avidity and high mechanical strength of FP-membrane binding.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stefan L. Schaefer", + "author_inst": "Max-Planck-Institute of Biophysics" + }, + { + "author_name": "Hendrik Jung", + "author_inst": "Max-Planck-Institute of Biophysics" + }, + { + "author_name": "Gerhard Hummer", + "author_inst": "Max Planck Institute of Biophysics" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.05.10.443404", "rel_title": "In-solution buffer-free digestion for the analysis of SARS-CoV-2 RBD proteins allows a full sequence coverage and detection of post-translational modifications in a single ESI-MS spectrum", @@ -753659,245 +752445,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.08.443253", - "rel_title": "SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies", - "rel_date": "2021-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.08.443253", - "rel_abs": "The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha). In vitro, B.1.617.2 is 6-fold less sensitive to serum neutralising antibodies from recovered individuals, and 8-fold less sensitive to vaccine-elicited antibodies as compared to wild type Wuhan-1 bearing D614G. Serum neutralising titres against B.1.617.2 were lower in ChAdOx-1 versus BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies against the receptor binding domain (RBD) and N-terminal domain (NTD), in particular to the clinically approved bamlavinimab and imdevimab monoclonal antibodies. B.1.617.2 demonstrated higher replication efficiency in both airway organoid and human airway epithelial systems as compared to B.1.1.7, associated with B.1.617.2 spike being in a predominantly cleaved state compared to B.1.1.7. Additionally we observed that B.1.617.2 had higher replication and spike mediated entry as compared to B.1.617.1, potentially explaining B.1.617.2 dominance. In an analysis of over 130 SARS-CoV-2 infected healthcare workers across three centres in India during a period of mixed lineage circulation, we observed substantially reduced ChAdOx-1 vaccine efficacy against B.1.617.2 relative to non-B.1.617.2. Compromised vaccine efficacy against the highly fit and immune evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.", - "rel_num_authors": 56, - "rel_authors": [ - { - "author_name": "Petra Mlcochova", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Steven A Kemp", - "author_inst": "UCL" - }, - { - "author_name": "Mahesh Shanker Dhar", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "Guido Papa", - "author_inst": "MRC LMB" - }, - { - "author_name": "Bo Meng", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Swapnil Mishra", - "author_inst": "Imperial College" - }, - { - "author_name": "Charlie Whittaker", - "author_inst": "Imperial" - }, - { - "author_name": "Thomas Mellan", - "author_inst": "Imperial" - }, - { - "author_name": "Isabella Ferreira", - "author_inst": "Cambridge" - }, - { - "author_name": "Rawlings Datir", - "author_inst": "Cambridge University" - }, - { - "author_name": "Dami Collier", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sujeet Singh", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Kalaiarasan Ponnusamy", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "V S Radhakrishnan", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "CSIR Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Jonathan Brown", - "author_inst": "Imperial" - }, - { - "author_name": "Robin Marwal", - "author_inst": "National Centre for Disease Control" - }, - { - "author_name": "Kalaiarasan Ponnusamy", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "V.S. Radhakrishnan", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "Niluka Goonawardne", - "author_inst": "Imperial" - }, - { - "author_name": "Adam Abdullahi", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Priti Devi", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Chand Wattal", - "author_inst": "Ganga Ram Hospital" - }, - { - "author_name": "Daniela Caputo", - "author_inst": "Cambridge NIHR Bioresource" - }, - { - "author_name": "Tom Peacock", - "author_inst": "Imperial" - }, - { - "author_name": "Neeraj Goel", - "author_inst": "Ganga Ram" - }, - { - "author_name": "Raju Vaishya", - "author_inst": "Indraprastha Apollo Hospital, New Delhi" - }, - { - "author_name": "Oscar Charles", - "author_inst": "UCL" - }, - { - "author_name": "Partha Chattopadhyay", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Meenakshi Agarwal", - "author_inst": "Northern Railway Central Hospital, New Delhi, India" - }, - { - "author_name": "Ambrish Satwik", - "author_inst": "Sri Ganga Ram Hospital, New Delhi, India" - }, - { - "author_name": "- INSACOG CONSORTIUM", - "author_inst": "-" - }, - { - "author_name": "- NIHR Bioresource Collaboration", - "author_inst": "-" - }, - { - "author_name": "Antranik Mavousian", - "author_inst": "Cambridge Stem Cell Institute" - }, - { - "author_name": "Jonathan Brown", - "author_inst": "Imperial College" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Imperial College" - }, - { - "author_name": "Niluka Goonawardne", - "author_inst": "Imperial College" - }, - { - "author_name": "Joo Hyeon Lee", - "author_inst": "Cambridge Stem Cell Institute" - }, - { - "author_name": "Jessica Bassi", - "author_inst": "Vir" - }, - { - "author_name": "Chiara Silacci-Fegni", - "author_inst": "Vir" - }, - { - "author_name": "Christian Saliba", - "author_inst": "Vir" - }, - { - "author_name": "Dora Pinto", - "author_inst": "Vir" - }, - { - "author_name": "Takashi Irie", - "author_inst": "Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan" - }, - { - "author_name": "Isao Yoshida", - "author_inst": "Tokyo Metropolitan Institute of Public Health, Tokyo 1690073, Japan" - }, - { - "author_name": "William L Hamilton", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Kei Sato", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Leo James", - "author_inst": "MRC LMB" - }, - { - "author_name": "Davide Corti", - "author_inst": "Vir" - }, - { - "author_name": "Luca Piccoli", - "author_inst": "Vir" - }, - { - "author_name": "Samir Bhatt", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Seth Flaxman", - "author_inst": "Imperial" - }, - { - "author_name": "Wendy Barlcay", - "author_inst": "Imperial" - }, - { - "author_name": "Partha Rakshit", - "author_inst": "National Centre for Disease Control, Delhi, India" - }, - { - "author_name": "Anurag Agrawal", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Ravindra K Gupta", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.07.443175", "rel_title": "Vaccination boosts naturally enhanced neutralizing breadth to SARS-CoV-2 one year after infection", @@ -754598,6 +753145,225 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.04.21256637", + "rel_title": "Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256637", + "rel_abs": "Many high-income countries have met the SARS-CoV-2 pandemic with overwhelming sequencing resources and have identified numerous distinct lineages, including some with notably altered biology. Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69{Delta}, Y144{Delta}, and LLA241/243{Delta}. This lineage - designated B.1.620 - is known to circulate in Lithuania and has now been found in several European states, but also in increasing numbers in central Africa owing to important recent increases in genome sequencing efforts on the continent. We provide evidence of likely ongoing local transmission of B.1.620 in Lithuania, France, Germany, Spain, Belgium and the Central African Republic. We describe the suite of mutations this lineage carries, its potential to be resistant to neutralising antibodies, travel histories for a subset of the European cases, and evidence of local B.1.620 transmission in Europe. We make a case for the likely Central African origin of this lineage by providing travel records as well as the outcomes of carefully crafted phylogenetic and phylogeographic inference methodologies, the latter of which is able to exploit individual travel histories recorded for infected travellers having entered different European countries.", + "rel_num_authors": 51, + "rel_authors": [ + { + "author_name": "Gytis Dudas", + "author_inst": "Gothenburg Global Biodiversity Centre" + }, + { + "author_name": "Samuel L Hong", + "author_inst": "KU Leuven" + }, + { + "author_name": "Barney I Potter", + "author_inst": "KU Leuven" + }, + { + "author_name": "Sebastien Calvignac-Spencer", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Frederic S Niatou-Singa", + "author_inst": "WWF Central African Republic Programme Office" + }, + { + "author_name": "Thais B Tombolomako", + "author_inst": "WWF Central African Republic Programme Office" + }, + { + "author_name": "Terence Fuh-Neba", + "author_inst": "WWF Central African Republic Programme Office" + }, + { + "author_name": "Ulrich Vickos", + "author_inst": "Amitie Hospital" + }, + { + "author_name": "Markus Ulrich", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Fabian H Leendertz", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Kamran Khan", + "author_inst": "BlueDot" + }, + { + "author_name": "Alexander Watts", + "author_inst": "BlueDot" + }, + { + "author_name": "Ingrida Olendraite", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Joost Snijder", + "author_inst": "Utrecht University" + }, + { + "author_name": "Kim N Wijnant", + "author_inst": "Utrecht University" + }, + { + "author_name": "Alexandre MJJ Bonvin", + "author_inst": "Utrecht University" + }, + { + "author_name": "Pascale Martres", + "author_inst": "Centre Hospitalier Rene Dubos" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ahidjo Ayouba", + "author_inst": "Universite de Montpellier" + }, + { + "author_name": "Martin F Maidadi", + "author_inst": "Institut de Recherches Medicales et D'etudes des Plantes Medicinales" + }, + { + "author_name": "Dowbiss M Djomsi", + "author_inst": "Institut de Recherches Medicales et D'etudes des Plantes Medicinales" + }, + { + "author_name": "Celestin Godwe", + "author_inst": "Institut de Recherches Medicales et D'etudes des Plantes Medicinales" + }, + { + "author_name": "Christelle Butel", + "author_inst": "Universite de Montpellier" + }, + { + "author_name": "Aistis Simaitis", + "author_inst": "The Office of the Government of the Republic of Lithuania" + }, + { + "author_name": "Migle Gabrielaite", + "author_inst": "Rigshospitalet" + }, + { + "author_name": "Monika Katenaite", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Rimvydas Norvilas", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Ligita Raugaite", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Rimvydas Jonikas", + "author_inst": "Hospital of Lithuanian University of Health Sciences Kauno Klinikos" + }, + { + "author_name": "Inga Nasvytiene", + "author_inst": "Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas" + }, + { + "author_name": "Zivile Zemeckiene", + "author_inst": "Hospital of Lithuanian University of Health Sciences Kauno Klinikos" + }, + { + "author_name": "Dovydas Gecys", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Kamile Tamusauskaite", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Milda Norkiene", + "author_inst": "Vilnius University" + }, + { + "author_name": "Emilija Vasiliunaite", + "author_inst": "Vilnius University" + }, + { + "author_name": "Danguole Ziogiene", + "author_inst": "Vilnius University" + }, + { + "author_name": "Albertas Timinskas", + "author_inst": "Vilnius University" + }, + { + "author_name": "Marius Sukys", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Mantas Sarauskas", + "author_inst": "Hospital of Lithuanian University of Health Sciences Kauno Klinikos" + }, + { + "author_name": "Gediminas Alzbutas", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Dovile Juozapaite", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Daniel Naumovas", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Arnoldas Pautienius", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Astra Vitkauskiene", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Rasa Ugenskiene", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Alma Gedvilaite", + "author_inst": "Vilnius University" + }, + { + "author_name": "Darius Cereskevicius", + "author_inst": "Lithuanian University of Health Sciences" + }, + { + "author_name": "Vaiva Lesauskaite", + "author_inst": "Hospital of Lithuanian University of Health Sciences Kauno Klinikos" + }, + { + "author_name": "Lukas Zemaitis", + "author_inst": "National Public Health Surveillance Laboratory" + }, + { + "author_name": "Laimonas Griskevicius", + "author_inst": "Vilnius University Hospital Santaros Klinikos" + }, + { + "author_name": "Guy Baele", + "author_inst": "KU Leuven" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.05.21256649", "rel_title": "Illness duration and symptom profile in a large cohort of symptomatic UK school-aged children tested for SARS-CoV-2", @@ -755381,81 +754147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.07.21252267", - "rel_title": "Evaluation of a multi-species SARS-CoV-2 surrogate virus neutralization test", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21252267", - "rel_abs": "Assays to measure SARS-CoV-2-specific neutralizing antibodies are important to monitor seroprevalence, to study asymptomatic infections and to reveal (intermediate) hosts. A recently developed assay, the surrogate virus-neutralization test (sVNT) is a quick and commercially available alternative to the \"gold standard\" virus neutralization assay using authentic virus, and does not require processing at BSL-3 level. The assay relies on the inhibition of binding of the receptor binding domain (RBD) on the spike (S) protein to human angiotensin-converting enzyme 2 (hACE2) by antibodies present in sera. As the sVNT does not require species- or isotype-specific conjugates, it can be similarly used for antibody detection in human and animal sera. In this study, we used 298 sera from PCR-confirmed COVID-19 patients and 151 sera from patients confirmed with other coronavirus or other (respiratory) infections, to evaluate the performance of the sVNT. To analyze the use of the assay in a One Health setting, we studied the presence of RBD-binding antibodies in 154 sera from nine animal species (cynomolgus and rhesus macaques, ferrets, rabbits, hamsters, cats, cattle, mink and dromedary camels). The sVNT showed a moderate to high sensitivity and a high specificity using sera from confirmed COVID-19 patients (91.3% and 100%, respectively) and animal sera (93.9% and 100%), however it lacked sensitivity to detect low titers. Significant correlations were found between the sVNT outcomes and PRNT50 and the Wantai total Ig and IgM ELISAs. While species-specific validation will be essential, our results show that the sVNT holds promise in detecting RBD-binding antibodies in multiple species.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Carmen W.E. Embregts", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Babs Verstrepen", - "author_inst": "Biomedical Primate Research Centre, Rijswijk, the Netherlands" - }, - { - "author_name": "Jan A.M. Langermans", - "author_inst": "Biomedical Primate Research Centre, Rijswijk, the Netherlands. Department Population Health Sciences, Division Animals in Science and Society, Faculty of Veteri" - }, - { - "author_name": "Kinga P Boszormenyi", - "author_inst": "Biomedical Primate Research Centre" - }, - { - "author_name": "Reina S. Sikkema", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Rory D. de Vries", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Insel Riems, Germany" - }, - { - "author_name": "Kerstin Wernike", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Lidwien A.M. Smit", - "author_inst": "Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands" - }, - { - "author_name": "Shan Zhao", - "author_inst": "Department of Biomolecular Health Sciences, Virology Division, Faculty of Veterinary Medicine, Utrecht University, the Netherlands" - }, - { - "author_name": "Barry Rockx", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Bart L. Haagmans", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Thijs Kuiken", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Corine GeurtsvanKessel", - "author_inst": "Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.05.21256257", "rel_title": "A Rapid and Reliable Liquid Chromatography/Mass Spectrometry Method for SARS-CoV-2 Diagnostics from Gargle Solutions and Saliva", @@ -756424,6 +755115,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.05.05.21254713", + "rel_title": "Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay", + "rel_date": "2021-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21254713", + "rel_abs": "BackgroundSARS-CoV-2 causes COVID-19, which can be fatal and is responsible for a global pandemic. Variants with increased transmissibility or the potential to evade immunity have emerged and represent a threat to global pandemic control. Variants of concern (VOC) can be identified by sequencing of viral RNA, or by more rapid methods for detection of subsets of signature mutations.\n\nMethodsWe developed a multiplex, real-time RT-PCR assay (cobas(R) SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Analytical sensitivity and accuracy were evaluated at three testing sites using clinical specimens from patients infected with SARS-CoV-2 variants belonging to several different lineages, including B.1.1.7, B.1.351, and P.1.\n\nResultsThe limit of detection for E484K was between 180 and 620 IU/mL for the three different isolates tested. For N501Y, the LOD was between 270 and 720 IU/mL (five isolates), while for del 69-70, it was 80 - 92 IU/mL (two isolates). Valid test results were obtained with all clinical specimens that were positive using routine diagnostic tests. Compared to sequencing (Sanger and next-generation), test results were 100% concordant at all three loci; no false positive or false negative results were observed.\n\nConclusionsData collected at three independent laboratories indicates excellent performance and concordance of cobas(R) SARS-CoV-2 Variant Set 1 with sequencing. New sets of primers and probes that target additional loci can be rapidly deployed in response to the identification of other emerging variants.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Carolin Bier", + "author_inst": "Roche Diagnostics International AG" + }, + { + "author_name": "Anke Edelmann", + "author_inst": "Labor Berlin Charite Vivantes GmbH" + }, + { + "author_name": "Kathrin Theil", + "author_inst": "Labor Berlin Charite Vivantes GmbH" + }, + { + "author_name": "Rolf Schwarzer", + "author_inst": "Labor Berlin Charite Vivantes GmbH" + }, + { + "author_name": "Maria Deichner", + "author_inst": "Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany" + }, + { + "author_name": "Andre Gessner", + "author_inst": "Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany" + }, + { + "author_name": "Andreas Hiergeist", + "author_inst": "Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany" + }, + { + "author_name": "Ute Rentschler", + "author_inst": "Bioscientia" + }, + { + "author_name": "Peter Gohl", + "author_inst": "Bioscientia" + }, + { + "author_name": "Alison Kuchta", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Chitra Manohar", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Chris Santini", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Dana Duncan", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Jesse Canchola", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Jingtao Sun", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Gene Spier", + "author_inst": "Roche Molecular Systems, Inc." + }, + { + "author_name": "Christian Simon", + "author_inst": "Roche Molecular Systems, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256012", "rel_title": "Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants.", @@ -757727,49 +756501,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.04.21256593", - "rel_title": "Obstructive sleep apnea is highly prevalent in COVID19 moderate to severe ARDS survivors: Findings of level I Polysomnography in a tertiary care hospital", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256593", - "rel_abs": "Study ObjectivesStudies have found Obstructive Sleep Apnea (OSA) as a risk factor for increased risk for COVID19 Acute respiratory Distress Syndrome (ARDS); but most of the studies were done in already known patients of OSA. This study was done to find prevalence of OSA in patients with COVID-19 related acute respiratory distress syndrome.\n\nMethodologyA hospital based longitudinal study was conducted among COVID 19 Intensive Care Unit (ICU) survivors. All consecutive COVID19 with moderate to severe ARDS were evaluated for OSA by Level I Polysomnography (PSG) after 4-6 weeks of discharge. Prevalence of OSA and PSG variables {Total sleep time, Sleep efficiency, sleep stage percentage, Apnea Hypopnea Index (AHI), T90, nadir oxygen} was estimated.\n\nResultsOut of 103 patients discharged from ICU during study period (October 2020 to 15 December 2020), 67 underwent Level I PSG. Mean Age was 52.6{+/-}10.9 years and mean Body Mass Index was 27.5 {+/-} 6.2 Kg/m2. Total sleep time was 343.2 {+/-} 86 minutes, sleep efficiency was 75.9{+/-}14.2%. OSA (AHI [≥]5) was seen in 65/67 patients and 49 patients had moderate to severe OSA (i.e. AHI [≥] 15).\n\nConclusionModerate-severe OSA was highly prevalent (73%) in COVID19 moderate to severe ARDS survivors. Role of OSA in pathophysiology of COVID19 ARDS needs further evaluation.\n\nHighlightsO_LIThis study was done to find prevalence of OSA in patients with COVID-19 related Acute respiratory distress syndrome\nC_LIO_LIModerate-severe OSA is highly prevalent (73%) in COVID19 ARDS survivors.\nC_LIO_LITo the best of our knowledge, it is first study in which level I PSG was done in COVID19 survivors.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Abhishek Goyal", - "author_inst": "All India INstitute of Medical Sciences Bhopal" - }, - { - "author_name": "Khushboo Saxena", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Avishek Kar", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Alkesh Khurana", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Abhijit P Pakhare", - "author_inst": "All India Institute of Medical Sciences, Bhopal" - }, - { - "author_name": "Parneet Kaur Bhagtana", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Chinta Siva Koti Rupa Sridevi", - "author_inst": "AIIMS Bhopal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.05.04.21256599", "rel_title": "Derivation and external validation of a simple risk score to predict in-hospital mortality in patients hospitalized for COVID-19", @@ -758706,6 +757437,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.03.21256532", + "rel_title": "COVID-19 infection and hospitalization according to the burden of chronic noncommunicable diseases in Brazil", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256532", + "rel_abs": "Chronic diseases, worse socioeconomic conditions and old age can increase infection and hospitalization rate due to Coronavirus disease (COVID-19). We assessed the association between the burden of NCDs and the occurrence of infections and hospitalizations of COVID-19 in Brazil in a large COVID-19 national survey data. We analyzed only data collected between July and November 2020 (n = 1,071,782). The frequencies of positive COVID-19 diagnosis and NCD burden were estimated according to age, sex, socioeconomic strata and skin color categories. We estimated hazard ratios and 95% confidence intervals using Cox regression models. There is a non-linear dose-response inverse association between per capita income and the rates of infection and hospitalization due to COVID-19. The presence of NCDs was associated with a higher incidence of COVID-19 infection (HR1NCD = 1.34; 95% CI: 1.26; 1.43; HR2 or more NCD= 1.54 95% CI: 1.39; 1.71) and incidence of hospitalization (HR1NCD = 3.08 95% CI: 2.26; 4.19; HR 2or more NCD= 6.81 95% CI: 4.88; 9.49).The difference between the risks of infection or hospitalization of COVID-19 attributable to the burden of NCDs is non-linearly associated with the income.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fabiana Ribeiro Ferraz", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Isabela Venancio", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Larissa Novais Lopes", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Catarina Azeredo", + "author_inst": "University Federal of Uberlandia" + }, + { + "author_name": "wolney Conde", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.05.21256527", "rel_title": "A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance", @@ -759520,61 +758286,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.04.30.21256228", - "rel_title": "Population Vaccine Effectiveness and its Implication for Control of the Spread of COVID-19 in the US", - "rel_date": "2021-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256228", - "rel_abs": "Realized vaccine efficacy in population is highly different from the individual vaccine efficacy measured in clinical trial. The realized vaccine efficacy in population is substantially affected by the vaccine age-stratified prioritization strategy, population age-structure, non-pharmaceutical intervention (NPI). We proposed a population vaccine efficacy which integrated individual vaccine efficacy, vaccine prioritization strategy and NPI to measure and monitor the control of the spread of COVID-19. We found that 11 states in the US had low population vaccine efficacy and 20 states had high population efficacy. We demonstrated that although the proportion of the population who received at least one dose of COVID-19 vaccine across 11 low population vaccine efficacy states, in general, was greater than that in 20 high population vaccine efficacy states, the 11 low population vaccine efficacy states experienced the recent COVID-19 surge, while the number of new cases in the 20 high population vaccine efficacy states exponentially decreased. We demonstrated that the proportions of adults in the population across 50 states were significantly associated with the forecasted ending date of the COVID-19. We show that it was recent low proportion of adults vaccinated in Michigan that caused its COVID-19 surge. Using population vaccination efficacy, we forecasted that the earliest COVID-19 ending states were Hawaii, Arizona, Arkansas, and California (in the end of June, 2021) and the last COVID-19 ending states were Colorado, New York and Michigan (in the Spring, 2022).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zixin Hu", - "author_inst": "Fudan University, China" - }, - { - "author_name": "Qiyang Ge", - "author_inst": "Fudan University, China" - }, - { - "author_name": "Li Luo", - "author_inst": "University of New Mexico, US" - }, - { - "author_name": "Tao Xu", - "author_inst": "University of Texas School of Public Health, US" - }, - { - "author_name": "Kai Zhang", - "author_inst": "University at Albany, State University of New York, US" - }, - { - "author_name": "Henry H Lu", - "author_inst": "Sanofi Pharmaceuticals, US" - }, - { - "author_name": "Wei Lin", - "author_inst": "Fudan University, China" - }, - { - "author_name": "Eric Boerwinkle", - "author_inst": "University of Texas Health Science Center at Houston, US" - }, - { - "author_name": "Li Jin", - "author_inst": "Fudan University, China" - }, - { - "author_name": "Momiao Xiong", - "author_inst": "University of Texas School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.01.21256090", "rel_title": "Effect of commuting on the risk of COVID-19 and COVID-19-induced anxiety", @@ -760431,6 +759142,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.02.21256492", + "rel_title": "Changes in work and health of Australians during the COVID-19 pandemic: a longitudinal cohort study", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.02.21256492", + "rel_abs": "ObjectivesTo determine the long-term effects of work loss on health during the COVID-19 pandemic, and whether any effects are persistent upon returning to work.\n\nMethodsA prospective longitudinal cohort study of 2603 participants across Australia monitored changes in health and work during between March and December 2020, with participants completing surveys at baseline and 1, 3 and 6 months later. Outcomes described psychological distress, and mental and physical health. Linear mixed regression models examined associations between changes in health and experiences of work loss, and return to work, over time.\n\nResultsLosing work during the early stages of the pandemic was associated with long-term poorer mental health, which began to recover over time as some returned to work. Physical health deteriorated over time, greater for people not working at baseline. Being out of work was associated with poorer mental health, but better physical health. These effects were larger for people that had recently lost work than for people with sustained work loss, and retaining employment played a protective role. Generally, returning to work resulted in poorer physical health and improvements in mental health, although this depended on the broader context of changes in work.\n\nConclusionsWork cessation during the pandemic led to poor health outcomes and had long-lasting effects. Returning to work benefits mental health but may reduce physical activity in the short-term. We encourage the provision of accessible mental health supports and services immediately following loss of work, and for people with prolonged forms of work loss.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Daniel Griffiths", + "author_inst": "Monash University" + }, + { + "author_name": "Luke Sheehan", + "author_inst": "Monash University" + }, + { + "author_name": "Caryn van Vreden", + "author_inst": "Monash University" + }, + { + "author_name": "Dennis Petrie", + "author_inst": "Monash University" + }, + { + "author_name": "Peter Whiteford", + "author_inst": "Australian National University" + }, + { + "author_name": "Malcolm Sim", + "author_inst": "Monash University" + }, + { + "author_name": "Alex Collie", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.04.26.21250357", "rel_title": "Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of COVID-19 in cancer patients with poor prognosis", @@ -761554,53 +760308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.05.03.21256482", - "rel_title": "The Physiologic Response to COVID-19 Vaccination", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256482", - "rel_abs": "Two mRNA vaccines and one adenovirus-based vaccine against SARS CoV-2 are currently being distributed at scale in the United States. Objective evidence of a specific individuals physiologic response to that vaccine are not routinely tracked but may offer insights into the acute immune response and personal and/or vaccine characteristics associated with that. We explored this possibility using a smartphone app-based research platform developed early in the pandemic that enabled volunteers (38,911 individuals between 25 March 2020 and 4 April 2021) to share their smartwatch and activity tracker data, as well as self-report, when appropriate, any symptoms, COVID-19 test results and vaccination dates and type. Of 4,110 individuals who reported at least one mRNA vaccination dose, 3,312 provided adequate resting heart rate data from the peri-vaccine period for analysis. We found changes in resting heart rate with respect to an individual baseline increased the days after vaccination, peaked on day 2, and returned to normal on day 6, with a much stronger effect after second dose with respect to first dose (average changes 1.6 versus 0.5 beats per minute). The changes were more pronounced for individuals who received the Moderna vaccine (on both doses), those who previously tested positive to COVID-19 (on dose 1), and for individuals aged <40 years, after adjusting for possible confounding factors. Taking advantage of continuous passive data from personal sensors could potentially enable the identification of a digital fingerprint of inflammation, which might prove useful as a surrogate for vaccine-induced immune response.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Giorgio Quer", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Matteo Gadaleta", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Jennifer M Radin", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Kristian G. Andersen", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Katie Baca-Motes", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Edward Ramos", - "author_inst": "Scripps Research Translational Institute" - }, - { - "author_name": "Eric J. Topol", - "author_inst": "Scripps ResearchTranslational Institute" - }, - { - "author_name": "Steven R. Steinhubl", - "author_inst": "Scripps Research Translational Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.01.21256389", "rel_title": "Latin American Registry of renal involvement in COVID-19 disease. The relevance of assessing proteinuria throughout the clinical course.", @@ -762149,6 +760856,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.03.442520", + "rel_title": "A novel highly potent inhibitor of TMPRSS2-like proteases blocks SARS-CoV-2 variants of concern and is broadly protective against infection and mortality in mice", + "rel_date": "2021-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.442520", + "rel_abs": "The COVID-19 pandemic caused by the SARS-CoV-2 virus remains a global public health crisis. Although widespread vaccination campaigns are underway, their efficacy is reduced against emerging variants of concern (VOCs) 1,2. Development of host-directed therapeutics and prophylactics could limit such resistance and offer urgently needed protection against VOCs 3,4. Attractive pharmacological targets to impede viral entry include type-II transmembrane serine proteases (TTSPs), such as TMPRSS2, whose essential role in the virus lifecycle is responsible for the cleavage and priming of the viral spike protein 5-7. Here, we identify and characterize a small-molecule compound, N-0385, as the most potent inhibitor of TMPRSS2 reported to date. N-0385 exhibited low nanomolar potency and a selectivity index of >106 at inhibiting SARS-CoV-2 infection in human lung cells and in donor-derived colonoids 8. Importantly, N-0385 acted as a broad-spectrum coronavirus inhibitor of two SARS-CoV-2 VOCs, B.1.1.7 and B.1.351. Strikingly, single daily intranasal administration of N-0385 early in infection significantly improved weight loss and clinical outcomes, and yielded 100% survival in the severe K18-human ACE2 transgenic mouse model of SARS-CoV-2 disease. This demonstrates that TTSP-mediated proteolytic maturation of spike is critical for SARS-CoV-2 infection in vivo and suggests that N-0385 provides a novel effective early treatment option against COVID-19 and emerging SARS-CoV-2 VOCs.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Tirosh Shapira", + "author_inst": "University of British Columbia" + }, + { + "author_name": "I. Abrrey Monreal", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "S\u00e9bastien P Dion", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Mason Jager", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Antoine D\u00e9silets", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Andrea D Olmstead", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Thierry Vandal", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "David W Buchholz", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Brian Imbiakha", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Guang Gao", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Aaleigha Chin", + "author_inst": "University of British Columbia" + }, + { + "author_name": "William D Rees", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Theodore Steiner", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Ivan Robert Nabi", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Eric Marsault", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Julie Sahler", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Avery August", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Gerlinde Van de Walle", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Gary R Whittaker", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Pierre-Luc Boudreault", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Hector C Aguilar", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Richard Leduc", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Fran\u00e7ois Jean", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.04.441029", "rel_title": "Sex-biased response to and brain cell infection by SARS-CoV-2 in a highly susceptible human ACE2 transgenic model", @@ -762866,57 +761680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.30.21256364", - "rel_title": "How are sociodemographic factors and risk preferences associated with seasonal influenza vaccination behavior under the COVID-19 pandemic?", - "rel_date": "2021-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256364", - "rel_abs": "The 2020/2021 seasonal influenza vaccination was carried out under unique situations during the coronavirus disease 2019 (COVID-19) pandemic. Examining the factors affecting vaccine inoculation in a pandemic situation may provide valuable insights. The purpose of the current study was to investigate how the COVID-19 pandemic affected the 2020/2021 seasonal influenza vaccine intake. A cross-sectional study was conducted on workers aged 20-65 years on December 22-25, 2020, using data from an Internet survey. We set the presence or absence of 2020/2021 seasonal influenza vaccination as the dependent variable, and each aspect of sociodemographic factors, including gender, age, marital status, education, annual household income, and underlying disease, as independent variables. We performed a multilevel logistic regression analysis nested by residence. In total, 26,637 respondents (13,600 men, 13,037 women) participated, and a total of 11,404 individuals (42.8%) received the 2020/2021 influenza vaccine. Significantly more women than men were vaccinated, and the vaccination rate was higher among younger adults, married people, highly educated people, high-income earners, and those with underlying disease. The current results suggested that the relationship between seasonal influenza vaccination behavior and sociodemographic factors differed from the results reported in previous studies in terms of age. These findings suggest that, during the COVID-19 pandemic, young people may have become more aware of the risk of contracting influenza and of the effectiveness of the influenza vaccine. In addition, information interventions may have had a positive effect.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "TAKAHIRO MORI", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Kazunori Ikegami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Koji Mori", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.30.21256366", "rel_title": "Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater", @@ -763621,6 +762384,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.02.21255857", + "rel_title": "Detection of SARS-CoV-2 infection in gargle, spit and sputum specimens", + "rel_date": "2021-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.02.21255857", + "rel_abs": "The gold standard for SARS-CoV-2 infection diagnosis is RT-PCR from nasopharyngeal specimen (NPS). Its collection involves a close contact between patients and healthcare workers requiring a significant amount of workforce and putting them at risk of infection. We evaluated self-collection of alternative specimens and compared their sensitivity and Ct values to NPS. We visited acute COVID-19 outpatients to collect concomitant nasopharyngeal and gargle specimens and had patients self-collect a gargle and either sputum or spit specimens on the next morning.\n\nWe included 40 patients and collected 40 concomitant nasopharyngeal and gargle specimens, as well as 40 gargle, 22 spit and 16 sputum specimens on the next day, as 2 patients could not produce sputum.\n\nAll specimens were as sensitive as NPS. Gargle specimens had a sensitivity of 0.97 (CI 95% 0.92-1,00), whether collected concomitantly to NPS or on the next morning. Next morning spit and sputum specimens showed a sensitivity of 1.00 CI (95% 1.00-1.00) and 0.94 (CI 95% 0.87-1.00), respectively. The gargle specimens had a significantly higher mean cycle threshold (Ct) values, 29.89 (SD 4.63) (p-value <0.001) and 29.25 (SD 3.99) (p-value <0.001) when collected concomitantly and on the next morning compared to NPS (22.07, SD 4.63). Ct value obtained with spit (23.51, SD 4.57, p-value 0.11) and sputum (25.82, SD 9.21, p-value 0.28) specimens were close to NPS.\n\nAll alternative specimen collection methods were as sensitive as NPS, but spit collection appeared more promising, with a low Ct value and ease of collection. Our findings warrant further investigation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Henna M\u00e4kel\u00e4", + "author_inst": "Finnish institute for Health and Welfare" + }, + { + "author_name": "Eero Poukka", + "author_inst": "Finnish institute for Health and Welfare" + }, + { + "author_name": "Lotta Hagberg", + "author_inst": "Finnish institute for Health and Welfare" + }, + { + "author_name": "Thuan Vo", + "author_inst": "University of Tampere" + }, + { + "author_name": "Hanna Nohynek", + "author_inst": "National Institute for Health and Welfare" + }, + { + "author_name": "Niina Ikonen", + "author_inst": "The National Institute for Health and Welfare" + }, + { + "author_name": "Kirsi Liitsola", + "author_inst": "National Institute of health and welfare" + }, + { + "author_name": "Otto Helve", + "author_inst": "Finnish institute for Health and Welfare" + }, + { + "author_name": "Carita Savolainen-Kopra", + "author_inst": "National Institute for Health and Welfare (THL)" + }, + { + "author_name": "Timoth\u00e9e Dub", + "author_inst": "Finnish institute for Health and Welfare" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.01.21256071", "rel_title": "Incidence and outcome of delirium during Helmet CPAP treatment in COVID-19 patients", @@ -764700,57 +763518,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.04.28.21256237", - "rel_title": "Cost-effectiveness of COVID-19 vaccination in low- and middle-income countries", - "rel_date": "2021-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256237", - "rel_abs": "Despite the advent of safe and highly effective COVID-19 vaccines1-4, pervasive inequities in global distribution persist5. In response, multinational partners have proposed programs to allocate vaccines to low- and middle-income countries (LMICs)6. Yet, there remains a substantial funding gap for such programs7. Further, the optimal vaccine supply is unknown and the cost-effectiveness of investments into global vaccination programs has not been described. We used a validated COVID-19 simulation model8 to project the health benefits and costs of reaching 20%-70% vaccine coverage in 91 LMICs. We show that funding 20% vaccine coverage over one year among 91 LMICs would prevent 294 million infections and 2 million deaths, with 26 million years of life saved at a cost of US$6.4 billion, for an incremental cost effectiveness ratio (ICER) of US$250/year of life saved (YLS). Increasing vaccine coverage up to 50% would prevent millions more infections and save hundreds of thousands of additional lives, with ICERs below US$8,000/YLS. Results were robust to variations in vaccine efficacy and hesitancy, but were more sensitive to assumptions about epidemic pace and vaccination costs. These results support efforts to fund vaccination programs in LMICs and complement arguments about health equity9, economic benefits10, and pandemic control11.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mark J. Siedner", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Christopher Alba", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kieran P. Fitzmaurice", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Rebecca F. Gilbert", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Justine A. Scott", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Fatma M. Shebl", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Andrea Ciaranello", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Krishna P. Reddy", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kenneth A. Freedberg", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.04.29.21256291", "rel_title": "Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19", @@ -765575,6 +764342,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.29.21256307", + "rel_title": "Modelling digital and manual contact tracing for COVID-19. Are low uptakes and missed contacts deal-breakers?", + "rel_date": "2021-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256307", + "rel_abs": "Comprehensive testing schemes, followed by adequate contact tracing and isolation, represent the best public health interventions we can employ to reduce the impact of an ongoing epidemic when no or limited vaccines are available and the implications of a full lockdown are to be avoided. However, the process of tracing can prove feckless for highly-contagious viruses such as SARS-Cov-2. The interview-based approaches often miss contacts and involve significant delays, while digital solutions can suffer from insufficient adoption rates or inadequate usage patterns. Here we present a novel way of modelling different contact tracing strategies using a generalized multi-site mean-field model, which can naturally assess the impact of both manual and digital approaches. Our methodology can readily be applied to any compartmental formulation, thus enabling the study of several complex pathogens. We use this technique to simulate a new epidemiological model, SEIR-T, and show that, given the right conditions, tracing in a COVID-19 epidemic can be effective even when digital uptakes are sub-optimal or interviewers miss a fair proportion of the contacts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrei Rusu", + "author_inst": "University of Southampton" + }, + { + "author_name": "Katayoun Farrahi", + "author_inst": "University of Southampton" + }, + { + "author_name": "Remi Emonet", + "author_inst": "Jean Monnet University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.29.21256332", "rel_title": "System inference via field inversion for the spatio-temporal progression of infectious diseases: Studies of COVID-19 in Michigan and Mexico", @@ -766450,45 +765244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.27.21256205", - "rel_title": "Evaluation of serological tests for detecting SARS-CoV-2 antibodies: implementation in assessing post vaccination status", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256205", - "rel_abs": "BackgroundThe anti-SARS-CoV-2 immunological assays have promising applications in the control and surveillance of the current COVID-19 pandemic. Therefore, large number of serological assays are developed in the commercial market to measure SARS-CoV-2 antibodies, which requires evaluation before their application in large scale.\n\nObjectivesTo evaluate the performances of commercially available serological assays for detecting SARS-CoV-2 antibodies.\n\nMethodsThe study compared the performances of six different methods for detection of antibodies against SARS-CoV-2 which includes (i) Genscript SARS-CoV-2 surrogate virus neutralization test kit [Test A] (ii) Diasorin - SARS-CoV-2 S1/S2 IgG detection [Test B] (iii) Alinity SARS-CoV-2 IgG II [Test C] (iv) Diasorin - SARS-CoV-2 TrimericS IgG [Test D] (v) Roche Elecsys Anti-SARS-CoV-2 - cobas [Test E] (vi) AESKULISA (AESKU Enzyme Linked Immunosorbent Assay) [Test F] against the gold standard Plaque Reduction Neutralization Test (PRNT).\n\nResultsTest E had the highest sensitivity and Test A had the highest specificity The ROC for tests A, C, D and E showed optimum cut-offs that differed from the manufacturers recommendation. Test D had the best performance considering all the performance indicators with the highest agreement with the PRNT results. Parallel testing of test A with test D and test B had the optimum performance.\n\nConclusionSerological assays that are commercially available are very promising and show good agreement with the standard PRNT results. Studies on large samples for optimization of the assay cut-off values and cost-effective evaluations on parallel testing methods are needed to make recommendations on these commercial assays.\n\nImportanceSerological assays that are commercially available are very promising and this paper adds new knowledge about the optimization of these kits for evaluating post vaccination antibodies status. It highlights the positive and negative aspects of each of these assays in terms of sensitivity, specificity, positive and negative predictive values, and the agreement of results with the standard neutralization test. When serological assays are being used to assess post-vaccine immune status, a balance of all parameters needs to be considered rather than emphasizing only on high specificity. This is particularly relevant in the current situation where vaccination is happening around the globe, high sensitivity assays will result in reporting a lower percentage of false negative reports and avoids panic about lack of vaccine response. It is important that we understand the strengths and limitations of commercially available serological assays for better application of these tests to understand immune response and the duration of protection post vaccination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Dr. Sally A Mahmoud", - "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" - }, - { - "author_name": "Subhashini Ganesan", - "author_inst": "G42 Healthcare, UAE" - }, - { - "author_name": "shivaraj Naik", - "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" - }, - { - "author_name": "Safaa Bissar", - "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" - }, - { - "author_name": "Isra Al zamil", - "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" - }, - { - "author_name": "Walid Zaher", - "author_inst": "G42 Healthcare, UAE" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256193", "rel_title": "Real-world effectiveness of Ad26.COV2.S adenoviral vector vaccine for COVID-19", @@ -767015,6 +765770,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.29.21256186", + "rel_title": "COVID-19 Vaccine Acceptance Among Healthcare Workers in a United States Medical Center", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256186", + "rel_abs": "BackgroundThe Centers for Disease Control and Prevention prioritized healthcare personnel for the first phase of COVID-19 vaccination in the United States to keep critical healthcare infrastructure open and functioning, but vaccine hesitancy may limit vaccine uptake.\n\nObjectiveTo evaluate vaccine intentions among healthcare workers eligible for COVID-19 vaccination and explore differences by sociodemographic and occupational characteristics.\n\nDesignFrom February 1-15, 2021, we conducted a cross-sectional, opt-in online survey at a Midwest U.S. academic healthcare center that began vaccinating employees in December 2020.\n\nParticipantsThe entire employee workforce of the study site was eligible.\n\nMain MeasuresCOVID-19 vaccination intention, categorized as Received/Scheduled/ASAP, Not Now, and Not Ever. Logistic regression models to assess the relationship between demographic and occupational characteristics and intention to receive COVID-19 vaccination.\n\nKey ResultsMost participants (n=11,387, of 39,259 individual and group email accounts invited) had received or were scheduled to receive the COVID-19 vaccine (n=9081, 79.8%) or planned to receive it as soon as possible (n=546, 4.8%), while fewer were hesitant (Not Now, n=954, 8.4%; Not Ever, n=369, 3.2%). In multivariable logistic regression models predicting vaccine intention, physicians (aOR 22.2, 9.1-54.3), trainees (aOR 5.9, 3.0-11.4), and nurse practitioners/nurse midwives/physician assistants (aOR 1.9, 1.2-3.0) were significantly more likely to demonstrate vaccine acceptance, compared to nurses, whereas other clinical staff were significantly less likely (aOR 0.8, 0.6-0.9). Prior infection with COVID-19, gender, race/ethnicity, and age were all significantly associated with vaccine intention. Overall, 29.6% reported at least one concern about COVID-19 vaccination.\n\nConclusionsIn a large, diverse sample of healthcare workers, over 11% delayed COVID-19 vaccination when it was available to them, with notable variation in vaccine hesitancy across professional roles and demographic groups. Our findings suggest immediate opportunities to empathetically engage those with COVID-19 vaccine concerns and optimize vaccine coverage across our healthcare system.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michelle H. Moniz", + "author_inst": "University of Michigan" + }, + { + "author_name": "Courtney Townsel", + "author_inst": "University of Michigan" + }, + { + "author_name": "Abram L. Wagner", + "author_inst": "University of Michigan" + }, + { + "author_name": "Brian J. Zikmund-Fisher", + "author_inst": "University of Michigan" + }, + { + "author_name": "Sarah Hawley", + "author_inst": "University of Michigan" + }, + { + "author_name": "Charley Jiang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Molly J. Stout", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.30.441093", "rel_title": "Allosteric Cross-Talk Among SARS-CoV-2 Spike's Receptor-Binding Domain Mutations Triggers an Effective Hijacking of Human Cell Receptor", @@ -768094,101 +766892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.28.21255834", - "rel_title": "Pyridostigmine in adults with severe SARS-CoV-2 infection: the PISCO trial", - "rel_date": "2021-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21255834", - "rel_abs": "BackgroundHospitalized patients with severe COVID-19 have an increased risk of developing severe systemic inflammatory response, pulmonary damage, and acute respiratory distress syndrome (ARDS), resulting in end-organ damage and death. Acetylcholine modulates the acute inflammatory response through a neuro-immune mechanism known as the inflammatory reflex. Pyridostigmine, an acetylcholine-esterase inhibitor, increases the half-life of endogenous ACh, chemically stimulating the inflammatory reflex. This trial aimed to evaluate whether pyridostigmine could decrease invasive mechanical ventilation (IMV) and death in patients with severe COVID-19.\n\nMethodsWe performed a parallel-group, multicenter, double-blinded, placebo-controlled, randomized clinical trial to evaluate if add-on pyridostigmine to standard treatment reduced the composite outcome of initiation of IMV and 28-day all-cause mortality among hospitalized patients with severe COVID-19.\n\nResults188 participants were randomly assigned to placebo (n=94) or pyridostigmine (n=94). The composite outcome occurred in 22 (23.4%) vs. 11 (11.7%) participants, respectively (hazard ratio 0.46, 95% confidence interval 0.22-0.96, p=0.03). Most of the adverse events were mild to moderate, with no serious adverse events related to pyridostigmine; discontinuation of the study drugs was similar in both groups.\n\nConclusionsWe provide evidence indicating that the addition of pyridostigmine to standard treatment resulted in a clinically significant reduction in the composite outcome (IMV/death) among patients hospitalized for severe COVID-19. (Funded by Consejo Nacional de Ciencia y Tecnologia, Mexico; ClinicalTrials.gov number: NCT04343963).", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sergio Fragoso-Saavedra", - "author_inst": "Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico" - }, - { - "author_name": "Isaac N\u00fa\u00f1ez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Belem Mercedes Audelo-Cruz", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Sarahi Arias-Mart\u00ednez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Daniel Manzur-Sandoval", - "author_inst": "Instituto Nacional de Cariolog\u00eda Ignacio Ch\u00e1vez" - }, - { - "author_name": "Alejandro Quintero-Villegas", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "H. Benjam\u00ed Garc\u00eda-Gonz\u00e1lez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Sergio L. Carbajal-Morelos", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Sergio Ponce de Le\u00f3n-Rosales", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Jos\u00e9 Got\u00e9s-Palazuelos", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Yanink Caro-Vega", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Jos\u00e9 Maza-Larrea", - "author_inst": "Instituto Nacional de Cariolog\u00eda Ignacio Ch\u00e1vez" - }, - { - "author_name": "Isabella Batina", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Le\u00f3n Islas-Weinstein", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Juan J Calva", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "David A. Iruegas-Nunez", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Pablo F. Belaunzar\u00e1n-Zamudio", - "author_inst": "Independent researcher, Bethesda, MD, USA" - }, - { - "author_name": "Ju\u00e1n Sierra-Madero", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Jos\u00e9 Carlos Crisp\u00edn", - "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n" - }, - { - "author_name": "Sergio I. Vald\u00e9s-Ferrer", - "author_inst": "Instituto Nacional De Ciencias M\u00e9dicas y Nutrici\u00e9n" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.28.441832", "rel_title": "An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose.", @@ -768917,6 +767620,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.26.21256118", + "rel_title": "Anti-SARS-CoV-2 antibody levels are concordant across multiple platforms but are not fully predictive of sterilizing immunity", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256118", + "rel_abs": "With the availability of widespread SARS-CoV-2 vaccination, high-throughput quantitative anti-spike serological testing will likely become increasingly important. Here, we investigated the performance characteristics of the recently FDA authorized semi-quantitative anti-spike AdviseDx SARS-CoV-2 IgG II assay compared to the FDA authorized anti-nucleocapsid Abbott Architect SARS-CoV-2 IgG, Roche elecsys Anti-SARS-CoV-2-S, EuroImmun Anti-SARS-CoV-2 ELISA, and GenScript surrogate virus neutralization assays and examined the humoral response associated with vaccination, natural protection, and breakthrough infection. The AdviseDx assay had a clinical sensitivity at 14 days post-symptom onset or 10 days post PCR detection of 95.6% (65/68, 95% CI: 87.8-98.8%) with two discrepant individuals seroconverting shortly thereafter. The AdviseDx assay demonstrated 100% positive percent agreement with the four other assays examined using the same symptom onset or PCR detection cutoffs. Using a recently available WHO International Standard for anti-SARS-CoV-2 antibody, we provide assay unit conversion factors to international units for each of the assays examined. We performed a longitudinal survey of healthy vaccinated individuals, finding median AdviseDx immunoglobulin levels peaked seven weeks post-first vaccine dose at approximately 4,000 IU/mL. Intriguingly, among the five assays examined, there was no significant difference in antigen binding level or neutralizing activity between two seropositive patients protected against SARS-CoV-2 infection in a previously described fishing vessel outbreak and five healthcare workers who experienced vaccine breakthrough of SARS-CoV-2 infection - all with variants of concern. These findings suggest that protection against SARS-CoV-2 infection cannot currently be predicted exclusively using in vitro antibody assays against wildtype SARS-CoV-2 spike. Further work is required to establish protective correlates of protection for SARS-CoV-2 infection.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Ben T Bradley", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Andrew Bryan", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Susan L Fink", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Erin A Goecker", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Meei-Li Huang", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Haiying Zhu", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Anu Chaudhary", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Bhanupriya Madarampalli", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Joyce Y-C Lu", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Kathy Strand", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Estella Whimbey", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Chloe Bryson-Cahn", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Adrienne Schippers", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Nandita S Mani", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Gregory Pepper", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Keith R Jerome", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Chihiro Morishima", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Robert W Coombs", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Mark Wener", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Seth Cohen", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Alexander L Greninger", + "author_inst": "University of Washington Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.27.21256149", "rel_title": "Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19", @@ -769992,29 +768798,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.26.21256126", - "rel_title": "Building Back Better after COVID-19: a systematic scoping review of wicked problems affecting developed countries and implications for global governance", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256126", - "rel_abs": "The COVID-19 pandemic is a textbook example of a wicked problem, one which is complex, open-ended, unpredictable, or intractable and seems resistant to any solution. This presents a window of opportunity to explore other wicked problems and their implications after the pandemic. A systematic scoping review was conducted to investigate the COVID-19 aftermath and identify public health topics which may be of great significance in the years to come. Through the adoption of three megadrivers as fundamental drivers of change (globalisation, demographic change, and digitalisation), it narratively explored how different wicked problems - and the driving mechanisms which sustain them - persist. It further explored the implications of these public health topics on global (health) governance. While the wicked problems mapped in this article show a large variance in where their apparent roots lie, they share one factor in common: health. These wicked problems must be first and foremost addressed if we as a globalised world are to successfully and sustainably build back better from COVID-19.\n\nSummary BoxO_ST_ABSWhat is already known?C_ST_ABS- COVID-19 is a textbook example of a wicked problem; a problem that is complex, open-ended, unpredictable, or intractable and seems resistant to any solution;\n- Digitalisation, globalisation, and demographic change are seen as the three megadrivers of change and are theorised to create and sustain modern wicked problems;\n- The megadrivers respectively have complex relationships with health; this includes both positive and negative associations.\n\n\nWhat are the new findings?- A series of wicked problems exist in multiple domains of society that continue to obstruct the progress of the 2030 Agenda for Sustainable Development;\n- These wicked problems each have roots in the three megadrivers: digitalisation, globalisation, and demographic change;\n- There exists a complex interrelation between the megadrivers, wicked problems, and health.\n\n\nWhat do the new findings imply?- It currently remains unclear to what extent wicked problems and megadrivers respectively affect health outcomes; therefore, further research is indicated;\n- A once in a generation opportunity has presented itself to build back better from the COVID-19 pandemic by addressing the existing wicked problems; therefore, governance mechanisms should follow and adapt accordingly;\n- Wicked problems have bidirectional implications for modern policy; this has created an environment for wicked problems to manifest and sustain themselves, which in turn produce further policies that sustain wicked problems.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Robin van Kessel", - "author_inst": "Maastricht University" - }, - { - "author_name": "Brian Li Han Wong", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.26.21256152", "rel_title": "Effectiveness of portable air filtration on reducing indoor aerosol counts: preclinical observational trials", @@ -770795,6 +769578,117 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.04.28.441474", + "rel_title": "Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drive rapid and potent immunogenicity capable of single-dose protection", + "rel_date": "2021-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.28.441474", + "rel_abs": "Antibodies from SARS-CoV-2 vaccines may target epitopes which reduce durability or increase the potential for escape from vaccine-induced immunity. Using a novel synthetic vaccinology pipeline, we developed rationally immune focused SARS-CoV-2 Spike-based vaccines. N-linked glycans can be employed to alter antibody responses to infection and vaccines. Utilizing computational modeling and comprehensive in vitro screening, we incorporated glycans into the Spike Receptor-Binding Domain (RBD) and assessed antigenic profiles. We developed glycan coated RBD immunogens and engineered seven multivalent configurations. Advanced DNA delivery of engineered nanoparticle vaccines rapidly elicited potent neutralizing antibodies in guinea pigs, hamsters and multiple mouse models, including human ACE2 and human B cell repertoire transgenics. RBD nanoparticles encoding wild-type and the P.1 SARS-CoV-2 variant induced high levels of cross-neutralizing antibodies. Single, low dose immunization protected against a lethal SARS-CoV-2 challenge. Single-dose coronavirus vaccines via DNA-launched nanoparticles provide a platform for rapid clinical translation of novel, potent coronavirus vaccines.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Kylie Konrath", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Kevin Liaw", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Yuanhan Wu", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Xizhou Zhu", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Susanne Walker", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Ziyang Xu", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Katherine Schultheis", + "author_inst": "Inovio" + }, + { + "author_name": "Neethu Chokkalingam", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Nicholas J Tursi", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Jianqiu Du", + "author_inst": "Indiana University" + }, + { + "author_name": "Matthew Sullivan", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Mansi Purwar", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Alan Moore", + "author_inst": "Indiana University" + }, + { + "author_name": "Viviane Machado", + "author_inst": "Inovio Pharmecuticals" + }, + { + "author_name": "Igor Maricic", + "author_inst": "Inovio Pharmecuticals" + }, + { + "author_name": "Emma Reuschel", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Drew Frase", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Christel Iffland", + "author_inst": "Ligand Pharmecuticals" + }, + { + "author_name": "Kate Broderick", + "author_inst": "Inovio Pharmaceuticals" + }, + { + "author_name": "Laurent Humeau", + "author_inst": "Inovio Pharmecuticals" + }, + { + "author_name": "Trevor Smith", + "author_inst": "Inovio Pharmecuticals" + }, + { + "author_name": "Jesper Pallesen", + "author_inst": "Indiana University" + }, + { + "author_name": "David B Weiner", + "author_inst": "Wistar Institute" + }, + { + "author_name": "Daniel W Kulp", + "author_inst": "The Wistar Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.28.441797", "rel_title": "Prophylactic protection against respiratory viruses conferred by a prototype live attenuated influenza virus vaccine.", @@ -771790,45 +770684,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.04.22.21255951", - "rel_title": "The Impact of Face Masks on Performance and Physiological Outcomes during Exercise: A Systematic Review and Meta-analysis", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255951", - "rel_abs": "Face masks are promoted for preventing spread of viruses; however, wearing a mask during exercise might increase CO2 rebreathing, decrease arterial oxygenation, and decrease exercise performance. A systematic review and meta-analysis was conducted on the impact of wearing a mask during exercise. Data sources included SPORTDiscus, PubMed, and Medline. Eligibility criteria included all study designs comparing surgical, N95, or cloth masks to a no mask condition during any type of exercise where exercise performance and/or physiological parameters were evaluated. Healthy and clinical participants were included. Mean differences (MD) or standardized mean differences (SMD) with 95% confidence intervals were calculated and pooled effects assessed. Twenty-two studies involving 1,573 participants (620 females, 953 males) were included. Surgical, or N95 masks did not impact exercise performance (SMD -0.05 [-0.16,0.07] and -0.16 [-0.54,0.22], respectively) but increased ratings of perceived exertion (RPE) (SMD 0.33 [0.09,0.58] and 0.61 [0.23,0.99]) and dyspnea (SMD 0.6 [0.3,0.9] for all masks). End-tidal CO2 (MD 3.3 [1.0, 5.6] and 3.7 [3.0,4.4] mmHg), and heart rate (MD 2 [0,4] beats/min with N95 masks) slightly increased. Face masks can be worn during exercise with no influences on performance and minimal impacts on physiological variables.\n\nPROSPERO RegistrationCRD42020224988\n\nNovelty PointsFace masks can be worn during exercise with no impacts on performance and minimal impacts on physiological variables.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Keely A Shaw", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Gordon Zello", - "author_inst": "University ofSaskatchewan" - }, - { - "author_name": "Scotty Butcher", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Jong Bum Ko", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Leandy A Bertrand", - "author_inst": "College of Kinesiology, University of Saskatchewan" - }, - { - "author_name": "Philip D Chilibeck", - "author_inst": "University of Saskatchewan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.04.23.21255973", "rel_title": "EVIDENCE FOR BIOLOGICAL AGE ACCELERATION AND TELOMERE2 SHORTENING IN COVID-19 SURVIVORS", @@ -772512,6 +771367,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.26.441498", + "rel_title": "Mechanical control of innate immune responses against viral infection revealed in a human Lung Alveolus Chip", + "rel_date": "2021-04-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.26.441498", + "rel_abs": "Mechanical forces associated with breathing play a fundamental role in lung development and disease but the molecular pathways remain largely unknown. Here, we used a mechanically actuatable Human Lung Alveolus Chip that recapitulates human lung alveolar type I and type II cell differentiation, alveolar-capillary interface formation, and genome-wide gene expression profiles characteristic of the distal lung to investigate the role of physical forces associated with cyclic breathing motions in lung innate immune responses to viral infection. When the mechanically active Alveolus Chips are infected with the influenza H3N2 virus, a cascade of host responses is elicited on-chip, including increased production of cytokines and expression of inflammation-associated genes in pulmonary epithelial and endothelial cells, resulting in enhanced recruitment of circulating immune cells as occurs during viral infection in vivo. Surprisingly, studies carried out in parallel with static chips revealed that physiological breathing motions suppress viral replication by activating protective innate immune responses in epithelial and endothelial cells. This is mediated at least in part through upregulation of S100 calcium-binding protein A7 (S100A7), which binds to the Receptor for Advanced Glycation End Products (RAGE), an inflammatory mediator that is most highly expressed in the lung alveolus in vivo. This mechano-immunological control mechanism is further supported by the finding that existing RAGE inhibitor drugs can suppress the production of inflammatory cytokines in response to influenza virus infection in this model. S100A7-RAGE interactions and modulation of mechanical ventilation parameters could therefore serve as new targets for therapeutic intervention in patients infected with influenza and other potential pandemic viruses that cause life-threatening lung inflammation.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Haiqing Bai", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Longlong Si", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Amanda Jiang", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Chaitra Belgur", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Crystal Yuri Oh", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Melissa Rodas", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Atiq Nurani", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Sarah Elizabeth Gilpin", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Rani K Powers", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Girija Goyal", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Rachelle Prantil-Baun", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + }, + { + "author_name": "Donald Elliot Ingber", + "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.26.441517", "rel_title": "Relative Mutant N501Y SARS-CoV-2 Spike Protein RBD Inhibition of Anti-Spike Protein IgG and ACE-2 Binding to Spike Protein Species", @@ -773391,141 +772309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.27.441510", - "rel_title": "Aerosol Exposure of Cynomolgus Macaques to SARS-CoV-2 Results in More Severe Pathology than Existing Models", - "rel_date": "2021-04-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441510", - "rel_abs": "The emergence of SARS-CoV-2 pandemic has highlighted the need for animal models that faithfully recapitulate the salient features of COVID-19 disease in humans; these models are necessary for the rapid down-selection, testing, and evaluation of medical countermeasures. Here we performed a direct comparison of two distinct routes of SARS-CoV-2 exposure, combined intratracheal/intranasal and small particle aerosol, in two nonhuman primate species: rhesus and cynomolgus macaques. While all four experimental groups displayed very few outward clinical signs, evidence of mild to moderate respiratory disease was present on radiographs and at the time of necropsy. Cynomolgus macaques exposed via the aerosol route also developed the most consistent fever responses and had the most severe respiratory disease and pathology. This study demonstrates that while all four models were suitable representations of mild COVID-like illness, aerosol exposure of cynomolgus macaques to SARS-CoV-2 produced the most severe disease, which may provide additional clinical endpoints for evaluating therapeutics and vaccines.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Sandra L Bixler", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Christopher P Stefan", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Alexandra Jay", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Franco D Rossi", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Keersten M Ricks", - "author_inst": "USAMRIID" - }, - { - "author_name": "Charles Jason Shoemaker", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Alicia M Moreau", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Xiankun Zeng", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jay Hooper", - "author_inst": "USAMRIID" - }, - { - "author_name": "David Dyer", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Ondraya Frick", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jeffrey W Koehler", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Brian Kearney", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Nina DiPinto", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jun Liu", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Samantha Tostenson", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Tamara L Clements", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jeffrey M Smith", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Joshua A Johnson", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Kerry Berrier", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Heather Esham", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Korey L Delp", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Susan R Coyne", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Holly Bloomfield", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Paul Kuehnert", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Kristen Akers", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Kathleen Gibson", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Timothy Minogue", - "author_inst": "United States Army Medical Research Institute for Infectious Diseases" - }, - { - "author_name": "Aysegul Nalca", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Margaret L.M Pitt", - "author_inst": "United States Army Medical Research Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.27.441661", "rel_title": "Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets", @@ -774254,6 +773037,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.23.441195", + "rel_title": "Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies", + "rel_date": "2021-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.23.441195", + "rel_abs": "Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD {beta}-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Claudia A Jette", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Alexander A Cohen", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Priyanthi N. P. Gnanapragasam", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Frauke Muecksch", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Yu E. Lee", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Kathryn E. Huey-Tubman", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Fabian Schmidt", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Paul D. Bieniasz", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Michel C. Nussenzweig", + "author_inst": "Rockefeller" + }, + { + "author_name": "Anthony P West", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jennifer R. Keeffe", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Pamela Bjorkman", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Christopher O Barnes", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.24.440952", "rel_title": "Household transmission of SARS-CoV-2 from humans to dogs in Washington and Idaho: burden and risk factors", @@ -775205,57 +774059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.24.21256029", - "rel_title": "6-Month Follow Up of 8679 Hospitalized COVID-19 Patients in Germany: A Nationwide Cohort Study", - "rel_date": "2021-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21256029", - "rel_abs": "BackgroundData on long-term outcomes of hospitalized COVID-19 patients are scarce.\n\nObjectiveTo provide a detailed account of hospitalized COVID-19 patients until 180 days after their initial hospitalization.\n\nDesignNationwide cohort study using claims data from the German Local Health Care Funds, the health insurer of one-third of the German population.\n\nSettingGermany.\n\nPatientsAdult patients hospitalized in Germany between Feb 1 and April 30, 2020 with PCR-confirmed COVID-19 and a related principal diagnosis.\n\nMeasurementsPatient characteristics and ventilation status, in-hospital, 30-, 90- and 180- day mortality measured from admission, and 180-day readmission measured from discharge. Multivariable logistic regression model of independent risk factors for 180-day mortality.\n\nResultsOf 8679 patients (median age, 72 years), 2161 (24.9%) died during the index hospitalization. 30-day mortality was 23.9% (2073/8679), 90-day mortality 27.9% (2425/8679), and 180-day mortality 29.6% (2566/8679). The latter was 52.3% (1472/2817) for patients aged [≥] 80 years, and 53.0% for patients who had been ventilated invasively (853/1608). Risk factors for 180-day mortality included coagulopathy, BMI [≥] 40, and age. Female sex was a protective factor. Of 6235 patients discharged alive, 1668 patients were readmitted a total of 2551 times within 180 days, resulting in an overall readmission rate of 26.8%.\n\nLimitationsWe could not stratify patients by ICU treatment as it is not coded separately. Furthermore, we cannot exclude residual confounding in our analysis of risk factors nor determine causality between risk factors and long-term mortality given the observational nature of this study.\n\nConclusionThis nationwide cohort study of hospitalized COVID-19 patients in Germany found considerable long-term mortality and readmission rates, especially among patients with coagulopathy. Close follow-up after hospital discharge may improve long-term outcome.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christian Guenster", - "author_inst": "Wissenschaftliches Institut der AOK" - }, - { - "author_name": "Reinhard Busse", - "author_inst": "Department of Health Care Management, Technische Universitaet Berlin, Berlin, Germany" - }, - { - "author_name": "Melissa Spoden", - "author_inst": "Research Institute of the Local Health Care Funds, Berlin, Germany/ Federal Association of the Local Health Care Funds, Berlin, Germany" - }, - { - "author_name": "Tanja Rombey", - "author_inst": "Department of Health Care Management, Technische Universitaet Berlin, Berlin, Germany" - }, - { - "author_name": "Gerhard Schillinger", - "author_inst": "Research Institute of the Local Health Care Funds, Berlin, Germany/ Federal Association of the Local Health Care Funds, Berlin, Germany" - }, - { - "author_name": "Wolfgang Hoffmann", - "author_inst": "Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany" - }, - { - "author_name": "Steffen Weber-Carstens", - "author_inst": "Department of Anesthesiology and Operative Intensive Care Medicine (CCM, CVK), Charite - Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Andreas Schuppert", - "author_inst": "Institute for Computational Biomedicine II, JRC for Computational Biomedicine / AICES RWTH Aachen University, Aachen, Germany" - }, - { - "author_name": "Christian Karagiannidis", - "author_inst": "ARDS and ECMO centre Cologne-Merheim, University Witten/ Herdecke" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.04.25.441271", "rel_title": "Production of a Highly Immunogenic Antigen from SARS-CoV-2 by Covalent Coupling of the Receptor Binding Domain of Spike Protein to a Multimeric Carrier", @@ -776008,6 +774811,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.25.21256085", + "rel_title": "Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21256085", + "rel_abs": "The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has killed millions of people worldwide. The current crisis has created an unprecedented demand for rapid test of SARS-CoV-2 infection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. However, the sensitivity and specificity of RT-LAMP were generally regarded as inferior when compared with the gold standard RT-qPCR. To address this issue, we combined bioinformatic and experimental analyses to improve the assay performance for COVID-19 diagnosis. First, we developed an improved algorithm to design LAMP primers targeting the nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV-2. Next, we rigorously validated these new assays for their efficacy and specificity. Further, we demonstrated that multiplexed RT-LAMP assays could directly detect as low as a few copies of SARS-CoV-2 RNA in saliva, without the need of RNA isolation. Importantly, further testing using saliva samples from COVID-19 patients indicated that the new RT-LAMP assays were in total agreement in sensitivity and specificity with standard RT-qPCR. In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xin Huang", + "author_inst": "University of Illinois at Chicago" + }, + { + "author_name": "Gongyu Tang", + "author_inst": "University of Illinois at Chicago" + }, + { + "author_name": "Nahed Ismail", + "author_inst": "University of Illinois at Chicago" + }, + { + "author_name": "Xiaowei Wang", + "author_inst": "University of Illinois at Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.23.21256009", "rel_title": "Paradox of Predictors in Critically ill COVID-19 Patients: Outcome of a COVID-dedicated Intensive Care Unit", @@ -776851,53 +775685,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.21255844", - "rel_title": "COVID-19 Vaccine Hesitancy among the Adult Population in Bangladesh: A Nationally Representative Cross-sectional Survey", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255844", - "rel_abs": "IntroductionThe study related to the COVID-19 vaccine hesitancy is scanty in the context of Bangladesh, despite the growing necessity of understanding the mass peoples vaccination-related behavior. Thus, the present study was conducted to assess the prevalence of the COVID-19 vaccine hesitancy and its associated factors in Bangladesh to fill the knowledge gap.\n\nMethodologyThis study adopted a cross-sectional study design to collect data from 1497 respondents using online (Google forms) and face-to-face interviews. We employed descriptive statistics and multiple hierarchical linear regression analysis.\n\nFindingsThe prevalence of vaccine hesitancy was 41.1%. Men had less hesitancy ({beta} = -0.046, p = 0.030) than women. The Muslims ({beta} = 0.057, p = 0.009) and the respondents living in the city corporation areas ({beta} = 0.132, p <0.001) had more hesitancy. There was significant variation in vaccine hesitancy by administrative divisions (geographic regions). The vaccine hesitancy tended to decrease with increasing knowledge about the vaccine ({beta} = -0.072, p=0.001) and the vaccination process ({beta}= -0.058, p = 0.018). On the other hand, hesitancy increased with the increased negative attitudes towards vaccine ({beta} = 0.291, p <0.001) and conspiracy beliefs towards the COVID-19 vaccine ({beta} = 0.105, p=0.004). The perceived severity of the COVID-19 ({beta} = -0.079, p=0.002) and perceived benefits of COVID-19 vaccination ({beta} = -0.180, p=0.001) were negatively associated with hesitancy, while perceived barriers ({beta} = 0.180, p <0.001) were positively associated. The participants were more hesitant to accept the vaccine from a specific manufacturer.\n\nConclusionThis study emphasizes that negative attitudes and conspiracies towards the COVID-19 vaccine should be reduced through effective communications and contracting with additional vaccine manufacturers should be prioritized. The barriers like online registration for receiving the COVID-19 vaccination need to be removed, and initiatives like text message service using the mobile phone operator can be introduced.\n\nHighlightsO_LIAbout 41% of the respondents had had hesitancy to accept the COVID-19 vaccine.\nC_LIO_LIThe hesitancy increased with negative attitudes about vaccines and conspiracy beliefs.\nC_LIO_LIPerceived barriers to receive the vaccine were increasing vaccine hesitancy.\nC_LIO_LIPerceived severity of the COVID-19 decreased the vaccine hesitancy.\nC_LIO_LIPerceived benefits of receiving the COVID-19 vaccine decreased the vaccine hesitancy.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mohammad Bellal Hossain", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Md. Zakiul Alam", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Md. Syful Islam", - "author_inst": "Jatiya Kabi Kazi Nazrul Islam University, Mymensingh" - }, - { - "author_name": "Shafayat Sultan", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Md. Mahir Faysal", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Sharmin Rima", - "author_inst": "3Ovibashi Karmi Unnayan Program (OKUP), Dhaka, Bangladesh" - }, - { - "author_name": "Md. Anwer Hossain", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Abdullah Al Mamun", - "author_inst": "University of Dhaka" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.23.21256007", "rel_title": "Effects of the COVID-19 Pandemic on Park Use in U.S. Cities", @@ -777442,6 +776229,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.04.21.21255878", + "rel_title": "Addressing racial/ethnic disparities in the COVID-19 vaccination campaign", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255878", + "rel_abs": "BackgroundAs of April 19, all adults aged 16 years and older are eligible for COVID-19 vaccination. Unequal vaccination rates across racial/ethnic groups may compound existing disparities in cases, hospitalizations, and deaths among Black, Indigenous, and Hispanic communities.\n\nMethodsFrom state websites, we extracted shares of people receiving [≥]1 vaccine dose, stratified by age and separately by race/ethnicity, through March 31, 2021. Combining these data with demographic data from the American Community Survey, we estimated relative uptake rates by race/ethnicity within each state as the observed share of vaccinations for a racial/ethnic group, divided by the expected share if uptake across racial/ethnic groups within each age group were proportional to population size, an approach that allowed us to control for historical age-based eligibility. We modeled vaccination scale-up within each census tract in a state under three scenarios: 1) a scenario in which unequal uptake rates persist, 2) a scenario in which uptake rates are equalized across race/ethnicity groups over six weeks, and 3) a scenario in which uptake is equalized and states employ place-based allocation strategies that prioritizes disadvantaged census tracts.\n\nResultsWhite adults received a disproportionate share of vaccinations compared to Black and Hispanic adults through March 31, 2021. Across states, relative uptake rates, adjusted for eligible population size, were a median 1.3 (IQR, 1.2-1.4) times higher for White compared to Black adults, and a median 1.4 (IQR, 1.2-1.8) times higher for White compared to Hispanic adults. Projecting vaccination coverage under persistence of current disparities in uptake, we found that Black and Hispanic populations would reach 75% coverage among adults almost one month later than White populations. In alternative scenarios, we found that interventions to equalize uptake rates across racial/ethnic groups could narrow but not erase these gaps, and that geographic targeting of vaccine doses to disadvantaged communities may be needed to produce a more equitable convergence of coverage by July.\n\nDiscussionInterventions are urgently needed to eliminate disparities in COVID-19 vaccination rates. Eliminating access barriers and increasing vaccine confidence among marginalized populations can narrow gaps in coverage. Combining these interventions with place-based allocation strategies can accelerate vaccination in disadvantaged communities, who have borne a disproportionate burden from COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marissa B Reitsma", + "author_inst": "Stanford University" + }, + { + "author_name": "Jeremy D Goldhaber-Fiebert", + "author_inst": "Stanford University" + }, + { + "author_name": "Joshua A Salomon", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.04.22.21255911", "rel_title": "The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom", @@ -778513,101 +777327,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.22.440848", - "rel_title": "Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.22.440848", - "rel_abs": "SARS-CoV-2 can cause a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of the host factors mediating viral infection or restriction is critical to elucidate SARS-CoV-2 host-pathogen interactions and the progression of COVID-19. To this end, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. These screens uncovered proviral and antiviral host factors across highly interconnected host pathways, including components implicated in clathrin transport, inflammatory signaling, cell cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high-molecular weight glycoproteins, as a prominent viral restriction network. We demonstrate that multiple membrane-anchored mucins are critical inhibitors of SARS-CoV-2 entry and are upregulated in response to viral infection. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and suggests interactions between SARS-CoV-2 and airway mucins of COVID-19 patients as a host defense mechanism.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Scott B Biering", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Sylvia A Sarnik", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Eleanor Wang", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "James R Zengel", - "author_inst": "Stanford University" - }, - { - "author_name": "Varun Sathyan", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Xammy Nguyenla", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Erik Van Dis", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Carmelle Catamura", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Livia H Yamashiro", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Adam Begeman", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Jessica C Stark", - "author_inst": "Stanford University" - }, - { - "author_name": "D. Judy Shon", - "author_inst": "Stanford University" - }, - { - "author_name": "Douglas M Fox", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Andreas S Puschnik", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Carolyn R Bertozzi", - "author_inst": "Stanford University" - }, - { - "author_name": "Jan E Carette", - "author_inst": "Stanford University" - }, - { - "author_name": "Sarah A Stanley", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Eva Harris", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Silvana Konermann", - "author_inst": "Stanford University" - }, - { - "author_name": "Patrick D Hsu", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.04.22.441041", "rel_title": "Prefusion conformation of SARS-CoV-2 receptor-binding domain favors interactions with human receptor ACE2", @@ -779536,6 +778255,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.04.21.21255832", + "rel_title": "Shut Down Schools, Knock Down the Virus? Causal Inference on the School Closures' Effect on the Spread of COVID-19", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255832", + "rel_abs": "As COVID-19 spread in 2020, most countries shut down schools in the hopes of slowing the pandemic. Yet, studies have not reached a consensus about the effectiveness of these policies partly because they lack rigorous causal inference. Our study aims to estimate the causal effects of school closures on the number of confirmed cases. To do so, we apply matching methods to municipal-level data in Japan. We do not find that school closures caused a reduction in the spread of the coronavirus. Our results suggest that policies on school closures should be reexamined given the potential negative consequences for children and parents.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kentaro Fukumoto", + "author_inst": "Gakushuin University" + }, + { + "author_name": "Charles T. McClean", + "author_inst": "Harvard University" + }, + { + "author_name": "Kuninori Nakagawa", + "author_inst": "Shizuoka University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.04.20.21255797", "rel_title": "Diagnostic accuracy of a novel SARS-CoV-2 antigen-detecting rapid diagnostic test from standardized self-collected anterior nasal swabs", @@ -780483,69 +779229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.14.21255431", - "rel_title": "Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255431", - "rel_abs": "BackgroundDistribution of mRNA-based SARS-CoV-2 vaccines to healthcare personnel (HCP) in the United States began in December 2020, with efficacy > 90%. However, breakthrough infections in fully vaccinated individuals have been reported. Meanwhile, multiple SARS-CoV-2 variants of concern have emerged worldwide, including the B.1.427/B.1.429 variant first described in California. Little is known about the real-world effectiveness of the mRNA-based SARS-CoV-2 vaccines against novel variants including B.1.427/B.1.429.\n\nMethodsIn this quality improvement project, post-vaccine SARS-CoV-2 cases (PVSCs) were defined as individuals with positive SARS-CoV-2 nucleic acid amplification test (NAAT) after receiving at least one dose of a SARS-CoV-2 vaccine. Chart extraction of demographic and clinical information was performed, and available specimens meeting cycle threshold value criteria were tested for L452R, N501Y and E484K mutations by RT-PCR.\n\nResultsFrom December 2020 to March 2021, 189 PVSCs were identified out of 22,729 healthcare personnel who received at least one dose of an mRNA-based SARS-CoV-2 vaccine. Of these, 114 (60.3%) occurred within 14 days of first vaccine dose (early post-vaccination), 49 (25.9%) within 14 days of the second vaccine dose (partially vaccinated), and 26 (13.8%) >14 days after the second dose (fully vaccinated). Of 115 samples available for mutation testing, 42 were positive for L452R alone, presumptive of B.1.427/B.1.429; three had N501Y mutation alone and none were found with E484K mutation. Though on univariate analysis partially- and fully-vaccinated PVSCs were more likely than early post-vaccination PVSCs to be infected with presumptive B.1.427/B.1.429, when adjusted for community prevalence of B.1.427/B.1.429 at the time of infection, partially- and fully-vaccinated PVSC did not have statistically significantly elevated risk ratios for infection with this variant (RR 1.40, 95% CI 0.81-2.43 and RR 1.13, 95% CI 0.59-2.16, respectively).\n\nConclusionsThe great majority of PVSCs occurred prior to the expected onset of full, vaccine-derived immunity. Although the B.1.427/B.1.429 variant did not represent a significantly higher proportion of PVSCs than expected, numbers were small and there was a trend towards higher representation in the partially- and fully-vaccinated subset. Continued infection control measures in the workplace and in the community including social distancing and masking, particularly in the early days post-vaccination, as well as continued variant surveillance in PVSCs, is imperative in order to anticipate and control future surges of infection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Karen Blake Jacobson", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Benjamin Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Maria E. Montez Rath", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Hannah Wang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Jacob A. Miller", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Mehdi Skhiri", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "John Shepard", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Roshni Mathew", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Grace Lee", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Bryan Bohman", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Julie Parsonnet", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marisa Holubar", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.15.21252192", "rel_title": "Previous COVID-19 infection but not Long-COVID is associated with increased adverse events following BNT162b2/Pfizer vaccination", @@ -781282,6 +779965,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.22.21255133", + "rel_title": "Verification of the Abbott Alinity m Resp-4-Plex Assay for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255133", + "rel_abs": "COVID-19 symptomology may overlap with other circulating respiratory viruses that may also cause severe disease and for which there are specific and potentially life-saving treatments. The Abbott Alinity m Resp-4-Plex assay is a multiplex PCR assay that simultaneously detects and differentiates infection with SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus (RSV). We characterized its accuracy, precision, and analytical sensitivity. All were found to be robust for measures examined. In the context of sample-to-answer, near random access automation on the Alinity m platform, we believe that the Resp-4-Plex assay offers significant utility in addressing the current needs of the SARS-CoV-2 pandemic and future needs during anticipated endemic circulation of SARS-CoV-2 with other respiratory viruses.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Annie Cheng", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Stefan Riedel", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "Ramy Arnaout", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "James E Kirby", + "author_inst": "Beth Israel Deaconess Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21254079", "rel_title": "Genetic mismatch explains sizable variation of COVID-19 vaccine efficacy in clinical trials", @@ -782452,33 +781166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.04.17.21255665", - "rel_title": "Characterization of the Second Wave of COVID-19 in India", - "rel_date": "2021-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255665", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe second wave of COVID-19, which began around 11 February 2021, has hit India very hard with the daily cases reaching nearly triple the first peak value as on April 19, 2021. The epidemic evolution in India is quite complex due to regional inhomogeneities and the spread of several coronavirus mutants. In this paper, we characterize the virus spread in the ongoing second wave in India and its states until April 19, 2021, and also study the dynamical evolution of the epidemic from the beginning of the outbreak. Variations in the effective reproduction number (Rt) are taken as quantifiable measures of the virus transmissibility. Rt value for every state, including those with large rural populations, has value greater than the self-sustaining threshold of 1. An exponential fit on recent data also shows that the infection rate is much higher than the first wave. Subsequently, characteristics of the COVID-19 spread are analyzed regionwise, by estimating test positivity rates (TPRs) and case fatality rates (CFRs). Very high TPR values for several states present an alarming situation. CFR values are lower than those in the first wave but recently showing signs of increase as healthcare systems become over-stretched with the surge in infections. Preliminary estimates with a classical epidemiological model suggest that the peak for the second wave could occur around mid-May 2021 with daily count exceeding 0.4 million. The study strongly suggests that an effective administrative intervention is needed to arrest the rapid growth of the epidemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rajesh Ranjan", - "author_inst": "I.I.T. Kanpur" - }, - { - "author_name": "Aryan Sharma", - "author_inst": "Indian Institute of Technology, Kanpur" - }, - { - "author_name": "Mahendra K. Verma", - "author_inst": "I. I. T. Kanpur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.20.440654", "rel_title": "Rapid and Efficient Inactivation of SARS-CoV-2 from Surfaces using UVC Light Emitting Diode Device", @@ -783151,6 +781838,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255442", + "rel_title": "Gender differences in the determinants of willingness to get the COVID-19 vaccine among the working-age population in Japan", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255442", + "rel_abs": "Many factors are related to vaccination intentions. However, gender differences in the determinants of intention to get the coronavirus disease 2019 (COVID-19) vaccine have not been fully investigated. This study examined gender differences in the determinants of willingness to get the COVID-19 vaccine among the working-age population in Japan. We conducted a cross-sectional study of Japanese citizens aged 20-65 years using an online self-administered questionnaire in December 2020. Logistic regression analysis was performed. Among 27,036 participants (13,814 men and 13,222 women), the percentage who were willing to get the COVID-19 vaccine was lower among women than among men (33.0% vs. 41.8%). Age and education level showed a gender gap regarding the association with willingness to get the COVID-19 vaccine: men who were older or had a higher level of education were more willing to get the vaccine, whereas women aged 30-49 years and those with a higher level of education showed a relatively low willingness to get the vaccine. For both men and women, marriage, higher annual household income, underlying disease, current smoking, vaccination for influenza during the current season, and fear of COVID-19 transmission were linked to a higher likelihood of being willing to get the COVID-19 vaccine. These findings give important insight into identifying target groups in need of intervention regarding COVID-19 vaccination, especially among women. Providing education about COVID-19 and influenza vaccination in the workplace may be an effective strategy to increase COVID-19 vaccine uptake.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Tomohiro Ishimaru", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Makoto Okawara", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Hajime Ando", + "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" + }, + { + "author_name": "Ayako Hino", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohisa Nagata", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.14.21255452", "rel_title": "A Real World Evaluation of the safety and immunogenicity of the Covishield vaccine, ChAdOx1 nCoV- 19 Corona Virus Vaccine (Recombinant) in Health Care Workers (HCW) in National Capital Region (NCR) of India: A preliminary report", @@ -784158,53 +782896,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.04.14.21255479", - "rel_title": "Unlocking low- and middle-income countries to detect SARS-CoV-2", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255479", - "rel_abs": "Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local development of molecular testing and accentuated by the international supply shortage. Here, we describe a molecular toolkit that can be readily produced and deployed in LMICs using minimal laboratory equipment. Our results show that mid-scale production of enzymes and nucleic acids can supply thousand tests per production batch. One-step RT-PCR was optimized for two SARS-CoV-2 loci and coupled to CRISPR/Cas12a detection. The clinical validation indicated a sensitivity near 100% for mid and high viral load samples (Cq [≤] 33). The specificity was around 100% regardless of viral load. The toolkit was used with the mobile laboratory BentoLab, potentially unlocking LMICs to implement detection services in unattended regions. Altogether, we provide detailed methods and performance evidence of molecular tools aiming to aid LMICs to deploy molecular testing for current or future pathogenic outbreaks.\n\nOne Sentence SummaryWe describe a molecular toolkit for the detection of SARS-CoV-2 that is compatible with available facilities in low- and middle-income countries (LMICs).", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Roberto Alcantara", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Katherin Penaranda", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Gabriel Mendoza", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Jose A. Nakamoto", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Johanna Martins-Luna", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Juana Del Valle", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Vanessa Adaui", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - }, - { - "author_name": "Pohl Milon", - "author_inst": "Universidad Peruana de Ciencias Aplicadas (UPC)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.13.21255345", "rel_title": "Self-collected oral, nasal and saliva samples yield sensitivity comparable to professional-collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis", @@ -784929,6 +783620,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.14.21255500", + "rel_title": "Modelling COVID-19 evolution in Italy with an augmented SIRD model using open data", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255500", + "rel_abs": "We propose an augmented version of the traditional SIRD epidemic model and we estimate its parameters using the SaRs-Cov-2 Italian open-data. The models parameters are estimated partly using numerical optimization and partly with ABC. Our estimation procedure provides a good fit to real data.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vincenzo Nardelli", + "author_inst": "University of Milan-Bicocca" + }, + { + "author_name": "Giuseppe Arbia", + "author_inst": "Catholic University of Sacred Heart" + }, + { + "author_name": "Andrea Palladino", + "author_inst": "Apheris AI" + }, + { + "author_name": "Luigi Giuseppe Atzeni", + "author_inst": "Boraso" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.16.21255649", "rel_title": "COVID-19 Vaccine Prioritisation in Japan and South Korea", @@ -785912,205 +784634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.19.440481", - "rel_title": "Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants", - "rel_date": "2021-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.19.440481", - "rel_abs": "Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus displayed remarkable efficacy against authentic B.1.351 virus. Each of these 3 mAbs in combination with one neutralizing Ab recognizing non-competing epitope exhibited synergistic effect against authentic SARS-CoV-2 virus. Surprisingly, structural analysis revealed that 58G6 and 13G9, encoded by the IGHV1-58 and the IGKV3-20 germline genes, both recognized the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly bound to another region S450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrated prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. These 2 ultrapotent neutralizing Abs can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Tingting Li", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "XiaoJian Han", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Chenjian Gu", - "author_inst": "Fudan University" - }, - { - "author_name": "Hangtian Guo", - "author_inst": "Shanghai Tech University" - }, - { - "author_name": "Huajun Zhang", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Yingming Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Chao Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Fangjiang Liu", - "author_inst": "Shanghai Tech University" - }, - { - "author_name": "Feiyang Luo", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yanan Zhang", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Jie Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Wang wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Shenglong Li", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yanan Hao", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Meiying Shen", - "author_inst": "Harbin Medical University Cancer Hospital" - }, - { - "author_name": "Jingjing Huang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yingyi Long", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Shuyi Song", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ruixin Wu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Song Mu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Qian Chen", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Fengxia Gao", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Jianwei Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Shunhua Long", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Luo Li", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Yang Wu", - "author_inst": "Fudan University" - }, - { - "author_name": "Yan Gao", - "author_inst": "Shanghai Tech University" - }, - { - "author_name": "Wei Xu", - "author_inst": "Fudan University" - }, - { - "author_name": "Xia Cai", - "author_inst": "Fudan University" - }, - { - "author_name": "Di Qu", - "author_inst": "Fudan University" - }, - { - "author_name": "Zherui Zhang", - "author_inst": "Chinese Academy of Sciences," - }, - { - "author_name": "Hongqing Zhang", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Na Li", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Qingzhu Gao", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "guiji Zhang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Changlong He", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Wei Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Xiaoyun Ji", - "author_inst": "Nanjing University" - }, - { - "author_name": "Ni Tang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Zhenghong Yuan", - "author_inst": "Fudan University" - }, - { - "author_name": "Youhua Xie", - "author_inst": "Fudan University" - }, - { - "author_name": "Bo Zhang", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Haitao Yang", - "author_inst": "ShanghaiTech University" - }, - { - "author_name": "Ailong Huang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Aishun Jin", - "author_inst": "Chongqing Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.20.439992", "rel_title": "Drug repurposing to face Covid-19: Celastrol, a potential leading drug capable of inhibiting SARS-CoV-2 replication and induced inflammation", @@ -786923,6 +785446,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.20.21255059", + "rel_title": "Infants have lower RT-PCR cycle threshold for SARS-CoV-2 in comparison with older children and adults", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255059", + "rel_abs": "BackgroundThe viral dynamics and the role of children in the spread of SARS-CoV-2 are not completely understood. Our aim was to evaluate how RT-PCR Ct values among children with confirmed SARS-CoV-2 compared with that of adult subjects.\n\nMethodsPatients (aged from 2 months to [≤]18 years, and adults) with signs and symptoms of acute SARS-CoV-2 infection for less than 7 days, were prospectively enrolled in the study from May to November 2020. All participants performed RT-PCR assay for SARS-CoV-2 detection; Ct values of ORF1ab, N, and S gene-targets, and the average of all the three probes were used as surrogates of viral load.\n\nResultsOf the total of 376 participants with confirmed SARS-CoV-2 infection there were 21 infants, 62 children and 293 adults. The RT-PCR Ct values of children under 18 were not significantly different from that of adults, as observed by the analyzed probes (namely ORF1ab, N, and S), and by the mean of all 3 gene-targets. However, infants had significantly lower Ct values compared to children and adults (P = 0.044).\n\nDiscussionCt values for children were not significantly different than that of adults with positive SARS-CoV-2. Interestingly, infants had even lower Ct values when compared to older children and adults. Although viral load is not the only determinant of transmission, infants may play a significant role in the spread of SARS-CoV-2 in the community, especially if or when this population returns to regular daycare activities.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Marcia Polese-Bonatto", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Fernanda Hammes-Varela", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Gabriela Luchiari Tumioto Gianinni", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Thais Raupp Azevedo", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Luciane Beatriz Kern", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Caroline Nespolo de David", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Walquiria Aparecida Ferreira de Almeida", + "author_inst": "Brazilian Ministry of Health" + }, + { + "author_name": "Victor Bertollo Gomes Porto", + "author_inst": "Brazilian Ministry of Health" + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Hospital Moinhos de Vento" + }, + { + "author_name": "Renato T. Stein", + "author_inst": "Hospital Moinhos de Vento" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.20.440593", "rel_title": "Antibody Conversion rates to SARS-CoV-2 in Saliva from Children Attending Summer Schools in Barcelona, Spain", @@ -788198,85 +786788,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.04.18.440302", - "rel_title": "SARS-CoV-2 receptor binding domain fusion protein efficiently neutralizes virus infection", - "rel_date": "2021-04-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.18.440302", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, causing health and economic problems. Currently, as dangerous mutations emerge there is an increased demand for specific treatments for SARS-CoV-2 infected patients. The spike glycoprotein on the virus membrane binds to the angiotensin converting enzyme 2 (ACE2) receptor on host cells through its receptor binding domain (RBD) to mediate virus entry. Thus, blocking this interaction may inhibit viral entry and consequently stop infection. Here, we generated fusion proteins composed of the extracellular portions of ACE2 and RBD fused to the Fc portion of human IgG1 (ACE2-Ig and RBD-Ig, respectively). We demonstrate that ACE2-Ig is enzymatically active and that it can be recognized by the SARS-CoV-2 RBD, independently of its enzymatic activity. We further show that RBD-Ig efficiently inhibits in vitro and in vivo SARS-CoV-2 infection, better than ACE2-Ig. Mechanistically we show that anti-spike antibodies generation, ACE2 enzymatic activity and ACE2 surface expression were not affected by RBD-Ig. Finally, we show that RBD-Ig is more efficient than ACE2-Ig at neutralizing high virus concentration infection. We thus propose that RBD-Ig physically blocks virus infection by binding to ACE2 and that RBD-Ig should be used for the treatment of SARS-CoV-2-infected patients.\n\nAuthor SummarySARS-CoV-2 infection caused serious socio-economic and health problems around the globe. As dangerous mutations emerge, there is an increased demand for specific treatments for SARS-CoV-2 infected patients. SARS-CoV-2 infection starts via binding of SARS-CoV-2 spike protein receptor binding domain (RBD) to its receptor, ACE2, on host cells. To intercept this binding, we generated Ig-fusion proteins. ACE2-Ig was generated to possibly block RBD by binding to it and RBD-Ig to block ACE2. We indeed showed that the fusion proteins bind to their respective target. We found that it is more efficient to inhibit SARS-CoV-2 infection by blocking ACE2 receptor with RBD-Ig. We also showed that RBD-Ig does not interfere with ACE2 activity or surface expression. Importantly, as our treatment does not target the virus directly, it may be efficient against any emerging variant. We propose here that RBD-Ig physically blocks virus infection by binding to ACE2 and thus it may be used for the treatment of SARS-CoV-2-infected patients.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Abigael Eva Chaouat", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Hagit Achdout", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Inbal Kol", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Orit Berhani", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Gil Roi", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Einat B Vitner", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Sharon Melamed", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Boaz Politi", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Eran Zahavi", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Ilija Brizic", - "author_inst": "University of Rijeka" - }, - { - "author_name": "Tihana Lenac Rovis", - "author_inst": "University of Rijeka" - }, - { - "author_name": "Or B. Alfi", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Dana Wolf", - "author_inst": "Hebrew University Hadassah Medical School" - }, - { - "author_name": "Stipan Jonjic", - "author_inst": "University of Rijeka" - }, - { - "author_name": "Tomer Israely", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Ofer Mandelboim", - "author_inst": "The Hebrew University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.15.440089", "rel_title": "Substantial Differences in SARS-CoV-2 Antibody Responses Elicited by Natural Infection and mRNA Vaccination", @@ -788953,6 +787464,73 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.04.14.21255104", + "rel_title": "Mortality reduction in ICU-admitted COVID-19 patients in Suriname after treatment with convalescent plasma acquired via gravity filtration", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255104", + "rel_abs": "BackgroundAlthough convalescent plasma (CP) treatment is a potential therapeutic option for patients with COVID-19, there is a paucity of data from studies in low-resource settings. The efficacy and safety of CP therapy in intensive care unit (ICU) patients with COVID-19 in Suriname was evaluated. A novel gravity-based filtration method was used to obtain CP. The design was an open-label, multi-centre, non-randomized prospective clinical trial performed in two hospitals in Suriname, from June 2020, to December 2020. A pre-planned interim analysis is reported in 78 PCR-confirmed COVID-19 patients admitted to the ICU with severe or life-threatening symptoms. CP in combination with standard treatment (n = 28) was compared to standard treatment alone (control) (n = 50), stratified by disease severity. The primary endpoint was 28-day ICU mortality. Secondary (exploratory) endpoints were changes two days after treatment initiation in pulmonary oxygen exchange capacity (PF ratio) and chest x-ray (CXR) score.\n\nFindingsThe median age of patients was 52 years with 43 [55.1%] being male. Twenty-eight day mortality occurred in 18% (5/28) of the CP group vs 36% (18/50) of the control group. Survival probability was significantly higher in the CP group compared to the control group with standard care (P=0.027). When stratifying into disease severity, the survival probability was the lowest for the control group with life-threatening disease (P=0.0051). CP treatment of severe COVID-19 resulted in a higher probability of survival, with a hazard ratio (HR) of 0.22 (95% CI, 0.074-0.067), correcting for age, the presence of diabetes and COVID-19 severity. Age significantly increased the mortality risk (HR, 1.08 [95%CI, 1.022-1.14]; P = 0.006). In the severe group, CP resulted in an improved CXR score (P =0.0013) and increase in PF ratio (P = 0.011) as compared to standard therapy. The gravity-based plasmapheresis method used for CP production was well-tolerated and no adverse events were observed in the donors.\n\nInterpretationAmong patients with severe or life-threatening COVID-19, CP therapy in combination with standard treatment resulted in 78% reduction of 28-day ICU mortality (HR = 0.22) compared to standard treatment alone. Both CXR-score and PF ratio changes represent indicators of treatment effect of CP after two days and can easily be implemented in low-resource settings. The novel CP production method was effective and represents a practical solution for low- and middle income countries (LMICs) to produce CP locally. Although interpretation is limited by the non-randomized design of the trial, these results offer a potential route for broader implementation of CP treatment in LMICs.\n\nFundingThis study was funded by the Academic Hospital Paramaribo, without additional third-party funding.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Rosita Bihariesingh", + "author_inst": "Academic Hospital Paramaribo" + }, + { + "author_name": "Rakesh Bansie", + "author_inst": "Department of Internal Medicine, Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Janeri Froberg", + "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" + }, + { + "author_name": "Navin Ramdhani", + "author_inst": "Department of Anesthesiology , Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Rishi Mangroo", + "author_inst": "Department of Internal Medicine, Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Debra Bustamente", + "author_inst": "Department of Anesthesiology , Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Ernesto Diaz", + "author_inst": "Department of Intensive Care, Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Ishwardath Thakoer", + "author_inst": "Department of Radiology, Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Stephen Vreden", + "author_inst": "Department of Internal Medicine, Academic Hospital Paramaribo, Suriname" + }, + { + "author_name": "Zaheeb Choudhry", + "author_inst": "Department of Nephrology and Therapeutic Apheresis, Horacia Oduber Hospital, Aruba." + }, + { + "author_name": "Wouter Jansen Klomp", + "author_inst": "Department of Cardiology. Deventer Hospital, Deventer, The Netherlands" + }, + { + "author_name": "Dimitri Diavatopoulos", + "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" + }, + { + "author_name": "Arno Nierich", + "author_inst": "Department of Anesthesiology and Intensive Care, Isala, Zwolle, The Netherlands" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.04.13.21255380", "rel_title": "Understanding the impact of the Covid-19 pandemic on delivery of rehabilitation in specialist palliative care services: An analysis of the CovPall-Rehab survey data.", @@ -790032,49 +788610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.16.21255390", - "rel_title": "Eating Disorders Spectrum during COVID Pandemic: a systematic review", - "rel_date": "2021-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255390", - "rel_abs": "BackgroundSeveral data suggest that COVID-19 pandemic might exacerbate or trigger Eating Disorders (EDs). The aim of this paper was to summarize present literature on COVID pandemic and EDs.\n\nMethodsLiterature search, study selection, methods, and quality evaluation were performed following PRISMA Guidelines.\n\nResultsThe systematic search permitted the identification of 91 studies; 21 papers were eligible and included in the review. Nine papers (42.9%) evaluated the effect of pandemic and associated protective and risk factors in EDs patients, ten (47.6%) explored the prevalence of disturbed eating behaviours and risk factors for exacerbating EDs in the general population, and the remaining two (9.5%) were qualitative studies describing the impact of lockdown and quarantine on EDs patients.\n\nTheir analysis revealed five main findings: 1) changes in physical activities routines were related to a worsening of preoccupation on weight/body shape; 2) food access limitation during pandemic represented a risk factors for both triggering and exacerbating EDs; 3) restriction in healthcare facilities contributed to increase anxiety levels and modifies treatment compliance; 4) social isolation was related to symptoms exacerbation in EDs patients who are home-confined with family members; 5) conflicts and difficulties in relationships with no way out were maintenance factors for EDs symptoms, especially in adolescents and young adults.\n\nConclusionCOVID-19 pandemic had a negative impact on EDs that might be triggered or worsened by the exceptional conditions deriving from COVID-19-related stress in predisposed subjects. Patients already affected by EDs experienced a worsening of their clinical conditions and related quality of life.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mario Miniati", - "author_inst": "university of Pisa" - }, - { - "author_name": "Francesca Marzetti", - "author_inst": "University of Pisa" - }, - { - "author_name": "Laura Palagini", - "author_inst": "university of Pisa" - }, - { - "author_name": "Donatella Marazziti", - "author_inst": "university of Pisa" - }, - { - "author_name": "Graziella Orru", - "author_inst": "university of Pisa" - }, - { - "author_name": "Ciro Conversano", - "author_inst": "university of Pisa" - }, - { - "author_name": "Angelo Gemignani", - "author_inst": "university of Pisa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.04.16.21255618", "rel_title": "Adverse effects of COVID-19 vaccination: machine learning and statistical approach to identify and classify incidences of morbidity and post-vaccination reactogenicity", @@ -790783,6 +789318,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.10.21255250", + "rel_title": "Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA", + "rel_date": "2021-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.10.21255250", + "rel_abs": "COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Aravind Natarajan", + "author_inst": "Stanford University" + }, + { + "author_name": "Alvin Han", + "author_inst": "Stanford University" + }, + { + "author_name": "Soumaya Zlitni", + "author_inst": "Stanford University" + }, + { + "author_name": "Erin F Brooks", + "author_inst": "Stanford University" + }, + { + "author_name": "Summer E Vance", + "author_inst": "Stanford University" + }, + { + "author_name": "Marlene Wolfe", + "author_inst": "Stanford University" + }, + { + "author_name": "Upinder Singh", + "author_inst": "Stanford University" + }, + { + "author_name": "Prasanna Jagannathan", + "author_inst": "Stanford University" + }, + { + "author_name": "Benjamin A Pinsky", + "author_inst": "Stanford University" + }, + { + "author_name": "Alexandria Boehm", + "author_inst": "Stanford University" + }, + { + "author_name": "Ami S Bhatt", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.11.21255278", "rel_title": "A Single Drop of Fingerstick Blood for Quantitative Antibody Response Evaluation After SARS-CoV-2 Vaccination", @@ -791738,49 +790332,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.16.21255256", - "rel_title": "Randomized, Comparative, Clinical Trial to Evaluate Efficacy and Safety of PNB001 in Moderate COVID-19 Patients", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255256", - "rel_abs": "ABSTARCTO_ST_ABSObjectiveC_ST_ABSTo evaluate the efficacy and safety of PNB001 a CCK-A agonist and CCK-B antagonist, a new chemical entity with anti-inflammatory and immune stimulation properties, along with Standard of Care (SOC) in patients with moderate COVID-19 infection.\n\nDesignMulti-center, randomized, parallel group, comparative, open label study.\n\nSettingTwo tertiary-care hospitals in India.\n\nParticipantsPatients with laboratory-confirmed SARS-CoV-2 infection as determined by polymerase chain reaction (PCR) within 2 days of randomization, having pneumonia with no signs of severe disease (severe disease means SpO2[≤]94% on room air), and any two of the following signs or symptoms suggestive of COVID-19: fever, cough, dyspnea, or hypoxia.\n\nInterventionsPatients were randomized 1:1 to receive PNB001 at an oral dose of 100 mg three times daily for 14 days with Standard of Care (PNB001+SOC) or only SOC.\n\nMain outcome measuresThe primary endpoints were mean change in the 8-point WHO Ordinal Scale score from baseline by Day 14 and mortality rate by Day 28. The key secondary endpoints were percentage of patients showing change in clinical status using the ordinal scale, improvement in inflammatory segments in X-ray chest, reduction of days of hospitalization, duration of supplemental oxygen use, days to negative PCR for COVID-19 and change in inflammation markers Interlukin-6 (IL6) and C-reactive protein (CRP) from baseline by Day 14.\n\nResultsA total of 40 (20 in PNB 001+SOC arm and 20 in SOC arm) patients were randomized and received treatment. The primary endpoint showed significant clinical improvement from baseline to Day 14 with PNB001+SOC (0.22 Vs 1.12; P=0.0421). One patient in PNB001+SOC arm and two patients in SOC arm died (1 Vs 2; HR: 2.0 [95%CI=0.18, 22.05]; P=0.5637) by Day 28. At the end of the treatment by Day 14, more patients achieved zero ordinal scale in PNB001+SOC arm (17 Vs 12; P=0.0766). In the PNB001+SOC arm, change in mean chest X-ray score showed significant improvement (2.05 Vs 1.16; P=0.0321), and more patients quickly showed complete improvement (10 Vs 7; HR: 1.48 [95%CI=0.64, 3.44]; P=0.4309). In the PNB001+SOC arm, patients needed shorter duration of hospitalization in days (9.45 Vs 9.80) and more patients attained earlier discharge from the hospital (19 Vs 15; P=0.0486) with respect to days. The mean duration of supplemental oxygen requirement in days was shorter (5.45 Vs 7.10) and complete withdrawal from supplemental oxygen was more frequent with PNB001+SOC compared to SOC by Day 14 (17 Vs 13; P=0.1441). All patients in both the arms had negative PCR by the end of the study (18 Vs 17; P=0.6265) by similar time (7.6 Vs 7.0). Exploratory analysis done for IL-6, CRP, Neutrophil-Lymphocyte-Ratio (NLR), Platelet-Lymphocyte-Ratio (PLR) and Erythrocyte Sedimentation Rate (ESR) showed statistically significant reduction by Day 14 demonstrating PNB001s anti-inflammatory and immunomodulatory properties. Lymphocyte and neutrophil counts also improved by Day 14. 11 adverse events (AE) in 8 patients were observed with PNB001+SOC compared to 13 AEs in 10 patients with SOC; none of the AEs in PNB001+SOC arm were related to PNB001. The most common AE were tachycardia and acute respiratory distress syndrome; there were isolated cases of hepatic enzyme elevation and hyperglycemia. Overall, safety profile was similar between PNB001+SOC and SOC arms.\n\nConclusionsPNB001 with standard of care showed significant clinical improvement in moderate COVID-19 patients when compared to standard of care and was well tolerated by moderate COVID-19 patients.\n\nTrial RegistrationCTRI/2020/10/028423", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Eric Lattman", - "author_inst": "PNB Vesper Life Science Pvt. Ltd." - }, - { - "author_name": "Pradnya Bhalerao", - "author_inst": "BJ Medical College and Sassoon General Hospital" - }, - { - "author_name": "ShashiBhushan BL", - "author_inst": "Victoria Hospital and Bangalore Medical College and Research Institute" - }, - { - "author_name": "Neeta Nargundkar", - "author_inst": "Biosphere Clinical Research Pvt. Ltd" - }, - { - "author_name": "Pornthip Lattmann", - "author_inst": "PNB Vesper Life Science Pvt. Ltd." - }, - { - "author_name": "Sadasivan Pillai K", - "author_inst": "PNB Vesper Life Science Pvt. Ltd." - }, - { - "author_name": "P.N. Balaram", - "author_inst": "PNB Vesper Life Science Pvt. Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.15.21253747", "rel_title": "Multiplex Fragment Analysis Identifies SARS-CoV-2 Variants", @@ -792617,6 +791168,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.16.440215", + "rel_title": "SARS-CoV-2 spike protein expressing epithelial cells promotes senescence associated secretory phenotype in endothelial cells and increased inflammatory response", + "rel_date": "2021-04-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.16.440215", + "rel_abs": "Increased mortality in COVID-19 often associates with thrombotic and microvascular complications. We have recently shown that SARS-CoV-2 spike protein promotes inflammatory cytokine IL-6/IL-6R induced trans-signaling responses which modulate MCP-1 expression in human endothelial cells. MCP-1 is secreted as a major component of the senescence associated secretory phenotype (SASP). Virus infected or Spike transfected human pulmonary epithelial cells (A549) exhibited an increase in senescence related marker proteins. TMNK; as a representative human endothelial cell line, when exposed to cell culture supernatant derived from A549 cells expressing SARS-CoV-2 spike protein (Spike CM) exhibited a senescence phenotype with enhanced p16, p21, and SA-{beta}-galactosidase expression. Inhibition of IL-6 trans-signaling by Tocilizumab, prior to exposure of supernatant to endothelial cells, inhibited p16 and p21 induction. Likewise, inhibition of receptor signaling by Zanabrutinib or Brd4 function by AZD5153 also led to limited induction of p16 expression. Senescence lead to an enhanced level of adhesion molecule, ICAM-1 and VCAM-1 in human endothelial cells, and TPH1 attachment by in vitro assay. Inhibition of senescence or SASP function prevented ICAM/VCAM expression and leukocyte attachment. We also observed an increase in oxidative stress in A549 spike transfected and endothelial cells exposed to Spike CM. ROS generation in TMNK was reduced after treatment with the IL-6 specific inhibitor Tociliximab, and with the specific inhibitors Zanabrutinib and AZD5153. Taken together, we identified that the exposure of human endothelial cells to cell culture supernatant derived from SARS-CoV-2 spike protein expression displayed cellular senescence markers leading to enhanced leukocyte adhesion with coronary blockade potential.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Keith Meyer", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Tapas Patra", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Vijay Mahantesh", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Ranjit Ray", + "author_inst": "Saint Louis University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.16.440141", "rel_title": "Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2", @@ -793484,33 +792066,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.13.21255091", - "rel_title": "Covid-19: Early evening curfews are not effective and may backfire", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255091", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, some countries have introduced early evening curfews. Several studies try measure the effectiveness of such measures across different countries, but clear identification of effects is elusive.\n\nObjectiveWe examined the impact of an early evening curfew on mobility by studying a shift in curfews from 9pm to 6pm in Greece.\n\nData and MethodsWe took advantage of a natural experiment in Greece, where curfews shifted from 9pm to 6pm in one Region, but not in another. We followed a difference-in-differences econometric approach, where we compared trends in mobility in groceries and pharmacies as well as residential spaces before and after the introduction of the 6pm curfew, in the two regions.\n\nResultsThe relative difference in the time spent in groceries and pharmacies between the two regions before and after the intervention, is statistically insignificant [coeff: -9.95; 95%CI -44.358 to 24.458]. The relative increase in time spent at residential spaces after the 6pm curfew was only 4.625 percentage points [coeff: 4.625; 95%CI 1.412 to 7.838].\n\nConclusionsWe found that the 6pm instead of 9pm curfew in Athens led to a 4.63 percentage point relative increase in time spent at home and had no effect on time spent in groceries and pharmacies. Considering that this was a result of a 18.75% reduction in hours where people were allowed to leave home, it seems that the early evening curfew led to more crowding in indoor spaces - which may facilitate the spread of disease. Interventions should be based on a thorough analysis of human behaviour, that anticipates substitution of activities.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sotiris Vandoros", - "author_inst": "King's College London" - }, - { - "author_name": "Alina Velias", - "author_inst": "City, University of London" - }, - { - "author_name": "Sotiris Georganas", - "author_inst": "City University London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.13.21255328", "rel_title": "Do people reduce compliance with COVID-19 guidelines following vaccination? A longitudinal analysis of matched UK adults", @@ -794283,6 +792838,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.15.440035", + "rel_title": "Scalable, methanol-free manufacturing of the SARS-CoV-2 receptor binding domain in engineered Komagataella phaffii", + "rel_date": "2021-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.15.440035", + "rel_abs": "Prevention of COVID-19 on a global scale will require the continued development of high-volume, low-cost platforms for the manufacturing of vaccines to supply on-going demand. Vaccine candidates based on recombinant protein subunits remain important because they can be manufactured at low costs in existing large-scale production facilities that use microbial hosts like Komagataella phaffii (Pichia pastoris). Here, we report an improved and scalable manufacturing approach for the SARS-CoV-2 spike protein receptor binding domain (RBD); this protein is a key antigen for several reported vaccine candidates. We genetically engineered a manufacturing strain of K. phaffii to obviate the requirement for methanol-induction of the recombinant gene. Methanol-free production improved the secreted titer of the RBD protein by >5x by alleviating protein folding stress. Removal of methanol from the production process enabled scale up to a 1,200 L pre-existing production facility. This engineered strain is now used to produce an RBD-based vaccine antigen that is currently in clinical trials and could be used to produce other variants of RBD as needed for future vaccines.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Neil C Dalvie", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Andrew M Biedermann", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Sergio A Rodriguez-Aponte", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Christopher A Naranjo", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Harish D Rao", + "author_inst": "Serum Institute of India Pvt. Ltd" + }, + { + "author_name": "Meghraj P Rajurkar", + "author_inst": "Serum Institute of India Pvt. Ltd" + }, + { + "author_name": "Rakesh R Lothe", + "author_inst": "Serum Institute of India Pvt. Ltd" + }, + { + "author_name": "Umesh S Shaligram", + "author_inst": "Serum Institute of India Pvt. Ltd" + }, + { + "author_name": "Ryan S Johnston", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Laura E Crowell", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Seraphin Castelino", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Mary Kate Tracey", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Charles A Whittaker", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "J Christopher Love", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.04.15.439918", "rel_title": "Multi-modal engineering of Bst DNA polymerase for thermostability in ultra-fast LAMP reactions", @@ -795390,53 +794016,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.08.21255099", - "rel_title": "Occupational risks of COVID-19 in NHS workers in England", - "rel_date": "2021-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255099", - "rel_abs": "ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England\n\nMethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression.\n\nResultsWith adjustment for employing trust, demographic characteristics, and previous frequency of sickness absence, risk relative to administrative/clerical occupations was highest in additional clinical services (including care assistants) (OR 2.31 [2.25-2.37]), registered nursing and midwifery professionals (OR 2.28 [2.23-2.34]) and allied health professionals (OR 1.94 [1.88-2.01]), and intermediate in doctors and dentists (OR 1.55 [1.50-1.61]). Differences in risk were higher after the employing trust had started to care for documented Covid-19 patients, and were reduced, but not eliminated, following additional adjustment for exposure to infected patients or materials, assessed by a job-exposure matrix. For prolonged Covid-19 sickness absence (episodes lasting >14 days), the variation in risk by staff group was somewhat greater.\n\nConclusionsAfter allowance for possible bias and confounding by non-occupational exposures, we estimated that relative risks for Covid-19 among most patient-facing occupations were between 1.5 and 2.5. The highest risks were in those working in additional clinical services, nursing and midwifery and in allied health professions. Better protective measures for these staff groups should be a priority. Covid-19 may meet criteria for compensation as an occupational disease in some healthcare occupations.\n\nKey messagesO_LIWhat is already known about this subject?\nHealthcare workers and other keyworkers (workers whose job was considered essential to societal functioning) had a higher likelihood of testing positive for COVID-19 than other workers during the first lockdown in England. Amongst healthcare workers, those working in inpatient settings had the highest rate of infection.\nC_LIO_LIWhat are the new findings?\nBetween March and July 2000, the overall risk of COVID-19 sickness absence in National Health Service staff in England was lower at older ages, higher in non-white staff, and (in comparison with administrative and clerical staff) more than doubled in registered nurses and among workers such as healthcare assistants providing support to health professionals. Risk in health care scientists was little different from that in administrative and clerical occupations\nC_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future?\nOur results suggest that the risk reduction strategies that were in place for healthcare scientists were effective. However, the protection for nursing and supporting health professionals was insufficient. In the event of a further wave of infections resulting in high hospital admissions, attention should be paid to ensuring that risk reduction strategies for nurses and supporting health professionals are improved.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Diana van der Plaat", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ira Madan", - "author_inst": "Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "David Coggon", - "author_inst": "Southampton General Hospital" - }, - { - "author_name": "Martie van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Rhiannon Edge", - "author_inst": "Lancaster University" - }, - { - "author_name": "Rupert Muiry", - "author_inst": "Guy's and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Vaughan Parsons", - "author_inst": "Guy's and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Paul Cullinan", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.04.12.21254876", "rel_title": "Behavioral nudges increase COVID-19 vaccinations: Two randomized controlled trials", @@ -796137,6 +794716,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.04.14.439844", + "rel_title": "The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD", + "rel_date": "2021-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439844", + "rel_abs": "The emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution.\n\nOne Sentence SummaryDeep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Allison J Greaney", + "author_inst": "University of Washington" + }, + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Lauren E Gentles", + "author_inst": "University of Washington" + }, + { + "author_name": "Katharine HD Crawford", + "author_inst": "University of Washington" + }, + { + "author_name": "Tyler N Starr", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Keara D Malone", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.08.21255157", "rel_title": "Compliance with Covid-19 measures: evidence from New Zealand", @@ -796988,33 +795614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.09.21255185", - "rel_title": "Changes in cardiorespiratory fitness and body mass index due to COVID-19 mitigation measures in Austrian children aged 7 to 10 years.", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255185", - "rel_abs": "ImportancePrevious studies showed reduced self-reported physical activity levels in children due to the coronavirus disease 2019 (COVID-19) mitigation measures, whereas limited data is available for objectively assessed health parameters.\n\nObjectiveTo examine the influence of these measures on the longitudinal development of cardiorespiratory fitness (CRF) and body mass index (BMI) of primary school children.\n\nDesignCohort study with baseline measurements in September 2019, before the COVID-19 mitigation measures and follow-ups in June and September 2020.\n\nSettingTwelve randomly selected primary schools in urban and rural districts of Klagenfurt, Austria.\n\nParticipantsLegal guardians of 860 children provided written consent. A total of 764 children (88.8%) aged 7-10 years completed all measurements and were included for analyses.\n\nExposureCOVID-19 mitigation measures.\n\nMain Outcomes and MeasuresThe study was planned as a randomized controlled trial, but analyzed as a longitudinal study due to stopped intervention because of COVID-19 mitigation regulations. CRF was measured with a 6-min run test. Height and weight were objectively measured. Age- and gender-specific national and international standard deviation scores (SDS) were calculated for CRF and BMI. Changes over time were analysed using ANOVAs. Secondary analyses were performed for subgroups divided by gender and sports club membership.\n\nResultsFrom September 2019 to September 2020, CRF SDS decreased by -1.06 (95% CI, - 1.13 to -1.00), with a similar rate of decrease in both boys and girls. In June 2020, BMI SDS had increased by 0.12 (95% CI, 0.06-0.16), and in September 2020 by 0.16 (95% CI, 0.12-0.20), compared to September 2019. The rate of increase in BMI SDS was higher in boys (0.23 [95% CI, 0.18-0.29]) than in girls (0.09 [95% CI, 0.04-0.15]). Over the 1-year period, the proportion of children with overweight or obesity increased from 20.3% to 24.1% (+3.8%, P < .001), according to International Obesity Taskforce thresholds.\n\nConclusions and RelevanceCOVID-19 mitigation measures have negative indirect consequences of on relevant health parameters of children. Since these mitigation measures continued after our last assessments, consequences will have increased. Collaborative efforts are required to negate and reverse these effects on childrens health, to prevent long-term negative health consequences.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSDo the COVID-19 mitigation measures have an impact on cardiorespiratory fitness (CRF) and body mass index (BMI) of primary school children?\n\nFindingsIn this longitudinal study, which included 764 primary school children, substantial reductions were found in CRF, which is a parameter related to long-term cardiovascular risk factors. In addition, increases in BMI standard deviation scores and in the proportion of children who are overweight or obese were evident.\n\nMeaningCollaborative efforts are required to negate and reverse these effects on childrens health, to prevent long-term negative health consequences.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gerald Jarnig", - "author_inst": "University of Graz" - }, - { - "author_name": "Johannes Jaunig", - "author_inst": "University of Graz" - }, - { - "author_name": "Mireille Van Poppel", - "author_inst": "University of Graz" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.04.09.21255229", "rel_title": "COVID-19 vaccine perceptions: An observational study on Reddit", @@ -797851,6 +796450,117 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.13.439482", + "rel_title": "Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice", + "rel_date": "2021-04-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439482", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Kai Wu", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Angela Choi", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Matthew Koch", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Sayda Elbashir", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "LingZhi Ma", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Diana Lee", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Angela Woods", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Carole Henry", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Charis Palandjian", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Anna Hill", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Hardik Jani", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Julian Quinones", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Naveen Nunna", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Adrian B McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Samantha Falcone", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Elisabeth Narayanan", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Tonya Colpitts", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Hamilton Bennett", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Kizzmekia Corbett", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Robert Seder", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Barney S Graham", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Guillaume BE Stewart-Jones", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna, Inc" + }, + { + "author_name": "Darin K Edwards", + "author_inst": "Moderna, Inc" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.13.439274", "rel_title": "Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease", @@ -798982,49 +797692,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.04.11.439360", - "rel_title": "Development of highly potent neutralising nanobodies against multiple SARS-CoV-2 variants including the variant of concern B.1.351", - "rel_date": "2021-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.11.439360", - "rel_abs": "The pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. During the years of 2020-2021, millions of humans have died due to SARS-CoV-2 infection and severe economic damage to the global economy has occurred. Unprecedented rapid investments in vaccine development have been made to counter the spread of SARS-CoV-2 among humans. While vaccines are a key pillar of modern medicine, SARS-CoV-2 has mutated as it spread among humans. Vaccines previously developed and approved by regulators are becoming less effective against new variants. One variant of SARS-CoV-2 known as B.1.351 that was first reported to be present in South Africa significantly reduces the efficacy of vaccines developed to date. Therapeutic options that work against the B.1.351 variant are therefore urgently needed to counteract reduced vaccine efficacy. We present here the discovery of recombinant alpaca antibodies that neutralise live virus of B.1.351 and other SARS-CoV-2 variants potently. The antibodies described here may be a useful tool for clinicians who are treating patients infected with B.1.351 and other SARS-CoV-2 for which there is currently no known highly effective treatment.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Agnieszka M Sziemel", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH" - }, - { - "author_name": "Shi-Hsia Hwa", - "author_inst": "Africa Health Research Institute, Durban, 4001 South Africa, Division of Infection and Immunity, University College London, London, WC1E 6BT,UK" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute, Durban, 4001 South Africa, Max Planck Institute for Infection Biology, Berlin, 10117, Germany, School of Laboratory Medicine a" - }, - { - "author_name": "Grace Tyson", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH" - }, - { - "author_name": "Nicola Logan", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH" - }, - { - "author_name": "Brian J Willett", - "author_inst": "MRC University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH" - }, - { - "author_name": "Peter Joseph Durcan", - "author_inst": "Afrobodies Pty Ltd Biociti Laboratory, Woodstock Exchange, Capetown, 7925, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.10.439300", "rel_title": "Combinatorial approach with mass spectrometry and lectin microarray dissected glycoproteomic features of virion-derived spike protein of SARS-CoV-2", @@ -799521,6 +798188,49 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.04.08.21254922", + "rel_title": "Development of a tool to prioritize the monitoring of COVID-19 patients by public health teams", + "rel_date": "2021-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21254922", + "rel_abs": "BackgroundIn the context of the COVID-19 pandemic, public health teams have struggled to conduct monitoring for confirmed or suspicious COVID-19 patients. However, monitoring these patients is critical to improving the chances of survival, and therefore, a prioritization strategy for these patients is warranted. This study developed a monitoring algorithm for COVID-19 patients for the Colombian Ministry of Health and Social Protection (MOH).\n\nMethodsThis work included 1) a literature review, 2) consultations with MOH and National Institute of Health officials, and 3) data analysis of all positive COVID-19 cases and their outcomes. We used clinical and socioeconomic variables to develop a set of risk categories to identify severe cases of COVID-19.\n\nResultsThis tool provided four different risk categories for COVID-19 patients. As soon as the time of diagnosis, this tool can identify 91% of all severe and fatal COVID-19 cases within the first two risk categories.\n\nConclusionThis tool is a low-cost strategy to prioritize patients at higher risk of experiencing severe COVID-19. This tool was developed so public health teams can focus their scarce monitoring resources on individuals at higher mortality risk. This tool can be easily adapted to the context of other lower and middle-income countries. Policymakers would benefit from this low-cost strategy to reduce COVID-19 mortality, particularly during outbreaks.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Andres I. Vecino-Ortiz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Nicolas Guzman-Tordecilla", + "author_inst": "Institute of Public Health, Pontificia Universidad Javeriana, Bogota, Colombia" + }, + { + "author_name": "Yenny Fernanda Guzman Ruiz", + "author_inst": "Department of Health Services. University of Washington. Seattle, WA USA." + }, + { + "author_name": "Rolando Enrique Penaloza-Quintero", + "author_inst": "Institute of Public Health, Pontificia Universidad Javeriana, Bogota, Colombia" + }, + { + "author_name": "Julian Alfredo Fernandez-Nino", + "author_inst": "Fundacion de la Universidad del Norte" + }, + { + "author_name": "Fernando Ruiz Gomez", + "author_inst": "Ministry of Health and Social Protection of Colombia. Bogota, Colombia." + }, + { + "author_name": "Antonio J. Trujillo", + "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.04.08.21254791", "rel_title": "Emergence of multiple SARS-CoV-2 antibody escape variants in an immunocompromised host undergoing convalescent plasma treatment", @@ -800716,45 +799426,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.09.439181", - "rel_title": "Theoretical causes of the Brazilian P.1 and P.2 lineages of the SARS-CoV-2 virus through molecular dynamics", - "rel_date": "2021-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439181", - "rel_abs": "The new {beta}-coronavirus has been causing sad losses around the world and the emergence of new variants has caused great concern. This pandemic is of a proportion not seen since the Spanish Flu in 1918. Thus, throughout this research, the B.1.1.28 lineage of the P.1 clade (K417T, N501Y, E484K) that emerged in Brazil was studied, as well as the latest Delta variant. This is because the molecular mechanisms by which phenotypic changes in transmissibility or mortality remain unknown. Through molecular dynamics simulations with the NAMD 3 algorithm in the 50ns interval, it was possible to understand the impact on structural stabilization on the interaction of the ACE2-RBD complex, as well as simulations in 30ns for the neutralizing antibody P2B-2F6, with this antibody was derived from immune cells from patients infected with SARS-CoV-2. Although not all molecular dynamics analyzes support the hypothesis of greater stability in the face of mutations, there was a predominance of low fluctuations. Thus, 3 (three) analyzes corroborate the hypothesis of greater ACE2-RBD stability as a result of P.1, among them: Low mean RMSF values, greater formation of hydrogen bonds and low solvent exposure measured by the SASA value. An inverse behavior occurs in the interaction with neutralizing antibodies, since the mutations induce greater instability and thus hinder the recognition of antibodies in neutralizing the Spike protein, where we noticed a smaller number of hydrogen bonds as a result of P.1. Through MM-PBSA energy decomposition, we found that Van der Waals interactions predominated and were more favorable when the structure has P.1 strain mutations. Therefore, we believe that greater stabilization of the ACE2-RBD complex may be a plausible explanation for why some mutations are converging in different strains, such as E484K and N501Y. The P.1 concern variant still makes the Spike protein recognizable by antibodies, and therefore, even if the vaccines efficacy can be diminished, there are no results in the literature that nullify them.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Micael Davi Lima de Oliveira", - "author_inst": "Federal University of Amazonas" - }, - { - "author_name": "Kelson Mota Teixeira de Oliveira", - "author_inst": "Federal University of Amazonas" - }, - { - "author_name": "Jonathas Nunes da Silva", - "author_inst": "Federal University of Amazonas" - }, - { - "author_name": "Clarice Santos", - "author_inst": "Federal University of Amazonas" - }, - { - "author_name": "Joao Bessa", - "author_inst": "Federal University of Amazonas" - }, - { - "author_name": "Rosiane de Freitas", - "author_inst": "Federal University of Amazonas" - } - ], - "version": "1", - "license": "cc_by", - "type": "confirmatory results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.04.08.439088", "rel_title": "The homology analysis of ACE2 gene and its distinct expression in laboratory and wild animals", @@ -801559,6 +800230,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.07.21255094", + "rel_title": "Modelling the impact of extending dose intervals for COVID-19 vaccines in Canada", + "rel_date": "2021-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255094", + "rel_abs": "BackgroundDual dose SARS-CoV-2 vaccines demonstrate high efficacy and will be critical in public health efforts to mitigate the COVID-19 pandemic and its health consequences; however, many jurisdictions face very constrained vaccine supply. We examined the impacts of extending the interval between two doses of mRNA vaccines in Canada in order to inform deliberations of Canadas National Advisory Committee on Immunization.\n\nMethodsWe developed an age-stratified, deterministic, compartmental model of SARS-CoV-2 transmission and disease to reproduce the epidemiologic features of the epidemic in Canada. Simulated vaccination comprised mRNA vaccines with explicit examination of effectiveness against disease (67% [first dose], 94% [second dose]), hospitalization (80% [first dose], 96% [second dose]), and death (85% [first dose], 96% [second dose]) in adults aged 20 years and older. Effectiveness against infection was assumed to be 90% relative to the effectiveness against disease. We used a 6-week mRNA dose interval as our base case (consistent with early program rollout across Canadian and international jurisdictions) and compared extended intervals of 12 weeks, 16 weeks, and 24 weeks. We began vaccinations on January 1, 2021 and simulated a third wave beginning on April 1, 2021.\n\nResultsExtending mRNA dose intervals were projected to result in 12.1-18.9% fewer symptomatic cases, 9.5-13.5% fewer hospitalizations, and 7.5-9.7% fewer deaths in the population over a 12-month time horizon. The largest reductions in hospitalizations and deaths were observed in the longest interval of 24 weeks, though benefits were diminishing as intervals extended. Benefits of extended intervals stemmed largely from the ability to accelerate coverage in individuals aged 20-74 years as older individuals were already prioritized for early vaccination. Conditions under which mRNA dose extensions led to worse outcomes included: first-dose effectiveness < 65% against death; or protection following first dose waning to 0% by month three before the scheduled 2nd dose at 24-weeks. Probabilistic simulations from a range of likely vaccine effectiveness values did not result in worse outcomes with extended intervals.\n\nConclusionUnder real-world effectiveness conditions, our results support a strategy of extending mRNA dose intervals across all age groups to minimize symptomatic cases, hospitalizations, and deaths while vaccine supply is constrained.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Austin Nam", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Raphael Ximenes", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Man Wah Yeung", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "University of Toronto" + }, + { + "author_name": "Jianhong Wu", + "author_inst": "York University" + }, + { + "author_name": "Matthew Tunis", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.07.21255089", "rel_title": "Convalescent Plasma Use in the United States was inversely correlated with COVID-19 Mortality: Did Convalescent Plasma Hesitancy cost lives?", @@ -802530,29 +801244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.06.21254993", - "rel_title": "Reopening Italy's Schools in September 2020: A Bayesian Estimation of the Change in the Growth Rate of New SARS-CoV-2 Cases", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254993", - "rel_abs": "ObjectivesCoViD-19s second wave started a debate on the potential role of schools as a primary factor in the contagion resurgence. Two opposite positions appeared: those convinced that schools played a major role in spreading SARS-CoV-2 infections and those who were not. We studied the growth rate of the total number of SARS-CoV-2 infections in all the Italian regions, before and after the school reopening (September - October 2020), investigating the hypothesis of an association between schools and the resurgence of the virus in Italy.\n\nMethodsUsing Bayesian piecewise linear regression to scrutinize the number of daily SARS-CoV-2 infections in each Italian, we looked for an estimate of a changepoint in the growth rate of those confirmed cases. We compared the changepoints with the school opening dates, for each Italian region. The regression allows to discuss the change in steepness of the infection curve, before and after the changepoint.\n\nResultsIn 15 out of 21 Italian regions (71%), an estimated change in the rate of growth of the total number of daily SARS-CoV-2 infection cases occurred after an average of 16.66 days (CI 95% 14.47 to 18.73) since the school reopening. The number of days required for the SARS-CoV-2 daily cases to double went from an average of 47.50 days (CI 95% 37.18 to 57.61) before the changepoint to an average of 7.72 days (CI 95% 7.00 to 8.48) after it.\n\nConclusionStudying the rate of growth of daily SARS-CoV-2 cases in all the Italian regions provides some evidence in favor of a link between school reopening and the resurgence of the virus in Italy. The number of factors that could have played a role are too many to give a definitive answer. Still, the temporal correspondence warrants for a controlled experiment to clarify how much reopening schools mattered.\n\nDesignNot Applicable\n\nSettingNot Applicable\n\nParticipantsNot Applicable\n\nInterventionsNot Applicable\n\nPrimary and Secondary Outcome MeasuresNot Applicable\n\nArticle SummaryO_ST_ABSStrengths and Limitations of this StudyC_ST_ABSO_LIThe use of a Bayesian linear regression model represents a reliable method to account for the uncertainty in the estimation of the changes of the growth rate of the number of daily SARS-CoV-2 infections.\nC_LIO_LIAnalyzing the variation of the total number of new daily SARS-CoV-2 confirmed cases per each Italian region, in coincidence with school reopening, has avoided the problems of looking for specific data collected in schools.\nC_LIO_LIThe problem has been avoided of many infections missed inside schools as positive children and adolescents tend to display less symptoms, therefore leading to a lower probability to be detected with a passive surveillance methodology.\nC_LIO_LIData, made available by the Italian Government, used to count the number of daily SARS-CoV-2 infections, amount to aggregated measures, uploaded daily: in some cases, those measures changed meaning over time and/or contained errors that were never corrected.\nC_LIO_LIMany confounding factors, besides schools, may have played a role, nonetheless in September 2020 in Italy those factors were still fewer than in the following months, when several various containment measures were put in place.\nC_LI\n\nAuthor ContributionLC and MR equally contributed to conceive, design, write, manage, and revise the manuscript.\n\nFundingThe authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.\n\nCompeting interestsNone declared.\n\nPatient consent for publicationNot required.\n\nProvenance and peer reviewNot commissioned, externally peer reviewed.\n\nData availability statementData are available in a public, open access repository (https://github.com/pcm-dpc/COVID-19). All data and code are available upon request to the corresponding author email: luca.casini7@unibo.it\n\nResearch Ethics Approval: Human ParticipantsNot applicable: neither humans nor animals nor personal data are being involved in this study.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Luca Casini", - "author_inst": "University of Bologna" - }, - { - "author_name": "Marco Roccetti", - "author_inst": "University of Bologna" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.06.21255013", "rel_title": "Reduction in the 2020 Life Expectancy in Brazil after COVID-19", @@ -803133,6 +801824,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.06.21253465", + "rel_title": "Social, demographic and behavioural determinants of SARS-CoV-2 infection: A case-control study carried out during mass community testing of asymptomatic individuals in South Wales, December 2020", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21253465", + "rel_abs": "BackgroundBetween 21 November and 22 December 2020, a SARS-CoV-2 community testing pilot took place in the South Wales Valleys. Lateral flow tests were offered to all people aged over 10 years living, studying or working in the area.\n\nMethodsWe conducted a case-control study in adults taking part in the pilot using an anonymous online questionnaire. Social, demographic and behavioural factors were compared in people with a positive test (cases) and a sample of negatives (controls). Population attributable fractions (PAF) were calculated for factors with significantly increased odds following multivariate analysis.\n\nResultsA total of 199 cases and 2,621 controls were recruited by SMS (response rates: 27.1% and 37.6% respectively). Following adjustment, cases were more likely to work in the hospitality sector (aOR: 3.39, 95% CI: 1.43-8.03), social care (aOR: 2.63, 95% CI: 1.22-5.67) or healthcare (aOR: 2.31, 95% CI: 1.29-4.13), live with someone self-isolating due to contact with a case (aOR: 3.07, 95% CI: 2.03-4.62), visit a pub (aOR: 2.87, 95% CI: 1.11-7.37), and smoke or vape (aOR: 1.54, 95% CI: 1.02-2.32). In this community, and at this point in the epidemic, reducing transmission from a household contact who is self-isolating would have the biggest public health impact (PAF: 0.2).\n\nConclusionInfection prevention and control should be strengthened to help reduce household transmission. As restrictions on social mixing are relaxed, hospitality venues will become of greater public health importance, and those working in this sector should be adequately protected. Smoking or vaping may be an important modifiable risk factor.\n\nWhat is already known on this subject?Certain populations are known to be at risk of severe COVID-19: Older people, males, people in minority ethnic groups, people with pre-existing chronic disease or disability, and people in certain public-facing occupations. However, limited information exists on the factors associated with acquiring SARS-CoV-2 in the community.\n\nWhat this study adds?This study provides an insight into the most important factors determining community transmission of SARS-CoV-2. We found that transmission within the household was the most important source of SARS-CoV-2 infection. Working in the hospitality sector, and visiting the pub were associated with infection but at the time of this study were relatively infrequent exposures. Smoking or vaping had a small but significant effect. Working in education, living with someone working in education, having caring responsibilities, attending a healthcare appointment and visiting a supermarket, restaurant, gym or leisure centre were not associated with infection. Whilst these findings relate to a specific community at a specific time in the course of the epidemic when social restrictions were in place, the information will be useful in supporting policy decisions. Mass testing exercises present an opportunity to conduct epidemiological studies to gather information to inform the local and national epidemic response.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daniel Rhys Thomas", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Laia Fina", + "author_inst": "Public Health Wales Communicable Disease Surveillance Centre" + }, + { + "author_name": "James Adamson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Clare Sawyer", + "author_inst": "Public Health Wales Communicable DiseaseSurveillance Centre" + }, + { + "author_name": "Angela Jones", + "author_inst": "Cwm Taf Morgannwg University Health Board" + }, + { + "author_name": "Kelechi Nnoaham", + "author_inst": "Cwm Taf Morgannwg University Health Board" + }, + { + "author_name": "Alicia Barrasa", + "author_inst": "Public Health England FETP" + }, + { + "author_name": "Giri Shankar", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Christopher Williams", + "author_inst": "Public Health Wales" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.07.21255026", "rel_title": "Evaluating and optimizing COVID-19 vaccination policies: a case study of Sweden", @@ -804456,181 +803198,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.04.07.438849", - "rel_title": "Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438849", - "rel_abs": "The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Jule Goike", - "author_inst": "UT Austin" - }, - { - "author_name": "Ching-Lin Hsieh", - "author_inst": "UT Austin" - }, - { - "author_name": "Andrew Horton", - "author_inst": "UT Austin" - }, - { - "author_name": "Elizabeth C Gardner", - "author_inst": "UT Austin" - }, - { - "author_name": "Foteini Bartzoka", - "author_inst": "UT Austin" - }, - { - "author_name": "Niahshuang Wang", - "author_inst": "UT Austin" - }, - { - "author_name": "Kamyab Javanmardi", - "author_inst": "UT Austin" - }, - { - "author_name": "Andrew Herbert", - "author_inst": "USAMRIID" - }, - { - "author_name": "Shawn Abbasi", - "author_inst": "USAMRIID" - }, - { - "author_name": "Rebecca Renberg", - "author_inst": "US Army Research Laboratory" - }, - { - "author_name": "Michael J Johanson", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jose A Cardona", - "author_inst": "UT Austin" - }, - { - "author_name": "Thomas Segall-Shapiro", - "author_inst": "US Army Research Laboratory" - }, - { - "author_name": "Ling Zhou", - "author_inst": "UT Austin" - }, - { - "author_name": "Ruth H Nissly", - "author_inst": "Penn State University" - }, - { - "author_name": "Abhinay Gontu", - "author_inst": "Penn State University" - }, - { - "author_name": "Michelle Byrom", - "author_inst": "UT Austin" - }, - { - "author_name": "Andre C Maranhao", - "author_inst": "UT Austin" - }, - { - "author_name": "Anna M Battenhouse", - "author_inst": "UT Austin" - }, - { - "author_name": "Varun Gejji", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Laura Soto-Sierra", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Emma R Foster", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Susan L Woodard", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Zivko L Nikolov", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jason Lavinder", - "author_inst": "UT Austin" - }, - { - "author_name": "Will N Voss", - "author_inst": "UT Austin" - }, - { - "author_name": "Ankur Annapareddy", - "author_inst": "UT Austin" - }, - { - "author_name": "Gregory C Ippolito", - "author_inst": "UT Austin" - }, - { - "author_name": "Andrew D Ellington", - "author_inst": "UT Austin" - }, - { - "author_name": "Edward M Marcotte", - "author_inst": "UT Austin" - }, - { - "author_name": "Ilya J Finkelstein", - "author_inst": "UT Austin" - }, - { - "author_name": "Randall A Hughes", - "author_inst": "US Army Research Laboratory" - }, - { - "author_name": "James M Musser", - "author_inst": "Houston Methodist Research Institute" - }, - { - "author_name": "Suresh V Kuchipudi", - "author_inst": "Penn State University" - }, - { - "author_name": "Vivek Kapur", - "author_inst": "Penn State University" - }, - { - "author_name": "George Georgiou", - "author_inst": "UT Austin" - }, - { - "author_name": "John M Dye", - "author_inst": "USAMRIID" - }, - { - "author_name": "Daniel R Boutz", - "author_inst": "US Army Research Laboratory" - }, - { - "author_name": "Jason S McLellan", - "author_inst": "UT Austin" - }, - { - "author_name": "Jimmy D Gollihar", - "author_inst": "US Army Research Laboratory" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2021.04.06.438540", "rel_title": "TMPRSS2 and RNA-dependent RNA polymerase are effective targets of therapeutic intervention for treatment of COVID-19 caused by SARS-CoV-2 variants (B.1.1.7 and B.1.351)", @@ -805535,6 +804102,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.07.21255081", + "rel_title": "Effectiveness of CoronaVac in the setting of high SARS-CoV-2 P.1 variant transmission in Brazil: A test-negative case-control study", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255081", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, Gamma, emerged in the city of Manaus in late 2020 during a large resurgence of coronavirus disease (COVID-19), and has spread throughout Brazil. The effectiveness of vaccines in settings with widespread Gamma variant transmission has not been reported.\n\nMethodsWe performed a matched test-negative case-control study to estimate the effectiveness of an inactivated vaccine, CoronaVac, in healthcare workers (HCWs) in Manaus, where the Gamma variant accounted for 86% of genotyped SARS-CoV-2 samples at the peak of its epidemic. We performed an early analysis of effectiveness following administration of at least one vaccine dose and an analysis of effectiveness of the two-dose schedule. The primary outcome was symptomatic SARS-CoV-2 infection.\n\nFindingsFor the early at-least-one-dose and two-dose analyses the study population was, respectively, 53,176 and 53,153 HCWs residing in Manaus and aged 18 years or older, with complete information on age, residence, and vaccination status. Among 53,153 HCWs eligible for the two-dose analysis, 47,170 (89%) received at least one dose of CoronaVac and 2,656 individuals (5%) underwent RT-PCR testing from 19 January, 2021 to 13 April, 2021. Of 3,195 RT-PCR tests, 885 (28%) were positive. 393 and 418 case- control pairs were selected for the early and two-dose analyses, respectively, matched on calendar time, age, and neighbourhood. Among those who had received both vaccine doses before the RT-PCR sample collection date, the average time from second dose to sample collection date was 14 days (IQR 7-24). In the early analysis, vaccination with at least one dose was associated with a 0.50-fold reduction (adjusted vaccine effectiveness (VE), 49.6%, 95% CI 11.3 to 71.4) in the odds of symptomatic SARS-CoV-2 infection during the period 14 days or more after receiving the first dose. However, we estimated low effectiveness (adjusted VE 36.8%, 95% CI -54.9 to 74.2) of the two-dose schedule against symptomatic SARS-CoV-2 infection during the period 14 days or more after receiving the second dose. A finding that vaccinated individuals were much more likely to be infected than unvaccinated individuals in the period 0-13 days after first dose (aOR 2.11, 95% CI 1.36-3.27) suggests that unmeasured confounding led to downward bias in the vaccine effectiveness estimate.\n\nInterpretationEvidence from this test-negative study of the effectiveness of CoronaVac was mixed, and likely affected by bias in this setting. Administration of at least one vaccine dose showed effectiveness against symptomatic SARS-CoV-2 infection in the setting of epidemic Gamma variant transmission. However, the low estimated effectiveness of the two-dose schedule underscores the need to maintain non-pharmaceutical interventions while vaccination campaigns with CoronaVac are being implemented.\n\nFundingFundacao Oswaldo Cruz (Fiocruz); Municipal Health Secretary of Manaus\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for articles published from inception of the pandemic until April 3, 2021, with no language restrictions, using the search terms \"P.1\" AND \"vaccine\" AND \"SARS-CoV-2\". Additionally, we searched for \"CoronaVac\" AND \"SARS-CoV-2\". Early studies have found plasma from convalescent COVID-19 patients and sera from vaccinated individuals have reduced neutralisation of the SARS-CoV-2 variant, Gamma or P.1, compared with strains isolated earlier in the pandemic. Pfizer BNT162b2 mRNA, Oxford-AstraZeneca ChAdOx1, and CoronaVac are the only vaccines for which such data has been published to date.\n\nNo studies reported effectiveness of any vaccine on reducing the risk of infection or disease among individuals exposed to P.1 or in settings of high P.1 transmission.\n\nAdded value of this studyThis study finds that vaccination with CoronaVac was 49.4% (95% CI 13.2 to 71.9) effective at preventing COVID-19 in a setting with likely high prevalence of the Gamma Variant of Concern. However, an analysis of effectiveness by dose was underpowered and failed to find significant effectiveness of the two-dose schedule of CoronaVac (estimated VE 37.1%, 95% CI -53.3 to 74.2).\n\nImplications of all the available evidenceThese findings are suggestive for the effectiveness of CoronaVac in healthcare workers in the setting of widespread P.1 transmission but must be strengthened by observational studies in other settings and populations. Based on this evidence, there is a need to implement sustained non-pharmaceutical interventions even as vaccination campaigns continue.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Matt Hitchings", + "author_inst": "Department of Biology, University of Florida, Gainesville, FL, USA;Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA" + }, + { + "author_name": "Otavio T. Ranzani", + "author_inst": "Universidade de Sao Paulo; Barcelona Institute for Global Health, ISGlobal" + }, + { + "author_name": "Mario S.S. Torres", + "author_inst": "Municipal Health Secretary of Manaus" + }, + { + "author_name": "Silvano Barbosa de Oliveira", + "author_inst": "Universidade de Bras\u00edlia, Bras\u00edlia, DF, Brazil;Pan American Health Organization" + }, + { + "author_name": "Maria Almiron", + "author_inst": "Pan American Health Organization" + }, + { + "author_name": "Rodrigo Said", + "author_inst": "Pan American Health Organization" + }, + { + "author_name": "Ryan Borg", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA" + }, + { + "author_name": "Wade L. Schulz", + "author_inst": "Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA; Department of Laboratory Medicine, Yale University School of Medicine," + }, + { + "author_name": "Roberto Dias de Oliveira", + "author_inst": "State University of Mato Grosso do Sul - UEMS, Dourados, MS, Brazil" + }, + { + "author_name": "Patricia Vieira da Silva", + "author_inst": "Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil" + }, + { + "author_name": "Daniel Barros de Castro", + "author_inst": "Funda\u00e7\u00e3o de Vigil\u00e2ncia em Sa\u00fade do Estado do Amazonas" + }, + { + "author_name": "Vanderson de Souza Sampaio", + "author_inst": "Funda\u00e7\u00e3o de Vigil\u00e2ncia em Sa\u00fade do Estado do Amazonas" + }, + { + "author_name": "Bernardino Cl\u00e1udio de Albuquerque", + "author_inst": "Funda\u00e7\u00e3o de Vigil\u00e2ncia em Sa\u00fade do Estado do Amazonas" + }, + { + "author_name": "Tatyana Costa Amorim Ramos", + "author_inst": "Funda\u00e7\u00e3o de Vigil\u00e2ncia em Sa\u00fade do Estado do Amazonas" + }, + { + "author_name": "Shadia Hussami Hauache Fraxe", + "author_inst": "Municipal Health Secretary of Manaus" + }, + { + "author_name": "Cristiano Fernandes da Costa", + "author_inst": "Funda\u00e7\u00e3o de Vigil\u00e2ncia em Sa\u00fade do Estado do Amazonas" + }, + { + "author_name": "Felipe Gomes Naveca", + "author_inst": "Fiocruz, Instituto Le\u00f4nidas e Maria Deane" + }, + { + "author_name": "Andr\u00e9 M. Siqueira", + "author_inst": "Instituto Nacional de Infectologia Carlos Chagas-Fiocruz, Rio de Janeiro, Brazil" + }, + { + "author_name": "Wildo Navegantes de Ara\u00fajo", + "author_inst": "Universidade de Bras\u00edlia, Bras\u00edlia, DF, Brazil;National Institute for Science and Technology for Health Technology Assessment, Porto Alegre, RS, Brazil;Pan Amer" + }, + { + "author_name": "Jason R. Andrews", + "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA" + }, + { + "author_name": "Derek A.T. Cummings", + "author_inst": "Department of Biology, University of Florida, Gainesville, FL, USA;Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA;Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Salvador, BA," + }, + { + "author_name": "Julio Croda", + "author_inst": "Fiocruz Mato Grosso do Sul, Funda\u00e7\u00e3o Oswaldo Cruz, Campo Grande, MS, Brazil;Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil;Departme" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.05.21254656", "rel_title": "Glucocorticoids and B Cell Depleting Agents Substantially Impair Immunogenicity of mRNA Vaccines to SARS-CoV-2", @@ -806522,53 +805196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.05.21254921", - "rel_title": "Impact of COVID-19 on Pediatric Emergency Department Visits: A Retrospective Cohort Study.", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254921", - "rel_abs": "Background & ObjectiveCOVID-19 has caused significant shifts in healthcare utilization, including pediatric emergency departments (EDs). We describe variations in visits made to two large pediatric EDs during the first three months of the COVID-19 pandemic, compared to a historical control period.\n\nMethodsWe performed a retrospective cohort study of children presenting to two academic pediatric EDs in Quebec, Canada. We compared the number of ED visits during the first wave of COVID-19 pandemic (March-May 2020) to historical controls (March-May 2015-2019), using Poisson regression, adjusting for site and the underlying baseline trend. Secondary analyses examined variations in ED visits by acuity, disposition, and disease categories.\n\nResultsFrom 2015 to 2019, the two EDs had a median of 1,632 visits per week [interquartile range (IQR) 1,548; 1,703]; in 2020, this number decreased to 536 visits per week [IQR 446; 744]. In multivariable analyses, this represent a 53.3% (95%CI: 52.1, 54.4) reduction in the number of ED visits. The reduction was larger among visits triage categories 4 and 5 (lower acuity) than categories 1, 2 and 3 (higher acuity): -54.2% vs. -42.0% (p<0.001). A greater proportion of children presenting to these sites were hospitalized during the COVID period than in pre-COVID period: 11.8% vs. 5.5% (p<0.001).\n\nConclusionsDuring the early stages of the COVID-19 pandemic, there was a large decrease in visits to pediatric EDs. Patients presented with higher acuity at triage and the proportion of patients requiring hospitalization increased.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Pierre Fontaine", - "author_inst": "Faculty of Medicine, University of Montreal" - }, - { - "author_name": "Esli Osmanlliu", - "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" - }, - { - "author_name": "Jocelyn Gravel", - "author_inst": "Department of Pediatric Emergency Medicine" - }, - { - "author_name": "Ariane Boutin", - "author_inst": "Department of Pediatric Emergency Medicine" - }, - { - "author_name": "Evelyne D. Trottier", - "author_inst": "Department of Pediatric Emergency Medicine" - }, - { - "author_name": "Nathalie O Gaucher", - "author_inst": "Department of Pediatric Emergency Medicine" - }, - { - "author_name": "Antonio D'Angelo", - "author_inst": "Department of Pediatric Emergency Medicine" - }, - { - "author_name": "Olivier Drouin", - "author_inst": "CHU Sainte-Justine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.04.05.21254024", "rel_title": "Strategies for antigen testing: An alternative approach to widespread PCR testing", @@ -807393,6 +806020,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.05.21254712", + "rel_title": "Evaluation of the performance of SARS-CoV-2 antibody assays for the longitudinal population-based study of COVID-19 spread in St. Petersburg, Russia", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254712", + "rel_abs": "BackgroundAn evident geographical variation in the SARS-CoV-2 spread requires seroprevalence studies based on local tests with robust validation against already available antibody tests and neutralization assays. This report summarizes the evaluation of antibody tests used in the representative population-based serological study of SARS-CoV-2 in Saint Petersburg, Russia.\n\nMethodsWe used three different antibody tests throughout the study: chemiluminescent microparticle immunoassay (CMIA) Abbott Architect SARS-CoV-2 IgG, Enzyme-linked immunosorbent assay (ELISA) CoronaPass total antibodies test, and ELISA SARS-CoV-2-IgG-EIA-BEST. Clinical sensitivity was estimated with the SARS-CoV-2 PCR test as the gold standard and specificity in pre-pandemic sera samples using the cut-off recommended by manufacturers. Paired and unpaired serum sets were used. Measures of concordance were also calculated in the seroprevalence study sample against the microneutralization test (MNA).\n\nFindingsSensitivity was equal to 91.1% (95% CI: 78.8-97.5) and 90% (95% CI: 76.4-96.4) for ELISA Coronapass and ELISA Vector-Best respectively. It was equal to 63.1% (95% CI (50.2-74.7) for CMIA Abbott. Specificity was equal to 100% for all the tests. Comparison of ROCs for three tests has shown lower AUC for CMIA Abbott, but not for ELISA Coronapass and CMIA Abbott. The cutoff SC/O ratio of 0.28 for CMIA-Abbott resulted in a sensitivity of 80% at the same full level of specificity. In less than one-third of the population-based study participants with positive antibody test results, we detected neutralizing antibodies in titers 1:80 and above. There was a moderate correlation between antibody assays results and MNA.\n\nInterpretationOur validation study encourages the use of local antibody tests for population-based SARS-CoV-2 surveillance and sets the reference for the seroprevalence correction. Available tests are sensitive enough to detect antibodies in most individuals with previous positive PCR tests with a follow-up of more than 5 months. The Abbott Architect SARS-CoV-2 IgGs sensitivity can be significantly improved by incorporating a new cut-off. Relying on manufacturers test characteristics for correction of reported prevalence estimates may introduce bias to the study results.\n\nFundingPolymetal International plc", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anton Barchuk", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Daniil Shirokov", + "author_inst": "ITMO University" + }, + { + "author_name": "Mariia Sergeeva", + "author_inst": "Smorodintsev Research Institute of Influenza" + }, + { + "author_name": "Rustam Tursun-zade", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Olga Dudkina", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Varvara Tychkova", + "author_inst": "Smorodintsev Research Institute of Influenza" + }, + { + "author_name": "Lubov Barabanova", + "author_inst": "Clinic 'Scandinavia' (LLC Ava-Peter)" + }, + { + "author_name": "Dmitriy Skougarevskiy", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Daria Danilenko", + "author_inst": "Smorodintsev Research Institute of Influenza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.05.21254918", "rel_title": "Unraveling Attributes of COVID-19 Vaccine Hesitancy in the U.S.: A Large Nationwide Study", @@ -808376,57 +807054,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.04.05.21254935", - "rel_title": "Clinical correlation of lung ultrasound profiles in patients with COVID-19 infection", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254935", - "rel_abs": "BackgroundLung ultrasound is a popular point of care test that correlates well with computed tomography for lung pathologies. While previous studies have shown its ability to detect COVID-19 related lung pathology, we aimed to evaluate the utility of lung ultrasound in the triage and prognostication of COVID-19 patients by determining its ability to predict clinical severity and outcomes.\n\nMethodsThis was a prospective, cross-sectional, observational, single centre study done at JPNATC and AIIMS, New Delhi, India. Consenting eligible patients aged 18 years or more were included if hospitalised with microbiologically confirmed COVID-19 and classified as mild, moderate (respiratory rate >24/min OR SpO2<94% on room air) and severe COVID-19 (respiratory rate >30/min OR SpO2<90% on room air) at the time of enrolment. The lungs were systematically assessed with ultrasound after division into 14 zones (4 anteriorly, 4 axillary and 6 posteriorly). Clinical and laboratory parameters including arterial blood gas analysis at the time of evaluation were recorded. Patients were followed till death or discharge. The primary objective was to determine the correlation between clinical severity and lung ultrasound profiles (no. of A, B and C profiles, and the total number of areas involved). Secondary objectives included assessment of the correlation between lung ultrasound profiles and clinical outcomes and development of a statistical model incorporating ultrasound and clinical parameters to allow prediction of COVID-19 related severity and outcomes.\n\nFindingsBetween October 1, 2020, and January 31,2021, patients were screened for inclusion and total n=60 patients were evaluated and included in the final analysis. The most common abnormality seen were B lines, seen in at least one zone in n=53 (88.33%) of cases. A median of 9 (IQR: 5-12) zones of the 14 assessed had a B-profile. The total number of abnormal areas (zones with a B or C profile) correlated significantly with the PaO2/FiO2 ratio ({rho}= -0.7232, p<0.0001) and SpO2/FiO2 ratio ({rho}= -0.6866, p<0.0001), and differed significantly between mild and moderate vs severe cases (p=0.0026 mild vs moderate, p<0.0001 mild vs severe, p=0.0175 moderate vs severe). The total number of B lines were predictors of mortality (p=0.0188, OR 1.03, 95% CI 1.003-1.060). Statistical models that incorporated total number of B-lines, CRP and anticoagulation use could predict mortality (p=0.0124, pseudo R2=0.1740) with an AUC= 0.7682 (95% CI=0.6176-0.9188), and the total number of involved areas and LDH levels could distinguish severe disease from mild/moderate disease (p<0.0001, Pseudo R2=0.3822), AUC = 0.8743 (95% CI=0.7752-0.9733). A simplified cut off of [≥]6 involved areas (of the 14 assessed) was 100% sensitive and 52% specific for differentiating severe disease from mild and moderate ones.\n\nInterpretationIn patients with COVID-19, increasing involvement of the lungs as assessed by ultrasonography correlates significantly with clinical severity and outcomes. These findings may be utilized in future prospective studies to validate the use of lung ultrasound to triage and prognosticate patients with COVID-19 infection.\n\nAuthor ApprovalAll authors have seen and approved the manuscript\n\nCompeting interestsThere are no potential competing interests\n\nData availability StatementAll data referred to in the manuscript shall be provided when asked for.\n\nDisclaimersThe authors have nothing to disclose\n\nFunding statementNo funding source was involved.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Chitrakshi Nagpal", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Sanchit Kumar", - "author_inst": "All India institute of medical sciences" - }, - { - "author_name": "Naveet Wig", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "Arvind Kumar", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "Praful Pandey", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "Manraj Singh Bhullar", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "Richa Aggarwal", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "kapil dev soni", - "author_inst": "all india institute of medical sciences" - }, - { - "author_name": "Anjan Trikha", - "author_inst": "all india institute of medical sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.04.06.21254840", "rel_title": "Patient perspectives on healthcare at the time of COVID-19 and suggestions for care redesign after the pandemic: a qualitative study in all six WHO regions", @@ -809191,6 +807818,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.06.21254014", + "rel_title": "COVID-19 vaccine hesitancy among individuals with cancer, autoimmune diseases, and other serious comorbid conditions", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254014", + "rel_abs": "BackgroundIndividuals with comorbid conditions have been disproportionately affected by COVID-19. Since regulatory clinical trials with COVID-19 vaccines excluded those with immunocompromising conditions, few patients with cancer and autoimmune diseases were enrolled. With limited vaccine safety data available, vulnerable populations may have conflicted vaccine attitudes.\n\nMethodsTo assess the incidence and reasons for COVID-19 vaccine hesitancy and to assess early vaccine safety, we conducted a cross-sectional online survey, fielded January 15, 2021 through February 22, 2021, with international participation (74% USA). A random sample of members of Inspire, anonline healthcommunityof over 2.2million individualswith comorbid conditions, completed a 55-item online survey.\n\nResults21,943 individuals completed the survey (100% with comorbidities including 27% cancer, 23% autoimmune diseases, 38% chronic lung diseases). 10% declared they would not, 4% stated they probably would not, and 5% were not sure they would agree to vaccination (hesitancy rate 19%). Factors associated with hesitancy included younger age, female gender, black-Pacific-Island-Native American heritage, less formal education, conservative political tendencies, resistance to masks or routine influenza vaccinations, and distrust of media coverage. 5501 (25%) had received at least one COVID-19 vaccine injection, including 29% of US participants. Following the first injection, 69% self-reported local and 40% systemic reactions, which increased following the second injection to 76% and 67%, respectively, with patterns mimicking clinical trials.\n\nConclusionNearly one in five individuals with serious comorbid conditions harbor COVID-19 hesitancy. Early safety experiences among those who have been vaccinated should be reassuring.\n\nHighlightsO_LIIndividuals with serious comorbid conditions, including cancer, have been disproportionately affected by COVID-19 and therefore have been prioritized for vaccination\nC_LIO_LIAn online survey of nearly 22,000 individuals with comorbid conditions revealed that nearly one in 5 expressed vaccine hesitancy.\nC_LIO_LIReasons for hesitancy in this comorbid population mimicked surveys of the general population.\nC_LIO_LISelf-reported safety profiles among individuals with comorbid conditions were acceptable, and generally milder than reports in clinical trials among the general population.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Richard Tsai", + "author_inst": "Inspire" + }, + { + "author_name": "John Hervey", + "author_inst": "Inspire" + }, + { + "author_name": "Kathleen D Hoffman", + "author_inst": "Inspire" + }, + { + "author_name": "Jessica Wood", + "author_inst": "Inspire" + }, + { + "author_name": "John Novack", + "author_inst": "Inspire" + }, + { + "author_name": "Jennifer Johnson", + "author_inst": "Inspire" + }, + { + "author_name": "Dana C Deighton", + "author_inst": "Inspire" + }, + { + "author_name": "Brian Loew", + "author_inst": "Inspire" + }, + { + "author_name": "Stuart L Goldberg", + "author_inst": "Hackensack Meridian School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.06.21253178", "rel_title": "New Zealand Emergency Department COVID-19 Preparedness Survey", @@ -810194,53 +808872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.30.21253126", - "rel_title": "High SARS-CoV-2 attack rates following exposure during singing events in the Netherlands, September-October 2020", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21253126", - "rel_abs": "BackgroundPrevious reports suggest SARS-CoV-2 transmission risk increases during singing events. From September-October 2020, several clusters of COVID-19 cases among singing events were reported across the Netherlands. Our aim was to investigate whether singing increased SARS-CoV-2 transmission risk during these events.\n\nMethodsData from 5 events were retrospectively collected from spokespersons and singing group members via questionnaires. Information was consolidated with the National Notifiable Diseases Surveillance System. Specimens were requested for sequencing for point source and cluster assessment. We described outbreaks in terms of person, place and time and depicted potential SARS-CoV-2 transmission routes. A previously published model (AirCoV2) was used to estimate mean illness risk of 1 person through airborne transmission under various scenarios.\n\nResultsEvents included 9-21 persons (mean: 16), aged 20-89 years (median: 62). Response rates ranged 58-100%. Attack rates were 53-74%. Limited sequencing data was obtained from 2 events. Events lasted 60-150 minutes (singing: 20-120). Rooms ranged 320-3000m3. SARS-CoV-2 transmission likely occurred during all events; with a possible index case identified in 4 events. AirCoV2 showed 86% (54-100%) mean illness risk for 120 minutes of singing, smaller room (300m3), 1 air exchange/hour (ACH), and supershedder presence.\n\nConclusionsDroplet transmission and indirect contact probably caused some cases, but unlikely explain the high attack rates. AirCoV2 indicated that airborne transmission due to singing is possible in case of supershedder presence. Airflow expelling respiratory droplets >1.5m possibly influenced transmission. It is possible that singing itself increased SARS-CoV-2 transmission risk through airborne transmission.\n\nSummaryThis outbreak investigation among five singing events with high SARS-CoV-2 attack rates (53-74%) suggested that airflow expelling respiratory droplets >1.5m possibly influenced transmission and it is possible that singing itself increased SARS-CoV-2 transmission risk through airborne transmission.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Anita A. Shah", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Florien Dusseldorp", - "author_inst": "Public Health Service Hollands Midden (GGD)" - }, - { - "author_name": "Irene K. Veldhuijzen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Margreet J.M. te Wierik", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Alvin Bartels", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Jack Schijven", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Lucie C. Vermeulen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Mirjam J. Knol", - "author_inst": "National Institute for Public Health and Environment (RIVM)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.02.21254493", "rel_title": "Humoral response to Pfizer mRNA vaccine against SARS CoV2, in patients with autoimmune inflammatory rheumatic diseases and the impact on the rheumatic disease activity", @@ -811077,6 +809708,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.31.21254695", + "rel_title": "A BIBLIOMETRIC ANALYSIS OF RHEUMATOLOGY AND COVID-19 RESEARCHES", + "rel_date": "2021-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254695", + "rel_abs": "ObjectivesCOVID-19 has had a substantial impact on rheumatology. This study provides a general overview of studies on rheumatology and COVID-19.\n\nMethodsData were taken from the Web of Science (WoS) website. Analysis and network visualization mapping processes were carried out using VOSviewer. A total of 234 publications were analyzed, and the correlations between citation numbers and reference counts, usage counts and page numbers were analyzed with Spearman correlation coefficients.\n\nResultsThe average number of citations per item was 6.03. The studies were cited 1,411 times in total, and 1,121 times without self-citations. The countries with the highest number of publications on rheumatology and COVID-19 were the USA and England; the countries with the highest number of citations were Italy and the USA, and Jinoos Yazdany was the most cited author. The Annals of the Rheumatic Diseases was the most cited journal, whereas the highest number of articles on rheumatology and COVID-19 were published in Arthritis and Rheumatology.\n\nConclusionsBibliometric analysis of rheumatology and COVID-19 can be useful to future studies because it provides a general perspective on the studies. This study provides an insight into the development of publications on rheumatology during the COVID-19 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ozge Pasin", + "author_inst": "Istanbul University Faculty of Medicine Biostatistics Department" + }, + { + "author_name": "Tugce Pasin", + "author_inst": "Department of Physical Medicine and Rehabilitation, Istanbul Goztepe Training and Research Hospital, Istanbul, Turkey" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.03.31.21254735", "rel_title": "Racial Disparities in the SOFA Score Among Patients Hospitalized with COVID-19", @@ -812064,89 +810718,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254687", - "rel_title": "SARS-CoV-2 infectivity by viral load, S gene variants and demographic factors and the utility of lateral flow devices to prevent transmission", - "rel_date": "2021-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254687", - "rel_abs": "BackgroundHow SARS-CoV-2 infectivity varies with viral load is incompletely understood. Whether rapid point-of-care antigen lateral flow devices (LFDs) detect most potential transmission sources despite imperfect sensitivity is unknown.\n\nMethodsWe combined SARS-CoV-2 testing and contact tracing data from England between 01-September-2020 and 28-February-2021. We used multivariable logistic regression to investigate relationships between PCR-confirmed infection in contacts of community-diagnosed cases and index case viral load, S gene target failure (proxy for B.1.1.7 infection), demographics, SARS-CoV-2 incidence, social deprivation, and contact event type. We used LFD performance to simulate the proportion of cases with a PCR-positive contact expected to be detected using one of four LFDs.\n\nResults231,498/2,474,066 (9%) contacts of 1,064,004 index cases tested PCR-positive. PCR-positive results in contacts independently increased with higher case viral loads (lower Ct values) e.g., 11.7%(95%CI 11.5-12.0%) at Ct=15 and 4.5%(4.4-4.6%) at Ct=30. B.1.1.7 infection increased PCR-positive results by [~]50%, (e.g. 1.55-fold, 95%CI 1.49-1.61, at Ct=20). PCR-positive results were most common in household contacts (at Ct=20.1, 8.7%[95%CI 8.6-8.9%]), followed by household visitors (7.1%[6.8-7.3%]), contacts at events/activities (5.2%[4.9-5.4%]), work/education (4.6%[4.4-4.8%]), and least common after outdoor contact (2.9%[2.3-3.8%]). Contacts of children were the least likely to test positive, particularly following contact outdoors or at work/education. The most and least sensitive LFDs would detect 89.5%(89.4-89.6%) and 83.0%(82.8-83.1%) of cases with PCR-positive contacts respectively.\n\nConclusionsSARS-CoV-2 infectivity varies by case viral load, contact event type, and age. Those with high viral loads are the most infectious. B.1.1.7 increased transmission by [~]50%. The best performing LFDs detect most infectious cases.\n\nKey pointsIn 2,474,066 contacts of 1,064,004 SARS-CoV-2 cases, PCR-positive tests in contacts increased with higher index case viral loads, the B.1.1.7 variant and household contact. Children were less infectious. Lateral flow devices can detect 83.0-89.5% of infections leading to onward transmission.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lennard YW Lee", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stefan Rozmanowski", - "author_inst": "UK Government Department of Health and Social Care" - }, - { - "author_name": "Matthew Pang", - "author_inst": "UK Government Department of Health and Social Care" - }, - { - "author_name": "Andre Charlett", - "author_inst": "Public Health England" - }, - { - "author_name": "Charlotte Anderson", - "author_inst": "Public Health England" - }, - { - "author_name": "Gareth J Hughes", - "author_inst": "Public Health England" - }, - { - "author_name": "Matthew Barnard", - "author_inst": "UK Government Department of Health and Social Care" - }, - { - "author_name": "Leon Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Vipond", - "author_inst": "Public Health England" - }, - { - "author_name": "Alex Sienkiewicz", - "author_inst": "Public Health England" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "John Bell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Derrick W Crook", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nick Gent", - "author_inst": "Public Health England" - }, - { - "author_name": "A Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim EA Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.31.21254434", "rel_title": "Impact of COVID-19 in Individuals with Autism Spectrum Disorders: Analysis of a National Private Claims Insurance Database", @@ -813031,6 +811602,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.04.03.21254847", + "rel_title": "Equity Impacts of Dollar Store Vaccine Distribution", + "rel_date": "2021-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.03.21254847", + "rel_abs": "We use geospatial data to examine the unprecedented national program currently underway in the United States to distribute and administer vaccines against COVID-19. We quantify the impact of the proposed federal partnership with the company Dollar General to serve as vaccination sites and compare vaccine access with Dollar General to the current Federal Retail Pharmacy Partnership Program. Although dollar stores have been viewed with skepticism and controversy in the policy sector, we show that, relative to the locations of the current federal program, Dollar General stores are disproportionately likely to be located in Census tracts with high social vulnerability; using these stores as vaccination sites would greatly decrease the distance to vaccines for both low-income and minority households. We consider a hypothetical alternative partnership with Dollar Tree and show that adding these stores to the vaccination program would be similarly valuable, but impact different geographic areas than the Dollar General partnership. Adding Dollar General to the current pharmacy partners greatly surpasses the goal set by the Biden administration of having 90% of the population within 5 miles of a vaccine site. We discuss the potential benefits of leveraging these partnerships for other vaccinations, including against influenza.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Judith A Chevalier", + "author_inst": "Yale University" + }, + { + "author_name": "Jason L. Schwartz", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Yihua Sabrina Su", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Kevin R Williams", + "author_inst": "Yale School of Management" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.04.02.21254514", "rel_title": "Signatures of COVID-19 severity and immune response in the respiratory tract microbiome", @@ -814050,53 +812652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.03.24.21254188", - "rel_title": "Controlling the pandemic during the SARS-CoV-2 vaccination rollout: a modeling study", - "rel_date": "2021-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254188", - "rel_abs": "There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point control of COVID-19 would be achieved for each scenario.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Joao Viana", - "author_inst": "Faculdade de Ciencias, Universidade de Lisboa, Lisbon, Portugal" - }, - { - "author_name": "Christiaan H. van Dorp", - "author_inst": "Los Alamos National Laboratory, Los Alamos, New Mexico, USA" - }, - { - "author_name": "Ana Nunes", - "author_inst": "BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciencias, Universidade de Lisboa, Lisbon, Portugal" - }, - { - "author_name": "Manuel C. Gomes", - "author_inst": "Faculdade de Ciencias, Universidade de Lisboa, Lisbon, Portugal" - }, - { - "author_name": "Michiel van Boven", - "author_inst": "National Institute for Public Health and the Environment, Bilthoven, The Netherlands" - }, - { - "author_name": "Mirjam E. Kretzschmar", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - }, - { - "author_name": "Marc Veldhoen", - "author_inst": "Instituto de Medicina Molecular, Lisbon, Portugal" - }, - { - "author_name": "Ganna Rozhnova", - "author_inst": "University Medical Center Utrecht, Utrecht, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.02.21254856", "rel_title": "Background rates of hospitalizations and emergency department visits for selected thromboembolic and coagulation disorders in Ontario, Canada, 2015 to 2020, to inform COVID-19 vaccine safety surveillance", @@ -814857,6 +813412,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.30.21254564", + "rel_title": "Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways", + "rel_date": "2021-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254564", + "rel_abs": "Coronavirus Disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 SARS-CoV-2), which infects host cells with help from the Viral Entry (VE) proteins ACE2, TMPRSS2, and CTSL1-4. Proposed risk factors for viral infection, as well as the rate of disease progression, include age5,6, sex7, chronic obstructive pulmonary disease7,8, cancer9, and cigarette smoking10-13. To investigate whether the proposed risk factors increase viral infection by modulation of the VE genes, we examined gene expression profiles of 796 nasal and 1,673 bronchial samples across four lung cancer screening cohorts containing individuals without COVID-19. Smoking was the only clinical factor reproducibly associated with the expression of any VE gene across cohorts. ACE2 expression was significantly up-regulated with smoking in the bronchus but significantly down-regulated with smoking in the nose. Furthermore, expression of individual VE genes were not correlated between paired nasal and bronchial samples from the same patients. Single-cell RNA-seq of nasal brushings revealed that an ACE2 gene module was detected in a variety of nasal secretory cells with the highest expression in the C15orf48+ secretory cells, while a TMPRSS2 gene module was most highly expressed in nasal keratinizing epithelial cells. In contrast, single-cell RNA-seq of bronchial brushings revealed that ACE2 and\n\nTMPRSS2 gene modules were most enriched in MUC5AC+ bronchial goblet cells. The CTSL gene module was highly expressed in immune populations of both nasal and bronchial brushings. Deconvolution of bulk RNA-seq showed that the proportion of MUC5AC+ goblet cells was increased in current smokers in both the nose and bronchus but proportions of nasal keratinizing epithelial cells, C15orf48+ secretory cells, and immune cells were not associated with smoking status. The complex association between VE gene expression and smoking in the nasal and bronchial epithelium revealed by our results may partially explain conflicting reports on the association between smoking and SARS-CoV-2 infection.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Ke Xu", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Xingyi Shi", + "author_inst": "Boston Univeristy School of Medicine" + }, + { + "author_name": "Chris Husted", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Rui Hong", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Yichen Wang", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Boting Ning", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Travis Sullivan", + "author_inst": "Lahey Hospital & Medical Center" + }, + { + "author_name": "Kimberly M Rieger-Christ", + "author_inst": "Lahey Hospital & Medical Center" + }, + { + "author_name": "Fenghai Duan", + "author_inst": "Brown University School of Public Health" + }, + { + "author_name": "Helga Marques", + "author_inst": "Brown University School of Public Health" + }, + { + "author_name": "Adam C Gower", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Xiaohui Xiao", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Hanqiao Liu", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Gang Liu", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Grant Duclos", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Avrum Spira", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Sarah A Mazzilli", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Ehab Billatos", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Marc E Lenburg", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Joshua D Campbell", + "author_inst": "Boston University" + }, + { + "author_name": "Jennifer Beane", + "author_inst": "Boston University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.03.30.21254323", "rel_title": "A novel variant of interest of SARS-CoV-2 with multiple spike mutations is identified from travel surveillance in Africa", @@ -815956,45 +814610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.437955", - "rel_title": "To knot and not: Multiple conformations of the SARS-CoV-2 frameshifting RNA element", - "rel_date": "2021-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437955", - "rel_abs": "The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, \"RAG\" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribo-some during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tamar Schlick", - "author_inst": "NYU" - }, - { - "author_name": "Qiyao Zhu", - "author_inst": "New York University" - }, - { - "author_name": "Abhishek Dey", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Swati Jain", - "author_inst": "New York University" - }, - { - "author_name": "Shuting Yan", - "author_inst": "New York University" - }, - { - "author_name": "Alain Laederach", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.31.437925", "rel_title": "SARS-CoV-2 immune evasion by variant B.1.427/B.1.429", @@ -817051,6 +815666,49 @@ "type": "new results", "category": "developmental biology" }, + { + "rel_doi": "10.1101/2021.04.01.438120", + "rel_title": "Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein", + "rel_date": "2021-04-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.01.438120", + "rel_abs": "The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to enrich the Golgi-resident fraction of a wild-type SARS-CoV-2 S glycoprotein trimer, and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on soluble and virion S trimers, is predominantly modified in the Golgi by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shijian Zhang", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Eden P. Go", + "author_inst": "University of Kansas" + }, + { + "author_name": "Haitao Ding", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Saumya Anang", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "John C. Kappes", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Heather Desaire", + "author_inst": "University of Kansas" + }, + { + "author_name": "Joseph G. Sodroski", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.01.438036", "rel_title": "Fine-tuning the Spike: Role of the nature and topology of the glycan shield structure and dynamics of SARS-CoV-2 S", @@ -818090,65 +816748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254544", - "rel_title": "Prevalence of anti-SARS-CoV-2 antibodies in Poznan, Poland, after the first wave of the COVID-19 pandemic", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254544", - "rel_abs": "A serosurvey of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was performed between July and September 2020. Within this study, we found that 0.93% of the Pozna[n] metropolitan areas population had been exposed to SARS-CoV-2 after the first wave of coronavirus disease 2019 (COVID-19).", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Dagny Lorent", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Rafal Nowak", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Carolina Roxo", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Elzbieta Lenartowicz", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Aleksandra Makarewicz", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Bartosz Zaremba", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Szymon Nowak", - "author_inst": "Department and Clinic of Tropical and Parasitic Diseases, Poznan University of Medical Sciences, Poznan, Poland" - }, - { - "author_name": "Lukasz Kuszel", - "author_inst": "Department of Human Genetics, Poznan University of Medical Sciences, Poznan, Poland" - }, - { - "author_name": "Jerzy Stefaniak", - "author_inst": "Department and Clinic of Tropical and Parasitic Diseases, Poznan University of Medical Sciences, Poznan, Poland" - }, - { - "author_name": "Ryszard Kierzek", - "author_inst": "Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland" - }, - { - "author_name": "Pawel Zmora", - "author_inst": "Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.30.21254635", "rel_title": "Validity of markers and indexes of systemic inflammation in predicting mortality in COVID 19 infection : A hospital based cross sectional study", @@ -818645,6 +817244,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.29.21254579", + "rel_title": "Clustering of patient comorbidities within electronic medical records enables high-precision COVID-19 mortality prediction", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254579", + "rel_abs": "We present an explainable AI framework to predict mortality after a positive COVID-19 diagnosis based solely on data routinely collected in electronic healthcare records (EHRs) obtained prior to diagnosis. We grounded our analysis on the [1/2] Million people UK Biobank and linked NHS COVID-19 records. We developed a method to capture the complexities and large variety of clinical codes present in EHRs, and we show that these have a larger impact on risk than all other patient data but age. We use a form of clustering for natural language processing of the clinical codes, specifically, topic modelling by Latent Dirichlet Allocation (LDA), to generate a succinct digital fingerprint of a patients full secondary care clinical history, i.e. their comorbidities and past interventions. These digital comorbidity fingerprints offer immediately interpretable clinical descriptions that are meaningful, e.g. grouping cardiovascular disorders with common risk factors but also novel groupings that are not obvious. The comorbidity fingerprints differ in both their breadth and depth from existing observational disease associations in the COVID-19 literature. Taking this data-driven approach allows us to avoid human-induction bias and confirmation bias during selection of what are important potential predictors of COVID-19 mortality. Together with age, these digital fingerprints are the single most important factor in our predictor. This holds the potential for improving individual risk profiling for clinical decisions and the identification of groups for public health interventions such as vaccine programmes. Combining our digital precondition fingerprints with demographic characteristics allow us to match or exceed the performance of existing state-of-the-art COVID-19 mortality predictors (EHCF) which have been developed through expert consensus. Our precondition fingerprinting and entire mortality prediction analytics pipeline are designed so as to be rapidly redeployable, e.g. for COVID-19 variants or other pre-existing diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Erwann Le Lannou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Benjamin Post", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shlomi Haar", + "author_inst": "Imperial College London" + }, + { + "author_name": "Stephen Brett", + "author_inst": "Imperial College London" + }, + { + "author_name": "Balasundaram Kadirvelu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aldo A. Faisal", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254565", "rel_title": "Pediatric household transmission of SARS-CoV-2 infection", @@ -819600,41 +818238,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.29.21254568", - "rel_title": "Nonpharmaceutical Interventions Remain Essential to Reducing COVID-19 Burden Even in a Well-Vaccinated Society: A Modeling Study", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254568", - "rel_abs": "Vaccination and non-pharmaceutical interventions (NPIs) reduce transmission of SARS-CoV-2 infection, but their effectiveness depends on coverage and adherence levels. We used scenario modeling to evaluate their effects on cases and deaths averted and herd immunity. NPIs and vaccines worked synergistically in different parts of the pandemic to reduce disease burden.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tom\u00e1s M. Le\u00f3n", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jason Vargo", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Erica S. Pan", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Priya B. Shete", - "author_inst": "California Department of Public Health, University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.29.21254583", "rel_title": "Migration of households from New York City and the Second Peak in Covid-19 cases in New Jersey, Connecticut and New York Counties.", @@ -820371,6 +818974,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.30.437704", + "rel_title": "Sequence analysis of SARS-CoV-2 in nasopharyngeal samples from patients with COVID-19 illustrates population variation and diverse phenotypes, placing the in vitro growth properties of B.1.1.7 and B.1.351 lineage viruses in context.", + "rel_date": "2021-03-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.30.437704", + "rel_abs": "New variants of SARS-CoV-2 are continuing to emerge and dominate the regional and global sequence landscapes. Several variants have been labelled as Variants of Concern (VOCs) because of perceptions or evidence that these may have a transmission advantage, increased risk of morbidly and/or mortality or immune evasion in the context of prior infection or vaccination. Placing the VOCs in context and also the underlying variability of SARS-CoV-2 is essential in understanding virus evolution and selection pressures. Sequences of SARS-CoV-2 in nasopharyngeal swabs from hospitalised patients in the UK were determined and virus isolated. The data indicated the virus existed as a population with a consensus level and non-synonymous changes at a minor variant. For example, viruses containing the nsp12 P323L variation from the Wuhan reference sequence, contained minor variants at the position including P and F and other amino acids. These populations were generally preserved when isolates were amplified in cell culture. In order to place VOCs B.1.1.7 (the UK Kent variant) and B.1.351 (the South African variant) in context their growth was compared to a spread of other clinical isolates. The data indicated that the growth in cell culture of the B.1.1.7 VOC was no different from other variants, suggesting that its apparent transmission advantage was not down to replicating more quickly. Growth of B.1.351 was towards the higher end of the variants. Overall, the study suggested that studying the biology of SARS-CoV-2 is complicated by population dynamics and that these need to be considered with new variants.\n\nImportanceSARS-CoV-2 is the causative agent of COVID-19. The virus has spread across the planet causing a global pandemic. In common with other coronaviruses, SARS-CoV-2 genetic material (genomes) can become quite diverse as a consequence of replicating inside cells. This has given rise to multiple variants from the original virus that infected humans. These variants may have different properties and in the context of a widespread vaccination program may render vaccines less ineffective. Our research confirms the degree of genetic diversity of SARS-CoV-2 in patients. By isolating viruses from these patients, we show that there is a 100-fold range in growth of even normal variants. Interestingly, by comparing this to the pattern seen with two Variants of Concern (UK and South African variants), we show that at least in cells the ability of the B.1.1.7 variant to grow is not substantially different to many of the previous variants.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Tessa Prince", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "Xiaofeng Dong", + "author_inst": "Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Rebekah Penrice-Randal", + "author_inst": "Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Nadine Randle", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "Catherine Hartley", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "Hannah Goldswain", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "Benjamin Jones", + "author_inst": "Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK." + }, + { + "author_name": "Malcolm G Semple", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Peter J. M. Openshaw", + "author_inst": "Imperial College, UK." + }, + { + "author_name": "Lance Turtle", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "- ISARIC4C Investigators", + "author_inst": "-" + }, + { + "author_name": "Grant Hughes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Enyia Anderson", + "author_inst": "Liverpool School of Tropical Medicine, UK" + }, + { + "author_name": "Edward I Patterson", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Julian Druce", + "author_inst": "University of Melbourne, Australia." + }, + { + "author_name": "Gavin Screaton", + "author_inst": "University of Oxford, UK." + }, + { + "author_name": "Miles Carroll", + "author_inst": "Public Health England, UK." + }, + { + "author_name": "James P Stewart", + "author_inst": "University of Liverpool, UK." + }, + { + "author_name": "Julian Alexander Hiscox", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.30.437622", "rel_title": "Rapid characterization of spike variants via mammalian cell surface display", @@ -821462,45 +820160,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.26.21254445", - "rel_title": "LncRNAs NEAT1 and MALAT1 Differentiate Inflammation in Severe COVID-19 Patients", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254445", - "rel_abs": "Hyperactive and damaging inflammation is a hallmark of severe rather than mild COVID-19 syndrome. To uncover key inflammatory differentiators between severe and mild COVID-19 disease, we applied an unbiased single-cell transcriptomic analysis. We integrated a bronchoalveolar lavage (BAL) dataset with a peripheral blood mononuclear cell dataset (PBMC) and analyzed the combined cell population, focusing on genes associated with disease severity. Distinct cell populations were detected in both BAL and PBMC where the immunomodulatory long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 were highly differentially expressed between mild and severe patients. The detection of other severity associated genes involved in cellular stress response and apoptosis regulation suggests that the pro-inflammatory functions of these lncRNAs may foster cell stress and damage. The lncRNAs NEAT1 andMALAT1 are potential components of immune dysregulation in COVID-19 that may provide targets for severity related diagnostic measures or therapy.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kai Huang", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Catherine Wang", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Christen Vagts", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Vanitha Raguveer", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Patricia Finn", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "David L Perkins", - "author_inst": "University of Illinois at Chicago" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.27.21253966", "rel_title": "Clinical performance evaluation of SARS-CoV-2 rapid antigen testing in point of care usage in comparison to RT-qPCR", @@ -822313,6 +820972,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.28.437426", + "rel_title": "COVID-19 dominant D614G mutation in the SARS-CoV-2 spike protein desensitizes its temperature-dependent denaturation", + "rel_date": "2021-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.28.437426", + "rel_abs": "The D614G mutation in the spike protein of SARS-CoV-2 alters the fitness of the virus, making it the dominant form in the COVID-19 pandemic. Here we demonstrated by cryo-electron microscopy that the D614G mutation does not significantly perturb the structure of the spike protein, but multiple receptor binding domains are in an upward conformation poised for host receptor binding. The impact of the mutation lies in its ability to eliminate the unusual cold-induced unfolding characteristics, and to significantly increase the thermal stability under physiological pH. Our findings shed light on how the D614G mutation enhances the infectivity of SARS-CoV-2 through a stabilizing mutation, and suggest an approach for better design of spike-protein based conjugates for vaccine development.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Tzu-Jing Yang", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taiwan" + }, + { + "author_name": "Pei-Yu Yu", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan" + }, + { + "author_name": "Yuan-Chih Chang", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Academia Sinica Cryo-EM Center, Academia Sinica, Taiwan" + }, + { + "author_name": "Chu-Wei Kuo", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan" + }, + { + "author_name": "Kay-Hooi Khoo", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taiwan" + }, + { + "author_name": "Shang-Te Danny Hsu", + "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taiwan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.03.29.437515", "rel_title": "Enrichment of SARS-CoV-2 entry factors and interacting intracellular genes in peripheral immune cells", @@ -823108,41 +821806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.25.21254293", - "rel_title": "Early experiences of rehabilitation for patients post-COVID to improve fatigue, breathlessness exercise capacity and cognition.", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254293", - "rel_abs": "Patients with lasting symptoms of COVID-19 should be offered a comprehensive recovery programme. Patients that completed a six week, twice supervised adapted pulmonary rehabilitation programme demonstrated statistically significant improvements in exercise capacity, respiratory symptoms, fatigue and cognition. Participants improved by 112m on the Incremental Shuttle Walking Test and 544 seconds on the Endurance Shuttle Walking Test. There were no serious adverse events recorded, and there were no dropouts related to symptom worsening. COVID-19 rehabilitation appears feasible and significantly improves clinical outcomes.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Enya Daynes", - "author_inst": "Centre of Exercise and Rehabilitation Sciences" - }, - { - "author_name": "Charlotte Gerlis", - "author_inst": "Centre of Exercise and Rehabilitation Sciences" - }, - { - "author_name": "Emma Chaplin", - "author_inst": "University Hospitals of Leicester" - }, - { - "author_name": "Nikki Gardiner", - "author_inst": "University Hospitals of Leicester" - }, - { - "author_name": "Sally J Singh", - "author_inst": "Centre of Exercise and Rehabilitation Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.03.25.21253908", "rel_title": "A unique SARS-CoV-2 spike protein P681H strain detected in Israel", @@ -823979,6 +822642,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.20.21254035", + "rel_title": "SARS-CoV-2 Acquisition and Immune Pathogenesis Among School-Aged Learners in Four K-12 Schools", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254035", + "rel_abs": "BackgroundUnderstanding SARS-CoV-2 infection in children is necessary to reopen schools safely.\n\nMethodsWe measured SARS-CoV-2 infection in 320 learners [10.5 {+/-} 2.1(sd); 7-17 y.o.] at four diverse schools with either remote or on-site learning. Schools A and B served low-income Hispanic learners; school C served many special-needs learners; and all provided predominantly remote instruction. School D served middle- and upper-income learners, with predominantly on-site instruction. Testing occurred in the fall (2020), and 6-8 weeks later during the fall-winter surge (notable for a tenfold increase in COVID-19 cases). Immune responses and mitigation fidelity were also measured.\n\nResultsWe found SARS-CoV-2 infections in 17 learners only during the surge. School A (97% remote learners) had the highest infection (10/70, 14.3%, p<0.01) and IgG positivity rates (13/66, 19.7%). School D (93% on-site learners) had the lowest infection and IgG positivity rates (1/63, 1.6%). Mitigation compliance [physical distancing (mean 87.4%) and face covering (91.3%)] was remarkably high at all schools. Documented SARS-CoV-2-infected learners had neutralizing antibodies (94.7%), robust IFN-{gamma}+ T cell responses, and reduced monocytes.\n\nConclusionSchools can implement successful mitigation strategies across a wide range of student diversity. Despite asymptomatic to mild SARS-CoV-2 infection, children generate robust humoral and cellular immune responses.\n\nKey PointsO_LISuccessful COVID-19 mitigation was implemented across a diverse range of schools.\nC_LIO_LISchool-associated SARS-CoV-2 infections reflect regional rates rather than remote or on-site learning.\nC_LIO_LISeropositive school-aged children with asymptomatic to mild SARS-CoV-2 infections generate robust humoral and cellular immunity.\nC_LI", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Dan M Cooper", + "author_inst": "Institute for Clinical and Translational Science, University of California at Irvine, Irvine, California; Department of Pediatrics, University of California at " + }, + { + "author_name": "Michael Z Zulu", + "author_inst": "Center for Virus Research, University of California at Irvine, School of Biological Sciences, Irvine, California" + }, + { + "author_name": "Allen Jankeel", + "author_inst": "Center for Virus Research, University of California at Irvine, School of Biological Sciences, Irvine, California" + }, + { + "author_name": "Izabela Coimbra Ibraim", + "author_inst": "Center for Virus Research, University of California at Irvine, School of Biological Sciences, Irvine, California" + }, + { + "author_name": "Jessica Ardo", + "author_inst": "Childrens Hospital of Orange County, Orange, California" + }, + { + "author_name": "Kirsten Kasper", + "author_inst": "Childrens Hospital of Orange County, Orange, California" + }, + { + "author_name": "Diana Stephens", + "author_inst": "Institute for Clinical and Translational Science, University of California at Irvine, Irvine, California" + }, + { + "author_name": "Andria Meyer", + "author_inst": "Institute for Clinical and Translational Science, University of California at Irvine, Irvine, California" + }, + { + "author_name": "Annamarie Stehli", + "author_inst": "Pediatric Exercise and Genomics Research Center, Department of Pediatrics, University of California Irvine, Irvine, California;" + }, + { + "author_name": "Curt Condon", + "author_inst": "Orange County Health Care Agency, Santa Ana, California" + }, + { + "author_name": "Mary E Londono", + "author_inst": "University of California Irvine School of Medicine, Irvine, California" + }, + { + "author_name": "Casey M Schreiber", + "author_inst": "University of California Irvine Health, Orange, California; Children's Hospital of Orange County, Orange, California" + }, + { + "author_name": "Nanette V Lopez", + "author_inst": "Center for Health Equity Research, Department of Health Sciences, Northern Arizona University, Flagstaff, Arizona" + }, + { + "author_name": "Ricky L Camplain", + "author_inst": "Center for Health Equity Research, Department of Health Sciences, Northern Arizona University, Flagstaff, Arizona" + }, + { + "author_name": "Michael Weiss", + "author_inst": "Children's Hospital of Orange County, Orange, California" + }, + { + "author_name": "Charles Golden", + "author_inst": "Children's Hospital of Orange County, Orange, California" + }, + { + "author_name": "Shlomit Aizik", + "author_inst": "Pediatric Exercise and Genomics Research Center, Department of Pediatrics, University of California Irvine, Irvine, California" + }, + { + "author_name": "Bernadette Boden-Albala", + "author_inst": "Program in Public Health, University of California Irvine, Irvine, California" + }, + { + "author_name": "Clayton Chau", + "author_inst": "Orange County Health Care Agency, Santa Ana, California" + }, + { + "author_name": "Ilhem Messaoudi", + "author_inst": "Center for Virus Research, University of California Irvine, School of Biological Sciences, Irvine, California" + }, + { + "author_name": "Erlinda R Ulloa", + "author_inst": "Department of Pediatrics, University of California at Irvine School of Medicine, Irvine, California; Division of Infectious Diseases, Children's Hospital of Ora" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.03.21.21254065", "rel_title": "The health effects in the US of quarantine policies based on predicted individual risk of severe COVID-19 outcomes", @@ -825270,49 +824032,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.22.21254100", - "rel_title": "A global database of COVID-19 vaccinations", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254100", - "rel_abs": "An effective rollout of vaccinations against COVID-19 offers the most promising prospect of bringing the pandemic to an end. We present the Our World in Data COVID-19 vaccination dataset, a global public dataset that tracks the scale and rate of the vaccine rollout across the world. This dataset is updated regularly, and includes data on the total number of vaccinations administered; first and second doses administered; daily vaccination rates; and population-adjusted coverage for all countries for which data is available (138 countries as of 17 March 2021). It will be maintained as the global vaccination campaign continues to progress. This resource aids policymakers and researchers in understanding the rate of current and potential vaccine rollout; the interactions with non-vaccination policy responses; the potential impact of vaccinations on pandemic outcomes such as transmission, morbidity, and mortality; and global inequalities in vaccine access.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Edouard Mathieu", - "author_inst": "Our World in Data" - }, - { - "author_name": "Hannah Ritchie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Esteban Ortiz-Ospina", - "author_inst": "University of Oxford" - }, - { - "author_name": "Max Roser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Joe Hasell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Cameron Appel", - "author_inst": "Our World in Data" - }, - { - "author_name": "Charlie Giattino", - "author_inst": "Our World in Data" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.22.21254082", "rel_title": "Epidemiology and transmission of COVID-19 in cases and close contacts in Georgia in the first four months of the epidemic", @@ -826085,6 +824804,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.22.21254125", + "rel_title": "Testing and Vaccination to Reduce the Impact of COVID-19 in Nursing Homes: An Agent-Based Approach", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254125", + "rel_abs": "BackgroundEfforts to protect residents in nursing homes involve non-pharmaceutical interventions, testing, and vaccine. We sought to quantify the effect of testing and vaccine strategies on the attack rate, length of the epidemic, and hospitalization.\n\nMethodsWe developed an agent-based model to simulate the dynamics of SARS-CoV-2 transmission in a nursing home with resident and staff agents. Interactions between 172 residents and 170 staff were assumed based on data from a nursing home in Los Angeles, CA. We simulated scenarios assuming different levels of non-pharmaceutical interventions, testing frequencies, and vaccine efficacy to block transmission.\n\nResultsUnder the hypothetical scenario of widespread SARS-CoV-2 in the community, 3-day testing frequency minimized the attack rate and the time to eradicate an outbreak. Prioritization of vaccine among staff or staff and residents minimized the cumulative number of infections and hospitalization, particularly in the scenario of high probability of an introduction. Reducing the probability of a virus introduction reduced the demand on testing and vaccine to reduce infections and hospitalizations.\n\nConclusionsImproving frequency of testing from 7-days to 3-days minimized the number of infections and hospitalizations, despite widespread community transmission. Vaccine prioritization of staff provides the best protection strategy, despite high risk of a virus introduction.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jose Pablo G\u00f3mez-V\u00e1zquez", + "author_inst": "Center for Animal Disease Modeling and Surveillance, University of California Davis, CA, USA" + }, + { + "author_name": "yury Garc\u00eda", + "author_inst": "Department of Public Health Sciences, University of California Davis, CA, USA" + }, + { + "author_name": "Alec J Schmidt", + "author_inst": "Department of Public Health Sciences, University of California Davis, CA, USA" + }, + { + "author_name": "Beatriz Mart\u00ednez-L\u00f3pez", + "author_inst": "Center for Animal Disease Modeling and Surveillance, University of California Davis, CA, USA" + }, + { + "author_name": "Miriam Nu\u00f1o", + "author_inst": "Department of Public Health Sciences, University of California Davis, CA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.23.21253727", "rel_title": "Development of a Codebook of Online Anti-Vaccination Rhetoric to Manage COVID-19 Vaccine Misinformation", @@ -827112,73 +825866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.25.21254376", - "rel_title": "A differential regulatory T cell signature distinguishes the immune landscape of COVID-19 hospitalized patients from those hospitalized with other respiratory viral infections", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254376", - "rel_abs": "SARS-CoV-2 infection has caused a lasting global pandemic costing millions of lives and untold additional costs. Understanding the immune response to SARS-CoV-2 has been one of the main challenges in the past year in order to decipher mechanisms of host responses and interpret disease pathogenesis. Comparatively little is known in regard to how the immune response against SARS-CoV-2 differs from other respiratory infections. In our study, we compare the peripheral blood immune signature from SARS-CoV-2 infected patients to patients hospitalized pre-pandemic with Influenza Virus or Respiratory Syncytial Virus (RSV). Our in-depth profiling indicates that the immune landscape in patients infected by SARS-CoV-2 is largely similar to patients hospitalized with Flu or RSV. Similarly, serum cytokine and chemokine expression patterns were largely overlapping. Unique to patients infected with SARS-CoV-2 who had the most critical clinical disease state were changes in the regulatory T cell (Treg) compartment. A Treg signature including increased frequency, activation status, and migration markers was correlated with the severity of COVID-19 disease. These findings are particularly relevant as Tregs are being discussed as a therapy to combat the severe inflammation seen in COVID-19 patients. Likewise, having defined the overlapping immune landscapes in SARS-CoV-2, existing knowledge of Flu and RSV infections could be leveraged to identify common treatment strategies.\n\nHighlightsO_LIThe immune landscapes of hospitalized pre-pandemic RSV and influenza patients are similar to SARS-CoV-2 patients\nC_LIO_LISerum cytokine and chemokine expression patterns are largely similar between patients hospitalized with respiratory virus infections, including SARS-CoV-2, versus healthy donors\nC_LIO_LISARS-CoV-2 patients with the most critical disease displayed unique changes in the Treg compartment\nC_LIO_LIadvances in understanding and treating SARS-CoV-2 could be leveraged for other common respiratory infections\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC=\"FIGDIR/small/21254376v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@1dddb4corg.highwire.dtl.DTLVardef@689a1corg.highwire.dtl.DTLVardef@15db5eaorg.highwire.dtl.DTLVardef@1521659_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sarah C Vick", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Marie Frutoso", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Florian Mair", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew J Konecny", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Evan Greene", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Caitlin R Wold", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Jim Boonyaratanakornkit", - "author_inst": "Fred Hutchinon Cancer Research Center" - }, - { - "author_name": "Raphael Gottardo", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Joshua T Schiffer", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Martin Prlic", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jennifer M. Lund", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.03.23.21254209", "rel_title": "Vascular Comorbidities Worsen Prognosis of Patients with Heart Failure Hospitalized with COVID-19", @@ -827727,6 +826414,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.24.21254227", + "rel_title": "COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254227", + "rel_abs": "The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Darryl P Leong", + "author_inst": "McMaster University" + }, + { + "author_name": "Amitava Banerjee", + "author_inst": "University College London" + }, + { + "author_name": "Salim Yusuf", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.23.21253730", "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 virus in the adult Norwegian population, winter 2020/2021: pre-vaccination period", @@ -828630,57 +827344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.24.21254240", - "rel_title": "Antibody response to first and second dose of BNT162b2 in a cohort of characterized healthcare workers", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254240", - "rel_abs": "BackgroundVaccine-induced population immunity is a key global strategy to control coronavirus disease 2019 (COVID-19). The rapid implementation and availability of several COVID-19 vaccines is now a global health-care priority but more information about humoral responses to single- and double-dose vaccine is needed\n\nMethods163 health care workers (HCW) of the Padua University Hospitals, who underwent a complete vaccination campaign with BNT162b2 vaccine were asked to collect serum samples at 12 (t12) and 28 (t28) days after the first inoculum to allow the measurement of SARS-CoV-2 Antibodies (Ab) using chemiluminescent assays against the spike (S) protein and the Receptor Binding Domain (RBD) of the virus, respectively.\n\nResultsSignificant differences were found at t12 for infection-naive and subjects with previous-natural infection who present higher values of specific antibodies, while no significant differences have been found between t12 and t28. No statistically significant difference was found between male and female, while lower Ab levels have been observed in subjects older than 60 years at t12 but not at t28.\n\nConclusionsOur study confirms observed differences in vaccine responses between infection-naive and subjects with previous natural infection at t12 but not for a longer time. The influence of sex and age deserves further studies, even if the relationship with age seems particularly significant.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Andrea Padoan", - "author_inst": "university of padova" - }, - { - "author_name": "Luigi Dall'Olmo", - "author_inst": "Padua University Hospital" - }, - { - "author_name": "Foscarina Della Rocca", - "author_inst": "University hospital of padova" - }, - { - "author_name": "Francesco Barbaro", - "author_inst": "University hospital of padova" - }, - { - "author_name": "Chiara Cosma", - "author_inst": "University hospital of padova" - }, - { - "author_name": "Daniela Basso", - "author_inst": "University of Padova" - }, - { - "author_name": "Annamaria Cattelan", - "author_inst": "University hospital of padova" - }, - { - "author_name": "Vito Cianci", - "author_inst": "University hospital of padova" - }, - { - "author_name": "Mario Plebani", - "author_inst": "University of Padova" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21252635", "rel_title": "Tenofovir-DF versus Hydroxychloroquine in the Treatment of Hospitalized Patients with COVID-19: An Observational Study (THEDICOV)", @@ -829321,6 +827984,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.25.21254315", + "rel_title": "Characterizing the incidence of adverse events of special interest for COVID-19 vaccines across eight countries: a multinational network cohort study", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254315", + "rel_abs": "BackgroundAs large-scale immunization programs against COVID-19 proceed around the world, safety signals will emerge that need rapid evaluation. We report population-based, age- and sex- specific background incidence rates of potential adverse events of special interest (AESI) in eight countries using thirteen databases.\n\nMethodsThis multi-national network cohort study included eight electronic medical record and five administrative claims databases from Australia, France, Germany, Japan, Netherlands, Spain, the United Kingdom, and the United States, mapped to a common data model. People observed for at least 365 days before 1 January 2017, 2018, or 2019 were included. We based study outcomes on lists published by regulators: acute myocardial infarction, anaphylaxis, appendicitis, Bells palsy, deep vein thrombosis, disseminated intravascular coagulation, encephalomyelitis, Guillain-Barre syndrome, hemorrhagic and non-hemorrhagic stroke, immune thrombocytopenia, myocarditis/pericarditis, narcolepsy, pulmonary embolism, and transverse myelitis. We calculated incidence rates stratified by age, sex, and database. We pooled rates across databases using random effects meta-analyses. We classified meta-analytic estimates into Council of International Organizations of Medical Sciences categories: very common, common, uncommon, rare, or very rare.\n\nFindingsWe analysed 126,661,070 people. Rates varied greatly between databases and by age and sex. Some AESI (e.g., myocardial infarction, Guillain-Barre syndrome) increased with age, while others (e.g., anaphylaxis, appendicitis) were more common in young people. As a result, AESI were classified differently according to age. For example, myocardial infarction was very rare in children, rare in women aged 35-54 years, uncommon in men and women aged 55-84 years, and common in those aged [≥]85 years.\n\nInterpretationWe report robust baseline rates of prioritised AESI across 13 databases. Age, sex, and variation between databases should be considered if background AESI rates are compared to event rates observed with COVID-19 vaccines.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Xintong Li", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Anna Ostropolets", + "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA" + }, + { + "author_name": "Rupa Makadia", + "author_inst": "Janssen Research and Development, Titusville, NJ, USA" + }, + { + "author_name": "Azza Shoaibi", + "author_inst": "Janssen Research and Development, Titusville, NJ, USA" + }, + { + "author_name": "Gowtham Rao", + "author_inst": "Janssen Research and Development, Titusville, NJ, USA" + }, + { + "author_name": "Anthony G. Sena", + "author_inst": "Janssen Research and Development, Titusville, NJ, USA . Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Eugenia Martinez-Hernandez", + "author_inst": "Neurology Department, Hospital Clinic de Barcelona and University of Barcelona, Barcelona, Spain" + }, + { + "author_name": "Antonella Delmestri", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Katia Verhamme", + "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Peter Rijnbeek", + "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Talita Duarte-Salles", + "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina" + }, + { + "author_name": "Marc A Suchard", + "author_inst": "Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles. Department of Human Genetics, David Geffen School of Medic" + }, + { + "author_name": "Patrick B Ryan", + "author_inst": "Janssen Research and Development, Titusville, NJ, USA. Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA" + }, + { + "author_name": "George Hripcsak", + "author_inst": "Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA" + }, + { + "author_name": "DANIEL PRIETO-ALHAMBRA", + "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford, Oxford, United Kingdom. Department of Medical Informatics, Erasmus University Medical Center, R" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.25.21254219", "rel_title": "Re-opening schools in a context of low COVID-19 contagion: Consequences for teachers, students and their parents", @@ -830372,37 +829110,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.25.437113", - "rel_title": "Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility", - "rel_date": "2021-03-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.437113", - "rel_abs": "We explore the energetic frustration patterns associated with the binding between the SARS-CoV-2 spike protein and the ACE2 receptor protein in a broad selection of animals. Using energy landscape theory and the concept of energy frustration--theoretical tools originally developed to study protein folding--we are able to identify interactions among residues of the spike protein and ACE2 that result in COVID-19 resistance. This allows us to identify whether or not a particular animal is susceptible to COVID-19 from the protein sequence of ACE2 alone. Our analysis predicts a number of experimental observations regarding COVID-19 susceptibility, demonstrating that this feature can be explained, at least partially, on the basis of theoretical means.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ryan R. Cheng", - "author_inst": "Rice University" - }, - { - "author_name": "Esteban Dodero-Rojas", - "author_inst": "Rice University" - }, - { - "author_name": "Michele Di Pierro", - "author_inst": "Northeastern University" - }, - { - "author_name": "Jos\u00e9 Nelson Onuchic", - "author_inst": "Rice University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.03.24.21254270", "rel_title": "Counties with lower insurance coverage are associated with both slower vaccine rollout and higher COVID-19 incidence across the United States", @@ -831091,6 +829798,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.20.21253990", + "rel_title": "Changes in live births, preterm birth, low birth weight, and cesarean deliveries in the United States during the SARS-CoV-2 pandemic", + "rel_date": "2021-03-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21253990", + "rel_abs": "BackgroundThe SARS-CoV-2 pandemic and associated social, economic, and clinical disruption have been widely speculated to affect pregnancy decision-making and outcomes. While a few US-based studies have examined subnational changes in fertility, preterm birth, and stillbirth, there remains limited knowledge of how the pandemic impacted childbearing and a broader set of perinatal health indicators at the national-level throughout 2020. Here, we use recently released national-level data to fill this gap. Importantly, we, unlike earlier work, use time-series methods to account for strong temporal patterning (e.g., seasonality, trend) that could otherwise lead to spurious findings.\n\nMethodsFor the years 2015 to 2020, we obtained national monthly counts of births and rates (per 100 births) for six perinatal indicators: preterm birth (<37 weeks gestation), early preterm birth (<34 weeks gestation), late preterm birth (34-36 weeks gestation), low birth weight birth (<2500 g), very low birth weight birth (<1500 g), and cesarean delivery. We use an interrupted time-series approach to compare the outcomes observed after the pandemic began (March 2020) to those expected had the pandemic not occurred.\n\nResultsFor total births as well as five of the six indicators (i.e., all but the rate of cesarean delivery), observed values fall well below expected levels (p<.0001 for each test) during the entire pandemic period. Declines in preterm birth and low birth weight were largest in magnitude in both early and later stages of the 2020 pandemic, while those for live births occurred at the end of the year.\n\nDiscussionOur findings provide some of the first national evidence of substantial reductions in live births and adverse perinatal outcomes during the SARS-CoV-2 pandemic. Only cesarean delivery appeared unaffected. These declines were not uniform across the pandemic, suggesting that several mechanisms, which require further study, may explain these patterns.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alison Gemmill", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joan A. Casey", + "author_inst": "Columbia University Mailman School of Public Health" + }, + { + "author_name": "Ralph Catalano", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Deborah Karasek", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tim-Allen Bruckner", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.03.21.21253418", "rel_title": "Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil", @@ -832333,89 +831075,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.18.21253633", - "rel_title": "Characterising long COVID more than 6 months after acute infection in adults; prospective longitudinal cohort study, England", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253633", - "rel_abs": "BackgroundMost individuals with COVID-19 will recover without sequelae, but some will develop long-term multi-system impairments. The definition, duration, prevalence and symptoms associated with long COVID, however, have not been established.\n\nMethodsPublic Health England (PHE) initiated longitudinal surveillance of clinical and non-clinical healthcare workers for monthly assessment and blood sampling for SARS-CoV-2 antibodies in March 2020. Eight months after enrolment, participants completed an online questionnaire including 72 symptoms in the preceding month. Symptomatic mild-to-moderate cases with confirmed COVID-19 were compared with asymptomatic, seronegative controls. Multivariable logistic regression was used to identify independent symptoms associated with long COVID.\n\nFindingsAll 2,147 participants were contacted and 1,671 (77.8%) completed the questionnaire, including 140 (8.4%) cases and 1,160 controls. At a median of 7.5 (IQR 7.1-7.8) months after infection, 20 cases (14.3%) had ongoing (4/140, 2.9%) or episodic (16/140, 11.4%) symptoms. We identified three clusters of symptoms associated with long COVID, those affecting the sensory (ageusia, anosmia, loss of appetite and blurred vision), neurological (forgetfulness, short-term memory loss and confusion/brain fog) and cardiorespiratory (chest tightness/pain, unusual fatigue, breathlessness after minimal exertion/at rest, palpitations) systems. The sensory cluster had the highest association with being a case (aOR 5.25, 95% CI 3.45-8.01). Dermatological, gynaecological, gastrointestinal or mental health symptoms were not significantly different between cases and controls.\n\nInterpretationMost persistent symptoms reported following mild COVID-19 were equally common in cases and controls. While all three clusters identified had a strong association with cases, the sensory cluster had the highest specificity and strength of association, and therefore, most likely to be characteristic of long COVID.\n\nFundingPHE.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed using search terms \"long covid*\" OR \"post COVID*\" in adults for studies including cohort, case reports, randomised control trials, cross-sectional and systematic reviews published up to 12 March 2020 without any language restrictions. Most reports included a small number of cases. Larger studies included very specific cohorts, including hospitalised cases and self-selected participants with COVID-19. A systematic review identified 15 studies and, using a broad case definition, concluded that 80% (95% CI 65-92) of patients with SARS-CoV-2 developed one or more long-term symptoms. The five most common symptoms were fatigue (58%), headache (44%), attention disorder (27%), hair loss (25%), and dyspnea (24%), but no assessment was made of these symptoms in uninfected adults.\n\nAdded value of this studyIn a prospective, longitudinal cohort of clinical and non-clinical healthcare workers recruited at the start of the pandemic, we found that most self-reported symptoms were as common in 140 adults who developed mild-to-moderate COVID-19 more than 6 months previously compared to 1,160 controls who were asymptomatic and SARS-CoV-2 antibody negative throughout the surveillance period. Compared to controls, we identified three clusters of symptoms affecting the sensory, neurological and cardiorespiratory systems that were more prevalent among cases. Notably, symptoms affecting other organ systems were as prevalent among cases as controls. The high proportion of cases and controls reporting mental health symptoms highlights the toll that the pandemic has had on healthcare workers\n\nImplications of all the available evidenceOur findings highlight the importance of including a representative cohort of cases to assess long-term outcomes of COVID-19 as well as appropriate controls to estimate the relative prevalence of self-reported symptoms to accurately define this new syndrome. Our study adds to the evidence-base for long COVID in adults with mild-to-moderate COVID-19 who contribute to the vast majority of 120+ million infections worldwide. This information is not only important for clinicians, patients and the public, but also for policy makers and healthcare providers who are investing heavily in long-term provisions for COVID-19 survivors.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Zahin Amin-Chowdhury", - "author_inst": "Public Health England" - }, - { - "author_name": "Ross J Harris", - "author_inst": "Public Health England" - }, - { - "author_name": "Felicity Aiano", - "author_inst": "Public Health England" - }, - { - "author_name": "Maria Zavala", - "author_inst": "Public Health England" - }, - { - "author_name": "Marta Bertran", - "author_inst": "Public Health England" - }, - { - "author_name": "Ray Borrow", - "author_inst": "Public Health England" - }, - { - "author_name": "Ezra Linley", - "author_inst": "Public Health England" - }, - { - "author_name": "Shazaad Ahmad", - "author_inst": "Manchester NHS Foundation Trust" - }, - { - "author_name": "Ben Parker", - "author_inst": "Manchester NHS Foundation Trust" - }, - { - "author_name": "Alex Horsley", - "author_inst": "Manchester NHS Foundation Trust" - }, - { - "author_name": "Bassam Hallis", - "author_inst": "Public Health England" - }, - { - "author_name": "Jessica Flood", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin E Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary E Ramsay", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Shamez N Ladhani", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253429", "rel_title": "SARS-CoV-2 Seroprevalence in 12 Cities of India from July-December 2020", @@ -832992,6 +831651,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.16.21253662", + "rel_title": "WiFi mobility models for COVID-19 enable less burdensome and more localized interventions for university campuses", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253662", + "rel_abs": "Infectious diseases, like COVID-19, pose serious challenges to university campuses, which typically adopt closure as a non-pharmaceutical intervention to control spread and ensure a gradual return to normalcy. Intervention policies, such as remote instruction (RI) where large classes are offered online, reduce potential contact but also have broad side-effects on campus by hampering the local economy, students learning outcomes, and community wellbeing. In this paper, we demonstrate that university policymakers can mitigate these tradeoffs by leveraging anonymized data from their WiFi infrastructure to learn community mobility --- a methodology we refer to as WiFi mobility models (WO_SCPLOWIC_SCPLOWMO_SCPLOWOBC_SCPLOW). This approach enables policymakers to explore more granular policies like localized closures (LC). WO_SCPLOWIC_SCPLOWMO_SCPLOWOBC_SCPLOW can construct contact networks that capture behavior in various spaces, highlighting new potential transmission pathways and temporal variation in contact behavior. Additionally, WO_SCPLOWIC_SCPLOWMO_SCPLOWOBC_SCPLOW enables us to design LC policies that close super-spreader locations on campus. By simulating disease spread with contact networks from WO_SCPLOWIC_SCPLOWMO_SCPLOWOBC_SCPLOW, we find that LC maintains the same reduction in cumulative infections as RI while showing greater reduction in peak infections and internal transmission. Moreover, LC reduces campus burden by closing fewer locations, forcing fewer students into completely online schedules, and requiring no additional isolation. WO_SCPLOWIC_SCPLOWMO_SCPLOWOBC_SCPLOW can empower universities to conceive and assess a variety of closure policies to prevent future outbreaks.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Vedant Das Swain", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jiajia Xie", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Maanit Madan", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Sonia Sargolzaei", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "James Cai", + "author_inst": "Brown University" + }, + { + "author_name": "Munmun De Choudhury", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Gregory D. Abowd", + "author_inst": "Northeastern University" + }, + { + "author_name": "Lauren N. Steimle", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "B. Aditya Prakash", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.18.21253734", "rel_title": "SARS-CoV-2 spike protein gene variants with N501T and G142D mutation dominated infections in minks in the US", @@ -833995,57 +832705,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.24.436830", - "rel_title": "New detection of SARS-CoV-2 in two cats height months after COVID-19 outbreak appearance in France", - "rel_date": "2021-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436830", - "rel_abs": "Although there are several reports in the literature of SARS-CoV-2 infection in cats, few SARS-CoV-2 sequences from infected cats have been published. In this report, SARS-CoV-2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (Microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS-CoV-2-infection in two cats, infection status was confirmed by RT-qPCR and, in one cat, serological analysis for antibodies against N-protein and S-protein, as well as neutralizing antibodies. Comparative analysis of five SARS-CoV-2 sequence-fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS-CoV-2. This study provides additional information on the clinical, molecular, and serological aspects of SARS-CoV-2 infection in cats.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Matthieu Fritz", - "author_inst": "Institut de Recherche pour le Developpement" - }, - { - "author_name": "Nicolas Nesi", - "author_inst": "Universite de Caen Normandie" - }, - { - "author_name": "Solene Denolly", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Bertrand Boson", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Vincent Legros", - "author_inst": "Centre International de Recherche en Infectiologie/VetAgro Sup" - }, - { - "author_name": "Serge G. Rosolen", - "author_inst": "Sorbonne Universite/Clinique Veterinaire Voltaire" - }, - { - "author_name": "Alexandra Briend-Marchal", - "author_inst": "Laboratoire de Biologie Veterinaire VEBIO" - }, - { - "author_name": "Meriadeg Ar Gouil", - "author_inst": "Universite de Caen Normandie/Centre Hospitalo-Universitaire Caen" - }, - { - "author_name": "Eric M. Leroy", - "author_inst": "Institut de Recherche pour le Developpement" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.24.436850", "rel_title": "Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants", @@ -834654,6 +833313,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.03.20.21253397", + "rel_title": "Incidence of and factors associated with SARS-CoV-2 infection among people living with HIV in Southern Spain", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21253397", + "rel_abs": "BackgroundWhether people living with HIV (PLWH) are at greater risk of acquiring SARS-CoV-2 infection is currently unknown. Prospective serologic studies may allow seroincidence analyses, where all infections are accurately identified. Because of this, we evaluated the incidence of and associated factors with SARS-CoV-2 infection in PLWH in Southern Spain.\n\nMethodsThis was a prospective cohort study including PLWH from a University Hospital in Southern Spain. Patients were enrolled if 1) they had attended as outpatients our Unit from August 1st, 2019 to February 8th, 2020; 2) had two subsequent evaluations from February 9th, 2020 to February 15th, 2021. Serum antibodies against SARS-CoV-2 were determined in baseline and intra-pandemic samples.\n\nResults710 PLWH were included in the study. Of them, 46 [6.5%, 95% confidence interval (95% CI): 4.8%-8.5%] patients developed SARS-CoV-2 infection. Between May 18th and November 29th, 2020, the rate of seroconversion was 5.3% (95% CI: 3.1%-9%) for the general population in the area of Seville and 2.3% (95% CI: 1.3%-3.6%) for PLWH in this study (p=0.001). After multivariate analysis, adjusted by age and sex, active tobacco smoking was the only factor independently associated with lower risk of SARS-Cov-2 infection (Incidence rate ratio 0.35, 95% CI: 0.18-0.68, p=0.002).\n\nConclusionsThe incidence of SARS-CoV-2 infection among PLWH in Southern Spain during the ongoing pandemic was lower than that reported for the general population in the same area. Tobacco smoking was the only factor independently associated with a lower risk of incident SARS-CoV-2 infection.\n\nSummaryThe incidence of SARS-CoV-2 infection among people living with HIV is lower than that of general population in Southern Spain. Active tobacco smoking could be associated with a lower risk of developing COVID-19.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2021.03.23.21253433", "rel_title": "Serious adverse events reported from the COVID-19 vaccines: A descriptive study based on WHO database", @@ -835600,25 +834273,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.17.21253791", - "rel_title": "Forecasting the Epidemiological Impact of Coronavirus Disease (COVID-19): Pre-vaccination Era", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253791", - "rel_abs": "BackgroundDuring this pandemic, many studies have been published on the virology, diagnosis, prevention, and control of the novel coronavirus. However, fewer studies are currently available on the quantitative future epidemiological impacts. Therefore, the purpose of this study is to forecast the COVID-19 morbidities and associated-mortalities among the top 20 countries with the highest number of confirmed COVID-19 cases globally prior to vaccination intervention.\n\nMethodWe conducted a secondary data analysis of the prospective geographic distribution of COVID-19 cases data worldwide as of 10 April 2020. The historical data was forecasted using Exponential-Smoothing to detect seasonality patterns and confidence intervals surrounding each predicted value in which 95 percent of the future points are expected to fall based on the forecast.\n\nResultsThe total mean forecasted cases and deaths were 99,823 and 8,801. Interestingly, the US has the highest forecasted cases, deaths, and percentage cases-deaths ratio of 45,338, 2 358, and 5.20% respectively. China has the lowest cases, deaths, and percentage cases-deaths ratio -267, -2, and 0.75% respectively. In addition, France has the highest forecasted percentage cases-deaths ratio of 26.40% with forecasted cases, and deaths of 6,246, and 1,649 respectively.\n\nConclusionOur study revealed the possibility of higher COVID-19 morbidities and associated-mortalities worldwide.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Saheed Oladele Amusat", - "author_inst": "Ladoke Akintola University of Technology Ogbomoso Nigeria" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.17.21253283", "rel_title": "COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review Update", @@ -836559,6 +835213,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.03.16.21253371", + "rel_title": "Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253371", + "rel_abs": "COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering axes of prognosis. We propose two innovative clustering approaches - Layered Axes and Prognosis Space - to apply on patients outcome data. We then show how these clusters can help predict a patients deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients hospital admission. Moreover, our method could be used to explore subtypes of long COVID and other diseases with heterogeneous outcomes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Emma Whitfield", + "author_inst": "Institute of Health Informatics, UCL, London, United Kingdom" + }, + { + "author_name": "Claire Coffey", + "author_inst": "University of Cambridge, Cambridge, United Kingdom" + }, + { + "author_name": "Huayu Zhang", + "author_inst": "Usher Institute, University of Edinburgh, United Kingdom" + }, + { + "author_name": "Ting Shi", + "author_inst": "Usher Institute, University of Edinburgh, United Kingdom" + }, + { + "author_name": "Xiaodong Wu", + "author_inst": "Shanghai East Hospital, Tongji University, Shanghai, China" + }, + { + "author_name": "Qiang Li", + "author_inst": "Shanghai East Hospital, Tongji University, Shanghai, China" + }, + { + "author_name": "Honghan Wu", + "author_inst": "Institute of Health Informatics, UCL, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.03.16.21253405", "rel_title": "Evaluation of albumin kinetics in mechanically ventilated patients with COVID-19 compared to those with sepsis-induced ARDS", @@ -837630,205 +836327,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.03.22.436522", - "rel_title": "The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection", - "rel_date": "2021-03-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436522", - "rel_abs": "Summary ParagraphWe identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone1, a compound in clinical trials for anti-fibrotic and anti-inflammatory applications2, as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry3. We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir4. Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginones translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Daniel R. Sandoval", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Thomas Mandel Clausen", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Chelsea Nora", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Jason A. Magida", - "author_inst": "Salk Institute" - }, - { - "author_name": "Adam P. Cribbs", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrea Denardo", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Alex E. Clark", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Aaron F. Garretson", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Joanna K.C. Coker", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Anoop Narayanan", - "author_inst": "Penn State University" - }, - { - "author_name": "Sydney A. Majowicz", - "author_inst": "Penn State University" - }, - { - "author_name": "Martin Philpott", - "author_inst": "University of Oxford" - }, - { - "author_name": "Catrine Johansson", - "author_inst": "University of Oxford" - }, - { - "author_name": "James E. Dunford", - "author_inst": "University of Oxford" - }, - { - "author_name": "Charlotte B. Spliid", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Gregory J. Golden", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "N. Connor Payne", - "author_inst": "Harvard University" - }, - { - "author_name": "Mark A. Tye", - "author_inst": "Harvard University" - }, - { - "author_name": "Cameron J. Nowell", - "author_inst": "Monash Institute of Pharmaceutical Sciences" - }, - { - "author_name": "Eric R. Griffis", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Ann Piermatteo", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Kaare V. Grunddal", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Thibault Alle", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Blake M. Hauser", - "author_inst": "Harvard University" - }, - { - "author_name": "Jared Feldman", - "author_inst": "Harvard University" - }, - { - "author_name": "Timothy M. Caradonna", - "author_inst": "Harvard University" - }, - { - "author_name": "Yuan Pu", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Xin Yin", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Racheal N. McVicar", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Elizabeth M. Kwong", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Sotirios Tsimikas", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Harvard University" - }, - { - "author_name": "Carlo Ballatore", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Karsten Zengler", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sumit K. Chanda", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Ryan J. Weiss", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Micheal Downes", - "author_inst": "Salk Institute" - }, - { - "author_name": "Ronald M. Evans", - "author_inst": "Salk Institute" - }, - { - "author_name": "Ben A. Croker", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sandra L. Leibel", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Joyce Jose", - "author_inst": "Penn State University" - }, - { - "author_name": "Ralph Mazitschek", - "author_inst": "Broad Institute" - }, - { - "author_name": "Udo Oppermann", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jeffrey D. Esko", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Aaron F. Carlin", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Philip L.S.M. Gordts", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.11.21253231", "rel_title": "Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.220 in Upstate New York", @@ -838645,6 +837143,45 @@ "type": "confirmatory results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.03.19.21253997", + "rel_title": "The Impact of Early or Late Lockdowns on the Spread of COVID-19 in US Counties", + "rel_date": "2021-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253997", + "rel_abs": "BackgroundCOVID-19 is a highly transmissible infectious disease that has infected over 122 million individuals worldwide. To combat this pandemic, governments around the world have imposed lockdowns. However, the impact of these lockdowns on the rates of COVID-19 transmission in communities is not well known. Here, we used COVID-19 case counts from 3,000+ counties in the United States (US) to determine the relationship between lockdown as well as other county factors and the rate of COVID-19 spread in these communities.\n\nMethodsWe merged county-specific COVID-19 case counts with US census data and the date of lockdown for each of the counties. We then applied a Functional Principal Component (FPC) analysis on this dataset to generate scores that described the trajectory of COVID-19 spread across the counties. We used machine learning methods to identify important factors in the county including the date of lockdown that significantly influenced the FPC scores.\n\nFindingsWe found that the first FPC score accounted for up to 92.81% of the variations in the absolute rates of COVID-19 as well as the topology of COVID-19 spread over time at a county level. The relation between incidence of COVID-19 and time at a county level demonstrated a hockey-stick appearance with an inflection point approximately 7 days prior to the county reporting at least 5 new cases of COVID-19; beyond this inflection point, there was an exponential increase in incidence. Among the risk factors, lockdown and total population were the two most significant features of the county that influenced the rate of COVID-19 infection, while the median family income, median age and within-county move also substantially affect COVID spread.\n\nInterpretationLockdowns are an effective way of controlling the COVID-19 spread in communities. However, significant delays in lockdown cause a dramatic increase in the case counts. Thus, the timing of the lockdown relative to the case count is an important consideration in controlling the pandemic in communities.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed using the term \"coronavirus\", OR \"COVID-19\", OR \"COVID-19 infection\", OR \"SARS-CoV-2\" combined with \"Lockdown\" or \"sociodemographic factor\" or \"Vulnerability\" for original articles published before March 18, 2021. Similar searches were done in medRxiv, Google Scholar, and Web of Science. Only papers published in English were reviewed. The most similar relevant works to our study were Acharya et al.1 and Karmakar et al.2, which investigated the associations between population-level social factors and COVID-19 incidence and mortality. Unlike our current study, which employed a longitudinal design, both of studies were cross-sectional in nature and thus fixed on a single time point. In addition, neither of these studies investigated the impact of lockdown measures on COVID-19 infection patterns. Another relevant study is Alfano et al.s work3, which focused on the efficacy of lockdown on COVID-19 case rates. However, this study did not evaluate the timing of lockdown on this endpoint.\n\nAdded value of this studyTo our knowledge, this is the first study to use functional principal component analysis (FPCA) to investigate COVID-19 infection trajectories (in a longitudinal manner) and their relationships with different sociodemographic factors and lockdown policy at a county level. The FPCA transformed a longitudinal vector with high-dimensions into a \"single\" surrogate variable, which retained 93% of the information. We used an advanced statistical model (segmented regression) to investigate the effects of lockdown on incidence of COVID-19 across the US. We found that the relationship had a \"hockey stick\" appearance with an inflection point at [~]7 days prior to a county reporting at least 5 cases of COVID-19. We also applied a machine learning model (i.e., elastic net) to explore joint effects of lockdown and other sociodemographic factors on COVID-19 infection patterns, which estimated the impact of each of factors, adjusted for each other.\n\nImplications of all the available evidenceOur study suggests that lockdown is an effective policy to reduce case counts of COVID-19 in communities; however, significant delays in its implementation result in exponential growth of COVID-19. The inflection point is approximately 7 days prior to a county reporting at least 5 cases of COVID-19. These data will help policy-makers to determine the optimal timing of lockdowns for their communities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Xiaolin Huang", + "author_inst": "University of Victoria" + }, + { + "author_name": "Xiaojian Shao", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Li Xing", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Yushan Hu", + "author_inst": "University of Victoria" + }, + { + "author_name": "Don Sin", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Xuekui Zhang", + "author_inst": "University of Victoria" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.03.19.21253975", "rel_title": "Mortality in individuals treated with COVID-19 convalescent plasma varies with the geographic provenance of donors", @@ -839672,53 +838209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253815", - "rel_title": "Vascular Inflammation in Lungs of Patients with Fatal Coronavirus Disease 2019 (COVID-19) Infection: Possible role for the NLRP3 inflammasome", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253815", - "rel_abs": "Hyperinflammation is a key event that occurs with SARS-CoV-2 infection. In the lung, hyperinflammation leads to structural damage to tissue. To date, numerous lung histological studies have shown extensive alveolar damage, but there is scarce documentation of vascular inflammation in postmortem lung tissue. Here we document histopathological features and monitor the NLRP3 inflammasome in fatal cases of disease caused by SARS Cov2 (COVID-19). We posit that inflammasome formation along the vessel wall is a characteristic of lung inflammation that accompanies COVID-19 and that it is a probable candidate that drives amplification of inflammation post infection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Oindrila Paul", - "author_inst": "Institute for Environmental Medicine and Department of Physiology, University of Pennsylvania" - }, - { - "author_name": "Jian Qin Tao", - "author_inst": "Institute for Environmental Medicine and Department of Physiology, University of Pennsylvania" - }, - { - "author_name": "Leslie Litzky", - "author_inst": "Department of Pathology, University of Pennsylvania" - }, - { - "author_name": "Michael Feldman", - "author_inst": "Department of Pathology, University of Pennsylvania" - }, - { - "author_name": "Kathleen Montone", - "author_inst": "Department of Pathology, University of Pennsylvania" - }, - { - "author_name": "Chamith Rajapakse", - "author_inst": "Department of Radiology, University of Pennsylvania" - }, - { - "author_name": "Christian Bermudez", - "author_inst": "Department of Surgery, University of Pennsylvania" - }, - { - "author_name": "Shampa Chatterjee", - "author_inst": "Institute for Environmental Medicine and Department of Physiology, University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.03.20.21254040", "rel_title": "Symptoms of COVID-19 in a population-based cohort study", @@ -840587,6 +839077,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.22.436427", + "rel_title": "Replicative fitness SARS-CoV-2 20I/501Y.V1 variant in a human reconstituted bronchial epithelium", + "rel_date": "2021-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.22.436427", + "rel_abs": "Since its emergence in 2019, circulating populations of the new coronavirus continuously acquired genetic diversity. At the end of 2020, a variant named 20I/501Y.V1 (lineage B.1.1.7) emerged and replaced other circulating strains in several regions. This phenomenon has been poorly associated to biological evidence that this variant and original strain exhibit different phenotypic characteristics. Here, we analyse the replication ability of this new variant in different cellular models using for comparison an ancestral D614G European strain (lineage B1). Results from comparative replication kinetics experiments in vitro and in a human reconstituted bronchial epithelium showed no difference. However, when both viruses were put in competition in a human reconstituted bronchial epithelium, the 20I/501Y.V1 variant outcompeted the ancestral strain. Altogether, these findings demonstrate that this new variant replicates more efficiently and could contribute to better understand the progressive replacement of circulating strains by the SARS-CoV-2 20I/501Y.V1 variant.\n\nImportanceThe emergence of several SARS-CoV-2 variants raised numerous questions concerning the future course of the pandemic. We are currently observing a replacement of the circulating viruses by the variant from the United Kingdom known as 20I/501Y.V1 from B.1.1.7 lineage but there is little biological evidence that this new variant exhibit a different phenotype. In the present study, we used different cellular models to assess the replication ability of the 20I/501Y.V1 variant. Our results showed that this variant replicate more efficiently in a human reconstituted bronchial epithelium, which may explain why it spreads so rapidly in human populations.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Franck Touret", + "author_inst": "Unite des Virus Emergents" + }, + { + "author_name": "Lea Luciani", + "author_inst": "Unite des virus Emergents" + }, + { + "author_name": "Cecile Baronti", + "author_inst": "Unite des virus Emergents" + }, + { + "author_name": "Maxime Cochin", + "author_inst": "Unite des virus Emergents" + }, + { + "author_name": "Jean-Selim Driouich", + "author_inst": "Unite des virus Emergents" + }, + { + "author_name": "Magali Gilles", + "author_inst": "Unite des virus emergents" + }, + { + "author_name": "Laurence Thirion", + "author_inst": "Unite des virus emergents" + }, + { + "author_name": "Antoine Nougairede", + "author_inst": "Unite des virus Emergents" + }, + { + "author_name": "Xavier de Lamballerie", + "author_inst": "Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospitals o" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.17.21253488", "rel_title": "A Queuing Model for Ventilator Capacity Management during the COVID-19 Pandemic", @@ -841830,45 +840371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.16.21253761", - "rel_title": "Details of COVID-19 Disease Mitigation Strategies in 17 K-12 Schools in Wood County, Wisconsin", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253761", - "rel_abs": "ImportanceWith the current COVID-19 return-to-school guidelines, over half of Americas K-12 students are being denied access to full time in-person education, leading to harmful academic, emotional and health consequences.\n\nObjectiveTo describe the specific details of mitigation strategies employed at 17 K-12 schools in Wisconsin during a time of exceptionally high COVID-19 community disease prevalence where in-school transmission was minimal. The aim of this report is to assist school districts and governing bodies in developing full-time return to school plans.\n\nDesignRetrospective cohort\n\nSettingWood County, Wisconsin, August 31-November 29, 2020\n\nParticipants5,530 students and staff from 17 schools in 4 school districts\n\nMain outcomes and measuresO_LIDistancing between primary and secondary students in school\nC_LIO_LISchool ventilation details\nC_LIO_LIMasking among teachers\nC_LIO_LILunch, recess and bussing practices\nC_LI\n\nResults89.3% of elementary students included in our study did not maintain 6 feet of physical distancing in the classroom and 94.8% were within 6 feet in lunchrooms. The majority of secondary students (86.2%) were able to maintain 6 feet of distancing in the classroom but no students were greater than 6 feet in the hallways. 58.8% of schools did not install new ventilation systems prior to the school year. Students ate lunch indoors. Bussing of students continued and all elementary children were allowed to go without masks at recess.\n\nConclusion and relevanceIn the setting of high community COVID-19 disease transmission, 6 feet of distance between elementary students and major ventilation system renovations in primary or secondary schools do not appear to be necessary to minimize disease spread. Requiring masks at recess and prohibiting bussing also appears unnecessary. These findings may inform guidance on the safe reopening of schools and allow for more children to return to in-person schooling.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amy Falk", - "author_inst": "1Department of Pediatrics, Aspirus Doctors Clinic, 2031 Peach St. Wisconsin Rapids WI. 2Medical College of Wisconsin - Central Wisconsin, Wausau WI." - }, - { - "author_name": "Alison Benda", - "author_inst": "Medical College of Wisconsin - Central Wisconsin, Wausau WI." - }, - { - "author_name": "Sarah Steffen", - "author_inst": "Medical College of Wisconsin - Central Wisconsin, Wausau WI." - }, - { - "author_name": "Mikaela DeCoster", - "author_inst": "Medical College of Wisconsin - Central Wisconsin, Wausau, WI" - }, - { - "author_name": "Monica Gandhi", - "author_inst": "Center for AIDS Research, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA" - }, - { - "author_name": "Tracy Beth Hoeg", - "author_inst": "1. Department of Physical Medicine & Rehabilitation, University of California - Davis and 2. Northern California Orthopaedic Associates, Grass Valley, CA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.19.21253945", "rel_title": "Sarcopenic obesity and the risk of hospitalisation or death from COVID-19: findings from UK Biobank", @@ -842709,6 +841211,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.03.20.21254005", + "rel_title": "Alternative splicing of OAS1 alters the risk for severe COVID-19", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254005", + "rel_abs": "A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of [~]75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jennifer Huffman", + "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Bostoon, MA, USA, 02130" + }, + { + "author_name": "Guillaume Butler-Laporte", + "author_inst": "Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, " + }, + { + "author_name": "Atlas Khan", + "author_inst": "Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY" + }, + { + "author_name": "Theodore G. Drivas", + "author_inst": "Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Department of Pediatri" + }, + { + "author_name": "Gina M. Peloso", + "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Bostoon, MA, USA, 02130; Department of Biostatistics" + }, + { + "author_name": "Tomoko Nakanishi", + "author_inst": "Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland; Department of Human Genetics, McGill University, Montreal, Quebec, Canada;" + }, + { + "author_name": "Anurag Verma", + "author_inst": "Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA" + }, + { + "author_name": "Krzysztof Kiryluk", + "author_inst": "Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Institute for Genomic Medicine, Col" + }, + { + "author_name": "J. Brent Richards", + "author_inst": "Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, " + }, + { + "author_name": "Hugo Zeberg", + "author_inst": "Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany; Department of Neuroscience, Karolinska Institutet, SE-17177 Sto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.03.20.21254008", "rel_title": "Exploring causal relationships between COVID-19 and cardiometabolic disorders: A bi-directional Mendelian randomization study", @@ -844148,49 +842705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253972", - "rel_title": "Factors Associated with Intention to Vaccinate against COVID-19 in Puerto Rico", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253972", - "rel_abs": "COVID-19 has been particularly devastating to Black and Latinx communities in the U.S. However, data on acceptability of the COVID-19 vaccines among minority populations are limited. We conducted an online survey among adults in Puerto Rico to identify factors associated with intention to vaccinate against COVID-19. Sociodemographic variables were analyzed independently for association with intention to vaccinate. Significant associations were included in the multivariate logistic regression analysis. A total of 1016 responses were available for analysis. In the bivariate analysis, younger age, higher education, pre-covid employment, male sex, gay/bisexual identity, and single marital status were associated with increased intention to vaccinate. In the multivariate logistic regression, younger, male respondents who had higher educational attainment reported higher intention to vaccinate. Lower-income and living outside the San Juan metro region were associated with lower intention to vaccinate. National and international health organizations were identified as the most reliable sources of information, followed by healthcare professionals. These findings highlight the importance of considering sociodemographic characteristics identified with low intention to vaccinate as well as using trusted sources of information when designing public messaging related to increasing COVID-19 vaccinations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kyle Melin", - "author_inst": "University of Puerto Rico-Medical Sciences Campus" - }, - { - "author_name": "Cheyu Zhang", - "author_inst": "George Washington University-Milken Institute School of Public Health" - }, - { - "author_name": "Juan Pablo Zapata", - "author_inst": "Marquette University-Department of Psychology" - }, - { - "author_name": "Yonaira Maria Rivera", - "author_inst": "Rutgers University-School of Communication and Information" - }, - { - "author_name": "Enbal Shacham", - "author_inst": "Saint Louis University-College for Public Health and Social Justice" - }, - { - "author_name": "Souhail Marie Malave-Rivera", - "author_inst": "University of Puerto Rico-Medical Sciences Campus" - }, - { - "author_name": "Carlos E Rodriguez-Diaz", - "author_inst": "George Washington University-Milken Institute School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.19.21253960", "rel_title": "Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: a mathematical modelling analysis", @@ -844783,6 +843297,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253291", + "rel_title": "Monitoring the propagation of SARS CoV2 variants by tracking identified mutation in wastewater using specific RT-qPCR", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253291", + "rel_abs": "Since the end of 2020, the COVID-19 pandemic has experienced a major turning point with the appearance and rapid spread of new variants, causing a significant increase in the number of new cases requiring hospitalization. These so-called UK, South African or Brazilian variants are characterized by combinations of mutations which allow them to be distinguished from the variants which have circulated since the start of the epidemic. The impact of these variants on the functioning of healthcare systems requires monitoring the spread of these variants, which are more contagious, more lethal and may reinfect people who are already immune to a natural infection or to a vaccination. Monitoring the viral genome in wastewater has shown great value in early detection of the dynamics of virus spreading in populations.\n\nThe sequencing of viral genomes is used in humans, but its application and interpretation on wastewater matrices are much more complex due to the diversity of circulating strains. Also this study demonstrates the possibility of following certain mutations found in these new variants by targeted RT-qPCR. This study is the first carried out in France demonstrating the spreading dynamics of the 69-70 deletion in the Spike protein of SARS-CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "SEBASTIEN WURTZER", + "author_inst": "EAU DE PARIS" + }, + { + "author_name": "Prunelle Waldman", + "author_inst": "Sorbonne university" + }, + { + "author_name": "Morgane Levert", + "author_inst": "Sorbonne university" + }, + { + "author_name": "Jeann-Marie Mouchel", + "author_inst": "Sorbonne university" + }, + { + "author_name": "Olivier Gorge", + "author_inst": "Institut de recherches biomedicales des armees" + }, + { + "author_name": "Mickael Boni", + "author_inst": "Institut de recherches biomedicales des armees" + }, + { + "author_name": "Yvon Maday", + "author_inst": "Sorbonne university" + }, + { + "author_name": "- Obepine consortium", + "author_inst": "" + }, + { + "author_name": "Vincent Marechal", + "author_inst": "Sorbonne university" + }, + { + "author_name": "Laurent Moulin", + "author_inst": "Eau de Paris" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.13.21253363", "rel_title": "Mental health of patients with mental illness during the COVID-19 pandemic lockdown: A questionnaire-based survey weighted for attrition", @@ -845758,61 +844327,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.19.436183", - "rel_title": "Reduced neutralization of SARS-CoV-2 variants by convalescent plasma and hyperimmune intravenous immunoglobulins for treatment of COVID-19", - "rel_date": "2021-03-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.19.436183", - "rel_abs": "Hyperimmune immunoglobulin (hCoV-2IG) preparations generated from SARS-CoV-2 convalescent plasma (CP) are under evaluation in several clinical trials of hospitalized COVID-19 patients. Here we explored the antibody epitope repertoire, antibody binding and virus neutralizing capacity of six hCoV-2IG batches as well as nine convalescent plasma (CP) lots against SARS-CoV-2 and emerging variants of concern (VOC). The Gene-Fragment Phage display library spanning the SARS-CoV-2 spike demonstrated broad recognition of multiple antigenic sites spanning the entire spike including NTD, RBD, S1/S2 cleavage site, S2-fusion peptide and S2-heptad repeat regions. Antibody binding to the immunodominant epitopes was higher for hCoV-2IG than CP, with predominant binding to the fusion peptide. In the pseudovirus neutralization assay (PsVNA) and in the wild-type SARS-CoV-2 PRNT assay, hCoV-2IG lots showed higher titers against the WA-1 strain compared with CP. Neutralization of SARS-CoV-2 VOCs from around the globe were reduced to different levels by hCoV-2IG lots. The most significant loss of neutralizing activity was seen against the B.1.351 (9-fold) followed by P.1 (3.5-fold), with minimal loss of activity against the B.1.17 and B.1.429 ([≤]2-fold). Again, the CP showed more pronounced loss of cross-neutralization against the VOCs compared with hCoV-2IG. Significant reduction of hCoV-2IG binding was observed to the RBD-E484K followed by RBD-N501Y and minimal loss of binding to RBD-K417N compared with unmutated RBD. This study suggests that post-exposure treatment with hCoV-2IG is preferable to CP. In countries with co-circulating SARS-CoV-2 variants, identifying the infecting virus strain could inform optimal treatments, but would likely require administration of higher volumes or repeated infusions of hCOV-2IG or CP, in patients infected with the emerging SARS-CoV-2 variants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Juanjie Tang", - "author_inst": "FDA" - }, - { - "author_name": "Your Lee", - "author_inst": "FDA" - }, - { - "author_name": "Supriya Ravichandran", - "author_inst": "FDA" - }, - { - "author_name": "Gabrielle Grubbs", - "author_inst": "FDA" - }, - { - "author_name": "Chang Huang", - "author_inst": "FDA" - }, - { - "author_name": "Charles Stauft", - "author_inst": "FDA" - }, - { - "author_name": "Tony Wang", - "author_inst": "U.S. Food and Drug Administration" - }, - { - "author_name": "Basil Golding", - "author_inst": "FDA" - }, - { - "author_name": "Hana Golding", - "author_inst": "FDA" - }, - { - "author_name": "Surender Khurana", - "author_inst": "US Food and Drug Administration" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.19.435806", "rel_title": "Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir", @@ -846669,6 +845183,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.15.21253570", + "rel_title": "Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253570", + "rel_abs": "In this current COVID - 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS-COV-2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer-Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS-CoV 2-testing.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Dr. Sally Mahmoud", + "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" + }, + { + "author_name": "Ms.Esra Ibrahim", + "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" + }, + { + "author_name": "Subhashini Ganesan", + "author_inst": "G42 Healthcare, UAE" + }, + { + "author_name": "Dr. Bhagyashree Thakre", + "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" + }, + { + "author_name": "Dr.Juliet Teddy", + "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" + }, + { + "author_name": "Ms.Preety Raheja", + "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE" + }, + { + "author_name": "Dr.Walid Zaher", + "author_inst": "G42 Healthcare, UAE" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.15.21253571", "rel_title": "Using Machine Learning along with Data Science algorithms to pre-process and forecast COVID-19 Cases and Deaths", @@ -847608,57 +846165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2021.03.15.21253593", - "rel_title": "Post-viral parenchymal lung disease of COVID-19 and viral pneumonitis: A systematic review and meta-analysis.", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253593", - "rel_abs": "BackgroundApproximately half of COVID-19 survivors present persisting breathlessness, which may include development of pulmonary fibrosis.\n\nResearch QuestionWhat is the prevalence of long-term radiological and functional pulmonary sequelae of parenchymal lung disease following hospitalisation with COVID-19 and other viral pneumonia?\n\nStudy design and methodsWe performed systematic review and random effects meta-analysis of studies in adults hospitalised with SARS-CoV-2, SARS-CoV, MERS-CoV, or Influenza pneumonia and followed within 12 months from discharge. Searches were run on MEDLINE and Embase, updated 29 July 2021. Primary outcomes were proportion of 1) radiologic sequelae at CT scans; 2) restrictive impairment; 3) impaired gas transfer. Heterogeneity was explored in meta-regression.\n\nResultsNinety-five studies were included for qualitative synthesis, of which 70 were suitable for meta-analysis, including 60 studies of SARS-CoV-2 with a median follow up of 3 months. In SARS-CoV-2 the overall estimated proportion of inflammatory changes during follow up was 0.50 (95%CI 0.41 to 0.58, I2=94.6%), whilst fibrotic changes were estimated at 0.29 (95%CI 0.22 to 0.37, I2=94.1%). Inflammatory changes reduced compared with CTs performed during hospitalisation (-0.47; 95%CI -0.56 to -0.37), whereas no significant resolution was observed in fibrotic changes (-0.09; 95%CI -0.25 to 0.07). Impaired gas transfer was estimated at 0.38 (95%CI 0.32 to 0.44, I2=92.1%), which was greater than estimated restrictive impairment (0.17; 95%CI 0.13 to 0.23, I2=92.5%). High heterogeneity means that estimates should be interpreted with caution. Confidence in the estimates was deemed low due to the heterogeneity and because studies were largely observational without controls.\n\nInterpretationA substantial proportion of radiological and functional sequelae consistent with parenchymal lung disease are observed following COVID-19 and other viral pneumonitis. Estimates of prevalence are limited by differences in case mix and initial severity. This highlights the importance of extended radiological and functional follow-up post hospitalisation.\n\nPROSPERO registrationCRD42020183139 (April 2020)", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Laura Fabbri", - "author_inst": "Imperial College London" - }, - { - "author_name": "Samuel Moss", - "author_inst": "Imperial College London" - }, - { - "author_name": "Fasihul Khan", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Wenjie Chi", - "author_inst": "Systematic Review Solutions Ltd." - }, - { - "author_name": "Jun Xia", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Karen Robinson", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Alan Smyth", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Gisli Jenkins", - "author_inst": "Imperial College London" - }, - { - "author_name": "Iain Stewart", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.03.15.21253566", "rel_title": "Understanding Convergence Between Non-Hispanic Black and White COVID-19 Mortality: A County-Level Approach", @@ -848371,6 +846877,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253782", + "rel_title": "B.1.1.7 became the dominant variant in Lebanon.", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253782", + "rel_abs": "Recently, a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) designated VOC 202012/01 (or B.1.1.7 lineage) has become highly prevalent in several countries, after first being described in the United Kingdom (UK). Its rate of transmission has been estimated to be increased compared to other lineages. In the present study, we show the emergence, dominance and the rapid spread of the B.1.1.7 lineage in Lebanon.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mahmoud younes", + "author_inst": "Beirut cardiac institute" + }, + { + "author_name": "Kassem Hamze", + "author_inst": "Lebanese University" + }, + { + "author_name": "Karen L. Osman", + "author_inst": "Public health england" + }, + { + "author_name": "Daniel P. Carter", + "author_inst": "public health england" + }, + { + "author_name": "Steven T Pullan", + "author_inst": "Public Health England" + }, + { + "author_name": "Miles Caroll", + "author_inst": "Public health england" + }, + { + "author_name": "Richard T Vipond", + "author_inst": "Public Health England" + }, + { + "author_name": "Nada Mohamad", + "author_inst": "University of Oxford" + }, + { + "author_name": "hassan nassar", + "author_inst": "bahman hospital" + }, + { + "author_name": "Mayssa Ghaddar", + "author_inst": "Bahman hospital" + }, + { + "author_name": "Mohammad Makki", + "author_inst": "Beirut cardiac institute" + }, + { + "author_name": "Paul Nguewa", + "author_inst": "University of Navarra" + }, + { + "author_name": "fadi Abdel Sater", + "author_inst": "Lebanese university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.17.21253793", "rel_title": "A feasible and more efficient SARS-Cov-2 vaccine allocation to states and counties in the USA", @@ -849338,189 +847911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.17.21253610", - "rel_title": "Characteristics and risk factors for SARS-CoV-2 among children in Italy: a cross-sectional study in 20 pediatric centers", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253610", - "rel_abs": "BackgroundNo study has described factors associated with COVID-19 diagnosis in children.\n\nAimDescribe characteristics and risk factors for COVID-19 diagnosis in children tested in 20 pediatric centers across Italy.\n\nMethodsCases aged 0-18 years tested for SARS-CoV-2 between February 23 and May 24 2020 were included. Our primary analysis focused on children tested because of COVID-19 suggestive symptoms.\n\nResultsAmong 2494 children tested for SARS-CoV-2, 2148 (86.1%) had symptoms suggestive of COVID-19. Clinical presentation of SARS-CoV-2 included - beside fever (82.4%) and respiratory signs or symptoms (60.4%) - also gastrointestinal (18.2%), neurological (18.9%), cutaneous (3.8%) and other flu-like presentations (17.8%). In multivariate analysis, factors significantly associated with SARS-CoV-2 were: exposure history (adjusted OR 39.83 95%CI 17.52-90.55 p<0.0001), cardiac disease (adjusted OR 3.10 95%CI 1.19-5.02 p<0.0001), fever (adjusted OR 3.05 % 95% CI 1.67-5.58 p=0.0003), and anosmia/ageusia (OR 4.08 95%CI 1.69 -9.84 p=0.002). Among 190 (7.6%) children diagnosed with SARS-CoV-2, only four (2.1%) required respiratory support and two (1.1%) were admitted in ICU, while 100% recovered.\n\nConclusionRecommendations for SARS-CoV-2 testing in children should be updated based on the evidence of broader clinical features. Exposure history, fever, and anosmia/ageusia are strong risk factors for COVID-19 in children, while other symptoms dont seem helping discriminating in between the SARS-CoV-2 positive and the negative cases. This study confirm that COVID-19 is a mild disease in the general population of children in Italy. Further studies are needed to understand the risk, clinical spectrum and outcomes of COVID-19 in children with specific preexisting conditions.", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Marzia Lazzerini", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Idanna Sforzi", - "author_inst": "Department of Pediatric Emergency Medicine and Trauma Center, Meyer Children's University Hospital,Viale Pieraccini 24, 50139, Florence, Italy" - }, - { - "author_name": "Sandra Trapani", - "author_inst": "Department of Health Sciences and Meyer Children's University Hospital, Viale Pieraccini 24, 50139, Florence, Italy" - }, - { - "author_name": "Paolo Biban", - "author_inst": "Department of Neonatal and Paediatric Critical Care, Verona University Hospital, Verona Italy" - }, - { - "author_name": "Davide Salvigni", - "author_inst": "Department of Neonatal and Paediatric Critical Care, Verona University Hospital, Verona Italy" - }, - { - "author_name": "Ilaria Mariani", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Giovanna Villa", - "author_inst": "Pediatric Emergency Unit, IRCCS Gaslini Children's Hospital, Genoa, Italy" - }, - { - "author_name": "Jessica Tibaldi", - "author_inst": "Pediatric Emergency Unit, IRCCS Gaslini Children's Hospital, Genoa, Italy" - }, - { - "author_name": "Luca Bertacca", - "author_inst": "Pediatric Emergency Unit and Department of Pediatric and Neonatology, Misericordia Hospital, Grosseto, Italy" - }, - { - "author_name": "Enrico Felici", - "author_inst": "Pediatric and Pediatric Emergency Unit, The Children Hospital, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy" - }, - { - "author_name": "Giuseppina Perricone", - "author_inst": "Pediatric and Pediatric Emergency Unit, The Children Hospital, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy" - }, - { - "author_name": "Roberta Parrino", - "author_inst": "Pediatria d'Urgenza e Pronto Soccorso P.O.G. Di Cristina, Palermo, Italy" - }, - { - "author_name": "Claudia Gioe'", - "author_inst": "Pediatric Infectious diseases, P.O.G. Di Cristina, Palermo, Italy" - }, - { - "author_name": "Sara Lega", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Mariasole Conte", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Federico Marchetti", - "author_inst": "Department of Pediatrics, Ravenna Hospital, Ravenna, Italy" - }, - { - "author_name": "Annamaria Magista", - "author_inst": "Department of Pediatrics, Community Pediatrics, Ravenna, Italy" - }, - { - "author_name": "Paola Berlese", - "author_inst": "Department of Pediatrics, Treviso Hospital, Treviso, Italy" - }, - { - "author_name": "Stefano Martelossi", - "author_inst": "Department of Pediatrics, Treviso Hospital, Treviso, Italy" - }, - { - "author_name": "Francesca Vaienti", - "author_inst": "Pediatric Department, G.B. Morgagni-L. Pierantoni Hospital, Forli, Italy" - }, - { - "author_name": "Enrico Valletta", - "author_inst": "Pediatric Department, G.B. Morgagni-L. Pierantoni Hospital, Forli, Italy" - }, - { - "author_name": "Margherita Mauro", - "author_inst": "Department of Pediatrics and Neonatology, Santa Maria degli Angeli Hospital, Pordenone, Italy" - }, - { - "author_name": "Roberto Dall Amico", - "author_inst": "Department of Pediatrics and Neonatology, Santa Maria degli Angeli Hospital, Pordenone, Italy" - }, - { - "author_name": "Silvia Fasoli", - "author_inst": "Paediatric Unit, Carlo Poma Hospital, Mantua, Italy" - }, - { - "author_name": "Antonio Gatto", - "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" - }, - { - "author_name": "Antonio Chiaretti", - "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" - }, - { - "author_name": "Danica Dragovic", - "author_inst": "Pediatric Department, San Polo Hospital, ASUGI, Monfalcone (GO), Italy" - }, - { - "author_name": "Paola Pascolo", - "author_inst": "Pediatric Department, San Polo Hospital, ASUGI, Monfalcone (GO), Italy" - }, - { - "author_name": "Chiara Pilotto", - "author_inst": "Division of Paediatrics, Department of Medicine DAME, Academic Hospital Santa Maria della Misericordia, University of Udine, Udine, Italy" - }, - { - "author_name": "Ilaria Liguoro", - "author_inst": "Division of Paediatrics, Department of Medicine DAME, Academic Hospital Santa Maria della Misericordia, University of Udine, Udine, Italy" - }, - { - "author_name": "Elisabetta Miorin", - "author_inst": "Department of Pediatrics, Latisana-Palmanova, ASUFC, Udine, Italy" - }, - { - "author_name": "Francesca Saretta", - "author_inst": "Department of Pediatrics, Latisana-Palmanova, ASUFC, Udine, Italy" - }, - { - "author_name": "Gianluca Trobia", - "author_inst": "Pediatric and Pediatric Emergency Room Unit Cannizzaro Emergency Hospital Catania, Italy" - }, - { - "author_name": "Antonella Di Stefano", - "author_inst": "Pediatric and Pediatric Emergency Room Unit Cannizzaro Emergency Hospital Catania, Italy" - }, - { - "author_name": "Azzurra Orlandi", - "author_inst": "Giovanni XXIII Pediatric Hospital, Department of Pediatrics, University of Bari, Bari, Italy" - }, - { - "author_name": "Fabio Cardinale", - "author_inst": "Giovanni XXIII Pediatric Hospital, Department of Pediatrics, University of Bari, Bari, Italy" - }, - { - "author_name": "Riccardo Lubrano", - "author_inst": "Department of Pediatrics Sapienza University of Rome, Santa Maria Goretti Hospital, Latina, Italy" - }, - { - "author_name": "Alessia Testa", - "author_inst": "Department of Pediatrics Sapienza University of Rome, Santa Maria Goretti Hospital, Latina, Italy" - }, - { - "author_name": "Marco Binotti", - "author_inst": "Neonatal and Pediatric Intensive Care Unit, Maggiore della Carita University Hospital, Novara, Italy" - }, - { - "author_name": "Valentina Moressa", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Egidio Barbi", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - }, - { - "author_name": "Benedetta Armocida", - "author_inst": "Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.03.17.21253131", "rel_title": "Interim results of the safety and immune-efficacy of 1 versus 2 doses of COVID-19 vaccine BNT162b2 for cancer patients in the context of the UK vaccine priority guidelines", @@ -850573,6 +848963,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.15.435497", + "rel_title": "Killed whole genome-reduced bacteria surface-expressed coronavirus fusion peptide vaccines protect against disease in a porcine model", + "rel_date": "2021-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.15.435497", + "rel_abs": "As the coronavirus disease 2019 (COVID-19) pandemic rages on, it is important to explore new evolution-resistant vaccine antigens and new vaccine platforms that can produce readily scalable, inexpensive vaccines with easier storage and transport. We report here a synthetic biology-based vaccine platform that employs an expression vector with an inducible Gram-negative autotransporter to express vaccine antigens on surface of genome-reduced bacteria to enhance interaction of vaccine antigen with immune system. As a proof of principle, we utilized genome-reduced E. coli to express SARS-CoV-2 and porcine epidemic diarrhea virus (PEDV) fusion peptide (FP) on the cell surface, and evaluated their use as a killed whole cell vaccine. The FP sequence is highly conserved across coronaviruses; the 6 FP core amino acid residues along with the 4 adjacent residues upstream and the 3 residues downstream the core are identical between SARS-CoV-2 and PEDV. We tested the efficacy of PEDV FP and SARS-CoV-2 FP vaccines in a PEDV challenge pig model. We demonstrated that both vaccines induced potent anamnestic responses upon virus challenge, potentiated IFN-{gamma} responses, reduced viral RNA loads in jejunum tissue, and provided significant protection against clinical disease. However, neither vaccines elicited sterilizing immunity. Since SARS-CoV-2 FP and PEDV FP vaccines provided similar clinical protection, the coronavirus FP could be a target for a broadly-protective vaccine using any platform. Importantly, the genome-reduced bacterial surface-expressed vaccine platform, when using a vaccine appropriate bacterial vector, has potential utility as an inexpensive, readily manufactured, and rapid vaccine platform for other pathogens.\n\nSignificance StatementWe report a new vaccine platform to express vaccine antigens on surface of genome-reduced bacteria to enhance vaccine immunogenicity. We demonstrated the utility of this vaccine platform by expressing the highly conserved fusion peptide (FP) of SARS-CoV-2 and porcine epidemic diarrhea virus on the surface of E.coli to produce killed whole cell bacterial vaccines. The vaccine primes a potent anamnestic response, potentiates IFN-{gamma} responses, and provides significant protection in pigs against disease following virus challenge. The FP could be a target for a broadly-protective coronavirus vaccine since a Betacoronavirus SARS-CoV-2 FP vaccine provided cross-protection against Alphacoronavirus PEDV. When using a vaccine appropriate bacteria vector, this inexpensive new vaccine platform offers the potential for use in developing countries.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Denicar Lina Nascimento Fabris Maeda", + "author_inst": "University of Virginia" + }, + { + "author_name": "Debin Tian", + "author_inst": "2Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State U" + }, + { + "author_name": "Hanna Yu", + "author_inst": "1Departments of Pediatrics and Microbiology, Immunology, and Cancer Biology; Pendleton Pediatric Infectious Disease Laboratory; and Child Health Research Center" + }, + { + "author_name": "Nakul Dar", + "author_inst": "Departments of Pediatrics and Microbiology, Immunology, and Cancer Biology; Pendleton Pediatric Infectious Disease Laboratory; and Child Health Research Center," + }, + { + "author_name": "Vignesh Rajasekaran", + "author_inst": "Departments of Pediatrics and Microbiology, Immunology, and Cancer Biology; Pendleton Pediatric Infectious Disease Laboratory; and Child Health Research Center," + }, + { + "author_name": "Sarah Meng", + "author_inst": "Departments of Pediatrics and Microbiology, Immunology, and Cancer Biology; Pendleton Pediatric Infectious Disease Laboratory; and Child Health Research Center," + }, + { + "author_name": "Hassan Mahsoub", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Harini Sooryanarain", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Bo Wang", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "C. Lynn Heffron", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Anna Hassebroek", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Tanya LeRoith", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Xiang-Jin Meng", + "author_inst": "Department of Biomedical Sciences and Pathobiology, and Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State Un" + }, + { + "author_name": "Steven L Zeichner", + "author_inst": "Departments of Pediatrics and Microbiology, Immunology, and Cancer Biology; Pendleton Pediatric Infectious Disease Laboratory; and Child Health Research Center," + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.15.435472", "rel_title": "Replication kinetic, cell tropism and associated immune responses in SARS-CoV-2 and H5N1 virus infected human iPSC derived neural models", @@ -851752,65 +850213,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.03.14.435299", - "rel_title": "S-acylation controls SARS-Cov-2 membrane lipid organization and enhances infectivity", - "rel_date": "2021-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.14.435299", - "rel_abs": "SARS-CoV-2 virions are surrounded by a lipid bilayer which contains membrane proteins such as Spike, responsible for target-cell binding and virus fusion, the envelope protein E and the accessory protein Orf3a. Here, we show that during SARS-CoV-2 infection, all three proteins become lipid modified, through action of the S-acyltransferase ZDHHC20. Particularly striking is the rapid acylation of Spike on 10 cytosolic cysteines within the ER and Golgi. Using a combination of computational, lipidomics and biochemical approaches, we show that this massive lipidation controls Spike biogenesis and degradation, and drives the formation of localized ordered cholesterol and sphingolipid rich lipid nanodomains, in the early Golgi where viral budding occurs. ZDHHC20-mediated acylation allows the formation of viruses with enhanced fusion capacity and overall infectivity. Our study points towards S-acylating enzymes and lipid biosynthesis enzymes as novel therapeutic anti-viral targets.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Francisco Sarmento Mesquita", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Laurence Abrami", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Oksana Sergeeva", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Priscilla Turelli", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Beatrice Kunz", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Charlene Raclot", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Jonathan Paz Montoya", - "author_inst": "Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Luciano Abriata", - "author_inst": "Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Matteo Dal Peraro", - "author_inst": "Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "Didier Trono", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - }, - { - "author_name": "F. Gisou van der Goot", - "author_inst": "Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.03.15.435309", "rel_title": "One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening", @@ -852999,6 +851401,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.12.21253481", + "rel_title": "Modeling the use of SARS-CoV-2 vaccination to safely relax non-pharmaceutical interventions", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253481", + "rel_abs": "In response to the COVID-19 pandemic, widespread non-pharmaceutical interventions (NPIs), including physical distancing, mask wearing, and enhanced hygiene, have been implemented. As of March 2021, three effective vaccines have been approved for emergency use in the United States, with several other vaccines in the pipeline. We use a transmission model to study when and how NPIs could be relaxed in the United States with relative safety as vaccination becomes more widespread. We compare different relaxation scenarios where NPIs begin to relax 0-9 months after vaccination begins for both a one dose and two dose strategy, with historical levels of social interactions being reached within 1 month to 1 year. In our model, vaccination can allow widespread relaxation of NPIs to begin safely within 2 to 9 months, greatly reducing deaths and peak health system burden compared to relaxing NPIs without vaccination. Vaccinated individuals can safely begin to relax NPIs sooner than unvaccinated individuals. The extent of delay needed to safely reopen depends primarily on the rate of vaccine rollout, with the degree of protection against asymptomatic infection playing a secondary role. If a vaccination rate of 3 million doses/day can be achieved, similar to the typical rollout speed of seasonal influenza vaccination, NPIs could begin to be safely relaxed in 2-3 months. With a vaccination rate of 1 million doses/day, a 6-9-month delay is needed. A one dose strategy is preferred if relative efficacy is similar to a two-dose series, but the relative benefit of this strategy is minimal when vaccine rollout is fast. Due to the urgent need to pursue strategies that enable safe relaxation of NPIs, we recommend a two-dose strategy with an initial delay of at least 3 months in relaxing restrictions further, and that the speed of vaccine rollout be given immediate priority.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Alicia N M Kraay", + "author_inst": "Emory University" + }, + { + "author_name": "Molly E. Gallagher", + "author_inst": "Emory University" + }, + { + "author_name": "Yang Ge", + "author_inst": "University of Georgia" + }, + { + "author_name": "Peichun Han", + "author_inst": "Emory University" + }, + { + "author_name": "Julia M Baker", + "author_inst": "Emory University Rollins School of Public Health" + }, + { + "author_name": "Katia Koelle", + "author_inst": "Emory University" + }, + { + "author_name": "Andreas Handel", + "author_inst": "University of Georgia" + }, + { + "author_name": "Benjamin A Lopman", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253472", "rel_title": "Clinical characteristics of COVID-19 in children and adolescents: a systematic review and meta-analysis", @@ -854230,41 +852679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.03.08.21253152", - "rel_title": "Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020 to February 2021: insights and limitations from uneven sequencing efforts", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253152", - "rel_abs": "The COVID-19 pandemic has already reached approximately 110 million people and it is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. International efforts have been established to share information about SARS-CoV-2 epidemiology and evolution. However, sequencing facilities and research investments are very heterogeneous across different regions and countries. The understanding of the SARS-CoV-2 evolution plays a significant role in the development of effective strategies for public health and disease management. We aimed to analyze the available and high-quality genome sequences from Brazil between February 2020 and February 2021 to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages by using phylogenetics and phylodynamics analyses. We describe heterogeneous and episodic sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of novel and specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades (4.2 and 5.3) related to the six most prevalent lineages in the country and described its spatial distribution and dynamics. The emergence and recent frequency shift of lineages (P.1 and P.2) containing mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers and enable evidence-based decisions to fight the COVID-19 pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vinicius Bonetti Franceschi", - "author_inst": "Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil" - }, - { - "author_name": "Patricia Aline Grohs Ferrareze", - "author_inst": "Graduate Program in Health Sciences, Universidade Federal de Ciencias da Saude de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil" - }, - { - "author_name": "Ricardo Ariel Zimerman", - "author_inst": "Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre, RS, Brazil" - }, - { - "author_name": "Gabriela Bettella Cybis", - "author_inst": "Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil" - }, - { - "author_name": "Claudia Elizabeth Thompson", - "author_inst": "Department of Pharmacosciences, Universidade Federal de Ciencias da Saude de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.03.09.21253186", "rel_title": "Forecasting the COVID-19 epidemic integrating symptom search behavior: an infodemiology study", @@ -854889,6 +853303,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.08.21253009", + "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Juba, South Sudan: a population-based study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253009", + "rel_abs": "BackgroundRelatively few COVID-19 cases and deaths have been reported through much of sub-Saharan Africa, including South Sudan, although the extent of SARS-CoV-2 spread remains unclear due to weak surveillance systems and few population-representative serosurveys.\n\nMethodsWe conducted a representative household-based cross-sectional serosurvey in Juba, South Sudan. We quantified IgG antibody responses to SARS-CoV-2 spike protein receptor-binding domain and estimated seroprevalence using a Bayesian regression model accounting for test performance.\n\nResultsWe recruited 2,214 participants from August 10 to September 11, 2020 and 22.3% had anti-SARS-CoV-2 IgG titers above levels in pre-pandemic samples. After accounting for waning antibody levels, age, and sex, we estimated that 38.5% (32.1 - 46.8) of the population had been infected with SARS-CoV-2. For each RT-PCR confirmed COVID-19 case, 104 (87-126) infections were unreported. Background antibody reactivity was higher in pre-pandemic samples from Juba compared to Boston, where the serological test was validated. The estimated proportion of the population infected ranged from 30.1% to 60.6% depending on assumptions about test performance and prevalence of clinically severe infections.\n\nConclusionsSARS-CoV-2 has spread extensively within Juba. Validation of serological tests in sub-Saharan African populations is critical to improve our ability to use serosurveillance to understand and mitigate transmission.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Kirsten E. Wiens", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Pinyi Nyimol Mawien", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "John Rumunu", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "Damien Slater", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Forrest K. Jones", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Serina Moheed", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Andrea Caflish", + "author_inst": "Displacement Tracking Matrix, International Organization for Migration, Juba, South Sudan" + }, + { + "author_name": "Bior K. Bior", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "Jacob Amanaya Iboyi", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "Richard Lino Loro Lako", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "Argata Guracha Guyo", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Olushayo Oluseun Olu", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Sylvester Maleghemi", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Andrew Baguma", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Juma John Hassen", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Sheila K. Baya", + "author_inst": "World Health Organization, Juba, South Sudan" + }, + { + "author_name": "Lul Deng", + "author_inst": "Republic of South Sudan Ministry of Health, Juba, South Sudan" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Maya N. Demby", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Vanessa Sanchez", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Rachel Mills", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Clare Fraser", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Richelle C. Charles", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Jason B. Harris", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Andrew S. Azman", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Joseph F. Wamala", + "author_inst": "World Health Organization, Juba, South Sudan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21252741", "rel_title": "Weak anti-SARS-CoV-2 antibody response after the first injection of an mRNA COVID-19 vaccine in kidney transplant recipients", @@ -855956,101 +854489,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.09.21253200", - "rel_title": "Cumulative incidence of SARS-CoV-2 infection and associated risk factors among frontline health care workers in Paris, France: the SEROCOV prospective cohort study", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253200", - "rel_abs": "BackgroundWith the COVID-19 pandemic, documenting whether health care workers (HCWs) are at increased risk of SARS-CoV-2 contamination and identifying risk factors is of major concern.\n\nMethodsIn this multicenter prospective cohort study, HCWs from frontline departments were included in March and April 2020 and followed for 3 months. SARS-CoV-2 serology was performed at month 0 (M0), M1, and M3 and RT-PCR in case of symptoms. The primary outcome was laboratory-confirmed SARS-CoV-2 infection at M3. Risk factors of laboratory-confirmed SARS-CoV-2 infection at M3 were identified by multivariate logistic regression.\n\nResultsAmong 1,062 HCWs (median [interquartile range] age, 33 [28-42] years; 758 [71.4%] women; 321 [30.2%] physicians), the cumulative incidence of SARS-CoV-2 infection at M3 was 14.6% (95% confidence interval [CI] [12.5; 16.9]). Risk factors were the working department specialty, with increased risk for intensive care units (odds ratio 1.80, 95%CI [0.38; 8.58]), emergency departments (3.91 [0.83; 18.43]) and infectious diseases departments (4.22 [0.92; 18.28]); active smoking was associated with reduced risk (0.36 [0.21; 0.63]). Age, sex, professional category, number of years of experience in the job or department, and public transportation use were not significantly associated with laboratory-confirmed SARS-CoV-2 infection at M3.\n\nConclusionThe rate of SARS-CoV-2 infection in frontline HCWs was 14.6% at the end of the first COVID-19 wave in Paris and occurred mainly early. The study argues for an origin of professional in addition to private life contamination and therefore including HCWs in the first-line vaccination target population. It also highlights that smokers were at lower risk.\n\nKey messagesO_LIDuring the first epidemic wave, 14.6% of 1,062 first-line Health Care Workers had a positive serology and/or RT-PCR test for SARS-CoV-2.\nC_LIO_LIMost infections occurred early\nC_LIO_LIRisk was increased by working in infectious diseases (OR 4.22, 95% confidence interval [0.92; 18.28]), emergency (3.91 [0.83; 18.43]) and intensive care units (1.80, [0.38; 8.58])\nC_LIO_LIBeing an active smoker was protective (0.36 [0.21; 0.3]).\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "pierre hausfater", - "author_inst": "sorbonne university emergency department, GRC-14 BIOSFAST INSERM 1166 IHU ICAN" - }, - { - "author_name": "david boutolleau", - "author_inst": "service de virologie sorbonne university" - }, - { - "author_name": "karine lacombe", - "author_inst": "Infectious Disease Department Sorbonne University Hopital Saint-Antoine" - }, - { - "author_name": "alexandra beurton", - "author_inst": "Service de pneumologie - medecine intensive reanimation, hopital Pitie-Salpetriere, APHP.Sorbonne University" - }, - { - "author_name": "margaux dumont", - "author_inst": "Emergency Department, hopital Pitie-Salpetriere, APHP. Sorbonne University" - }, - { - "author_name": "jean michel constantin", - "author_inst": "Sorbonne University, GRC 29, AP-HP, DMU DREAM, Department of Anaesthesiology and critical care" - }, - { - "author_name": "jade ghosn", - "author_inst": "AP-HP, Nord, Service des Maladies Infectieuses et Tropicales, Hopital Bichat - Claude Bernard, and Universite de Paris, INSERM, UMR 1137 IAME" - }, - { - "author_name": "alain combes", - "author_inst": "Sorbonne Universite, INSERM, UMRS 1166-ICAN, Institute of Cardiometabolism and Nutrition, and Service de medecine intensive-reanimation" - }, - { - "author_name": "nicolas cury", - "author_inst": "Emergency Department, APHP.Sorbonne Universite Hopital Saint-Antoine, Paris" - }, - { - "author_name": "romain guedj", - "author_inst": "Pediatric Emergency Deparment, APHP Hopital Armand Trousseau Sorbonne Universite" - }, - { - "author_name": "michel djibre", - "author_inst": "Service de Medecine intensive Reanimation, APHP.Sorbonne Universite Hopital Tenon" - }, - { - "author_name": "rudy pierre bompard", - "author_inst": "Emergency Department, hopital Tenon, APHP.Sorbonne Universite" - }, - { - "author_name": "sandie mazerand", - "author_inst": "Service de medecine intensive-reanimation, APHP.Sorbonne Universite Hopital Saint-Antoine" - }, - { - "author_name": "valerie pourcher", - "author_inst": "Sorbonne Universite, APHP, Hopitaux Universitaires Pitie-Salpetriere Charles Foix, Service de Maladies infectieuses et Tropicales" - }, - { - "author_name": "linda gimeno", - "author_inst": "APHP.Sorbonne Universite, Unite de Recherche Clinique Pitie Salpetriere Charles Foix" - }, - { - "author_name": "clemence marois", - "author_inst": "Unite de Medecine Intensive Reanimation Neurologique, Departement de Neurologie, DMU Neurosciences, APHP.Sorbonne Universite" - }, - { - "author_name": "elisa teyssou", - "author_inst": "INSERM, Institut Pierre Louis d Epidemiologie et de Sante Publique Service de Virologie, Paris" - }, - { - "author_name": "anne genevieve marcelin", - "author_inst": "INSERM, Institut Pierre Louis d Epidemiologie et de Sante Publique Service de Virologie, Paris" - }, - { - "author_name": "david hajage", - "author_inst": "APHP.Sorbonne Universite, Unite de Recherche Clinique Pitie Salpetriere Charles Foix, F75013, Paris, France" - }, - { - "author_name": "florence tubach", - "author_inst": "APHP.Sorbonne Universite, Unite de Recherche Clinique Pitie Salpetriere Charles Foix, F75013, Paris, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.09.21253242", "rel_title": "Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission in England, October to December 2020", @@ -856791,6 +855229,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21252001", + "rel_title": "The BioNTech / Pfizer vaccine BNT162b2 induces class-switched SARS-CoV-2-specific plasma cells and potential memory B cells as well as IgG and IgA serum and IgG saliva antibodies upon the first immunization", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21252001", + "rel_abs": "To treat the SARS-CoV-2 virus, that enters the body through the respiratory tract, different vaccines in particular against the SARS-CoV-2 spike (S)-protein have been developed or are in the development process. For the BioNTech / Pfizer mRNA vaccine BNT162b2, which is injected twice, protection against COVID-19 has been described for the first weeks after the second vaccination. The underlying mechanisms of defense and the long-term effectiveness of this vaccine against COVID-19 are currently under investigation.\n\nIn addition to the induction of systemic antibodies (Abs), Ab responses in the respiratory tract would help to form a first line of defense against SARS-CoV-2. Furthermore, protection depends on Fab-part-dependent neutralizing capacities, however, Fc-part-mediated effector mechanisms might also be important. Long-term defense would be based on the induction of long-lived antibody-producing plasma cells (PCs) and memory B cells.\n\nHere, we established different assays to analyze anti-SARS-CoV-2-S IgG and IgA Abs in blood serum and saliva as well as SARS-CoV-2-S1-reactive IgG and IgA PCs and potential memory B cells in the blood of individuals upon their first immunization with BNT162b2.\n\nWe show that the vaccine induces in particular anti-SARS-CoV-2-S IgG1 and IgG3 as well as IgA1 and in some individuals also IgG2 and IgA2 serum Abs. In the saliva, we found no anti-SARS-CoV-2-S IgA, but instead IgG Abs. Furthermore, we found SARS-CoV-2-S reactive IgG+ blood PCs and potential memory B cells as well as SARS-CoV-2-S reactive IgA+ PCs and/or potential memory B cells in some individuals.\n\nOur data suggest that the vaccine induces a promising CD4+ T cell-dependent systemic IgG1 and IgG3 Ab response with IgG+ PCs and potential memory B cells. In addition to the systemic IgG response, the systemic IgA and saliva IgG response might help to improve a first line of defense in the respiratory tract against SARS-CoV-2 and its mutants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Anne Sophie Lixenfeld", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "inga Kuensting", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Emily L. Martin", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Vera von Kopylow", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Selina Lehrian", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Hanna B. Lunding", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Jana Sophia Buhre", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Janna L. Quack", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Moritz Steinhaus", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + }, + { + "author_name": "Tobias Graf", + "author_inst": "Medical Department 3, University Medical Center of Schleswig-Holstein, Luebeck, Germany;" + }, + { + "author_name": "Marc Ehlers", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Johann Rahmoeller", + "author_inst": "Institut fuer Ernaehrungsmedizin, Universitaet zu Luebeck" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253311", "rel_title": "Bayesian inference across multiple models suggests a strong increase in lethality of COVID-19 in late 2020 in the UK", @@ -857634,45 +856135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.03.11.21253225", - "rel_title": "Are vaccines safe in patients with Long COVID? A prospective observational study.", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253225", - "rel_abs": "IntroductionAlthough the efficacy of SARS-CoV-2 vaccination to prevent symptomatic COVID-19 is well established, there are no published studies on the impact on symptoms in patients with Long Covid. Anecdotal reports have suggested both a potential benefit and worsening of symptoms post vaccination with the uncertainty leading to some vaccine hesitancy amongst affected individuals.\n\nMethodsPatients initially hospitalised with COVID-19 were prospectively recruited to an observational study with clinical follow-up at 3 months (June-July 2020) and 8 months (Dec 2020-Jan 2021) post-admission. Participants who received the Pfizer-BioNTech (BNT162b2) or Oxford-AstraZeneca (ChAdOx1 nCoV-19) vaccine between January to February 2021 were identified and matched 2:1 (in terms of 8-month symptoms) with participants from the same cohort who were unvaccinated. All were re-assessed at 1 month post vaccination (or matched timepoint for unvaccinated cohort). Validated quality of life (SF-36), mental wellbeing (WEMWBS) and ongoing symptoms were assessed at all timepoints. Formal statistical analysis compared the effect of vaccination on recent quality of life using baseline symptoms, age, and gender in linear regression.\n\nResultsForty-four vaccinated participants were assessed at a median of 32 days (IQR 20-41) post vaccination with 22 matched unvaccinated participants. Most were highly symptomatic of Long Covid at 8 months (82% in both groups had at least 1 persistent symptom), with fatigue (61%), breathlessness (50%) and insomnia (38%) predominating. There was no significant worsening in quality-of-life or mental wellbeing metrics pre versus post vaccination. Nearly two-thirds (n=27) reported transient (<72hr duration) systemic effects (including fever, myalgia and headache).\n\nWhen compared to matched unvaccinated participants from the same cohort, those who had receive a vaccine had a small overall improvement in Long Covid symptoms, with a decrease in worsening symptoms (5.6% vaccinated vs 14.2% unvaccinated) and increase in symptom resolution (23.2% vaccinated vs 15.4% unvaccinated) (p=0.035). No difference in response was identified between Pfizer-BioNTech or Oxford-AstraZeneca vaccines.\n\nConclusionsReceipt of vaccination with either an mRNA or adenoviral vector vaccine was not associated with a worsening of Long Covid symptoms, quality of life, or mental wellbeing. Individuals with prolonged COVID-19 symptoms should receive vaccinations as suggested by national guidance.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "David T Arnold", - "author_inst": "University of Bristol" - }, - { - "author_name": "Alice Milne", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Emma Samms", - "author_inst": "Patient representative" - }, - { - "author_name": "Louise Stadon", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Nick A Maskell", - "author_inst": "University of Bristol" - }, - { - "author_name": "Fergus W Hamilton", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.11.21252969", "rel_title": "Reducing the Cost of Rapid Antigen Tests through Swab Pooling and Extraction in a Device", @@ -858313,6 +856775,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.03.11.21253350", + "rel_title": "Oxygen provision to severely ill COVID-19 patients at the peak of the 2020 pandemic in a Swedish district hospital: medical records-based cohort study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253350", + "rel_abs": "Oxygen is a low-cost and life-saving therapy for patients with COVID-19. Yet, it is a limited resource in many hospitals in low income countries and in the 2020 pandemic even hospitals in richer countries reported oxygen shortages. An accurate understanding of oxygen requirements is needed for capacity planning. The World Health Organization estimates the average flow-rate of oxygen to severe COVID-19-patients to be 10 l/min. However, there is a lack of empirical data about the oxygen provision to patients. This study aimed to estimate the oxygen provision to COVID-19 patients with severe disease in a Swedish district hospital.\n\nA retrospective, medical records-based cohort study was conducted in March to May 2020 in a Swedish district hospital. All adult patients with severe COVID-19 - those who received oxygen in the ward and had no ICU-admission during their hospital stay - were included. Data were collected on the oxygen flow-rates provided to the patients throughout their hospital stay, and summary measures of oxygen provision calculated.\n\nOne-hundred and twenty six patients were included, median age was 70 years and 43% were female. On admission, 27% had a peripheral oxygen saturation of [≤]91% and 54% had a respiratory rate of [≥]25/min. The mean oxygen flow-rate to patients while receiving oxygen therapy was 3.0 l/min (SD 2.9) and the mean total volume of oxygen provided per patient admission was 16,000 l (SD 23,000).\n\nIn conclusion, the provision of oxygen to severely ill COVID-19-patients was lower than previously estimated. Further research is required before global estimates are adjusted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Anna Hvarfner", + "author_inst": "Uppsala University" + }, + { + "author_name": "Ahmed Al-Djaber", + "author_inst": "Nykoping Hospital" + }, + { + "author_name": "Hampus Ekstrom", + "author_inst": "Nykoping Hospital" + }, + { + "author_name": "Malin Enarsson", + "author_inst": "Eskilstuna Hospital" + }, + { + "author_name": "Markus Castegren", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Tim Baker", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Carl Otto Schell", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.11.21253263", "rel_title": "Seroprevalence of SARS-CoV-2 Infection in Cincinnati Ohio USA from August to December 2020", @@ -859376,85 +857881,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.11.21253402", - "rel_title": "Comprehensive evaluation of the impact of sociodemographic inequalities on adverse outcomes and excess mortality during the COVID-19 pandemic in Mexico City", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253402", - "rel_abs": "The impact of the COVID-19 pandemic in Mexico City has been sharp, as several social inequalities coexist with chronic comorbidities. Here, we conducted an in-depth evaluation of the impact of social, municipal, and individual factors on the COVID-19 pandemic in working-age population living in Mexico City. To this end, we used data from the National Epidemiological Surveillance System; furthermore, we used a multidimensional metric, the social lag index (DISLI), to evaluate its interaction with mean urban population density (MUPD) and its impact on COVID-19 rates. Influence DISLI and MUPD on the effect of vehicular mobility policies on COVID-19 rates were also tested. Finally, we assessed the influence of MUPD and DISLI on discrepancies of COVID-19 and non-COVID-19 excess mortality compared with death certificates from the General Civil Registry. We detected vulnerable groups who belonged to economically active sectors and who experienced increased risk of adverse COVID-19 outcomes. The impact of social inequalities transcends individuals and has significant effects at a municipality level, with and interaction between DISLI and MUPD. Marginalized municipalities with high population density experienced an accentuated risk for adverse COVID-19 outcomes. Additionally, policies to reduce vehicular mobility had differential impacts across marginalized municipalities. Finally, we report an under-registry of COVID-19 deaths and significant excess mortality associated with non-COVID-19 deaths closely related to MUPD/DISLI in an ambulatory setting, which could be a negative externality of hospital reconversion. In conclusion, social, individual, and municipality-wide factors played a significant role in shaping the course of the COVID-19 pandemic in Mexico City.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Neftali Eduardo Antonio-Villa", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Luisa Fern\u00e1ndez-Chirino", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Julio Pisanty-Alatorre", - "author_inst": "Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Javier Mancilla-Galindo", - "author_inst": "Instituto Nacional de Cardiologia" - }, - { - "author_name": "Ashuin Kammar-Garc\u00eda", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Arsenio Vargas-V\u00e1zquez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Armando Gonz\u00e1lez-D\u00edaz", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Carlos A. Ferm\u00edn-Mart\u00ednez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Alejandro M\u00e1rquez-Salinas", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Enrique Ca\u00f1edo Guerra", - "author_inst": "National Autonomous University of Mexico" - }, - { - "author_name": "Jessica Paola Bahena-L\u00f3pez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Marco Villanueva-Reza", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Jessica M\u00e1rquez-S\u00e1nchez", - "author_inst": "Instituto Nacional de Pediatria" - }, - { - "author_name": "M\u00e1ximo Ernesto Jaramillo-Molina", - "author_inst": "International Inequalities Institute, London School of Economics, London, UK." - }, - { - "author_name": "Luis Miguel Guti\u00e9rrez-Robledo", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "Instituto Nacional de Geriatria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.10.21253324", "rel_title": "Dynamic versus Continuous Interventions: Optimizing Lockdown Policies for COVID-19", @@ -859967,6 +858393,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.12.21253454", + "rel_title": "Modelling, prediction and design of national COVID-19 lockdowns by stringency and duration", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253454", + "rel_abs": "The implementation of lockdowns has been a key policy to curb the spread of COVID-19 and to keep under control the number of infections. However, quantitatively predicting in advance the effects of lockdowns based on their stringency and duration is a complex task, in turn making it difficult for governments to design effective strategies to stop the disease. Leveraging a novel mathematical \"hybrid\" approach, we propose a new epidemic model that is able to predict the future number of active cases and deaths when lockdowns with different stringency levels or durations are enforced. The key observation is that lockdown-induced modifications of social habits may not be captured by traditional mean-field compartmental models because these models assume uniformity of social interactions among the population, which fails during lockdown. Our model is able to capture the abrupt social habit changes caused by lockdowns. The results are validated on the data of Israel and Germany by predicting past lockdowns and providing predictions in alternative lockdown scenarios (different stringency and duration). The findings show that our model can effectively support the design of lockdown strategies by stringency and duration, and quantitatively forecast the course of the epidemic during lockdown.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alberto Mellone", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zilong Gong", + "author_inst": "Imperial College London" + }, + { + "author_name": "Giordano Scarciotti", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253448", "rel_title": "SARS-CoV-2 infection and risk of clinical sequelae during the post-acute phase: a retrospective cohort study", @@ -860945,97 +859398,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.09.21253208", - "rel_title": "Point-of-care ultrasonography for risk stratification of non-critical suspected COVID-19 patients on admission (POCUSCO): a prospective binational study", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253208", - "rel_abs": "BackgroundLung point-of-care ultrasonography (L-POCUS) is highly effective in detecting pulmonary peripheral patterns and may allow early identification of patients who are likely to develop an acute respiratory distress syndrome (ARDS). We hypothesized that L-POCUS performed during the initial examination would identify non-severe COVID-19 patients with a high risk of getting worse.\n\nMethodsPOCUSCO was a prospective, multicenter study. Non-critical adult patients who were admitted to the emergency department (ED) for suspected or confirmed COVID-19 were included and had L-POCUS performed within 48 hours following admission. The severity of lung damage was assessed using the L-POCUS score based on 36 points for ARDS. The primary outcome was the rate of patients requiring intubation or who died within 14 days following inclusion.\n\nResultsAmong 296 participating patients, 8 (2.7%) had primary outcome. The area under the curve (AUC) of the receiver operating characteristic of L-POCUS was 0.80 [95%CI:0.60-0.94]. The score values which achieved a sensibility > 95% in defining low-risk patients and a specificity > 95% in defining high-risk patients were <1 and [≥]16, respectively. The rate of patients with an unfavorable outcome was 0/95 (0%[95%CI:0-3.9]) for low-risk patients (score=0) versus 4/184 (2.17%[95%CI:0.8-5.5]) for intermediate-risk patients (score 1-15) and 4/17 (23.5%[95%CI:11.4-42.4]) for high-risk patients (score [≥]16). In patients with confirmed COVID-19 (n=58), the AUC of L-POCUS was 0.97 [95%CI:0.92-1.00].\n\nConclusionsL-POCUS allows risk-stratification of patients with suspected or confirmed COVID-19. These results should be confirmed in a population with a higher risk of an unfavorable outcome.\n\nTrial registration numberNCT04338100", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Francois Morin", - "author_inst": "Department of Emergency Medicine, University Hospital of Angers, Angers, France" - }, - { - "author_name": "Delphine Douillet", - "author_inst": "Department of Emergency Medicine, University Hospital of Angers, Angers, France" - }, - { - "author_name": "Jean Francois Hamel", - "author_inst": "Department of Methodology and Biostatistics, University Hospital of Angers, Univ Angers, France" - }, - { - "author_name": "Dominique Savary", - "author_inst": "Department of Emergency Medicine, University Hospital of Angers, Angers, France" - }, - { - "author_name": "Christophe Aube", - "author_inst": "Department of Radiology, University Hospital of Angers, Univ Angers, Angers, France" - }, - { - "author_name": "Karim Tazarourte", - "author_inst": "Groupement hospitalier Edouard-Herriot, Hospices Civils de Lyon, Emergency Department, Lyon, France" - }, - { - "author_name": "Kamelia Marouf", - "author_inst": "Department of Emergency Medicine, Hospital of Cholet, Cholet, France" - }, - { - "author_name": "Florence Dupriez", - "author_inst": "Department of Emergency Medicine, Cliniques Universitaires Saint-Luc, Brussels, Belgium" - }, - { - "author_name": "Philippe Le Conte", - "author_inst": "Department of Emergency Medicine, University Hospital of Nantes, Nantes, France" - }, - { - "author_name": "Thomas Flament", - "author_inst": "Department of Pulmonology University Hospital of Tours, Tours, France" - }, - { - "author_name": "Thomas Delomas", - "author_inst": "Department of Emergency Medicine, Hospital of Saint-Lo, Saint-Lo, France" - }, - { - "author_name": "Mehdi Taalba", - "author_inst": "CHU Rouen, Department of Emergency Medicine Rouen, Normandie" - }, - { - "author_name": "Nicolas Marjanovic", - "author_inst": "Poitiers University Faculty of Medicine and Pharmacy Poitiers, FR" - }, - { - "author_name": "Francis Couturaud", - "author_inst": "University hospital of Brest, Department of internal medicine and chest diseases BREST cedex" - }, - { - "author_name": "Nicolas Peschanski", - "author_inst": "CHU Rennes, Department of Emergency Medicine Rennes, Bretagne, FR" - }, - { - "author_name": "Thomas Boishardy", - "author_inst": "CHU Angers, Department of Emergency Medicine, Angers, Pays de la Loire, FR" - }, - { - "author_name": "Jeremie Riou", - "author_inst": "UNIV Angers INSERM, UMR 1066, CNRS 6021, MINT Angers, Pays de la Loire, FR" - }, - { - "author_name": "Vincent Dubee", - "author_inst": "CHU Angers Maladies infectieuses et tropicales, Infectious Diseases and Tropical Medicine Angers, FR" - }, - { - "author_name": "Pierre-Marie Roy", - "author_inst": "CHU Angers, Department of Emergency Medicine Angers, FR" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.03.09.21253212", "rel_title": "Exploring the short-term role of particulate matter in the COVID-19 outbreak in USA cities", @@ -861695,6 +860057,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.08.21253110", + "rel_title": "Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 Long Term Care Facilities (VIVALDI study)", + "rel_date": "2021-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253110", + "rel_abs": "BackgroundSARS-CoV-2 infection represents a major challenge for Long Term Care Facilities (LTCFs) and many residents and staff are now sero-positive following persistent outbreaks. We investigated the relationship between the presence of SARS-CoV-2 specific antibodies and subsequent infection in this population.\n\nMethodsProspective cohort study of infection in staff and residents in 100 LTCFs in England between October 2020 and February 2021. Blood samples were collected at baseline (June 2020), 2 and 4 months and tested for IgG antibodies to nucleocapsid and spike protein. PCR testing for SARS-CoV-2 was undertaken weekly in staff and monthly in residents. The primary analysis estimated the relative hazard of a PCR-positive test by baseline antibody status, from Cox regression adjusted for age and gender, and stratified by LTCF.\n\nFindingsStudy inclusion criteria were met by 682 residents and 1429 staff. Baseline IgG antibodies to nucleocapsid were detected in 226 residents (33%) and 408 staff (29%). A total of 93 antibody-negative residents had a PCR-positive test (0.054 per month at risk) compared to 4 antibody-positive residents (0.007 per month at risk). There were 111 PCR-positive tests in antibody-negative staff (0.042 per month at risk) compared to 10 in antibody-positive staff (0.009 per month at risk). The adjusted hazard ratios for reinfection in staff and residents with a baseline positive versus negative antibody test were 0.13 (95% CI 0.05-0.40) and 0.39 ((95% CI: 0.19-0.77) respectively. Of 12 reinfected participants with data on symptoms, 11 were symptomatic. Antibody titres to spike and nucleocapsid were comparable in PCR-positive and PCR-negative cases.\n\nInterpretationThe presence of IgG antibodies to nucleocapsid was associated with substantially reduced risk of reinfection in staff and residents for up to 10 months after primary infection.\n\nFundingUK Government Department of Health and Social Care\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe performed a systematic search of MEDLINE (Ovid) and MedRxiv on 18 January 2021 for studies in LTCFs that described the risk of infection in individuals who were seropositive for SARS-CoV-2 compared to individuals who were seronegative. Search terms were deliberately broad to improve capture of relevant literature and included \"SARS-CoV-2\"OR \"COVID-19\" OR \"coronavirus\" AND \"care home\" OR \"nursing home\" OR \"long term care facility\" with no date or language restrictions. We did not identify any publications that focussed on risk of reinfection in seropositive individuals, but subsequent to our search one study has been published using data from two LTCFs in London, UK. This study reported a 96% reduction in the odds of reinfection in individuals who were seropositive compared to those who were seronegative based on 4-month follow-up in 161 participants. We found 10 studies that performed seroprevalence surveys in either staff or staff and residents in LTCFs in 8 cohorts. Five of these were carried out in response to SARS-CoV-2 outbreaks within the care homes, either as part of the subsequent investigation or as post-infection surveillance. The largest of these, which enrolled both staff and residents, was performed in 6 LTCFs and performed longitudinal antibody testing.\n\nAdded value of this studyWe undertook a cohort study in staff and residents from 100 LTCFs in England to investigate whether individuals with evidence of prior SARS-CoV-2 infection could be infected twice. Staff and residents were offered up to three rounds of antibody testing and antibody results were linked to PCR test results which were obtained weekly from staff and monthly from residents through the national SARS-CoV-2 testing programme. This study, which was conducted in >2000 staff and residents, suggests that antibodies provide high levels of protection against reinfection for up to 10 months. Almost all cases of reinfection were symptomatic, but no cases required hospital treatment. Amongst those with detectable baseline antibodies, quantitative antibody titres against spike protein and nucleocapsid were comparable between cases of reinfection and those who did not become reinfected.\n\nImplications of all available evidenceDespite high background rates of infection in LTCFs, the overall risk of reinfection was low in this population. This is broadly consistent with findings from large cohort studies of hospital staff, but, importantly, extends the evidence of substantial protection to frail elderly, who are vulnerable to severe outcomes of SARS-CoV-2 due to age-related changes in immunity (immune-senescence) and high levels of comorbidity. The low risk of reinfection in our study suggests identification of immune correlates of protection in this population will require pooling of data across multiple cohorts.\n\nAs vaccination coverage in residents approaches 100% in England, it will be important to understand whether vaccination and natural infection provide comparable levels of protection against infection. Such insights will inform future policy decisions regarding re-vaccination schedules in LTCF, and the longer-term need for non-pharmaceutical interventions to prevent SARS-CoV-2 transmission, such as asymptomatic testing and visitor restrictions.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Maria Krutikov", + "author_inst": "UCL" + }, + { + "author_name": "Tom Palmer", + "author_inst": "UCL" + }, + { + "author_name": "Gokhan Tut", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Chris Fuller", + "author_inst": "UCL" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "UCL" + }, + { + "author_name": "Haydn Williams", + "author_inst": "Four Seasons Healthcare Group" + }, + { + "author_name": "Daniel Davies", + "author_inst": "Palantir Ltd" + }, + { + "author_name": "Aidan Irwin-Singer", + "author_inst": "UK Department of Health and Social Care" + }, + { + "author_name": "James Robson", + "author_inst": "Four Seasons Healthcare Group" + }, + { + "author_name": "Andrew Hayward", + "author_inst": "UCL" + }, + { + "author_name": "Paul Moss", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Andrew Copas", + "author_inst": "UCL" + }, + { + "author_name": "Laura J Shallcross", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2021.03.02.21252438", "rel_title": "Detection of autoimmune antibodies in severe but not in moderate or asymptomatic COVID-19 patients", @@ -863062,77 +861491,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.10.434733", - "rel_title": "Structures and function of locked conformations of SARS-CoV-2 spike", - "rel_date": "2021-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.10.434733", - "rel_abs": "The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct \"S-R/x3\" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kun Qu", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Qiuluan Chen", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Katarzyna A Ciazynska", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Banghui Liu", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xixi Zhang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Jingjing Wang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Yujie He", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Jiali Guan", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Jun He", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Tian Liu", - "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" - }, - { - "author_name": "Xiaofei Zhang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Andrew P Carter", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Xiaoli Xiong", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "John A G Briggs", - "author_inst": "MRC Laboratory of Molecular Biology" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.09.434592", "rel_title": "Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes", @@ -864397,6 +862755,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.07.21253080", + "rel_title": "COVID-19 vaccine distrust in Colombian university students: Frequency and associated variables", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.07.21253080", + "rel_abs": "The study aimed to know the frequency and variables associated with COVID-19 vaccine distrust in students of a Colombian university. A cross-sectional study was carried out which participated emerging adult students of a Colombian university. A total of 1,136 students between 18 and 29 years (M= 22.0, SD = 3.0); most of them were female (66.0%), non-health students (82.8%), low-income (79.0%), and residents of urban areas (84.9%). It was frequent low institutional trust (74.8%), low cognitive, social capital (27.9%), low fear of COVID-19 (49.5%), low perceived stress related to COVID-19 (83.5%), and high COVID-19 vaccine distrust (78.9%). Non-health carrier (Adjusted OR = 3.63, 95%CI 2.58-5.10), rural residence (AOR = 1.85, 95%CI 1.13-3.04), low income (AOR = 1.84, 95%CI 1.31-2.57), and perceived stress related to COVID-19 (AOR = 1.74, 95%CI 1.20-2.54) were related to high COVID-19 vaccine distrust. In conclusion, COVID-19 vaccine distrust is high among emerging adult Colombian university students. The COVID-19 vaccine distrust is related to non-health science carriers, rural residents, low-income, and low-perceived stress related to COVID-19. The COVID-19 related health literacy should be improved in students of this university considering socio-cultural background.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Adalberto Campo-Arias", + "author_inst": "Universidad del Magdalena" + }, + { + "author_name": "John C Pedrozo-Pupo", + "author_inst": "Universidad del Magdalena" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.06.21252601", "rel_title": "COVID-19 risk score as a public health tool to guide targeted testing: A demonstration study in Qatar", @@ -865592,85 +863973,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.03.09.434641", - "rel_title": "A recombinant ACE2 Triple Decoy that traps and neutralizes SARS-CoV-2 shows enhanced affinity for highly transmissible SARS-CoV-2 variants", - "rel_date": "2021-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434641", - "rel_abs": "The highly-transmissible SARS-CoV-2 variants now replacing the first wave strain pose an increased threat to human health by their ability, in some instances, to escape existing humoral protection conferred by previous infection, neutralizing antibodies, and possibly vaccination. Thus, other therapeutic options are necessary. One such therapeutic option that leverages SARS-CoV-2 initiation of infection by binding of its spike receptor binding domain (S RBD) to surface-expressed host cell angiotensin-converting enzyme 2 (ACE2) is an ACE2 decoy that would trap the virus by competitive binding and thus inhibit propagation of infection. Here, we used Molecular Dynamic (MD) simulations to predict ACE2 mutations that might increase its affinity for S RBD and screened these candidates for binding affinity in vitro. A double mutant ACE2(T27Y/H34A)-IgG1FC fusion protein was found to have very high affinity for S RBD and to show greater neutralization of SARS-CoV-2 in a live virus assay as compared to wild type ACE2. We further modified the double mutant ACE2 decoy by addition of an H374N mutation to inhibit ACE2 enzymatic activity while maintaining high S RBD affinity. We then confirmed the potential efficacy of our ACE2(T27Y/H34A/H374N)-IgG1FC Triple Decoy against S RBD expressing variant-associated E484K, K417N, N501Y, and L452R mutations and found that our ACE2 Triple Decoy not only maintains its high affinity for S RBD expressing these mutations, but shows enhanced affinity for S RBD expressing the N501Y or L452R mutations and the highest affinity for S RBD expressing both the E484K and N501Y mutations. The ACE2 Triple Decoy also demonstrates the ability to compete with wild type ACE2 in the cPass surrogate virus neutralization in the presence of S RBD with these mutations. Additional MD simulation of ACE2 WT and decoy interactions with S RBD WT or B.1.351 variant sequence S RBD provides insight into the enhanced affinity of the ACE2 decoy for S RBD and reveals its potential as a tool to predict affinity and inform therapeutic design. The ACE2 Triple Decoy is now undergoing continued assessment, including expression by a human adenovirus serotype 5 (hAd5) construct to facilitate delivery in vivo.\n\nSummary sentenceAn ACE2(N27Y/H34A/H374N)-IgG1FC fusion protein decoy sustains high affinity to all SARS-CoV-2 spike receptor binding domain (RBD) protein variants tested, shows enhanced affinity for the N501Y and L452R variants, and the highest affinity for combined N501Y and E484K variants.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Shiho Tanaka", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Gard Nelson", - "author_inst": "ImmunityBio" - }, - { - "author_name": "Anders Olson", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Oleksandr Buzko", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Wendy Higashide", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Annie Shin", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Marcos Gonzales", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Justin Taft", - "author_inst": "Icahn School of Medicine, New York" - }, - { - "author_name": "Roosheel Sandeep Patel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sofija Buta", - "author_inst": "Icahn School of Medicine, New York" - }, - { - "author_name": "Marta Martin-Fernandez", - "author_inst": "Icahn School of Medicine, New York" - }, - { - "author_name": "Dusan Sandeep Bogunovic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Patricia R Spilman", - "author_inst": "ImmunityBio, Inc" - }, - { - "author_name": "Kayvan Niazi", - "author_inst": "ImmunityBio, Inc" - }, - { - "author_name": "Shahrooz Rabizadeh", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Patrick Soon-Shiong", - "author_inst": "ImmunityBio, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.03.05.433897", "rel_title": "COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19", @@ -866647,6 +864949,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.05.434168", + "rel_title": "Deletion disrupts a conserved antibody epitope in a SARS-CoV-2 variant of concern", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.434168", + "rel_abs": "Multiple SARS-CoV-2 variants with altered antigenicity have emerged and spread internationally. In one lineage of global concern, we identify a transmitted variant with a deletion in its receptor binding domain (RBD) that disrupts an epitope which is conserved across sarbecoviruses. Overcoming antigenic variation by selectively focusing immune pressure on this conserved site may, ultimately, drive viral resistance.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Linda L. Rennick", + "author_inst": "The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA" + }, + { + "author_name": "Lindsey R. Robinson-McCarthy", + "author_inst": "Department of Pathology, University of Pittsburgh" + }, + { + "author_name": "Sham Nambulli", + "author_inst": "The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA" + }, + { + "author_name": "W. Paul Duprex", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Kevin Raymond McCarthy", + "author_inst": "The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.08.433449", "rel_title": "Drug development of an affinity enhanced, broadly neutralizing heavy chain only antibody that restricts SARS-CoV-2 in hamsters", @@ -867742,41 +866079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.03.04.21252550", - "rel_title": "Estimating the super-spreading rate at workplaces using bluetooth technology", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252550", - "rel_abs": "Workplaces deploy internal guidelines to remain operational during the ongoing COVID-19 pandemic. It is challenging to assess whether those interventions will prevent super-spreading events, where an infected individual transmits the disease to 10 or more secondary cases. Here we provide a model of infectious disease at the level of a workplace to address that problem. We take as input proximity contact records based on bluetooth technology and the infectious disease parameters from the literature. Using proximity contact data for a case-study workplace and an infection transmission model, we estimate the SARS-CoV-2 transmission rate as 0.014 per proximity contact, going up to 0.041 for the SARS-CoV-2 B.1.1.7 variant first detected in the UK. Defining super-spreading as events with 10 or more secondary infections, we obtain a super-spreading event rate of 2.3 per 1000 imported SARS-CoV-2 cases, rising up to 13.7 for SARS-CoV-2 B.1.1.7. This methodology provides the means for workplaces to determine their internal super-spreading rate or other infection related risks.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alexei Vazquez", - "author_inst": "German Aerospace Center (DLR), Institute for the Protection of Terrestrial Infrastructures" - }, - { - "author_name": "Maximilian Staebler", - "author_inst": "German Aerospace Center (DLR), Institute for the Protection of Terrestrial Infrastructures" - }, - { - "author_name": "Alexander Khanin", - "author_inst": "German Aerospace Center (DLR), Institute for the Protection of Terrestrial Infrastructures" - }, - { - "author_name": "Daniel Lichte", - "author_inst": "German Aerospace Center (DLR), Institute for the Protection of Terrestrial Infrastructures" - }, - { - "author_name": "Eva Brucherseifer", - "author_inst": "German Aerospace Center (DLR), Institute for the Protection of Terrestrial Infrastructures" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.04.21252913", "rel_title": "Comparison of IgG and neutralizing antibody responses after one or two doses of COVID-19 mRNA vaccine in previously infected and uninfected persons", @@ -868401,6 +866703,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.03.04.21252903", + "rel_title": "Impact of remdesivir on 28 day mortality in hospitalized patients with COVID-19: February 2021 Meta-analysis", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252903", + "rel_abs": "BackgroundThe COVID-19 pandemic has stimulated worldwide investigation into a myriad of potential therapeutic agents, including antivirals such as remdesivir. The first RCT reporting results on the impact of remdesivir on COVID-19 in a peer reviewed journal was the ACTT-1 trial published in November, 2020. The ACTT-1 trial showed more rapid clinical improvement and a reduced risk of 28-day mortality in patients who received remdesivir.\n\nThis study is a meta-analysis of peer reviewed RCTs aims to estimate the association of remdesivir therapy compared to the usual care or placebo on all-cause mortality in hospitalized patients with COVID-19. Software based tools to accelerate the analysis process.\n\nMethodsMeta-analysis of peer reviewed RCTs comparing remdesivir to usual care or placebo. The protocol for this meta-analysis was registered and published in the PROSPERO database (CRD42021229985) on February 5, 2021.\n\nResultsFour English language RCTs were identified, including data from 7,333 hospitalized patients worldwide using remdesivir in COVID-19 positive patients.\n\nMeta-analysis of all identified RCTs showed no difference in survival in patients who received remdesivir therapy compared to usual care or placebo. The random effects meta-analysis has a summary odd ratio is 0.89 (95% CI 0.65-1.21, p = 0.30). Considerable variability in the severity of illness is noted with the rates of IMV at the time of randomization ranging from 0% to 27%.\n\nConclusionsThis meta-analysis of randomized controlled trials published in peer-reviewed literature by February 1, 2021 did not show reduced mortality in hospitalized patients with COVID-19 who received remdesivir. Further research is needed to clarify the role of remdesivir therapy in the management of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Robert Robinson", + "author_inst": "SIU School of Medicine" + }, + { + "author_name": "Vidhya Prakash", + "author_inst": "SIU School of Medicine" + }, + { + "author_name": "Raad Al Tamimi", + "author_inst": "College of Medicine, Alfaisal University, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nour Albast", + "author_inst": "College of Medicine, Alfaisal University, Riyadh, Saudi Arabia" + }, + { + "author_name": "Elizabeth Wieland", + "author_inst": "SIU School of Medicine" + }, + { + "author_name": "Carlos Garcia", + "author_inst": "SIU School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.04.21251264", "rel_title": "Comparison of COVID-19 vaccine prioritization strategies in the United States", @@ -869504,65 +867845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.04.21252949", - "rel_title": "High-frequency screening combined with diagnostic testing for control of SARS-CoV-2 in high-density settings: an economic evaluation of resources allocation for public health benefit", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252949", - "rel_abs": "SARS-CoV-2 spreads quickly in dense populations, with serious implications for universities, workplaces, and other settings where exposure reduction practices are difficult to implement. Rapid screening has been proposed as a tool to slow the spread of the virus; however, many commonly used diagnostic tests (e.g., RT-qPCR) are expensive, difficult to deploy (e.g., require a nasopharyngeal specimen), and have extended turn-around times. We evaluated testing regimes that combined diagnostic testing using qPCR with high-frequency screening using a novel reverse-transcription loop-mediated isothermal amplification (RT-LAMP, herein LAMP) assay. We used a compartmental susceptible-exposed-infectious-recovered (SEIR) model to simulate screening of a university population. We also developed a Shiny application to allow administrators and public health professionals to develop optimal testing strategies given site-specific assumptions about testing investment, target population, and cost. The frequency of screening, especially when pooling samples, was more important for minimizing epidemic size than test sensitivity, behavioral compliance, contact tracing capacity, and time between testing and results. Our results suggest that when testing budgets are limited, it is safer and more cost-effective to allocate the majority of funds to screening. Rapid, cost-effective, and scalable screening tests, like LAMP, should be viewed as critical components of SARS-CoV-2 testing in high-density populations.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Will Rogers", - "author_inst": "Montana State University" - }, - { - "author_name": "Manuel Ruiz-Aravena", - "author_inst": "Montana State University" - }, - { - "author_name": "Dale Hansen", - "author_inst": "Montana State University" - }, - { - "author_name": "Wyatt Madden Sonoma", - "author_inst": "Montana State University" - }, - { - "author_name": "Maureen Kessler", - "author_inst": "Montana State University" - }, - { - "author_name": "Matthew W Fields", - "author_inst": "Montana State University" - }, - { - "author_name": "Matthew J Ferrari", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Connie B Chang", - "author_inst": "Montana State University" - }, - { - "author_name": "Jayne Morrow", - "author_inst": "Montana State University" - }, - { - "author_name": "Andrew Hoegh", - "author_inst": "Montana State University" - }, - { - "author_name": "Raina K Plowright", - "author_inst": "Montana State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.05.21253022", "rel_title": "Non-uniform UV-C dose across N95 facepieces can cause 2.9-log variation in SARS-CoV-2 inactivation", @@ -870243,6 +868525,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.05.21252998", + "rel_title": "COVID-19 mRNA vaccine is not detected in human milk", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252998", + "rel_abs": "Several countries have recently approved the use of mRNA vaccines against COVID-19 under an emergency use authorization. However, no pregnant or lactating individuals were included in the Phase 3 clinical trials of these vaccines despite belonging to a group at high risk for severe complications of COVID-19 infection. We show here that the mRNA from anti-COVID BNT162b2 (Pfizer) and mRNA-1273 (Moderna) vaccines is not detected in human breast milk samples collected 4-48 hours post-vaccine. These results strengthen the recommendation of ABM and WHO that lactating individuals who receive the anti-COVID-19 mRNA-based vaccine should continue to breastfeed their infants uninterrupted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yarden Golan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mary Prahl", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Arianna Cassidy", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Christine Y Lin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nadav Ahituv", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Valerie J Flaherman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Stephanie L Gaw", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.03.06.21253048", "rel_title": "More than the eye can see; shedding new light on SARS-CoV-2 Lateral Flow Device-based immunoassays", @@ -871242,53 +869567,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.03.06.434214", - "rel_title": "Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics", - "rel_date": "2021-03-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434214", - "rel_abs": "Coronavirus (CoV) non-structural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase (RdRp) and other nsps. To date, no structure of full-length SARS-CoV-2 nsp7:nsp8 complex has been published. Current understanding of this complex is based on structures from truncated constructs or with missing electron densities and complexes from related CoV species with which SARS-CoV-2 nsp7 and nsp8 share upwards of 90% sequence identity. Despite available structures being solved using crystallography and cryo-EM representing detailed snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the complex and how it assembles to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the structural dynamics of the SARS-CoV-2 full-length nsp7:nsp8 complex. The results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without altering nsp7-nsp8 interactions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Valentine Courouble", - "author_inst": "Scripps Research" - }, - { - "author_name": "Sanjay Dey", - "author_inst": "Rutgers" - }, - { - "author_name": "Ruchi Yadav", - "author_inst": "Rutgers" - }, - { - "author_name": "Jennifer Timm", - "author_inst": "Rutgers" - }, - { - "author_name": "Jerry Harrison", - "author_inst": "Rutgers" - }, - { - "author_name": "Francesc X Ruiz", - "author_inst": "Rutgers" - }, - { - "author_name": "Eddy Arnold", - "author_inst": "Rutgers" - }, - { - "author_name": "Patrick R Griffin", - "author_inst": "Scripps Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.03.06.434193", "rel_title": "SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies", @@ -872457,6 +870735,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.20134866", + "rel_title": "Clinical course and risk factors for in-hospital mortality of 205 patients with SARS-CoV-2 pneumonia in Como, Lombardy Region, Italy", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.20134866", + "rel_abs": "ImportanceWith randomized clinical trials ongoing and vaccine still a long distance away, efforts to repurpose old medications used for other diseases provide hope for the treatment of COVID-19\n\nObjectivesTo examine the risk factors for in-hospital mortality and describe the effectiveness of different treatment strategies in a real-life setting of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia.\n\nDesignReal-life single-center study during the Lombardy COVID-19 outbreak.\n\nSettingValduce Hospital in Como, Lombardy Region, Italy.\n\nParticipants205 laboratory-confirmed patients presenting with SARS-Cov-2 pneumonia requiring hospitalization.\n\nInterventionsAll patients received best supportive care and, based on their clinical needs and comorbidities, specific interventions that included the main drugs being tested for repurposing to treat COVID-19, such as hydroxychloroquine, anticoagulation, antiviral drugs, steroids or interleukin-6 pathway inhibitors.\n\nMain outcomes and measuresClinical, laboratory and treatment characteristics were analyzed with univariate and multivariate logistic regression methods to explore their impact on in-hospital mortality and compared with current literature data.\n\nResultsUnivariate analyses for clinical variables showed prognostic significance for age equal or greater than 70 years (estimated 28-days survival: 21.4 vs 67.4%; p<0.0001), presence of 2 or more relevant comorbidities (35.3 vs 61.8%; p=0.0008), ratio of arterial oxygen partial pressure to fractional inspired oxygen (P/F) less than 200 at presentation (21-days survival: 14.7 vs 52.4%;p<0.0001), high levels of lactate dehydrogenase (LDH) (26.4 vs 65.3%; p=0.0001), and elevated C-reactive protein (CRP) values (25.4 vs 74.9%; p=0.0001), while no statistical significance was found for all the other clinical variables tested. At univariate analysis for the different treatment scheduled, prognostic significance for survival was showed for intermediate or therapeutic-dose anticoagulation (estimated 28-days survival: 37.1 vs 23.4%; p=0.0001), hydroxychloroquine (35.7 vs 27.3%; p=0.0029), early antiviral therapy with lopinavir/ritonavir (60.1 vs 22.4%; p<0.0001), late short-course of steroids (47.9 vs 18.2%; p<0.0001) or tocilizumab therapy (69.4 vs 29.4%; p=0.0059). Multivariable regression confirmed increasing odds of in-hospital death associated with age older than 70 years (odds ratio 3.26, 95% CI 1.81-5.86; p<0.0001) and showed a reduction in mortality for patients treated with anticoagulant (-0.37, 0.49-0.95; p=0.0273), antiviral (-1.22, 0.16-0.54; p<0.0001), or steroids (-0.59, 0.35-0.87; p=0.0117) therapy.\n\nConclusions and RelevanceResults from this real-life single-center experience are in agreement and confirm actual literature data on SARS-CoV-2 pneumonia, both in terms of clinical risk factors for in-hospital mortality and as regards the effectiveness of the different therapies proposed for the management of COVID-19 disease. Waiting the results from randomized clinical trials, these data could help clinicians to identify patients with poor prognosis at an early stage and guide the choice between the different treatments implied in COVID-19 disease.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSAmong the main drugs that have been tested for repurposing to treat COVID-19, what are the most effective medical treatments for SARS-CoV-2 pneumonia?\n\nFindingsResults from these real-life cohort of 205 patients confirm at multivariate regression model an increasing odds of in-hospital death associated with age older than 70 years (OR 3.26) and a reduction in mortality for patients treated with anticoagulant (OR -0.37), antiviral lopinavir/ritonavir (OR -1.22), or steroids therapy (OR -0.59). In contrast, hydroxychloroquine and tocilizumab have not been confirmed to have a significant effect in the treatment of SARS-CoV-2 pneumonia, in accordance with the latest data from the international literature.\n\nMeaningWaiting the results from randomized clinical trials, these data could help clinicians to identify patients with poor prognosis at an early stage and guide the choice between the different treatments implied in COVID-19 disease.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Mauro Turrini", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Angelo Gardellini", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Livia Beretta", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Lucia Buzzi", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Stefano Ferrario", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Sabrina Vasile", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Raffaella Clerici", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Andrea Colzani", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Luigi Liparulo", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Giovanni Scognamiglio", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Gianni Imperiali", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Giovanni Corrado", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Antonella Strada", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Marco Galletti", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Nunzio Castiglione", + "author_inst": "Valduce Hospital" + }, + { + "author_name": "Claudio Zanon", + "author_inst": "Valduce Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.02.21252448", "rel_title": "Dramatic Rise of Seroprevalence Rates of SARS-CoV-2 Antibodies among Healthy Blood Donors: The evolution of a Pandemic", @@ -873316,73 +871673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.03.21252844", - "rel_title": "Kinetics of SARS-CoV-2 anti-s IgG after BNT162b2 vaccination", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252844", - "rel_abs": "Deployment of the BNT162b2 mRNA Covid-19 Vaccine in Israel began in December 2020.\n\nThis is a retrospective analysis of serological data, describing SARS-CoV-2 anti-S IgG kinetics in 116 Israeli healthcare workers administrated the BNT162b2 vaccine.\n\nSeroconversion occurred by day 14 in all individuals, with IgG levels peaking approximately 30 days post inoculation.\n\nThis study demonstrated the kinetics of the antibody response post vaccination with BNT162b2. The robustness of seroconversion was observed, alongside a statistically significant difference in IgG levels between employees over and younger 50 years of afge. Further research is required in order to examine the antibody kinetics overtime, as well as whether the age-dependent difference persists.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Daniel Grupel", - "author_inst": "Ben Gurion University, Beer Sheva, Israel" - }, - { - "author_name": "Sivan Gazit", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Israel." - }, - { - "author_name": "Licita Schreiber", - "author_inst": "Maccabi Healthcare Services, Central Laboratory, Rehovot, Israel" - }, - { - "author_name": "Varda Nadler", - "author_inst": "Maccabi Healthcare Services, Central Laboratory, Rehovot, Israel" - }, - { - "author_name": "Tamar Wolf", - "author_inst": "Maccabi Healthcare Services, Central Laboratory, Rehovot, Israel" - }, - { - "author_name": "Rachel Lazar", - "author_inst": "Maccabi Healthcare Services, Central Laboratory, Rehovot, Israel" - }, - { - "author_name": "Lia Supino-Rosin", - "author_inst": "Maccabi Healthcare Services, Central Laboratory, Rehovot, Israel" - }, - { - "author_name": "Galit Perez", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Israel." - }, - { - "author_name": "Asaf Peretz", - "author_inst": "Internal Medicine COVID-19 Ward, Samson Assuta Ashdod University Hospital, Ashdod, Israel." - }, - { - "author_name": "Amir Ben Tov", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Israel. Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel." - }, - { - "author_name": "Miri Mizrahi-Reuveni", - "author_inst": "Health Division, Maccabi Healthcare Services, Tel Aviv, Israel." - }, - { - "author_name": "Gabriel Chodick", - "author_inst": "Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Tel Aviv, Israel. Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Is" - }, - { - "author_name": "Tal Patalon", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Israel." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.03.21252509", "rel_title": "Efficacy of Nitazoxanide in reducing the viral load in COVID-19 patients. Randomized, placebo-controlled, single-blinded, parallel group, pilot study.", @@ -874171,6 +872461,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.21252234", + "rel_title": "SWIFT: A Deep Learning Approach to Prediction of Hypoxemic Events in Critically-Ill Patients Using SpO2 Waveform Prediction", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252234", + "rel_abs": "Hypoxemia is a significant driver of mortality and poor clinical outcomes in conditions such as brain injury and cardiac arrest in critically ill patients, including COVID-19 patients. Given the host of negative clinical outcomes attributed to hypoxemia, identifying patients likely to experience hypoxemia would offer valuable opportunities for early and thus more effective intervention. We present SWIFT (SpO2 Waveform ICU Forecasting Technique), a deep learning model that predicts blood oxygen saturation (SpO2) waveforms 5 and 30 minutes in the future using only prior SpO2 values as inputs. When tested on novel data, SWIFT predicts more than 80% and 60% of hypoxemic events in critically ill and COVID-19 patients, respectively. SWIFT also predicts SpO2 waveforms with average MSE below .0007. SWIFT provides information on both occurrence and magnitude of potential hypoxemic events 30 minutes in advance, allowing it to be used to inform clinical interventions, patient triaging, and optimal resource allocation. SWIFT may be used in clinical decision support systems to inform the management of critically ill patients during the COVID-19 pandemic and beyond.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Akshaya V Annapragada", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joseph L Greenstein", + "author_inst": "Institute for Computational Medicine, The Johns Hopkins University" + }, + { + "author_name": "Sanjukta N Bose", + "author_inst": "The Johns Hopkins University" + }, + { + "author_name": "Bradford D Winters", + "author_inst": "Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sridevi V Sarma", + "author_inst": "The Johns Hopkins University School of Medicine & Whiting School of Engineering" + }, + { + "author_name": "Raimond L Winslow", + "author_inst": "The Johns Hopkins University School of Medicine & Whiting School of Engineering" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.03.05.433713", "rel_title": "Zoonotic spillover of SARS-CoV-2: mink-adapted virus in humans", @@ -875258,45 +873587,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.04.430128", - "rel_title": "The mRNA-LNP platform's lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory", - "rel_date": "2021-03-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.430128", - "rel_abs": "Vaccines based on mRNA-containing lipid nanoparticles (LNPs) are a promising new platform used by two leading vaccines against coronavirus disease in 2019 (COVID-19). Clinical trials and ongoing vaccinations present with very high protection levels and varying degrees of side effects. However, the nature of the reported side effects remains poorly defined. Here we present evidence that LNPs used in many preclinical studies are highly inflammatory in mice. Intradermal injection of these LNPs led to rapid and robust inflammatory responses, characterized by massive neutrophil infiltration, activation of diverse inflammatory pathways, and production of various inflammatory cytokines and chemokines. The same dose of LNP delivered intranasally led to similar inflammatory responses in the lung and resulted in a high mortality rate.\n\nIn summary, here we show that the LNPs used for many preclinical studies are highly inflammatory. Thus, their potent adjuvant activity and reported superiority comparing to other adjuvants in supporting the induction of adaptive immune responses likely stem from their inflammatory nature. Furthermore, the preclinical LNPs are similar to the ones used for human vaccines, which could also explain the observed side effects in humans using this platform.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sonia Ndeupen", - "author_inst": "Thomas Jefferson University" - }, - { - "author_name": "Zhen Qin", - "author_inst": "Thomas Jefferson University" - }, - { - "author_name": "Sonya Jacobsen", - "author_inst": "Thomas Jefferson University" - }, - { - "author_name": "Henri Estanbouli", - "author_inst": "Thomas Jefferson University" - }, - { - "author_name": "Aurelie Bouteau", - "author_inst": "Thomas Jefferson University" - }, - { - "author_name": "Botond Z Igyarto", - "author_inst": "Thomas Jefferson University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.04.433846", "rel_title": "SARS-CoV-2 viability in time on experimental surfaces", @@ -876117,6 +874407,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.01.21252710", + "rel_title": "Public perception of ethical issues related to COVID-19 control measures in Singapore, Hong Kong, and Malaysia: A cross-sectional survey", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252710", + "rel_abs": "BackgroundSeveral countries have implemented control measures to limit SARS-CoV-2 spread, including digital contact tracing, digital monitoring of quarantined individuals and testing of travelers. These raise ethical issues around privacy, personal freedoms and equity. However, little is known regarding public acceptability of these measures.\n\nMethodsIn December 2020, we conducted surveys among 3635 respondents in Singapore, Hong Kong and Malaysia to understand public perceptions on the ethical acceptability of COVID-19 control measures.\n\nFindingsHong Kong respondents were much less supportive of digital contact tracing and monitoring devices than those in Malaysia and Singapore. Around three-quarters of Hong Kong respondents perceived digital contact tracing as an unreasonable restriction of individual freedom; <20% trusted that there were adequate local provisions preventing these data being used for other purposes. This was the opposite in Singapore, where nearly three-quarters of respondents agreed that there were adequate data protection rules locally. In contrast, only a minority of Hong Kong respondents viewed mandatory testing and vaccination for travelers as unreasonable infringements of privacy or freedom. Less than two-thirds of respondents in all territories were willing to be vaccinated against COVID-19, with a quarter of respondents undecided. However, support for differential travel restrictions for vaccinated and unvaccinated individuals was high in all settings.\n\nInterpretationOur findings highlight the importance of socio-political context in public perception of public health measures and emphasize the need to continually monitor public attitudes towards such measures to inform implementation and communication strategies.\n\nFundingThis work was funded by the World Health Organization.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Google Scholar for research articles published between 29 February 2020 to 20 January 2021 to identify empirical studies on public perception of restrictive and control measures imposed during COVID-19. We used the following terms: \"COVID-19\", \"SARS-COV-2\", \"pandemic\", \"public\", \"population\", \"survey\", \"cross-sectional\", \"national\", \"international\", \"perception\", \"attitudes\", \"opinions\", \"views\", \"acceptance\", \"acceptability\", \"support\", \"ethics\", \"restrictive measures\", \"restrictions\", \"control measures\", travel\", \"contact tracing\", \"testing\", \"tests\", \"quarantine\", \"monitoring\", \"vaccines\" \"vaccination\", \"immunity\", \"certificates\", \"passports\", \"digital\", \"applications\", \"apps\", \"mandatory\" and \"compulsory\". We found 4 peer-reviewed publications: three population surveys on public acceptance of and ethical issues in digital contact tracing in France, Jordan, and Ireland, and one population survey on perceptions of immunity and vaccination certificates in Geneva, Switzerland. We found no studies that studied the relative acceptance of different types of control measures.\n\nAdded valueThere is a paucity of literature on public perception of the ethics of control measures that have been or may be implemented in response to the COVID-19 pandemic. In this study, we found differing levels of public support in Singapore, Hong Kong, and Malaysia for digital contact tracing, wearable quarantine monitoring devices, and mandatory testing and vaccination for travelers. Hong Kong respondents sharply differed from Singapore and Malaysia respondents on perceptions of risks and benefits, the extent of intrusion into individual freedom, and assurance of privacy and data protection related to use of digital contact tracing and monitoring devices. These differences are likely to be substantially influenced by socio-political climate and governmental trust. Although less than two-thirds of respondents in all territories expressed a willingness to be vaccinated against COVID-19, we found high support for differential travel restrictions for vaccinated and unvaccinated individuals in all settings.\n\nImplications of all the available evidenceOur survey provides evidence of strong public support of vaccination requirements for travelers within an Asian context, and differential restrictions for vaccinated and non-vaccinated travelers. It highlights the importance of wider socio-political influences on public perception and ethical issues related to control measures and emphasizes the need to continually monitor public attitudes towards such measures to inform implementation and communication strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Teck Chuan Voo", + "author_inst": "Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore" + }, + { + "author_name": "Angela Ballantyne", + "author_inst": "Department of Primary Health Care and General Practice, University of Otago, Otago, New Zealand" + }, + { + "author_name": "Chirk Jenn Ng", + "author_inst": "Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia" + }, + { + "author_name": "Benjamin J Cowling", + "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative" + }, + { + "author_name": "Jingyi Xiao", + "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative" + }, + { + "author_name": "Kean Chang Phang", + "author_inst": "University of Malaya Medical Centre, Faculty of Medicine, Kuala Lumpur, Malaysia" + }, + { + "author_name": "Sharon Kaur", + "author_inst": "Faculty of Law, University of Malaya, Kuala Lumpur Malaysia" + }, + { + "author_name": "Grazele Jenarun", + "author_inst": "Medical Research Ethics Committee, University of Malaya Medical Centre, Kuala Lumpur, Malaysia" + }, + { + "author_name": "Vishakha Kumar", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore" + }, + { + "author_name": "Jane Mingjie Lim", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore" + }, + { + "author_name": "Zaw Myo Tun", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore" + }, + { + "author_name": "Nigel Chong Boon Wong", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore" + }, + { + "author_name": "Clarence C Tam", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.01.21252700", "rel_title": "Lack of lockdown, open borders, and no vaccination in sight: is Bosnia and Herzegovina a control group?", @@ -877188,57 +875545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.02.21252772", - "rel_title": "Recent Gains in Life Expectancy Reversed by the COVID-19 Pandemic", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252772", - "rel_abs": "Variations in the age patterns and magnitudes of excess deaths, as well as differences in population sizes and age structures make cross-national comparisons of the cumulative mortality impacts of the COVID-19 pandemic challenging. Life expectancy is a widely-used indicator that provides a clear and cross-nationally comparable picture of the population-level impacts of the pandemic on mortality. Life tables by sex were calculated for 29 countries, including most European countries, Chile, and the USA for 2015-2020. Life expectancy at birth and at age 60 for 2020 were contextualised against recent trends between 2015-19. Using decomposition techniques, we examined which specific age groups contributed to reductions in life expectancy in 2020 and to what extent reductions were attributable to official COVID-19 deaths. Life expectancy at birth declined from 2019 to 2020 in 27 out of 29 countries. Males in the USA and Lithuania experienced the largest losses in life expectancy at birth during 2020 (2.2 and 1.7 years respectively), but reductions of more than an entire year were documented in eleven countries for males, and eight among females. Reductions were mostly attributable to increased mortality above age 60 and to official COVID-19 deaths. The COVID-19 pandemic triggered significant mortality increases in 2020 of a magnitude not witnessed since WW-II in Western Europe or the breakup of the Soviet Union in Eastern Europe. Females from 15 countries and males from 10 ended up with lower life expectancy at birth in 2020 than in 2015.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jos\u00e9 Manuel Aburto", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford and the Interdisciplinary Centre on Population Dynamics, University " - }, - { - "author_name": "Jonas Sch\u00f6ley", - "author_inst": "Interdisciplinary Centre on Population Dynamics, University of Southern Denmark and the Max Planck Institute for Demographic Research, Rostock" - }, - { - "author_name": "Ilya Kashnitsky", - "author_inst": "Interdisciplinary Centre on Population Dynamics, University of Southern Denmark" - }, - { - "author_name": "Luyin Zhang", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford" - }, - { - "author_name": "Charles Rahal", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford" - }, - { - "author_name": "Trifon Missov", - "author_inst": "Interdisciplinary Centre on Population Dynamics, University of Southern Denmark" - }, - { - "author_name": "Melinda C Mills", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford" - }, - { - "author_name": "Jennifer Beam Dowd", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford" - }, - { - "author_name": "Ridhi Kashyap", - "author_inst": "Leverhulme Centre for Demographic Science and Department of Sociology, University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.09.21251168", "rel_title": "A novel, multiplexed RT-qPCR assay to distinguish lineage B.1.1.7 from the remaining SARS-CoV-2 lineages", @@ -878163,6 +876469,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.03.433699", + "rel_title": "Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses", + "rel_date": "2021-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.03.433699", + "rel_abs": "The Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Neetu Tyagi", + "author_inst": "RCB, Faridabad" + }, + { + "author_name": "Rahila Sardar", + "author_inst": "ICGEB, New Delhi" + }, + { + "author_name": "Dinesh Gupta", + "author_inst": "ICGEB, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.02.26.21252554", "rel_title": "Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil", @@ -879438,29 +877771,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.28.21252638", - "rel_title": "Modelled Optimization of SARS-Cov-2 Vaccine Distribution: an Evaluation of Second Dose Deferral Spacing of 6, 12, and 24 weeks", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252638", - "rel_abs": "BackgroundMultiple recent studies have shown strong first dose vaccine efficacy for both Moderna mRNA-1273 and Pfizer/BioNTech BNT 162b2, which has stimulated discussion of maximizing initial population immunity during a time of vaccine shortage by using a deferred second dose strategy for these vaccines.\n\nMethodsOur model examines the size of the effect of spacing of the second dose with 6, 12, and 24 week deferred spacing regimens relative to 3 week spacing.\n\nResultsDeferring the second dose from 3 weeks to 6 weeks, 12 weeks, and 24 weeks shows progressive benefit to population immunity for any given time period, even with significant one dose efficacy decay. The benefits are influenced by vaccine supply per capita.\n\nConclusionThe longer the second dose is deferred the larger the benefit in initial population immunity, provided one dose efficacy does not significantly wane. Monitoring one dose efficacy duration from the UK or Quebec minimizes this risk, as the gathered data will help ensure the second dose is given at an optimal time. How this information is implemented should vary depending on the population and whether the goal is to optimally protect high risk groups or to increase total population immunity as quickly as possible. Benefits to deferring the second dose are influenced by the length of deferral, one dose efficacy, and vaccine supply per capita. The time to herd immunity could be shortened by 4 weeks with the implementation of a 12 week spacing regimen or 10 weeks with a 24 week spacing regimen.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Graham Jurgens", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Kyle Lackner", - "author_inst": "Unaffiliated" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.28.21252633", "rel_title": "A new accessible adaptable COVID-19 model", @@ -880201,6 +878511,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.28.21252536", + "rel_title": "COVID-19 Related Chemosensory Changes in Individuals with Self-Reported Obesity", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252536", + "rel_abs": "Background/objectivesIndividuals with obesity show alterations in smell and taste abilities. Smell and taste loss are also the most prominent neurological symptoms of COVID-19, yet how chemosensory ability present in individuals with obesity with a positive COVID-19 diagnosis is unknown.\n\nSubjects/MethodsIn this secondary analysis of a cross-sectional global dataset, we compared self-reported chemosensory ability in participants with a respiratory illness reporting a positive (C19+; n = 5156) or a negative (C19-; n = 659) COVID-19 laboratory test outcome, who also self-reported to be obese (C19+; n = 433, C19-; n = 86) or non-obese.\n\nResultsCompared to the C19- group, C19+ exhibited a greater decline in smell, taste, and chemesthesis during illness, though these symptoms did not differ between participants with obesity and without obesity. In 68% of participants who reported recovery from respiratory illness symptoms (n=3431 C19+ and n= 539 C19-), post-recovery chemosensory perception did not differ in C19+ and C19- diagnosis, and by self-reported obesity. Finally, we found that all chemosensory and other symptoms combined predicted the C19+ diagnosis in participants with obesity with a moderately good estimate (63% accuracy). However, in C19+ participants with obesity, we observed a greater relative prevalence of non-chemosensory symptoms, including respiratory as respiratory and GI symptoms.\n\nConclusionsWe conclude that despite a presumed lower sensitivity to chemosensory stimuli, COVID-19 respondents with obesity experience a similar self-reported chemosensory loss as those without obesity, and in both groups self-reported chemosensory symptoms are similarly predictive of COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Surabhi Bhutani", + "author_inst": "San Diego State University" + }, + { + "author_name": "Geraldine Coppin", + "author_inst": "University of Geneva" + }, + { + "author_name": "Maria Geraldine Veldhuizen", + "author_inst": "Mersin University" + }, + { + "author_name": "Valentina Parma", + "author_inst": "Temple University" + }, + { + "author_name": "Paule Valery Joseph", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.27.21252099", "rel_title": "Persistent SARS-CoV-2 infection and increasing viral variants in children and young adults with impaired humoral immunity", @@ -881284,93 +879629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.26.21252543", - "rel_title": "Covid-19 lockdown: Ethnic differences in childrens self-reported physical activity and the importance of leaving the home environment. A longitudinal and cross-sectional", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252543", - "rel_abs": "BackgroundIn England, the onset of COVID-19 and a rapidly increasing infection rate resulted in a lockdown (March-June 2020) which placed strict restrictions on movement of the public, including children. Using data collected from children living in a multi-ethnic city with high levels of deprivation, this study aimed to: (1) report childrens self-reported physical activity (PA) during the first COVID-19 UK lockdown and identify associated factors; (2) examine changes of childrens self-reported PA prior to and during the first UK lockdown.\n\nMethodsThis study is part of the Born in Bradford (BiB) COVID-19 Research Study. PA (amended Youth Activity Profile), sleep, sedentary behaviours, daily frequency/time/destination/activity when leaving the home, were self-reported by 949 children (9-13 years). A sub-sample (n=634) also self-reported PA (Physical Activity Questionnaire for Children) pre-pandemic (2017-February 2020). Univariate analysis assessed differences in PA between sex and ethnicity groups; multivariable logistic regression identified factors associated with childrens PA. Differences in childrens levels of being sufficiently active were examined using the McNemar test examined change in PA prior to and during the lockdown, and multivariable logistic regression to identify factors explaining change.\n\nResultsDuring the pandemic, White British (WB) children were more sufficiently active (34.1%) compared to Pakistani Heritage children (PH) (22.8%) or Other ethnicity children (O) (22.8%). WB children reported leaving the home more frequently and for longer periods than PH and O children. Modifiable variables related to being sufficiently active were frequency, duration, type of activity, and destination away from the home environment. There was a large reduction in children being sufficiently active during the first COVID-19 lockdown (28.9%) compared to pre-pandemic (69.4%).\n\nConclusionsPromoting safe extended periods of PA everyday outdoors is important for all children, in particular for children from ethnic minority groups. Childrens PA during the first COVID-19 UK lockdown has drastically reduced from before. Policy and decision makers, and practitioners should consider the findings in order to begin to understand the impact and consequences that COVID-19 has had upon childrens PA which is a key and vital behaviour for health and development.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Daniel David Bingham", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Andy Daly-Smith", - "author_inst": "Faculties of Life Sciences and Health Studies, University of Bradford, Richmond Road, Bradford, BD7 1DP, UK" - }, - { - "author_name": "Jennifer Hall", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Amanda Seims", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Sufyan Abid Dogra", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Stuart J Fairclough", - "author_inst": "Health Research Institute and Movement Behaviours, Health, and Wellbeing Research Group, Dept. Sport and Physical Activity, Edge Hill University, Ormskirk, L39 " - }, - { - "author_name": "Mildred Ajebon", - "author_inst": "Department of Health Sciences, University of York, Seebohm Rowntree Building, University of York, Heslington, York, YO10 5DD, UK" - }, - { - "author_name": "Brian Kelly", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Bo Hou", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Katy A Shire", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Kirsty L Crossley", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Mark Mon-Williams", - "author_inst": "University of Leeds" - }, - { - "author_name": "John Wright", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Kate Pickett", - "author_inst": "Department of Health Sciences, University of York, Seebohm Rowntree Building, University of York, Heslington, York, YO10 5DD, UK" - }, - { - "author_name": "Rosemary McEachan", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Josie Dickerson", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "Sally E Barber", - "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK" - }, - { - "author_name": "- on behalf of the Bradford Institute for Health Research COVID-19 Scientific Advisory Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.26.21252504", "rel_title": "Opening schools and trends in SARS-CoV-2 transmission in European countries", @@ -882103,6 +880361,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.27.21252535", + "rel_title": "Modeling infection dynamics and mitigation strategies to support K-6 in-person instruction during the COVID-19 pandemic", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252535", + "rel_abs": "ObjectiveTo support safer in-person K-6 instruction during the coronavirus disease 2019 (COVID- 19) pandemic by providing public health authorities and school districts with a practical model of transmission dynamics and mitigation strategies.\n\nMethodsWe developed an agent-based model of infection dynamics and preventive mitigation strategies such as distancing, health behaviors, surveillance and symptomatic testing, daily symptom and exposure screening, quarantine policies, and vaccination. The model parameters can be updated as the science evolves and are adjustable via an online user interface, enabling users to explore the effects of interventions on outcomes of interest to states and localities, under a variety of plausible epidemiological and policy assumptions.\n\nResultsUnder default assumptions, secondary infection rates and school attendance are substantially affected by surveillance testing protocols, vaccination rates, class sizes, and effectiveness of safety education.\n\nConclusionsOur model helps policymakers consider how mitigation options and the dynamics of school infection risks affect outcomes of interest. The models parameters can be immediately updated in response to changes in epidemiological conditions, science of COVID-19 transmission dynamics, testing and vaccination resources, and reliability of mitigation strategies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Douglas Ezra Morrison", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Roch Nianogo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Vladimir Manuel", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Onyebuchi A Arah", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Nathaniel Anderson", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Tony Kuo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Moira Inkelas", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.27.21252592", "rel_title": "Evaluating the trade-off between transmissibility and virulence of SARS-CoV-2 by mathematical modeling", @@ -883202,49 +881503,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.01.433340", - "rel_title": "The impact of mutations on the structural and functional properties of SARS-CoV-2 proteins: A comprehensive bioinformatics analysis", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433340", - "rel_abs": "An in-depth analysis of first wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we have performed comprehensive in-silico mutational analysis of 3C-like protease (3CLpro), RNA dependent RNA polymerase (RdRp), and spike (S) proteins with the aim of gaining important insights into first wave virus mutations and their functional and structural impact on SARS-CoV-2 proteins. Our integrated analysis gathered 3465 SARS-CoV-2 sequences and identified 92 mutations in S, 37 in RdRp, and 11 in 3CLpro regions. The impact of those mutations was also investigated using various in silico approaches. Among these 32 mutations in S, 15 in RdRp, and 3 in 3CLpro proteins are found to be deleterious in nature and could alter the structural and functional behavior of the encoded proteins. D614G mutation in spike and P323L in RdRp are the globally dominant variants with a high frequency. Most of them have also been found in the binding moiety of the viral proteins which determine their critical involvement in the host-pathogen interactions and drug targets. The findings of the current study may facilitate better understanding of COVID-19 diagnostics, vaccines, and therapeutics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Aqsa Ikram", - "author_inst": "The University of Lahore" - }, - { - "author_name": "Anam Naz", - "author_inst": "The University of Lahore" - }, - { - "author_name": "Faryal Awan", - "author_inst": "University of Haripur" - }, - { - "author_name": "Bisma Rauff", - "author_inst": "The University of Lahore" - }, - { - "author_name": "Ayesha Obaid", - "author_inst": "University of Haripur" - }, - { - "author_name": "Mohamad S. Hakim", - "author_inst": "Universitas Gadjah Mada Fakultas Kedokteran: Universitas Gadjah Mada Fakultas Kedokteran Kesehatan Masyarakat dan Keperawatan" - }, - { - "author_name": "Arif Malik", - "author_inst": "The University of Lahore" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.01.433379", "rel_title": "Meta-Research: Citation needed? Wikipedia and the COVID-19 pandemic", @@ -883857,6 +882115,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.21252410", + "rel_title": "Consistency of performance of adverse outcome prediction models for hospitalized COVID-19 patients", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252410", + "rel_abs": "BackgroundWe previously reported and validated a risk prediction tool based on COVID-19 hospitalizations prior to June 2020. Here, we report performance of that model on subsequent data from 6 hospitals and among individual patient subgroups.\n\nMethodWe included individuals age 18 or older hospitalized at one of 2 academic medical centers and 4 community hospitals from 6/7/2020 through 1/22/2021 with positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within 5 days of admission. Coefficients from our previously reported least absolute shrinkage and selection operator (Lasso) risk models were applied to estimate probability of a mortality, as well as a composite severe illness outcome, including admission to the ICU, mechanical ventilation or mortality.\n\nResultsOverall model performance for mortality included AUC of 0.83 (95% CI:0.80-0.87) for mortality, with a PPV 0.55 and NPV of 0.95 when using a cutoff corresponding to the highest 20% of predicted risk derived in the training set. For all adverse outcomes, AUC was 0.79 (95% CI:0.75-0.81) and PPV 0.48 and NPV 0.98 in the top 20% risk group. Model discrimination was generally similar between genders and race/ethnicity groups, but markedly poorer for younger age groups.\n\nConclusionAlthough the population of individuals hospitalized for COVID-19 has shifted and outcomes have improved overall, prediction models derived earlier in the pandemic may maintain utility.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Victor M Castro", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Thomas H McCoy Jr.", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Roy H Perlis", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.21252315", "rel_title": "Reanalysis of the Pfizer mRNA BNT162b2 SARS-CoV-2 vaccine data fails to find any increased efficacy following the boost: Implications for vaccination policy and our understanding of the mode of action", @@ -884772,81 +883057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.25.21252490", - "rel_title": "Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252490", - "rel_abs": "Tracking the spread of SARS-CoV-2 variants of concern is crucial to inform public health efforts and control the ongoing pandemic. Here, we report genetic evidence for circulation of the P.1 variant in Northeast Brazil. We advocate for increased active surveillance to ensure adequate control of this variant throughout the country.\n\nArticle Summary LineActive genomic surveillance of SARS- CoV-2 suspected cases from recent travelers reveals the circulation of the P1 variant of concern in Bahia state, Northeast Brazil.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Stephane Tosta", - "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Vanessa Brandao Nardy", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Luciana Reboredo de Oliveira da Silva", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Marcela Kelly Astete Gomez", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Jaqueline Gomes Lima", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Cristiane Wanderley Cardoso", - "author_inst": "Secretaria Municipal de Saude de Salvador" - }, - { - "author_name": "Tarcisio Oliveira Silva", - "author_inst": "Secretaria Municipal de Saude de Irece" - }, - { - "author_name": "Marcia SaoPedro Leal de Souza", - "author_inst": "Diretoria de Vigilancia Epidemiologica do Estado da Bahia (DIVEP) (M. Souza)" - }, - { - "author_name": "Pedro H. Presta Dia", - "author_inst": "Centro e Informacoes Estrategicas de Vigilancia em Saude do estado da Bahia (CIEVS)" - }, - { - "author_name": "Vagner Fonseca", - "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Jose Lourenco", - "author_inst": "University of Oxford" - }, - { - "author_name": "Luiz Carlos Junior Alcantara", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Felicidade Pereira", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Arabela Leal", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN-BA, Salvador, Bahia, Brazil" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.26.21252336", "rel_title": "What is the effect of lockdown upon hospitalisation due to COVID-19 amongst patients from a heart failure registry?", @@ -885351,6 +883561,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.02.20.21251598", + "rel_title": "A statewide analysis of SARS-CoV-2 transmission in New York", + "rel_date": "2021-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.20.21251598", + "rel_abs": "New York State, in particular the New York City metropolitan area, was the early epicenter of the SARS-CoV-2 pandemic in the United States. Similar to initial pandemic dynamics in many metropolitan areas, multiple introductions from various locations appear to have contributed to the swell of positive cases. However, representation and analysis of samples from New York regions outside the greater New York City area were lacking, as were SARS-CoV-2 genomes from the earliest cases associated with the Westchester County outbreak, which represents the first outbreak recorded in New York State. The Wadsworth Center, the public health laboratory of New York State, sought to characterize the transmission dynamics of SARS-CoV-2 across the entire state of New York from March to September with the addition of over 600 genomes from under-sampled and previously unsampled New York counties and to more fully understand the breadth of the initial outbreak in Westchester County. Additional sequencing confirmed the dominance of B.1 and descendant lineages (collectively referred to as B.1.X) in New York State. Community structure, phylogenetic, and phylogeographic analyses suggested that the Westchester outbreak was associated with continued transmission of the virus throughout the state, even after travel restrictions and the on-pause measures of March, contributing to a substantial proportion of the B.1 transmission clusters as of September 30th, 2020.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Navjot Singh", + "author_inst": "Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Alexis Russell", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Daryl Lamson", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "John Kelly", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Jonathan Plitnick", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Ryan D Pfeiffer", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Nathan Tucker", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Erasmus Schneider", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Kirsten St. George", + "author_inst": "Wadsworth Center - NYSDOH" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.17.21251943", "rel_title": "Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak", @@ -886458,89 +884723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.22.21252209", - "rel_title": "Association between Functional Inhibitors of Acid Sphingomyelinase and Reduced Risk of Intubation or Death in Individuals Hospitalized for Severe COVID-19: results from an observational multicenter study", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252209", - "rel_abs": "Several medications commonly used for a number of medical conditions share a property of functional inhibition of acid sphingomyelinase (ASM), or FIASMA. Preclinical and clinical evidence suggest that the (ASM)/ceramide system may be central to SARS-CoV-2 infection. We examined the potential usefulness of FIASMA use among patients hospitalized for severe COVID-19 in an observational multicenter retrospective study conducted at Greater Paris University hospitals. Of 2,846 adult patients hospitalized for severe COVID-19, 277 (9.7%) were taking a FIASMA medication at the time of their hospital admission. The primary endpoint was a composite of intubation and/or death. We compared this endpoint between patients taking vs. not taking a FIASMA medication in time-to-event analyses adjusted for sociodemographic characteristics and medical comorbidities. The primary analysis was a Cox regression model with inverse probability weighting (IPW). Over a mean follow-up of 9.2 days (SD=12.5), the primary endpoint occurred in 104 patients (37.5%) who were taking a FIASMA medication, and 1,060 patients (41.4%) who were not. Taking a FIASMA medication was associated with reduced likelihood of intubation or death in both crude (HR=0.71; 95%CI=0.58-0.87; p<0.001) and the primary IPW (HR=0.58; 95%CI=0.46-0.72; p<0.001) analyses. This association remained significant in multiple sensitivity analyses and was not specific to one FIASMA class or medication. These results show the potential importance of the ASM/ceramide system as a treatment target in COVID-19. Double-blind controlled randomized clinical trials of these medications for COVID-19 are needed.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nicolas Hoertel", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Marina S\u00e1nchez-Rico", - "author_inst": "Universit\u00e9 de Paris & Universidad Complutense de Madrid" - }, - { - "author_name": "Erich Gulbins", - "author_inst": "University of Duisburg-Essen" - }, - { - "author_name": "Johannes Kornhuber", - "author_inst": "Friedrich-Alexander-University of Erlangen-Nuremberg" - }, - { - "author_name": "Alexander Carpinteiro", - "author_inst": "University of Duisburg-Essen" - }, - { - "author_name": "Eric J. Lenze", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Angela M. Reiersen", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Miriam Abell\u00e1n", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Pedro de la Muela", - "author_inst": "Universit\u00e9 de Paris & Universidad Complutense de Madrid" - }, - { - "author_name": "Rapha\u00ebl Vernet", - "author_inst": "AP-HP. Centre-Universit\u00e9 de Paris" - }, - { - "author_name": "Carlos Blanco", - "author_inst": "National Institute on Drug Abuse" - }, - { - "author_name": "Nathana\u00ebl Beeker", - "author_inst": "Hopital Cochin" - }, - { - "author_name": "Antoine Neuraz", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Philip Gorwood", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Jes\u00fas M. Alvarado", - "author_inst": "Universidad Complutense de Madrid" - }, - { - "author_name": "Pierre Meneton", - "author_inst": "UPMC University of Paris" - }, - { - "author_name": "Fr\u00e9d\u00e9ric Limosin", - "author_inst": "Universit\u00e9 de Paris" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.24.21252335", "rel_title": "The neurology and neuropsychiatry of COVID-19: a systematic review and meta-analysis of the early literature reveals frequent CNS manifestations and key emerging narratives", @@ -887597,6 +885779,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.25.432893", + "rel_title": "Graphene oxide/silver nanoparticle ink formulations rapidly inhibit influenza A virus and OC43 coronavirus infection in vitro", + "rel_date": "2021-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432893", + "rel_abs": "Respiratory tract infections present a significant risk to the human population, both through seasonal circulation and novel introductions with pandemic potential. There is a strong need for antiviral compounds with broad antimicrobial activity that can be coated onto filtration systems and personal protective equipment to augment their ability to remove infectious particles from the environment. Graphene oxide and silver nanoparticles are both materials with documented antimicrobial properties. Here, we tested the in vitro antiviral properties of several graphene oxide-silver nanoparticle composite materials, which were prepared through three different methods: reduction with silver salt, direct addition of silver nanospheres, and direct addition of silver nanospheres to thiolized graphene. These materials were tested over short time scales for their antiviral activity against two enveloped RNA viruses, influenza A virus and OC43 coronavirus, by performing viral plaque assays after exposure of the viruses to each material. It was found that the graphene oxide - silver nanoparticle materials generated by direct addition of the silver nanospheres were able to completely inhibit plaque formation by both viruses within one minute of exposure. Materials generated by the other two methods had varying levels of efficacy against influenza A virus. These studies indicate that graphene oxide-silver nanoparticle composite materials can rapidly neutralize RNA viruses and demonstrate their potential for use in a wide range of applications.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC=\"FIGDIR/small/432893v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (39K):\norg.highwire.dtl.DTLVardef@7940d4org.highwire.dtl.DTLVardef@8f3207org.highwire.dtl.DTLVardef@11d9c1eorg.highwire.dtl.DTLVardef@f489a2_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Meredith J Crane", + "author_inst": "Brown University" + }, + { + "author_name": "Stephen Devine", + "author_inst": "Graphene Composites, Ltd." + }, + { + "author_name": "Amanda M. Jamieson", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.26.433062", "rel_title": "Comparative infectivity and pathogenesis of emerging SARS-CoV-2 variants in Syrian hamsters", @@ -888352,413 +886561,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.25.430130", - "rel_title": "A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2", - "rel_date": "2021-02-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.430130", - "rel_abs": "The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63+ intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.", - "rel_num_authors": 98, - "rel_authors": [ - { - "author_name": "Toni M. Delorey", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Carly G. K. Ziegler", - "author_inst": "Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA" - }, - { - "author_name": "Graham Heimberg", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Rachelly Normand", - "author_inst": "Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA" - }, - { - "author_name": "Yiming Yang", - "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02013, USA" - }, - { - "author_name": "Asa Segerstolpe", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Domenic Abbondanza", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Stephen J. Fleming", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142" - }, - { - "author_name": "Ayshwarya Subramanian", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Daniel T. Montoro", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA," - }, - { - "author_name": "Karthik A. Jagadeesh", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Kushal Dey", - "author_inst": "Department of Epidemiology, Harvard School of Public Health" - }, - { - "author_name": "Pritha Sen", - "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Michal Slyper", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Yered Pita-Juarez", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Devan Phillips", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Zohar Bloom-Ackermann", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Nick Barkas", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142" - }, - { - "author_name": "Andrea Ganna", - "author_inst": "Institue for Molecular Medicine Finland, Helsinki, Finland" - }, - { - "author_name": "James Gomez", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Erica Normandin", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Pourya Naderi", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Yury V. Popov", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Siddharth S. Raju", - "author_inst": "Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA" - }, - { - "author_name": "Sebastian Niezen", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Linus T.-Y. Tsai", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Katherine J. Siddle", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Malika Sud", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Victoria M. Tran", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Shamsudheen Karuthedath Vellarikkal", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Liat Amir-Zilberstein", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Joseph M Beechem", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Olga R. Brook", - "author_inst": "Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA" - }, - { - "author_name": "Jonathan Chen", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Prajan Divakar", - "author_inst": "NanoString Technologies Inc., Seattle, WA 98109, USA" - }, - { - "author_name": "Phylicia Dorceus", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Jesse M Engreitz", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Adam Essene", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Donna M. Fitzgerald", - "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Robin Fropf", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Steven Gazal", - "author_inst": "Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA" - }, - { - "author_name": "Joshua Gould", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142" - }, - { - "author_name": "Tyler Harvey", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Jonathan Hecht", - "author_inst": "Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Shapiro 4, Boston, MA, 02215-5400, USA" - }, - { - "author_name": "Tyler Hether", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Judit Jane-Valbuena", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Michael Leney-Greene", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Hui Ma", - "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02013, USA" - }, - { - "author_name": "Cristin McCabe", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Daniel E. McLoughlin", - "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Eric M. Miller", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Christoph Muus", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA, John A. Paulson School of Engineering and Applied Sciences, HarvardUniversity, Cambridge, MA 02138" - }, - { - "author_name": "Mari Niemi", - "author_inst": "Institue for Molecular Medicine Finland, Helsinki, Finland" - }, - { - "author_name": "Robert Padera", - "author_inst": "Department of Pathology, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Liuliu Pan", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Deepti Pant", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Jenna Pfiffner-Borges", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Christopher J. Pinto", - "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Jason Reeves", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Marty Ross", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Melissa Rudy", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Erroll H. Rueckert", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Michelle Siciliano", - "author_inst": "Department of Pathology, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Alexander Sturm", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Ellen Todres", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Avinash Waghray", - "author_inst": "Harvard Stem Cell Institute, Cambridge, MA, USA" - }, - { - "author_name": "Sarah Warren", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Shuting Zhang", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Dan Zollinger", - "author_inst": "NanoString Technologies, Seattle, WA, USA" - }, - { - "author_name": "Lisa Cosimi", - "author_inst": "Infectious Diseases Division, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA" - }, - { - "author_name": "Rajat M Gupta", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Nir Hacohen", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Winston Hide", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Alkes L. Price", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Jayaraj Rajagopal", - "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Purushothama Rao Tata", - "author_inst": "Duke University School of Medicine, Durham, NC" - }, - { - "author_name": "Stefan Riedel", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Gyongyi Szabo", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Timothy L. Tickle", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142" - }, - { - "author_name": "Deborah Hung", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Pardis C. Sabeti", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Richard Novak", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University" - }, - { - "author_name": "Robert Rogers", - "author_inst": "Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Shapiro 4, Boston, MA, 02215-5400, USA" - }, - { - "author_name": "Donald E. Ingber", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA" - }, - { - "author_name": "Z Gordon Jiang", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Dejan Juric", - "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Mehrtash Babadi", - "author_inst": "Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142" - }, - { - "author_name": "Samouil L. Farhi", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "James R. Stone", - "author_inst": "Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA" - }, - { - "author_name": "Ioannis S. Vlachos", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA" - }, - { - "author_name": "Isaac H. Solomon", - "author_inst": "Department of Pathology, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Orr Ashenberg", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Caroline B.M. Porter", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Bo Li", - "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02013, USA" - }, - { - "author_name": "Alex K. Shalek", - "author_inst": "Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" - }, - { - "author_name": "Alexandra-Chloe Villani", - "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Orit Rozenblatt-Rosen", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - }, - { - "author_name": "Aviv Regev", - "author_inst": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.02.25.432853", "rel_title": "Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells", @@ -889507,6 +887309,57 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.02.23.21252276", + "rel_title": "Inequalities in the decline and recovery of pathological cancer diagnoses during the first six months of the COVID-19 pandemic: a population-based study", + "rel_date": "2021-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252276", + "rel_abs": "BackgroundThe restructuring of healthcare systems to cope with the demands of the COVID-19 pandemic has led to a reduction in clinical services such as cancer screening and diagnostics.\n\nMethodsData from the four Northern Ireland pathology labs was used to assess trends in pathological cancer diagnoses from 1st March to 12th September 2020 overall and by cancer site, gender and age. These trends were compared to the same timeframe from 2017-2019.\n\nResultsBetween 1st March and 12th September 2020 there was a 23% reduction in cancer diagnoses compared to the same time period in the preceding three years. Although some recovery occurred in August and September 2020, this revealed inequalities across certain patient groups. Pathological diagnoses of lung, prostate and gynaecological malignancies remained well below pre-pandemic levels. Males and younger/middle-aged adults, particularly the 50-59 year old patient group, also lagged behind other population demographic groups in terms of returning to expected numbers of pathological cancer diagnoses.\n\nConclusionsThere is a critical need to protect cancer diagnostic services in the ongoing pandemic to facilitate timely investigation of potential cancer cases. Targeted public health campaigns may be needed to reduce emerging inequalities in cancer diagnoses as the COVID-19 pandemic continues.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ashleigh C. Hamilton", + "author_inst": "Centre for Public Health, Queen's University Belfast" + }, + { + "author_name": "David W. Donnelly", + "author_inst": "Northern Ireland Cancer Registry" + }, + { + "author_name": "Maurice B. Loughrey", + "author_inst": "Department of Pathology, Belfast Health and Social Care Trust, Northern Ireland" + }, + { + "author_name": "Richard C. Turkington", + "author_inst": "Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast" + }, + { + "author_name": "Colin Fox", + "author_inst": "Northern Ireland Cancer Registry" + }, + { + "author_name": "Deirdre Fitzpatrick", + "author_inst": "Northern Ireland Cancer Registry" + }, + { + "author_name": "Ciaran E. O'Neill", + "author_inst": "Northern Ireland Cancer Registry" + }, + { + "author_name": "Anna T. Gavin", + "author_inst": "Northern Ireland Cancer Registry" + }, + { + "author_name": "Helen G. Coleman", + "author_inst": "Centre for Public Health, Queen's University Belfast" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21252253", "rel_title": "SARS-CoV-2 genomic surveillance identifies naturally occurring truncations of ORF7a that limit immune suppression", @@ -890438,65 +888291,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.24.432634", - "rel_title": "A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432634", - "rel_abs": "Over the past 20 years, the emergence of three highly pathogenic coronaviruses (CoV) - SARS-CoV, MERS-CoV, and most recently SARS-CoV-2 - has shown that CoVs pose a serious risk to human health and highlighted the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycle. Here, we conducted two independent genome-wide CRISPR/Cas9 knockout screens to identify pan-CoV host factors required for the replication of both endemic and emerging CoVs, including the novel CoV SARS-CoV-2. Strikingly, we found that several autophagy-related genes, including the immunophilin FKBP8, TMEM41B, and MINAR1, were common host factors required for CoV replication. Importantly, inhibition of the immunophilin family with the compounds Tacrolimus, Cyclosporin A, and the non-immunosuppressive derivative Alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures that resemble the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrate that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Annika Kratzel", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - }, - { - "author_name": "Jenna N. Kelly", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - }, - { - "author_name": "Yannick Brueggemann", - "author_inst": "Department for Molecular and Medical Virology, Ruhr-University Bochum, Germany" - }, - { - "author_name": "Jasmine Portmann", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - }, - { - "author_name": "Daniel Todt", - "author_inst": "Department of Molecular and Medical Virology, Ruhr-University Bochum" - }, - { - "author_name": "Nadine Ebert", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - }, - { - "author_name": "Eike Steinmann", - "author_inst": "Department for Molecular & Medical Virology, Ruhr-University Bochum, Germany" - }, - { - "author_name": "Ronald Dijkman", - "author_inst": "Institute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Gert Zimmer", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - }, - { - "author_name": "Stephanie Pfaender", - "author_inst": "Department for Molecular and Medical Virology, Ruhr-University Bochum, Germany" - }, - { - "author_name": "Volker Thiel", - "author_inst": "Institute for Virology and Immunology, Bern and Mittelhaeusern, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.24.432721", "rel_title": "A missense variant effect prediction and annotation resource for SARS-CoV-2", @@ -891353,6 +889147,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.19.21252080", + "rel_title": "In search for the SARS-CoV-2 protection correlate: A head-to-head comparison of two quantitative S1 assays in a group of pre-characterized oligo-/asymptomatic patients", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252080", + "rel_abs": "BackgroundQuantitative serological assays detecting response to SARS-CoV-2 infection are urgently needed to quantify immunity. This study analyzed the performance and correlation of two independent quantitative anti-S1 assays in oligo-/asymptomatic individuals from a previously characterized population-based cohort.\n\nMethodsA total of 362 samples included 108 from individuals who had viral RNA detected in pharyngeal swabs, 111 negative controls and 143 samples with positive serology but not confirmed by RT-PCR. Blood plasma was tested with quantitative assays Euroimmun Anti-SARS-CoV-2 QuantiVac ELISA (IgG) (EI-S1-IgG-quant) and Roche Elecsys(R) Anti-SARS-CoV-2 CoV-2 S (Ro-RBD-Ig-quant), which were compared with each other and with confirmatory tests, including wild-type virus micro-neutralization (NT) and GenScript(R)cPass. Results were analyzed using square roots R of coefficients of determination for association among continuous variables and non-parametric tests for paired comparisons.\n\nResultsQuantitative anti-S1 serology correlated well with each other (96%/97% for true-positives and true-negatives, respectively). Antibody titers decreased over time (from <30 days to >240 days after initial positive RT-PCR). Agreement with GenScript-cPass was 96%/99% for true-positives and true-negatives, respectively, for Ro-RBD-Ig-quant and 93%/97% for EI-S1-IgG-quant. Ro-RBD-Ig-quant allowed a distinct separation between positive and negative values, and less non-specific reactivity compared with EI-S1-IgG-quant. Raw values (with 95% CI) [≥]28.7 U/mL (22.6-36.4) for Ro-RBD-Ig-quant and [≥]49.8 U/mL (43.4-57.1) for EI-S1-IgG-quant predicted virus neutralization >1:5 in 95% of cases.\n\nConclusionsBoth quantitative anti-S1 assays, Ro-RBD-Ig-quant and EI-S1-IgG-quant, may replace direct neutralization assays in quantitative measurement of immune protection against SARS-CoV-2 in certain circumstances in the future.\n\nKey pointsTwo quantitative anti-S1 assays showed similar performance and a high level of agreement with direct virus neutralization and surrogate neutralization tests, arguing for their utility in quantifying immune protection against SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Raquel Rubio-Acero", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "Noemi Castelletti", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "Volker Fingerle", + "author_inst": "Bavarian Health and Food Safety Authority (LGL)" + }, + { + "author_name": "Laura Olbich", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "Abhishek Bakuli", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "Roman Woelfel", + "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" + }, + { + "author_name": "Philipp Girl", + "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" + }, + { + "author_name": "Katharina Mueller", + "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" + }, + { + "author_name": "Simon Jochum", + "author_inst": "Roche Diagnostics GmbH, 82377 Penzberg, Germany" + }, + { + "author_name": "Matthias Strobl", + "author_inst": "Roche Diagnostics GmbH, 82377 Penzberg, Germany" + }, + { + "author_name": "Michael Hoelscher", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "Andreas Wieser", + "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universitaet (LMU) Munich, 80802 Munich, Germany" + }, + { + "author_name": "- KoCo19 study team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.18.21251955", "rel_title": "Role of Heterogeneous Transmission in the Decline of COVID-19 Cases During Winter of 2020/2021 in Massachusetts", @@ -892400,33 +890261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.22.21252241", - "rel_title": "COVID-19 Spreading dynamics in an age-structured population with selective relaxation of restrictions for vaccinated individuals : a mathematical modeling study", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252241", - "rel_abs": "BackgroundCOVID-19 vaccination of healthcare and other essential workers is underway in many countries while immunization of the general public is expected to begin in the next several weeks. We consider the question of whether people who have received the vaccine can be selectively and immediately permitted to return to normal activities.\n\nMethodsWe use a delay differential equation model to calculate the effects of vaccinee \"immunity passports\" on the epidemic spreading trajectories. The model incorporates age-structuring to account for children who are ineligible for vaccination, and senior citizens who are especially vulnerable to the disease. We consider consensus strains of virus as well as high-transmissibility variants such as B1.1.7 and B1.351 in our analysis.\n\nResultsWe find that with high vaccine efficacy of 80 percent or greater, unrestricted vaccinee--vaccinee interactions do not derail the epidemic from a path towards elimination. Vaccinee--non-vaccinee interactions should however be treated with far more caution. At current vaccine administration rates, it may be the better part of a year before COVID-19 transmission is significantly reduced or ceased. With lower vaccine efficacy of approximately 60 percent, restrictions for vaccinees may need to remain in place until the elimination of the disease is achieved. In all cases, the death tolls can be reduced by vaccinating the vulnerable population first.\n\nConclusionsDesigning high-efficacy vaccines with easily scalable manufacturing and distribution capacity should remain on the priority list in academic as well as industrial circles. Performance of all vaccines should continue to be monitored in real time during vaccination drives with a view to analysing socio-demographic determinants of efficacy, if any, and optimizing distribution accordingly. A speedy and efficacious vaccination drive augmented with selective relaxations for vaccinees will provide the smoothest path out of the pandemic with the least additional caseloads, death tolls and socio-economic cost.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "B Shayak", - "author_inst": "Cornell University" - }, - { - "author_name": "Mohit Manoj Sharma", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Anand Kumar Mishra", - "author_inst": "Cornell University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.22.21252237", "rel_title": "Group IIA Secreted Phospholipase A2 Plays a Central Role in the Pathobiology of COVID-19", @@ -893203,6 +891037,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.19.21251949", + "rel_title": "Temporal and geographical variation of COVID-19 in-hospital fatality rate in Brazil", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21251949", + "rel_abs": "BackgroundPrevious studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies between regions and has been diminishing over time. It is believed that the continuous improvement in the treatment of patients, age group of hospitalized, and the availability of hospital resources might be affecting the temporal and regional variation of IHFR. In this study, we explored how the IHFR varied over time and among age groups and federative states in Brazil. In addition, we also assessed the relationship between hospital structure availability and peaks of IHFR.\n\nMethodsA retrospective analysis of all COVID-19 hospitalizations with confirmed outcomes in 22 states between March 01 and September 22, 2020 (n=345,281) was done. We fit GLM binomial models with additive and interaction effects between age groups, epidemiological weeks, and states. We also evaluated the association between the modeled peak of IHFR in each state and the variables of hospital structure using the Spearman rank correlation test.\n\nResultsWe found that the temporal variation of the IHFR was heterogeneous among the states, and in general it followed the temporal trends in hospitalizations. In addition, the peak of IHFR was higher in states with a smaller number of doctors and intensivists, and in states in which a higher percentage of people relied on the Public Health System (SUS) for medical care.\n\nConclusionsOur results suggest that the pressure over the healthcare system is affecting the temporal trends of IHFR in Brazil.\n\nKey MessagesO_LITemporal variation of age adjusted In-Hospital Fatality Rate (IHFR) was markedly heterogeneous among Brazilian states from March to September of 2020.\nC_LIO_LIIn several states, the IHFR increased in association with the increase in the number of hospitalizations, which suggests that the overload of the healthcare system might be affecting the temporal trends of IHFR in Brazil.\nC_LIO_LIThe IHFR remained low in the states with higher rates of hospital resources, even with the high demand for hospitalization.\nC_LIO_LIThe number of doctors and intensivist physicians per habitant was more strongly correlated with the peak of IHFR in the Brazilian states than the number of ICU beds.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tatiana P. Portella", + "author_inst": "Universidade de Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Sara R. Mortara", + "author_inst": "Instituto Internacional para Sustentabilidade IIS-Rio, Rio de Janeiro, RJ, Brazil." + }, + { + "author_name": "Rafael Lopes", + "author_inst": "Universidade Estadual Paulista- UNESP" + }, + { + "author_name": "Andrea Sanchez-Tapia", + "author_inst": "Jardim Botanico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Maria R. Donalisio", + "author_inst": "Universidade Estadual de Campinas, Campinas, SP Brazil" + }, + { + "author_name": "Marcia C. Castro", + "author_inst": "Harvard TH Chan School of Public Health" + }, + { + "author_name": "Vito R. Venturieri", + "author_inst": "Hospital Sirio Libanes, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Camila G. Estevam", + "author_inst": "Universidade Estadual de Campinas, Campinas, SP Brazil" + }, + { + "author_name": "Ana F. Ribeiro", + "author_inst": "Instituto de Infectologia Emilio Ribas, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Renato M. Coutinho", + "author_inst": "Universidade Federal do ABC, Santo Andre, SP, Brazil" + }, + { + "author_name": "Maria Amelia S.M. Veras", + "author_inst": "Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo" + }, + { + "author_name": "Paulo I. Prado", + "author_inst": "Universidade de Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Roberto A. Kraenkel", + "author_inst": "Universidade Estadual Paulista- UNESP, Sao Paulo, SP, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.02.20.21252134", "rel_title": "Real-time analysis of a mass vaccination effort via an Artificial Intelligence platform confirms the safety of FDA-authorized COVID-19 vaccines", @@ -894314,217 +892215,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.23.432486", - "rel_title": "A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem inflammatory syndrome in children (MIS-C) with severe myocarditis", - "rel_date": "2021-02-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.23.432486", - "rel_abs": "SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often including myocarditis. To better understand these cases, we applied a multi-parametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. The most severe forms of MIS-C (multisystem inflammatory syndrome in children related to SARS-CoV-2), that resulted in myocarditis, were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomic analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of severe myocarditis, characterized by sustained NF-{kappa}B activity, TNF- signaling, associated with decreased gene expression of NF-{kappa}B inhibitors. We also found a weak response to type-I and type-II interferons, hyperinflammation and response to oxidative stress related to increased HIF-1 and VEGF signaling. These results provide potential for a better understanding of disease pathophysiology.", - "rel_num_authors": 49, - "rel_authors": [ - { - "author_name": "Camille de Cevins", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Marine Luka", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Nikaia Smith", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sonia Meynier", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Aude Magerus", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Francesco Carbone", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Victor Garcia Paredes", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Laura Barnabei", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Maxime Batignes", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Alexandre Boulle", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Marie-Claude Stolzenberg", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Brieuc P Perot", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Bruno Charbit", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Tinhinane Fali", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Vithura Pirabarakan", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Boris Sorin", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Quentin Riller", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Ghaith Abdessalem", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Maxime Beretta", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludivine Grzelak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pedro Goncalves", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Hugo Mouquet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Mohammed Zarhrate", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Melanie Parisot", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Christine Bole-Feysot", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Cecile Masson", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Nicolas Cagnard", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Aurelien Corneau", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Camille Bruneau", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Shen-Ying Zhang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Jean-Laurent Casanova", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Brigitte Bader Meunier", - "author_inst": "APHP" - }, - { - "author_name": "Julien Haroche", - "author_inst": "APHP" - }, - { - "author_name": "Isabelle Melki", - "author_inst": "APHP" - }, - { - "author_name": "Mathie Lorrot", - "author_inst": "APHP" - }, - { - "author_name": "Mehdi Oualha", - "author_inst": "APHP" - }, - { - "author_name": "Florence Moulin", - "author_inst": "APHP" - }, - { - "author_name": "Damien Bonnet", - "author_inst": "APHP" - }, - { - "author_name": "Zahra Belhadjer", - "author_inst": "APHP" - }, - { - "author_name": "Mariane Leruez", - "author_inst": "APHP" - }, - { - "author_name": "Slimane Allali", - "author_inst": "APHP" - }, - { - "author_name": "Christele Gras Leguen", - "author_inst": "CHU Nantes" - }, - { - "author_name": "Loic de Pontual", - "author_inst": "APHP" - }, - { - "author_name": "Alain Fischer", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Darragh Duffy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Frederic Rieux-Laucat", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Julie Toubiana", - "author_inst": "APHP" - }, - { - "author_name": "Mickael M Menager", - "author_inst": "Institut Imagine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.22.21252190", "rel_title": "A cross-sectional study of socioeconomic status and treatment interruption among Japanese workers during the COVID-19 pandemic", @@ -895173,6 +892863,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.22.432379", + "rel_title": "Using mixed-effects modeling to estimate decay kinetics of response to SARS-CoV-2 infection", + "rel_date": "2021-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.22.432379", + "rel_abs": "The duration of natural immunity in response to SARS-CoV-2 is a matter of some debate in the literature at present. For example, in a recent publication characterizing SARS-CoV-2 immunity over time, the authors fit pooled longitudinal data, using fitted slopes to infer the duration of SARS-CoV-2 immunity. In fact, such approaches can lead to misleading conclusions as a result of statistical model-fitting artifacts. To exemplify this phenomenon, we reanalyzed one of the markers (pseudovirus neutralizing titer) in the publication, using mixed-effects modeling, a methodology better suited to longitudinal datasets like these. Our findings showed that the half-life was both longer and more variable than reported by the authors. The example selected by us here illustrates the utility of mixed-effects modeling in provide more accurate estimates of the duration and heterogeneity of half-lives of molecular and cellular biomarkers of SARS-CoV-2 immunity.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dean Bottino", + "author_inst": "Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceuticals" + }, + { + "author_name": "Greg Hather", + "author_inst": "Takeda California" + }, + { + "author_name": "Lin Yuan", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "contradictory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.23.432479", "rel_title": "Oral Hsp90 inhibitor, SNX-5422, attenuates SARS-CoV-2 replication and dampens inflammation in airway cells.", @@ -896212,29 +893941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.17.21251917", - "rel_title": "What is the extent of COVID-19 vaccine hesitancy in Bangladesh? : A cross-sectional rapid national survey", - "rel_date": "2021-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251917", - "rel_abs": "objectivesTo assess COVID-19 vaccine hesitancy in Bangladesh and identify population subgroups with higher odds of vaccine hesitancy.\n\ndesignA nationally representative cross-sectional survey was used. Univariate analysis was employed to compute vaccine hesitancy proportions and compare them across groups and multiple logistic regression analyses were performed to compute the adjusted odds ratio.\n\nsettingBangladesh\n\nparticipantsA total of 1134 participants from the general population, aged 18 years and above.\n\noutcome measuresPrevalence and predictors of vaccine hesitancy.\n\nresults32.5% of participants showed COVID-19 vaccine hesitancy. Hesitancy was high among respondents who were males, over age 60, unemployed, from low-income families, from central Bangladesh including Dhaka, living in rented houses, tobacco users, politically affiliated, participants who did not believe in the vaccines effectiveness for Bangladeshis and those who did not have any physical illnesses in the last year. In the multilevel logistic regression models, respondents who were transgender (AOR= 3.62), married (AOR=1.49), tobacco users (AOR=1.33), those who did not get any physical illnesses in the last year (AOR=1.49), those with political affiliations with opposition parties (AOR= 1.48), those who believed COVID-19 vaccines will not be effective for Bangladeshis (AOR= 3.20), and those who were slightly concerned (AOR = 2.87) or not concerned at all (AOR = 7.45) about themselves or a family member getting infected with COVID-19 in the next one year were significantly associated with vaccine hesitancy (p < 0.05).\n\nconclusionsGiven the high prevalence of COVID-19 vaccine hesitancy, it is important to promote evidence-based communication, mass media campaigns, and policy initiatives across Bangladesh to reduce vaccine hesitancy among the Bangladeshi population.\n\nStrengths and Limitations of the studyO_LIThis study is the first its kind to measure COVID-19 vaccine hesitancy in Bangladesh.\nC_LIO_LIIn this study, randomly selected participants were interviewed face to face, enabling a nearly true representative sample of the Bangladeshi general population.\nC_LIO_LIThis study identified a wide range of sub-groups of the general population with higher odds of COVID-19 vaccine hesitancy relating to their sociodemographic characteristics in Bangladesh; thus, providing baseline evidence for the low and middle-income and low-resourced countries worldwide.\nC_LIO_LITraditional media and social media influence on COVID-19 vaccine hesitancy was not measured which is a major limitation of this study.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mohammad Ali", - "author_inst": "Bangladesh University of Professionals" - }, - { - "author_name": "Ahmed Hossain", - "author_inst": "North South University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.18.21250271", "rel_title": "Effectiveness of Non-Pharmaceutical Interventions on Child and Staff COVID-19 Cases in US Summer Camps", @@ -896847,6 +894553,69 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.02.20.431855", + "rel_title": "A cannabinoid receptor agonist shows anti-inflammatory and survival properties in human SARS-CoV-2-infected iPSC-derived cardiomyocytes", + "rel_date": "2021-02-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.431855", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can infect several organs, especially impacting respiratory capacity. Among the extrapulmonary manifestations of COVID-19 is myocardial injury, which is associated with a high risk of mortality. Myocardial injury, caused directly or indirectly by SARS-CoV-2 infection, can be triggered by inflammatory processes that cause damage to the heart tissue. Since one of the hallmarks of severe COVID-19 is the \"cytokine storm\", strategies to control inflammation caused by SARS-CoV-2 infection have been considered. Cannabinoids are known to have anti-inflammatory properties by negatively modulating the release of pro-inflammatory cytokines. Herein, we investigated the effects of the cannabinoid agonist WIN 55,212-2 (WIN) in human iPSC-derived cardiomyocytes (hiPSC-CMs) infected with SARS-CoV-2. WIN did not modify angiotensin-converting enzyme II protein levels, nor reduced viral infection and replication in hiPSC-CMs. On the other hand, WIN reduced the levels of interleukins 6, 8, 18 and tumor necrosis factor-alpha (TNF-) released by infected cells, and attenuated cytotoxic damage measured by the release of lactate dehydrogenase (LDH). Our findings suggest that cannabinoids should be further explored as a complementary therapeutic tool for reducing inflammation in COVID-19 patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jairo R Temerozo", + "author_inst": "National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janei" + }, + { + "author_name": "Carla Verissimo", + "author_inst": "Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Carolina Q. Sacramento", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Natalia Fintelman-Rodrigues", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Suelen da Silva Gomes Dias", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Vinicius Cardoso Soares", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Diogo Biagi", + "author_inst": "PluriCell Biotech" + }, + { + "author_name": "Estela M. Cruvinel", + "author_inst": "Pluricell Biotech, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Rafael Dariolli", + "author_inst": "Pluricell Biotech, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Patricia T. Bozza", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Helena L. Borges", + "author_inst": "Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Thiago Moreno L. Souza", + "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.02.20.432092", "rel_title": "Inhibition of SARS-CoV-2 infection in human cardiomyocytes by targeting the Sigma-1 receptor disrupts cytoskeleton architecture and contractility", @@ -897762,45 +895531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, - { - "rel_doi": "10.1101/2021.02.18.21251437", - "rel_title": "Preservation of neutralizing antibody function in COVID-19 convalescent plasma treated using a riboflavin and ultraviolet light-based pathogen reduction technology", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251437", - "rel_abs": "Background and ObjectiveConvalescent plasma (CP) has been embraced as a safe therapeutic option for coronavirus disease 2019 (COVID-19) while other treatments are developed. However, transfusion-transmitted disease is a risk, particularly in regions with high endemic prevalence of transfusion-transmissible diseases. Pathogen reduction can mitigate this risk; thus, the objective of this study was to evaluate the effect of riboflavin and ultraviolet light (R+UV) pathogen reduction technology on the functional properties of CCP.\n\nMaterials and MethodsCCP units (n = 6) from recovered COVID-19 research donors were treated with R+UV. Pre- and post-treatment samples were tested for coagulation factor and immunoglobulin retention. Antibody binding to spike protein receptor binding domain (RBD), S1, and S2 epitopes of SARS-CoV-2 was assessed by ELISA.\n\nNeutralizing antibody (nAb) function was assessed by pseudovirus reporter viral particle neutralization (RVPN) assay and plaque reduction neutralization test (PRNT).\n\nResultsMean retention of coagulation factors was [≥] 70% while retention of immunoglobulins was 100%. Starting nAb titers were low, but PRNT50 titers did not differ between pre- and post-treatment samples. No statistically significant differences were detected in levels of IgG (P [≥] 0.3665) and IgM (P [≥] 0.1208) antibodies to RBD, S1, and S2 proteins before and after treatment.\n\nConclusionR+UV PRT effects on coagulation factors were similar to previous reports, but no significant effects were observed on immunoglobulin concentration and antibody function. SARS-CoV-2 nAb function in COVID-19 convalescent plasma is conserved following R+UV PRT treatment.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Susan Yonemura", - "author_inst": "Terumo Blood and Cell Technologies, Lakewood, CO, USA" - }, - { - "author_name": "Lindsay Hartson", - "author_inst": "Colorado State University, Infectious Disease Research Center, Fort Collins, CO, USA" - }, - { - "author_name": "Taru Dutt", - "author_inst": "Colorado State University, Department of Microbiology, Immunology & Pathology, Fort Collins, CO, USA" - }, - { - "author_name": "Marcela Henao Tamayo", - "author_inst": "Colorado State University, Department of Microbiology, Immunology & Pathology, Fort Collins, CO, USA" - }, - { - "author_name": "Raymond Goodrich", - "author_inst": "Colorado State University, Infectious Disease Research Center, Fort Collins, CO, USA" - }, - { - "author_name": "Susanne Marschner", - "author_inst": "Terumo Blood and Cell Technologies, Lakewood, CO, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.02.18.21251776", "rel_title": "Rapid increase of SARS-CoV-2 seroprevalence during the 2020 pandemic year in the population of the city of Tirana, Albania", @@ -898453,6 +896183,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.09.21250937", + "rel_title": "Increased hazard of mortality in cases compatible with SARS-CoV-2 variant of concern 202012/1 - a matched cohort study", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21250937", + "rel_abs": "ObjectivesTo establish whether there is any change in mortality associated with infection of a new variant of SARS-CoV-2 (VOC-202012/1), first detected in UK in December 2020, compared to that associated with infection with circulating SARS-CoV-2 variants.\n\nDesignMatched cohort study. Cases are matched by age, gender, ethnicity, index of multiple deprivation, lower tier local authority region, and sample date of positive specimen, and differing only by detectability of the spike protein gene using the TaqPath assay - a proxy measure of VOC-202012/1 infection.\n\nSettingUnited Kingdom, Pillar 2 COVID-19 testing centres using the taqPath assay.\n\nParticipants54,773 pairs of participants testing positive for SARS-CoV-2 in Pillar 2 between 1st October 2020 and 29th January 2021.\n\nMain outcome measures - Death within 28 days of first positive SARS-CoV-2 test.\n\nResultsThere is a high probability that the risk of mortality is increased by infection with VOC-202012/01 (p <0.001). The mortality hazard ratio associated with infection with VOC-202012/1 compared to infection with previously circulating variants is 1.7 (95% CI 1.3 - 2.2) in patients who have tested positive for COVID-19 in the community. In this comparatively low risk group, this represents an increase of deaths from 1.8 in 1000 to 3.1 in 1000 detected cases.\n\nConclusionsIf this finding is generalisable to other populations, VOC-202012/1 infections have the potential to cause substantial additional mortality over and previously circulating variants. Healthcare capacity planning, national and international control policies are all impacted by this finding, with increased mortality lending weight to the argument that further coordinated and stringent measures are justified to reduce deaths from SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Robert Challen", + "author_inst": "University of Exeter / Taunton NHS Trust" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol, Bristol Veterinary School, Langford, Bristol, UK." + }, + { + "author_name": "Jonathan M Read", + "author_inst": "Lancaster University" + }, + { + "author_name": "Louise Dyson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Krasimira Tsaneva-Atanasova", + "author_inst": "College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, Devon, UK" + }, + { + "author_name": "Leon Danon", + "author_inst": "Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.17.21251884", "rel_title": "Repurposing Colchicine for the management of COVID-19: A systematic review and meta-analysis", @@ -899304,49 +897073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.16.21251834", - "rel_title": "SEIR Filter: A Stochastic Model of Epidemic", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251834", - "rel_abs": "There are many epidemiological models at hand to cope with the present pandemic; it is, however, difficult to calibrate these models when data are noisy, partial or observed only indirectly. It is also difficult to distinguish relevant data from noise, and to distinguish the impact of individual determinants of the epidemic.\n\nIn mathematical statistics, the tools to handle all of these phenomena exist; however, they are seldom used for epidemiological models. The goal of this paper is to start filling this gap by proposing a general stochastic epidemiological model, which we call SEIR Filter.\n\nTechnically our model is a heterogeneous partially observable vector autoregression model, in which we are able to express closed form formulas for the distribution of compartments and observations, so both maximum likelihood and least square estimators are analytically tractable. We give conditions for vanishing, explosion and stationary behaviour of the epidemic and we are able to express a closed form formula for reproduction number.\n\nFinally, we present several examples of the models application. We construct an estimate age-cohort model of the COVID-19 pandemic in the Czech Republic. To demonstrate the strengths of the model, we employ it to analyse and compare three vaccination scenarios.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Martin Smid", - "author_inst": "Czech Acad. Sci." - }, - { - "author_name": "Ludek Berec", - "author_inst": "South Bohemian Univ." - }, - { - "author_name": "Ales Antonin Kubena", - "author_inst": "Czech Acad. Sci." - }, - { - "author_name": "Rene Levinsky", - "author_inst": "CERGE-EI" - }, - { - "author_name": "Jan Trnka", - "author_inst": "Charles Univ." - }, - { - "author_name": "Vit Tucek", - "author_inst": "Univ. Zagreb" - }, - { - "author_name": "Milan Zajicek", - "author_inst": "Czech Acad. Sci." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.15.21251765", "rel_title": "When efficacy and adherence conflict: preferences and patterns of response to public health advice during the COVID-19 pandemic", @@ -899879,6 +897605,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.16.21251802", + "rel_title": "Knowledge, attitudes and perceptions towards COVID-19 vaccinations: a cross-sectional community survey in Bangladesh", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251802", + "rel_abs": "BackgroundSeveral vaccines have been approved against coronavirus disease (COVID-19) and distributed globally in different regions. However, general community knowledge, attitudes and perceptions towards COVID-19 vaccinations are poorly understood. Thus, the study aimed to investigate community knowledge, attitudes and perceptions towards COVID-19 vaccinations in Bangladesh.\n\nMethodsAn exploratory and anonymous population-based e-survey was conducted among 1658 general individuals (55.6% male; mean age=23.17{+/-}6.05 years; age range=18-65 years). The survey was conducted using a semi-structured and self-reported questionnaire containing informed consent along with four sections (i.e., socio-demographics, knowledge, attitudes, and perceptions). Multiple linear regression was performed to determine the variables predicting knowledge, and attitudes towards COVID-19 vaccinations.\n\nResultsThe mean scores of knowledge and attitudes were 2.83{+/-}1.48 (out of 5) and 9.34{+/-}2.39 (out of 12) respectively. About a quarter of participants thought that the COVID-19 vaccination available in Bangladesh is safe, only 60% will have the vaccination and about two-thirds will recommend it to family and friends. In the multiple regression model, higher SES, having university/ higher levels of education, holding nuclear families and having previous history of essential vaccines uptake were associated with knowledge; whilst attitudes were significantly associated with being female and having previous history of essential vaccines uptake. Just over half of the participants thought that everyone should be vaccinated and 61% responded that health workers should be vaccinated first on priority basis. 95% vaccine should be administered free of charge in Bangladesh and almost 90% believed that the COVID-19 vaccine used in Bangladesh may have side effects.\n\nConclusionsThe findings reflect inadequate knowledge but more positive attitudes towards COVID-19 vaccine among the general population in Bangladesh. In order to improve knowledge, immediate health education programs need to be initiated before mass vaccination schedule.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Md.Saiful Islam", + "author_inst": "Jahangirnagar University" + }, + { + "author_name": "Abu Bakkar Siddique", + "author_inst": "Jahangirnagar University" + }, + { + "author_name": "Rejina Akter", + "author_inst": "Jahangirnagar University" + }, + { + "author_name": "Rafia Tasnim", + "author_inst": "Jahangirnagar University" + }, + { + "author_name": "Md. Safaet Hossain Sujan", + "author_inst": "Jahangirnagar University" + }, + { + "author_name": "Paul R Ward", + "author_inst": "Flinders University" + }, + { + "author_name": "Md. Tajuddin Sikder", + "author_inst": "Jahangirnagar University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.17.21251735", "rel_title": "Experiences of supported isolation in returning travellers during the early COVID-19 response: an interview study", @@ -901046,81 +898815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.18.21251978", - "rel_title": "Service user experiences and views regarding telemental health during the COVID-19 pandemic: a co-produced framework analysis", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251978", - "rel_abs": "BackgroundThe prominence of telemental health, including providing care by video call and telephone, has greatly increased during the COVID-19 pandemic. However, there are clear variations in uptake and acceptability, and concerns that digital exclusion may exacerbate previous inequalities in accessing good quality care. Greater understanding is needed of how service users experience telemental health, and what determines whether they engage and find it acceptable.\n\nMethodsWe conducted a collaborative framework analysis of data from semi-structured interviews with a sample of people already experiencing mental health problems prior to the pandemic. Data relevant to participants experiences and views regarding telemental health during the pandemic was identified and extracted. Data collection and analysis used a participatory, coproduction approach where lived experience researchers, clinical and academic researchers contributed to all stages of data collection, analysis and interpretation of findings.\n\nFindingsParticipants experiences and preferences regarding telemental health care were dynamic and varied across time, settings, and individuals. Participants preferences were shaped by the reason for contacting providers, their relationship with the care provider, and both parties access or acceptability to use remote technology. While face-to-face care tended to be the preferred option, participants identified benefits of remote care including making care more accessible for some populations and improved efficiency for functional appointments such as prescription reviews. Participants highlighted important new challenges around safety and privacy in online settings, and gave examples of good remote care strategies, including scheduling regular phone calls and developing guidelines about how to access remote care tools.\n\nDiscussionParticipants in our study and previous literature have highlighted advantages of telemental health care, as well as significant limitations which hinder mental health support and exacerbate inequalities in access to services. Some of these limitations are seen as potentially removable, for example through staff training or better digital access for staff or service users. Others indicate a need to maintain traditional face-to-face contact at least for some appointments. There is a clear need for care to be flexible and individualised to service user circumstances and preferences. Further research is needed on ways of minimising digital exclusion and to support staff in making effective and collaborative use of relevant technologies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Norha Vera San Juan", - "author_inst": "Department of Health Service and Population Research, NIHR Mental Health Policy Research Unit, King's College London. UK" - }, - { - "author_name": "Prisha Shah", - "author_inst": "NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group. UK" - }, - { - "author_name": "Merle Schlief", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Rebecca Appleton", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Patrick Nyikavaranda", - "author_inst": "NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group. UK" - }, - { - "author_name": "Mary Birken", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Una Foye", - "author_inst": "Department of Health Service and Population Research, NIHR Mental Health Policy Research Unit, King's College London. UK" - }, - { - "author_name": "Natasha Lyons", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Luke Sheridan-Rains", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Zainab Dedat", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Brynmor Lloyd-Evans", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Justin J Needle", - "author_inst": "Division of Health Services Research and Management. City University of London. UK" - }, - { - "author_name": "Alan Simpson", - "author_inst": "Department of Health Service and Population Research, NIHR Mental Health Policy Research Unit, King's College London. UK" - }, - { - "author_name": "Nicola Morant", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - }, - { - "author_name": "Sonia Johnson", - "author_inst": "Division of Psychiatry, NIHR Mental Health Policy Research Unit, University College London. UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.02.18.21251981", "rel_title": "Assessing Age-Specific Vaccination Strategies and Post-Vaccination Reopening Policies for COVID-19 Control Using SEIR Modeling Approach", @@ -901657,6 +899351,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.18.431844", + "rel_title": "Predicting the zoonotic capacity of mammal species for SARS-CoV-2", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431844", + "rel_abs": "Back and forth transmission of SARS-CoV-2 between humans and animals may lead to wild reservoirs of virus that can endanger efforts toward long-term control of COVID-19 in people, and protecting vulnerable animal populations that are particularly susceptible to lethal disease. Predicting high risk host species is key to targeting field surveillance and lab experiments that validate host zoonotic potential. A major bottleneck to predicting animal hosts is the small number of species with available molecular information about the structure of ACE2, a key cellular receptor required for viral cell entry. We overcome this bottleneck by combining species ecological and biological traits with 3D modeling of virus and host cell protein interactions using machine learning methods. This approach enables predictions about the zoonotic capacity of SARS-CoV-2 for over 5,000 mammals -- an order of magnitude more species than previously possible. The high accuracy predictions achieved by this approach are strongly corroborated by in vivo empirical studies. We identify numerous common mammal species whose predicted zoonotic capacity and close proximity to humans may further enhance the risk of spillover and spillback transmission of SARS-CoV-2. Our results reveal high priority areas of geographic overlap between global COVID-19 hotspots and potential new mammal hosts of SARS-CoV-2. With molecular sequence data available for only a small fraction of potential host species, predictive modeling integrating data across multiple biological scales offers a conceptual advance that may expand our predictive capacity for zoonotic viruses with similarly unknown and potentially broad host ranges.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ilya R Fischhoff", + "author_inst": "Cary Institute of Ecosystem Studies" + }, + { + "author_name": "Adrian A. Castellanos", + "author_inst": "Cary Institute of Ecosystem Studies" + }, + { + "author_name": "Joao P.G.L.M. Rodrigues", + "author_inst": "Stanford University" + }, + { + "author_name": "Arvind Varsani", + "author_inst": "Arizona State University; University of Cape Town" + }, + { + "author_name": "Barbara A Han", + "author_inst": "Cary Institute of Ecosystem Studies" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2021.02.17.21251899", "rel_title": "Chyawanprash for the prevention of COVID-19 infection among healthcare workers: A Randomized Controlled Trial", @@ -902856,29 +900585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.15.21251791", - "rel_title": "Quantification of the tradeoff between test sensitivity and test frequency in COVID-19 epidemic - a multi-scale modeling approach", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251791", - "rel_abs": "Control strategies that employ real time polymerase chain reaction (RT-PCR) tests for the diagnosis and surveillance of COVID-19 epidemic are inefficient in fighting the epidemic due to high cost, delays in obtaining results, and the need of specialized personnel and equipment for laboratory processing. Cheaper and faster alternatives, such as antigen and paper-strip tests, have been proposed. They return results rapidly, but have lower sensitivity thresholds for detecting virus. To quantify the effects of the tradeoffs between sensitivity, cost, testing frequency, and delay in test return on the overall course of an outbreak, we built a multi-scale immuno-epidemiological model that connects the virus profile of infected individuals with transmission and testing at the population level. We investigated various randomized testing strategies and found that, for fixed testing capacity, lower sensitivity tests with shorter return delays slightly flatten the daily incidence curve and delay the time to the peak daily incidence. However, compared with RT-PCR testing, they do not always reduce the cumulative case count at half a year into the outbreak. When testing frequency is increased to account for the lower cost of less sensitive tests, we observe a large reduction in cumulative case counts, from 57% to as low as 1.5% half a year into the outbreak and to 3.2% three years into the outbreak. The improvement is preserved even when the testing budget is reduced by one half or one third. Our results predict that surveillance testing that employs low-sensitivity tests at high frequency is an effective tool for epidemic control.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jonathan E Forde", - "author_inst": "Hobart and William Smith Colleges" - }, - { - "author_name": "Stanca M. Ciupe", - "author_inst": "Virginia Tech" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.15.21251753", "rel_title": "Severe SARS-CoV-2 infection induces a distinct nasal cytokine profile", @@ -903483,6 +901189,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.02.15.21251766", + "rel_title": "Moderators of changes in smoking, drinking, and quitting behaviour associated with the first Covid-19 lockdown in England", + "rel_date": "2021-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251766", + "rel_abs": "AimTo estimate changes in smoking, drinking, and quitting behaviour from before to during the first Covid-19 lockdown in England, and whether changes differed by age, sex, or social grade.\n\nDesignRepresentative cross-sectional surveys of adults, collected monthly between August 2018 and July 2020.\n\nSettingEngland.\n\nParticipants36,980 adults ([≥]18y).\n\nMeasurementsIndependent variables were survey month (pre-lockdown: August-February vs. lockdown months: April-July) and year (pandemic: 2019/20 vs. comparator: 2018/19). Smoking outcomes were smoking prevalence, cessation, quit attempts, quit success, and use of evidence-based or remote cessation support. Drinking outcomes were high-risk drinking prevalence, alcohol reduction attempts, and use of evidence-based or remote support. Moderators were age, sex, and occupational social grade (ABC1=more advantaged/C2DE=less advantaged).\n\nFindingsRelative to changes over the same time period in 2018/19, lockdown was associated with significant increases in smoking prevalence (+24.7% in 2019/20 vs. 0.0% in 2018/19, ORadj=1.35[95%CI=1.12-1.63]) and quit attempts (+39.9% vs. -22.2%, ORadj=2.48[1.76-3.50]) among 18-34 year-olds, but not older groups. Increases in cessation (+156.4% vs. -12.5%, ORadj=3.08[1.86-5.09]) and the success rate of quit attempts (+99.2% vs. +0.8%, ORadj=2.29[1.31-3.98]) were also observed, and did not differ significantly by age, sex, or social grade. Lockdown was associated with a significant increase in high-risk drinking prevalence across all sociodemographic groups (+39.5% vs. -7.8%, ORadj=1.80[1.64-1.98]), with particularly high increases among women (ORadj=2.17[1.87-2.53]) and social grades C2DE (ORadj=2.34[2.00-2.74]). Alcohol reduction attempts increased significantly among high-risk drinkers from social grades ABC1 (ORadj=2.31[1.78-3.00]) but not C2DE (ORadj=1.25[0.83-1.88]), with larger increases among those aged 18-34 (ORadj=2.56[1.72-3.81]) and [≥]60 (ORadj=1.43[1.05-1.95]) than 35-59 (ORadj=2.51[1.51-4.18]). There were few significant changes in use of support for smoking cessation or alcohol reduction, although samples were small.\n\nConclusionsIn England, the first Covid-19 lockdown was associated with increased smoking prevalence among younger adults, and increased high-risk drinking prevalence among all adults. Smoking cessation activity also increased: more younger smokers made quit attempts during lockdown and more smokers quit successfully. Socioeconomic disparities in drinking behaviour were evident: high-risk drinking increased by more among women and those from less advantaged social grades (C2DE) but the rate of reduction attempts increased only among the more advantaged social grades (ABC1).", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sarah E Jackson", + "author_inst": "UCL" + }, + { + "author_name": "Emma Beard", + "author_inst": "UCL" + }, + { + "author_name": "Colin Angus", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Matt Field", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jamie Brown", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2021.02.15.21249676", "rel_title": "Epidemiological, Clinical Characteristics and Risk Factors for Severe Condition and ICU Admission of COVID-19 Patients of Early Stage in China: A review", @@ -904490,133 +902231,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.17.431591", - "rel_title": "Delayed induction of type I and III interferons and nasal epithelial cell permissiveness to SARS-CoV-2", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431591", - "rel_abs": "The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we applied single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrated widespread tropism for nasal epithelial cell types. The host response was dominated by type I and III IFNs and interferon-stimulated gene products. This response was notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response began to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFN{beta} or IFN{lambda}1 induced an efficient antiviral state that potently restricted SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data suggest that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Catherine F Hatton", - "author_inst": "Newcastle University" - }, - { - "author_name": "Rachel A Botting", - "author_inst": "Newcastle University" - }, - { - "author_name": "Maria Emilia Duenas", - "author_inst": "Newcastle University" - }, - { - "author_name": "Iram J Haq", - "author_inst": "Newcastle University" - }, - { - "author_name": "Bernard Verdon", - "author_inst": "Newcastle University" - }, - { - "author_name": "Benjamin J Thompson", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jarmila Stremenova Spegarova", - "author_inst": "Newcastle University" - }, - { - "author_name": "Florian Gothe", - "author_inst": "Newcastle University" - }, - { - "author_name": "Emily A Stephenson", - "author_inst": "Newcastle University" - }, - { - "author_name": "Aaron I Gardner", - "author_inst": "Newcastle University" - }, - { - "author_name": "Sandra Murphy", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jonathan Scott", - "author_inst": "Newcastle University" - }, - { - "author_name": "James P Garnett", - "author_inst": "Newcastle University" - }, - { - "author_name": "Sean Carrie", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jason Powell", - "author_inst": "Newcastle University" - }, - { - "author_name": "Anjam C M Khan", - "author_inst": "Newcastle University" - }, - { - "author_name": "Lei Huang", - "author_inst": "Newcastle University" - }, - { - "author_name": "Rafiqul Hussain", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jonathan Coxhead", - "author_inst": "Newcastle University" - }, - { - "author_name": "Tracey Davey", - "author_inst": "Newcastle University" - }, - { - "author_name": "John Simpson", - "author_inst": "Newcastle University" - }, - { - "author_name": "Muzlifah Haniffa", - "author_inst": "Newcastle University" - }, - { - "author_name": "Sophie Hambleton", - "author_inst": "Newcastle University" - }, - { - "author_name": "Malcolm Brodlie", - "author_inst": "Newcastle University" - }, - { - "author_name": "Chris Ward", - "author_inst": "Newcastle University" - }, - { - "author_name": "Matthias Trost", - "author_inst": "Newcastle University" - }, - { - "author_name": "Gary Reynolds", - "author_inst": "Newcastle University" - }, - { - "author_name": "Christopher J A Duncan", - "author_inst": "Newcastle University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.17.431492", "rel_title": "SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys", @@ -905384,6 +902998,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.10.21251507", + "rel_title": "Responsive caregiving, opportunities for early learning, and children's safety and security during COVID-19: A rapid review", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251507", + "rel_abs": "IntroductionDuring the COVID-19 pandemic, there have been drastic changes in family life and programs and services that promote and protect early childhood development. Global stakeholders have raised concerns that the pandemic is putting enormous strain on parents and other caregivers, compromising capabilities and enabling environments for nurturing care of young children and therefore likely impacting childrens development.\n\nMethodologyThis rapid review takes stock of emerging research on nurturing care for young children during the COVID-19 crisis. Two databases were searched in addition to an extensive search for grey literature, drawing on 112 scholarly and scientific studies from more than 30 countries that have examined components of nurturing care during the pandemic, namely: responsive caregiving, early learning and play, and childrens safety and security.\n\nResultsThere are some reports of unexpected positive benefits of the pandemic on families, including increased father involvement in caregiving. But more commonly, the studies findings reveal numerous issues of concern, including parental and caregiver mental health difficulties and less responsive parent-child relationships, increased screen time among children, limited opportunities for outdoor play, and fractured systems for responding to potential child neglect and maltreatment. Evidence suggests limited access and challenges in the provision of remote learning for the youngest learners, such as those in early childhood education.\n\nConclusionThe findings can inform global stakeholders, who have advocated for increased support and funding to ensure young children and other caregivers are supported and protected during the COVID-19 pandemic. There is an urgent need for action-oriented implementation studies - those that go beyond identifying trends and begin to pinpoint \"what works\" to effectively promote and protect nurturing care during emergencies such as the COVID-19 pandemic.\n\nKey questionsO_ST_ABSWhat is already known?C_ST_ABSThe most fundamental promotive experiences in the early years of life to reach optimal development come from nurturing care and protection received from parents, family, and community, which have lifelong benefits including improved health and wellbeing. Health and other emergencies are detrimental to the provision of nurturing care.\n\nWhat are the new findings?Findings from this rapid review reveal numerous areas of concern, including families reporting mental health difficulties and less responsive parent-child relationships, increased screen time among children, limited opportunities for outdoor play, and fractured systems for responding to potential child neglect and maltreatment. As with other features of this pandemic, not all families are affected equally: financially vulnerable families are much more likely to experience negative ramifications. The pandemic is also disproportionately affecting parents and other caregivers with young children, particularly mothers, those with pre-existing mental health difficulties, and those caring for children with disabilities.\n\nWhat do the new findings imply?Findings highlight the need for action by governments, civil society, international and community-based organizations to improve support for families so that the pandemic does not break the provision of nurturing care and wipe out decades of progress, especially for vulnerable families and children.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kerrie Proulx", + "author_inst": "FHI360" + }, + { + "author_name": "Rachel Lenzi-Weisbecker", + "author_inst": "FHI360" + }, + { + "author_name": "Rachel Rachel", + "author_inst": "FHI360" + }, + { + "author_name": "Kristy Hackett", + "author_inst": "FHI360" + }, + { + "author_name": "Vanessa Cavallera", + "author_inst": "Department of Mental Health and Substance Abuse Use, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Bernadette Daelmans", + "author_inst": "Department of Maternal, Newborn, Child and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland" + }, + { + "author_name": "Tarun Dua", + "author_inst": "Department of Mental Health and Substance Abuse Use, World Health Organization, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.12.21251445", "rel_title": "Fear and death anxiety among Latin American doctors during the Covid-19 pandemic", @@ -906406,25 +904063,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.02.12.21251654", - "rel_title": "The impact of armed conflict on the epidemiological situation of Coronavirus disease (COVID-19) in Libya, Syria, and Yemen.", - "rel_date": "2021-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.12.21251654", - "rel_abs": "BackgroundSince the Arab uprising 2011, Libya, Syria, and Yemen have gone through a major armed conflict. This resulted in a high rate of mortality, injury, and population displacement with a collapse of the health care system. Furthermore, it was complicated by the emergence of, COVID-19 as a global pandemic which made the population of these countries strive under unusual conditions to tackle both the pandemic and the ongoing wars. The objectives of this study were to determine the impacts and influence of armed conflicts on the epidemiology of Novel Coronavirus (SARS-CoV-2) within these war-torn countries and outline the needed strategies to combat the spread of the pandemic and its upcoming consequences.\n\nMethodsThe official and public data regarding the dynamics of armed conflict and the spread, of SARS-COV-19 in Libya, Syria, and Yemen were collected from all available sources. Starting from the early emergence of the COVID-19 in each country until the end of December 2020. Datasets were analyzed through a set of statistical techniques and the weekly resolved data were used to probe the link between the intensity levels of the armed conflict and the spread of the pandemic.\n\nResultsData indicated that there is an increase in the intensity of violence levels at an early stage from March to August reached up to two folds in the three countries particularly in Libya. In this violent period, few cases of COVID-19 were reported ranging from 5-53 cases/day. From September to December, a significant decline in the level of the armed conflict was accompanied by steep upsurges in the number of reported COVID-19 cases reached up to 500 cases/day. The highest accumulative cases of COVID-19 were reported in Libya, Syria, and Yemen respectively.\n\nConclusionsOur analysis demonstrates that the armed conflict has provided an opportunity for SARS-COV-19 to spread. At the early weeks of the pandemic that coincided with high levels of the armed conflict few cases were officially reported indicating a vast undercount, which may suggest a hidden mitigating spread at an early stage. Then the pandemic increased immensely as the armed conflict decline to reach the highest by December. A full-blown transmission of the COVID-19 pandemic in these countries is expected. Therefore, urgent national and international strategies should be implemented to combat the pandemic and its upcoming consequences.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Mohamed A Daw Sr.", - "author_inst": "University of Tripoli, Faculty of Medicine" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.13.21251682", "rel_title": "Mortality from injury, overdose and suicide during the 2020 COVID-19 pandemic, March-July, 2020", @@ -907013,6 +904651,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.13.21251681", + "rel_title": "Biological attributes of age and gender variations in Indian COVID-19 cases: A retrospective data analysis", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.13.21251681", + "rel_abs": "BackgroundThe associated risk factors, co-morbid conditions and biological variations varying with gender and age might be the cause of higher COVID-19 infection and deaths among males and older persons. The objective of this study was to predict and specify the biological attributes of variation in age and gender-based on COVID-19 status (deceased/recovered).\n\nMethodsIn this retrospective study, the data was extracted from a recognised web-based portal. A total of 112,860 patients record was filtered out and an additional 9,131 records were separately analyzed to examine age and gender relationship with patients COVID-19 status (recovered/deceased). Chi-square, t-test, binary logistic regression, and longitudinal regression analysis were conducted.\n\nResultsThe male COVID-19 cases (65.39%) were more than females (34.61%) and mean age of infected and recovered patients was 39.47{+/-}17.59 years and 36.85{+/-}18.51 years respectively. The odds for infection was significantly higher among females for lower age categories, which declines with age. The age-adjusted odds for recovery were significantly higher among females (O.R.=1.779) and odds for recovery was highest in 5-17 years age category (O.R.=88.286) independent of gender.\n\nConclusionThe chances of being COVID-19 infected was higher for females of lower age categories (<35 years) which decreases with age. The odds for recovery among females was significantly higher than males. The chances of recovery declines with increasing age and the variation could be attributed to the biological differences between age categories and gender.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Savitesh Kushwaha", + "author_inst": "PGIMER" + }, + { + "author_name": "Poonam Khanna", + "author_inst": "PGIMER, CHANDIGARH, INDIA" + }, + { + "author_name": "Vineeth Rajagopal", + "author_inst": "PGIMER, CHANDIGARH, INDIA" + }, + { + "author_name": "Tanvi Kiran", + "author_inst": "PGIMER, CHANDIGARH, INDIA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.12.21251659", "rel_title": "Recent SARS-CoV-2 seroconversion in a national, community-based prospective cohort of U.S. adults", @@ -908036,221 +905705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.10.21251540", - "rel_title": "Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251540", - "rel_abs": "The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "Tara Alpert", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Anderson F. Brito", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Erica Lasek-Nesselquist", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" - }, - { - "author_name": "Jessica Rothman", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Andrew L. Valesano", - "author_inst": "Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA" - }, - { - "author_name": "Matthew J. MacKay", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Mary E. Petrone", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Mallery I. Breban", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Anne E. Watkins", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Chantal B.F. Vogels", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Chaney C. Kalinich", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Simon Dellicour", - "author_inst": "Spatial Epidemiology Lab (SpELL), Universite Libre de Bruxelles, Bruxelles, Belgium and Laboratory of Clinical and Epidemiological Virology, Department of Micro" - }, - { - "author_name": "Alexis Russell", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" - }, - { - "author_name": "John P. Kelly", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" - }, - { - "author_name": "Matthew Shudt", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA and Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222" - }, - { - "author_name": "Jonathan Plitnick", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA and Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222" - }, - { - "author_name": "Erasmus Schneider", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA and Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222" - }, - { - "author_name": "William J. Fitzsimmons", - "author_inst": "Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA" - }, - { - "author_name": "Gaurav Khullar", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Jessica Metti", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Joel T. Dudley", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Megan Nash", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Nike Beaubier", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA" - }, - { - "author_name": "Jianhui Wang", - "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" - }, - { - "author_name": "Chen Liu", - "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" - }, - { - "author_name": "Pei Hui", - "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" - }, - { - "author_name": "Anthony Muyombwe", - "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" - }, - { - "author_name": "Randy Downing", - "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" - }, - { - "author_name": "Jafar Razeq", - "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" - }, - { - "author_name": "Stephen M. Bart", - "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA and Centers for Disease Control and Prevention, Atlanta, GA 30329, USA" - }, - { - "author_name": "Ardath Grills", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA 30329, USA" - }, - { - "author_name": "Stephanie M. Morrison", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA 30329, USA" - }, - { - "author_name": "Steven Murphy", - "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" - }, - { - "author_name": "Caleb Neal", - "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" - }, - { - "author_name": "Eva Laszlo", - "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" - }, - { - "author_name": "Hanna Rennert", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "Melissa Cushing", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "Lars Westblade", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "Priya Velu", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "Arryn Craney", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "Kathy A. Fauntleroy", - "author_inst": "Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA" - }, - { - "author_name": "David R. Peaper", - "author_inst": "Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA" - }, - { - "author_name": "Marie L. Landry", - "author_inst": "Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA" - }, - { - "author_name": "Peter W. Cook", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA 30329, USA" - }, - { - "author_name": "Joseph R. Fauver", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" - }, - { - "author_name": "Christopher E. Mason", - "author_inst": "Tempus Labs, Chicago, IL 60654, USA and Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 100" - }, - { - "author_name": "Adam S. Lauring", - "author_inst": "Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA" - }, - { - "author_name": "Kirsten St. George", - "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA and Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222" - }, - { - "author_name": "Duncan R. MacCannell", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA 30329, USA" - }, - { - "author_name": "Nathan D. Grubaugh", - "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA and Department of Ecology and Evolutionary Biology, Yal" - } - ], - "version": "2", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.11.21251548", "rel_title": "Association of demographic and occupational factors with SARS-CoV-2 vaccine uptake in a multi-ethnic UK healthcare workforce: a rapid real-world analysis", @@ -908747,6 +906201,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.02.10.21251527", + "rel_title": "Outcomes of COVID-19 among Patients with End Stage Renal Disease on Remdesivir", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251527", + "rel_abs": "BACKGROUNDSince the beginning of the COVID-19 pandemic, there has been widespread use of remdesivir in adults and children. There is little known information about its outcomes in patients with severe renal dysfunction or end-stage renal disease who are on hemodialysis.\n\nMETHODSA retrospective, multicenter study was conducted on patients with end-stage renal disease on hemodialysis that were discharged after treatment for COVID-19 between April 1st and December 31st, 2020. Primary endpoints were the length of stay, mortality, maximum oxygen requirements along with the escalation of care needing mechanical ventilation. Secondary endpoints included change in C reactive protein, d dimer levels, and disposition.\n\nRESULTSA total of 52 charts were reviewed, of which 28 met the inclusion criteria. 14 patients received remdesivir, and 14 patients did not receive remdesivir. The majority of patients were caucasian, female, with diabetes mellitus and hypertension. The mean age was 65.33 +14.14 years. All the patients in the remdesivir group received dexamethasone as compared to only 30% of patients in the non-remdesivir group. There was no significant difference in C reactive protein, d dimer levels, and disposition between the two groups. Approximately 35% of the patients died, 18% required intensive ventilation, and the mean length of stay was 12.21 days.\n\nDISCUSSIONThe study demonstrated no clinically significant difference in length of stay, maximum oxygen requirements, or mortality in COVID-19 patients with end-stage renal disease in the remdesivir group as compared to the non-remdesivir group. Further studies are needed to study the effects of remdesivir on the renal function and disease course in patients with chronic kidney disease stage 4 or 5 that are not on dialysis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Vijairam Selvaraj", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "Muhammad Baig", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "Kwame Dapaah-Afriyie", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "Arkadiy Finn", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "Atin Jindal", + "author_inst": "The Miriam Hospital" + }, + { + "author_name": "George Bayliss", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.02.11.21251571", "rel_title": "Returning to nursing during the COVID-19 pandemic: experiences and needs of re-entering nurses", @@ -909686,173 +907179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.09.430269", - "rel_title": "Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19", - "rel_date": "2021-02-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.09.430269", - "rel_abs": "The biological determinants of the wide spectrum of COVID-19 clinical manifestations are not fully understood. Here, over 1400 plasma proteins and 2600 single-cell immune features comprising cell phenotype, basal signaling activity, and signaling responses to inflammatory ligands were assessed in peripheral blood from patients with mild, moderate, and severe COVID-19, at the time of diagnosis. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identified and independently validated a multivariate model classifying COVID-19 severity (multi-class AUCtraining = 0.799, p-value = 4.2e-6; multi-class AUCvalidation = 0.773, p-value = 7.7e-6). Features of this high-dimensional model recapitulated recent COVID-19 related observations of immune perturbations, and revealed novel biological signatures of severity, including the mobilization of elements of the renin-angiotensin system and primary hemostasis, as well as dysregulation of JAK/STAT, MAPK/mTOR, and NF-{kappa}B immune signaling networks. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for the prevention of COVID-19 progression.\n\nSummaryFeyaerts et al. demonstrate that an integrated analysis of plasma and single-cell proteomics differentiates COVID-19 severity and reveals severity-specific biological signatures associated with the dysregulation of the JAK/STAT, MAPK/mTOR, and NF-{kappa}B immune signaling networks and the mobilization of the renin-angiotensin and hemostasis systems.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Dorien Feyaerts", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Julien Hedou", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Joshua Gillard", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Han Chen", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Eileen S Tsai", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Laura S Peterson", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Kazuo Ando", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Monali Manohar", - "author_inst": "Stanford University" - }, - { - "author_name": "Evan Do", - "author_inst": "Stanford University" - }, - { - "author_name": "Gopal K.R. Dhondalay", - "author_inst": "Stanford University" - }, - { - "author_name": "Jessica Fitzpatrick", - "author_inst": "Stanford University" - }, - { - "author_name": "Maja Artandi", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Iris Chang", - "author_inst": "Stanford University" - }, - { - "author_name": "Theo T Snow", - "author_inst": "Stanford University" - }, - { - "author_name": "R Sharon Chinthrajah", - "author_inst": "Stanford University" - }, - { - "author_name": "Christopher M Warren", - "author_inst": "Stanford University" - }, - { - "author_name": "Rich Wittman", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Justin G Meyerowitz", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Edward A Ganio", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ina A Stelzer", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Xiaoyuan Han", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Franck Verdonk", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Dyani K Gaudilliere", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nilanjan Mukherjee", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Amy S Tsai", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Kristen K Rumer", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Sizun J Jiang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Sergio I Valdes-Ferrer", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "J. Daniel Kelly", - "author_inst": "UCSF" - }, - { - "author_name": "David Furman", - "author_inst": "Buck Institute for Research on Aging" - }, - { - "author_name": "Nima Aghaeepour", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Martin S Angst", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Scott D Boyd", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Benjamin A Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Garry P Nolan", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Kari C Nadeau", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Brice Gaudilliere", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "David R McIlwain", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.12.430907", "rel_title": "A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients", @@ -910583,6 +907909,32 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.09.21251052", + "rel_title": "Emerging SARS-CoV-2 Lineages in Middle Eastern Jordan with Increasing Mutations Near Antibody Recognition Sites", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251052", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rima Hajjo", + "author_inst": "Al-Zaytoonah University of Jordan" + }, + { + "author_name": "Dima A Sabbah", + "author_inst": "Al-Zaytoonah University of Jordan" + }, + { + "author_name": "Sanaa K Bardaweel", + "author_inst": "The University of Jordan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.09.21251225", "rel_title": "Rapid Rise of S-Gene Target Failure and the UK variant B.1.1.7 among COVID-19 isolates in the Greater Toronto Area, Canada", @@ -911505,128 +908857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.10.21251518", - "rel_title": "Antigen-based multiplex strategies to discriminate SARS-CoV-2 natural and vaccine induced immunity from seasonal human coronavirus humoral responses", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251518", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Eric D Laing", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Spencer L Sterling", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Stephanie A Richard", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Nusrat J Epsi", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Si'Ana Coggins", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Emily C Samuels", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Shreshta Phogat", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Lianying Yan", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Nicole Moreno", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Christian L Coles", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Matthew Drew", - "author_inst": "NCI RAS Initiative, Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Jennifer Mehalko", - "author_inst": "NCI RAS Initiative, Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Scott Merritt", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation, Brooke Army Medical Center" - }, - { - "author_name": "Katrin Mende", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation, Brooke Army Medical Center" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Kevin K Chung", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Eugene V Millar", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "David R Tribble", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Mark P Simons", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Simon D Pollett", - "author_inst": "Uniformed Services University, Henry M Jackson Foundation" - }, - { - "author_name": "Dominic Esposito", - "author_inst": "NCI RAS Initiative, Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Charlotte Lanteri", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "G Travis Clifton", - "author_inst": "Brooke Army Medical Center" - }, - { - "author_name": "Edward Mitre", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Timothy H Burgess", - "author_inst": "Uniformed Services University" - }, - { - "author_name": "Christopher C Broder", - "author_inst": "Uniformed Services University" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.10.21251523", "rel_title": "Decline in mitigation readiness facilitated second waves of SARS-CoV-2", @@ -912555,6 +909785,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.08.21251393", + "rel_title": "A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251393", + "rel_abs": "Introductory paragraphSARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution in a small landlocked East African country. Here we show a recent shift in the local epidemic with a newly emerging lineage A.23 evolving into A.23.1 which is now dominating the Uganda cases and has spread to 26 other countries. Although the precise changes in A.23.1 as it has adapted are different from the changes in the variants of concern (VOC), the evolution shows convergence on a similar set of proteins. The A.23.1 spike protein coding region has accumulated changes that resemble many of the changes seen in VOC including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif, and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1lineage encodes changes in non-spike proteins that other VOC show (nsp6, ORF8 and ORF9). The clinical impact of the A.23.1 variant is not yet clear, however it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Daniel Lule Bugembe", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "My V.T. Phan", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Isaac Ssewanyana", + "author_inst": "Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda" + }, + { + "author_name": "Patrick Semanda", + "author_inst": "Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda" + }, + { + "author_name": "Hellen Nansumba", + "author_inst": "Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda" + }, + { + "author_name": "Beatrice Dhaala", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda" + }, + { + "author_name": "Susan Nabadda", + "author_inst": "Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda" + }, + { + "author_name": "Aine O'Toole", + "author_inst": "Institute of Evolutionary Biology, University of Edinburgh" + }, + { + "author_name": "Andrew Rambaut", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Pontiano Kaleebu", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda & Uganda Virus Research Institute, Entebbe, Uganda" + }, + { + "author_name": "Matthew Cotten", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda & MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.08.21251303", "rel_title": "Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report", @@ -913874,37 +911163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.08.21251383", - "rel_title": "SARS-CoV-2 transmission, vaccination rate and the fate of resistant strains", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251383", - "rel_abs": "Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic [1,2]. However, the emergence of vaccine-resistant strains [3-6] may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic [7,8]. To quantify and characterize the risk of such a scenario, we created a SIR-derived model [9,10] with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. We found a counterintuitive result that the highest probability for the establishment of the resistant strain comes at a time of reduced non-pharmaceutical intervention measures when most individuals of the population have been vaccinated. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions [7,11,12] throughout the entire vaccination period.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Simon Rella", - "author_inst": "IST, Austria" - }, - { - "author_name": "Yuliya Kulikova", - "author_inst": "Bank of Spain" - }, - { - "author_name": "Emmanouil Dermitzakis", - "author_inst": "Geneva Medical School" - }, - { - "author_name": "Fyodor Kondrashov", - "author_inst": "IST, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.08.21251290", "rel_title": "Confirmed forecasts for the expansion of the COVID-19 epidemic in the S. Paulo city, Brazil", @@ -914597,6 +911855,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.09.430547", + "rel_title": "SARS-CoV-2 infection models using in vivo and in vitro hACE2-lentivirus transduction", + "rel_date": "2021-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.09.430547", + "rel_abs": "SARS-CoV-2 uses the human ACE2 (hACE2) receptor for cell attachment and entry, with mouse ACE2 (mACE2) unable to support infection. Herein we describe an ACE2-lentivirus system and illustrate its utility for in vitro and in vivo SARS-CoV-2 infection models. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K substitutions, to match hACE2, rescued SARS-CoV-2 replication. Intranasal hACE2-lentivirus transduction of C57BL/6J mice permitted significant virus replication in lungs. RNA-Seq analyses illustrated that the model involves an acute inflammatory disease followed by resolution and tissue repair, with a transcriptomic profile similar to that seen in COVID-19 patients. Intranasal hACE2-lentivirus transduction of IFNAR-/- and IL-28RA-/- mice lungs was used to illustrate that loss of type I or III interferon responses have no significant effect on virus replication. However, their importance in driving inflammatory responses was illustrated by RNA-Seq analyses. We also demonstrate the utility of the hACE2-lentivirus transduction system for vaccine evaluation in C57BL/6J mice. The ACE2-lentivirus system thus has broad application in SARS-CoV-2 research, providing a tool for both mutagenesis studies and mouse model development.\n\nAUTHOR SUMMARYSARS-CoV-2 uses the human ACE2 (hACE2) receptor to infect cells, but cannot infect mice because the virus cannot bind mouse ACE2 (mACE2). We use an ACE2-lentivirus system in vitro to identify four key amino acids in mACE2 that explain why SARS-CoV-2 cannot infect mice. hACE2-lentivirus was used to express hACE2 in mouse lungs in vivo, with the inflammatory responses after SARS-CoV-2 infection similar to those seen in human COVID-19. Genetically modified mice were used to show that type I and III interferon signaling is required for the inflammatory responses. We also show that the hACE2-lentivirus mouse model can be used to test vaccines. Overall this paper demonstrates that our hACE2-lentivirus system has multiple applications in SARS-CoV-2 and COVID-19 research.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Daniel J Rawle", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Thuy T Le", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Troy Dumenil", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Kexin Yan", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Bing Tang", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Cameron Bishop", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Andreas Suhrbier", + "author_inst": "QIMR Berghofer Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.01.429199", "rel_title": "In vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2", @@ -915640,53 +912941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.07.21251312", - "rel_title": "An integrated rural health system baseline assessment of COVID-19 preparedness in Siaya Kenya", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251312", - "rel_abs": "ObjectiveOur aim was to assess Siaya county COVID-19 preparedness at community and health facility levels and measure baseline household prevalences of fever and cough.\n\nDesignThere was retrospective and prospective data collection using standard tools. We determined the prevalence of fever and cough in households. We evaluated household knowledge about COVID-19 prevention and adherence to preventive measures. We evaluated the presence of a workforce, essential infrastructure and equipment needed for COVID-19 case management, and the availability of essential maternal and child health services in health facilities.\n\nSettingSiaya in rural Western Kenya\n\nParticipantshouseholds and health facilities in Siaya\n\nResultsWe visited 19474 households and assessed 152 facilities. The prevalences of fever and cough ranged from 1.4% to 4.3% and 0.2 to 0.8% respectively; 97% and 98% of households had not received a guest from nor travelled outside Siaya respectively; 97% knew about frequent handwashing, 66% knew about keeping distance, and 80% knew about wearing a mask; 63% washed their hands countless times; 53% remained home; and 74% used a mask when out in public. The health facility assessment showed: 93.6% were dispensaries and health centers; 90.4% had nurses; 40.5% had oxygen capacity; 13.5% had pulse oximeters; and 2 ventilators were available; 94.2% of facilities did not have COVID-19 testing kits; 94% and 91% of facilities continued to provide antenatal care and immunization services respectively. Health care worker training in COVID-19 had been planned.\n\nConclusionsHousehold prevalence of fever and cough was low suggesting Siaya had not entered the active community transmission phase in June 2020. Our assessment revealed a need for training in COVID-19 case management, and a need for basic equipment and supplies including pulse oximeters and oxygen. Future interventions should address these gaps.\n\nStrengths and limitationsO_LIThis study provides an example of how to successfully carry out an integrated rural health system baseline assessment of COVID-19 preparedness; an approach that would be useful for any country experiencing COVID-19 with a significant rural population.\nC_LIO_LISome of our data were retrospective in nature and therefore vulnerable to multiple sources of bias including: recall bias and misclassification.\nC_LI\n\nClinical Trial registrationClinicaltrials.gov NCT04501458 5/8/2020\n\nProtocolThe full protocol has been accepted for publication: Kaseje N, Kaseje D, Oruenjo K, Milambo J and Kaseje M: Engaging community health workers, technology, and youth in the COVID-19 response with concurrent critical care capacity building: A protocol for an integrated community and health system intervention to reduce mortality related to COVID-19 infection in Western Kenya. Wellcome Open Research.\n\nEthical review approvalsreceived from the University of Nairobi Ethics Review Committee and Jaramogi Oginga Odinga Teaching and Referral Hospital Ethics Review Committee (approval number IERC/JOOTR/219/20)", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Neema Kaseje", - "author_inst": "Surgical Systems Research Group, Kisumu, Kenya (1) London School of Hygiene & Tropical Medicine, UK (2)" - }, - { - "author_name": "Dan Kaseje", - "author_inst": "Tropical Institute of Community Health, Kisumu, Kenya" - }, - { - "author_name": "Kennedy Oruenjo", - "author_inst": "Siaya Ministry of Health, Siaya, Kenya" - }, - { - "author_name": "Penina Ocholla Odhiambo", - "author_inst": "Tropical Institute of Community Health, Kisumu, Kenya" - }, - { - "author_name": "Margaret Kaseje", - "author_inst": "Tropical Institute of Community Health, Kisumu, Kenya" - }, - { - "author_name": "Stephen Achola", - "author_inst": "Surgical Systems Research Group, Siaya, Kenya" - }, - { - "author_name": "Marcel Tanner", - "author_inst": "Swiss Tropical & Public Health Institute, Basel, Switzerland" - }, - { - "author_name": "Andrew Haines", - "author_inst": "London School of Hygiene & Tropical Medicine, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.07.21251281", "rel_title": "Galectin-3 as a potential prognostic biomarker of severe COVID-19 in SARS-CoV-2 infected patients", @@ -916379,6 +913633,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.02.08.430344", + "rel_title": "Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids", + "rel_date": "2021-02-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.08.430344", + "rel_abs": "Nucleocapsid (N) protein of the SARS-CoV-2 virus packages the viral genome into well-defined ribonucleoprotein particles, but the molecular pathway is still unclear. N-protein is dimeric and consists of two folded domains with nucleic acid (NA) binding sites, surrounded by intrinsically disordered regions that promote liquid-liquid phase separation. Here we use biophysical tools to study N-protein interactions with oligonucleotides of different length, examining the size, composition, secondary structure, and energetics of the resulting states. We observe formation of supramolecular clusters or nuclei preceding growth into phase-separated droplets. Short hexanucleotide NA forms compact 2:2 N-protein/NA complexes with reduced disorder. Longer oligonucleotides expose additional N-protein interactions and multi-valent protein-NA interactions, which generate higher-order mixed oligomers and simultaneously promote growth of droplets. Phase separation is accompanied by a significant increase in protein secondary structure, different from that caused by initial NA binding, which may contribute to the assembly of ribonucleoprotein particles within molecular condensates.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Huaying Zhao", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Di Wu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ai Nguyen", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Yan Li", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Regina Ad\u00e3o", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Eugene Valkov", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "George H Patterson", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Grzegorz Piszczek", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Peter Schuck", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.02.09.430446", "rel_title": "GABA administration limits viral replication and pneumonitis in a mouse model of COVID-19", @@ -917370,73 +914675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.04.21251087", - "rel_title": "Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level Linked Data Approach", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251087", - "rel_abs": "BackgroundBetter understanding of the role that children and school staff play in the transmission of SARS-CoV-2 is essential to guide policy development on controlling infection whilst minimising disruption to childrens education and wellbeing.\n\nMethodsOur national e-cohort (n=500,779) study used anonymised linked data for pupils, staff and associated households linked via educational settings. We estimated the risk of testing positive for SARS-CoV-2 infection for staff and pupils over the period August - December 2020, dependent on measures of recent exposure to known cases linked to their educational settings.\n\nResultsThe total number of cases in a school was not associated with a subsequent increase in the risk of testing positive (Staff OR per case 0.92, 95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst pupils, the number of recent cases within the same year group was significantly associated with subsequent increased risk of testing positive (OR per case 1.12, 95%CI 1.08 - 1.15). These effects were adjusted for a range of demographic covariates, and in particular any known cases within the same household, which had the strongest association with testing positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 - 9.88).\n\nConclusionsIn a national school cohort, the odds of staff testing positive for SARS-CoV-2 infection were not significantly increased in the 14-day period after case detection in the school. However, pupils were found to be at increased risk, following cases appearing within their own year group, where most of their contacts occur. Strong mitigation measures over the whole of the study period may have reduced wider spread within the school environment.\n\nO_TEXTBOXWhat is knownO_LIEvidence of the role schools play in the transmission of SARS-CoV-2 is limited\nC_LIO_LIHigher positivity rates are observed in school staff compared to pupils\nC_LIO_LILack of evidence on transmission pathways transmission into and within schools\nC_LI\n\nWhat this study addsO_LIFirst UK national level study of transmission between pupils and staff in a school environment during the SARS-CoV-2 pandemic.\nC_LIO_LISchools opening September-December 2020 was not associated with an increased subsequent risk of testing positive in staff\nC_LIO_LIPupils were found to be at increased risk of testing positive, following cases appearing within their own year group\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Daniel A Thompson", - "author_inst": "Swansea University" - }, - { - "author_name": "Hoda Abbasizanjani", - "author_inst": "Swansea University" - }, - { - "author_name": "Richard Fry", - "author_inst": "Swansea University" - }, - { - "author_name": "Emily Marchant", - "author_inst": "Swansea University" - }, - { - "author_name": "Lucy J Griffiths", - "author_inst": "Swansea University" - }, - { - "author_name": "Ashley Akbari", - "author_inst": "Swansea University" - }, - { - "author_name": "Joseph Hollinghurst", - "author_inst": "Swansea University" - }, - { - "author_name": "Laura North", - "author_inst": "Swansea University" - }, - { - "author_name": "Jane Lyons", - "author_inst": "Swansea University" - }, - { - "author_name": "Fatemeh Torabi", - "author_inst": "Swansea University" - }, - { - "author_name": "Gareth Davies", - "author_inst": "Swansea University" - }, - { - "author_name": "Mike B Gravenor", - "author_inst": "Swansea University" - }, - { - "author_name": "Ronan A Lyons", - "author_inst": "Swansea University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.02.04.21251167", "rel_title": "A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic", @@ -917993,6 +915231,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.05.21251231", + "rel_title": "Design and Estimation for the Population Prevalence of Infectious Diseases", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251231", + "rel_abs": "Understanding the prevalence of infections in the population of interest is critical for making data-driven public health responses to infectious disease outbreaks. Accurate prevalence estimates, however, can be difficult to calculate due to a combination of low population prevalence, imperfect diagnostic tests, and limited testing resources. In addition, strategies based on convenience samples that target only symptomatic or high-risk individuals will yield biased estimates of the population prevalence. We present Bayesian multilevel regression and poststratification models that incorporate probability sampling designs, the sensitivity and specificity of a diagnostic test, and specimen pooling to obtain unbiased prevalence estimates. These models easily incorporate all available prior information and can yield reasonable inferences even with very low base rates and limited testing resources. We examine the performance of these models with an extensive numerical study that varies the sampling design, sample size, true prevalence, and pool size. We also demonstrate the relative robustness of the models to key prior distribution assumptions via sensitivity analyses.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Eric J Oh", + "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" + }, + { + "author_name": "Alyssa Mikytuck", + "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" + }, + { + "author_name": "Vicki Lancaster", + "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" + }, + { + "author_name": "Joshua Goldstein", + "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" + }, + { + "author_name": "Sallie Keller", + "author_inst": "Biocomplexity Institute and Initiative, University of Virginia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.05.21251174", "rel_title": "INCLUSIVE HEALTH: MODELING COVID-19 IN CORRECTIONAL FACILITIES AND COMMUNITIES", @@ -919328,77 +916601,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.06.21249256", - "rel_title": "Chronic COVID-19 Syndrome and Chronic Fatigue Syndrome (ME/CFS) following the first pandemic wave in Germany: a first analysis of a prospective observational study", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21249256", - "rel_abs": "ObjectiveCharacterization of the clinical features of patients with persistent symptoms after mild to moderate COVID-19 infection and exploration of factors associated with the development of Chronic COVID-19 Syndrome (CCS).\n\nMethodsSetting: Charite Fatigue Center with clinical immunologists and rheumatologist, neurologists and cardiologists at Charite University hospital.\n\nParticipants: 42 patients who presented with persistent moderate to severe fatigue six months following a mostly mild SARS-CoV-2 infection at the Charite Fatigue Center from July to November 2020.\n\nMain outcome measures: The primary outcomes were clinical and paraclinical data and meeting diagnostic criteria for Chronic Fatigue Syndrome (ME/CFS). Relevant neurological and cardiopulmonary morbidity was excluded.\n\nResultsThe median age was 36.5, range 22-62, 29 patients were female and 13 male. At six months post acute COVID-19 all patients had fatigue (Chalder Fatigue Score median 25 of 33, range 14-32), the most frequent other symptoms were post exertional malaise (n=41), cognitive symptoms (n=40), headache (n=38), and muscle pain (n=35). Most patients were moderately to severely impaired in daily live with a median Bell disability score of 50 (range 15-90) of 100 (healthy) and Short Form 36 (SF-36) physical function score of 63 (range 15-80) of 100. 19 of 42 patients fulfilled the 2003 Canadian Consensus Criteria for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). These patients reported more fatigue in the Chalder Fatigue Score (p=0.006), more stress intolerance (p=0.042) and more frequent and longer post exertional malaise (PEM) (p=0.003), and hypersensitivity to noise (p=0.029), light (p=0.0143) and temperature (p=0.024) compared to patients not meeting ME/CFS criteria. Handgrip force was diminished in most patients compared to healthy control values, and lower in CCS/CFS compared to non-CFS CCS (Fmax1 p=0.085, Fmax2, p=0.050, Fmean1 p=0.043, Fmean2 p=0.034, mean of 10 repeat handgrips, 29 female patients). Mannose-binding lectin (MBL) deficiency was observed frequently (22% of all patients) and elevated IL-8 levels were found in 43% of patients.\n\nConclusionsChronic COVID-19 Syndrome at months 6 is a multisymptomatic frequently debilitating disease fulfilling diagnostic criteria of ME/CFS in about half of the patients in our study. Research in mechanisms and clinical trials are urgently needed.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Claudia Kedor", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Helma Freitag", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Lil-Antonia Meyer-Arndt", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Kirsten Wittke", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "thomas Zoller", - "author_inst": "Charite universitaetmedizin Berlin" - }, - { - "author_name": "Fridolin Steinbeis", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Milan Haffke", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Rudolf Gordon", - "author_inst": "Charite Univarsitaetsmedizin Berlin" - }, - { - "author_name": "Bettina Heidecker", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Hans Dieter Volk", - "author_inst": "Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charite unuversitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Carsten Skurk", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Friedemann Paul", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Judith Bellmann-Strobl", - "author_inst": "Charite Universitaetsmedizin Berlin" - }, - { - "author_name": "Carmen Scheibenbogen", - "author_inst": "Charite Universitaetsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.06.21251246", "rel_title": "Dynamics of neutralizing antibody responses in acute-phase COVID-19: A potential relationship between disease progression and rapid neutralizing antibody response", @@ -920251,6 +917453,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.07.429299", + "rel_title": "A human antibody with blocking activity to RBD proteins of multiple SARS-CoV-2 variants including B.1.351 showed potent prophylactic and therapeutic efficacy against SARS-CoV-2 in rhesus macaques", + "rel_date": "2021-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.07.429299", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease-2019 (COVID-19), interacts with the host cell receptor angiotensin-converting enzyme 2 (hACE2) via its spike 1 protein for infection. After the virus sequence was published, we identified two potent antibodies against SARS-CoV-2 RBD from antibody libraries using a phage-to-yeast (PtY) display platform in only 10 days. Our lead antibody JMB2002, now in a phase I clinical trial, showed broad-spectrum in vitro blocking activity against hACE2 binding to the RBD of multiple SARS-CoV-2 variants including B.1.351 that was reportedly much more resistant to neutralization by convalescent plasma, vaccine sera and some clinical stage neutralizing antibodies. Furthermore, JMB2002 has demonstrated complete prophylactic and potent therapeutic efficacy in a rhesus macaque disease model. Prophylactic and therapeutic countermeasure intervention of SARS-CoV-2 using JMB2002 would likely slow down the transmission of currently emerged SARS-CoV-2 variants and result in more efficient control of the COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yanfeng Yao", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Ge Gao", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Yun Peng", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Juan Min", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Haixia Ma", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Donglin Song", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Zhiming Yuan", + "author_inst": "National Biosafety Laboratory, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.06.430072", "rel_title": "Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants.", @@ -921342,41 +918587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.02.02.21251039", - "rel_title": "Could the new COVID-19 mutant strain undermine vaccination efforts? A mathematical modelling approach for estimating the spread of the UK mutant strain using Ontario, Canada, as a case study", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251039", - "rel_abs": "BackgroundInfections represent highly dynamic processes, characterized by evolutionary changes and events that involve both the pathogen and the host. Among infectious agents, viruses, such as the \"Severe Acute Respiratory Syndrome-related Coronavirus type 2\" (SARS-CoV-2), the infectious agent responsible for the currently ongoing \"Coronavirus disease 2019\" (COVID-2019) pandemic, have a particularly high mutation rate. Taking into account the mutational landscape of an infectious agent, it is important to shed light on its evolution capability over time. As new, more infectious strains of COVID-19 emerge around the world, it is imperative to estimate when these new strains may overtake the wild-type strain in different populations. Therefore, we developed a general-purpose framework to estimate the time at which a mutant variant is able to takeover a wild-type strain during an emerging infectious diseases outbreak. In this study, we used COVID-19 as a case-study, but the model is adaptable to any emerging pathogens.\n\nMethods and findingsWe devise a two-strain mathematical framework, to model a wild- and a mutant-type viral population and fit cumulative case data to parameterize the model, using Ontario as a case study. We found that, in the context of under-reporting and the current case levels, a variant strain is unlikely to dominate until March/April 2021. Current non-pharmaceutical interventions in Ontario need to be kept in place longer even with vaccination in order to prevent another outbreak. The spread of a variant strain in Ontario will mostly likely be observed by a widened peak of the daily reported cases. If vaccine efficacy is maintained across strains, then it is still possible to have an immune population by end of 2021.\n\nConclusionsOur findings have important practical implications in terms of public health as policy-and decision-makers are equipped with a mathematical tool that can enable the estimation of the take-over of a mutant strain of an emerging infectious disease.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matthew Betti", - "author_inst": "Mount Allison University" - }, - { - "author_name": "Nicola Bragazzi", - "author_inst": "York University" - }, - { - "author_name": "Jane Marie Heffernan", - "author_inst": "York University" - }, - { - "author_name": "Jude Dzevela Kong", - "author_inst": "York University" - }, - { - "author_name": "Angie Raad", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.01.21249903", "rel_title": "Quantifying transmissibility of COVID-19 and impact of intervention within long-term health care facilities", @@ -922061,6 +919271,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.03.21251078", + "rel_title": "Antibody responses boosted in seropositive healthcare workers after single dose of SARS-CoV-2 mRNA vaccine", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251078", + "rel_abs": "Current guidelines recommend that individuals who have had COVID-19 should receive the identical vaccine regimen as those who have not had the infection. This includes two doses of the mRNA platform vaccines (BNT162b2/Pfizer; mRNA-1273/Moderna) that are approved for use in the United States. In this brief report, we show that after a single dose of the Pfizer SARS-CoV-2 vaccine, individuals that had prior SARS-CoV-2 infection had significantly higher antibody levels than individuals that had no history of infection. This provides the rationale for changing vaccination policy to deliver only a single dose to individuals with recent SARS-CoV-2 infection that may free up additional doses for individuals that have no preexisting immunity to the virus. Future study of other immune parameters such as T cell response and durability of immune response should be rapidly undertaken in individuals that had COVID-19 prior to vaccination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Todd Bradley", + "author_inst": "Children's Mercy Kansas City" + }, + { + "author_name": "- CODIEFY study team", + "author_inst": "" + }, + { + "author_name": "Elin Grundberg", + "author_inst": "Children's Mercy Kansas City" + }, + { + "author_name": "Rangaraj Selvarangan", + "author_inst": "Children's Mercy Kansas City" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.02.21250940", "rel_title": "IgA autoantibodies target pulmonary surfactant in patients with severe COVID-19", @@ -922992,73 +920233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.02.03.21251007", - "rel_title": "Intention to receive a COVID-19 vaccine: Results from a population-based survey in Canada", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251007", - "rel_abs": "BackgroundThe success of any COVID-19 vaccine program ultimately depends on high vaccine uptake. This study determined overall intention to receive a COVID-19 vaccine and identified factors that predict intentions to be vaccinated against COVID-19 in Canada, specifically in key priority groups identified by the American Committee on Immunization Practice (ACIP) and the National Advisory Committee on Immunization (NACI) for early immunization.\n\nMethodsIndividuals from research cohorts from the general population of British Columbia aged 25-69 were invited complete an online survey based on validated scales and theoretical frameworks to explore intention to receive a COVID-19 vaccine. Two multivariable logistic regression models were conducted to determine factors associated with intention to receive the COVID-19 vaccine.\n\nResultsOf 4,948 respondents, 79.8% intended to receive a COVID-19 vaccine. In multivariable modeling, respondents who intended to receive the vaccine had higher vaccine attitudinal scores (p <0.001), reported greater influence of direct social norms (p = 0.001), and indirect social norms, including their family physician (p = 0.024), and Provincial Health Officer (p = 0.011). Older individuals (>60 years) were more likely to intend to receive the vaccine, while females (95%CI 0.57,0.93), those with less than high school education (95%CI 0.5,0.76), those who self-identified as non-white (95%CI 0.60,0.92), self-identified as Indigenous (95%CI 0.36,0.84) and essential non-health care workers (95%CI 0.59,0.86) had lower adjusted odds of intending to receive a COVID-19 vaccine.\n\nConclusionsTo optimize vaccine coverage, public health should focus on key messages around vaccine safety and benefit, and leverage trusted practitioners for messaging. As certain key populations identified by NACI and ACIP for early immunization report a lower intention to vaccinate, there is a need for in-depth education and support for these communities to ensure optimal uptake.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Gina Ogilvie", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Shanlea Gordon", - "author_inst": "BC Children's Hospital Research Institute" - }, - { - "author_name": "Laurie Smith", - "author_inst": "BC Cancer Agency" - }, - { - "author_name": "Arianne Albert", - "author_inst": "Women's Health Research Institute" - }, - { - "author_name": "Amy Booth", - "author_inst": "University of British Columbia" - }, - { - "author_name": "C Sarai Racey", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Anna Gottschlich", - "author_inst": "University of British Columbia" - }, - { - "author_name": "David M Goldfarb", - "author_inst": "Children's and Women's Health Centre of British Columbia" - }, - { - "author_name": "Melanie C. M. Murray", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Liisa A.M Galea", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Angela Kaida", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Lori A Brotto", - "author_inst": "Women's Health Research Institute" - }, - { - "author_name": "Manish Sadarangani", - "author_inst": "Vaccine Evaluation Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.03.429628", "rel_title": "Development of a highly sensitive bioanalytical assay for the quantification of favipiravir.", @@ -924975,6 +922149,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.01.21250946", + "rel_title": "Usability of saliva collection devices for SARS-CoV-2 diagnostics", + "rel_date": "2021-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250946", + "rel_abs": "There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance of medical professionals, impeding the implementation of large-scale testing. Self-collection of saliva may solve these problems, as it can be completed without specialized training and uses generic materials. In this study, we observed thirty individuals who self-collected saliva using four different collection devices and analyzed their feedback. Two of these devices, a funnel and bulb pipette, were used to evaluate at-home saliva collection by 60 individuals. All devices enabled the safe, unsupervised self-collection of saliva. The quantity and quality of the samples received were acceptable for SARS-CoV-2 diagnostic testing, as determined by RNase P detection. Here, we demonstrate inexpensive, generic, buffer free collection devices suitable for unsupervised and home saliva self-collection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Orchid Allicock", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Mary E. Petrone", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Devyn Yolda-Carr", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Mallery Breban", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Hannah Walsh", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Anne E. Watkins", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Jessica Rothman", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Shelli Farhadian", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Anne L Wyllie", + "author_inst": "Yale School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.01.21250971", "rel_title": "Estimation of infection rate and the population size potentially exposed to SARS-CoV-2 in Japan during 2020", @@ -925750,33 +922979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.29.21250791", - "rel_title": "Bayesian Calibration of Using CO2 Sensors to Assess Ventilation Conditions and Associated COVID-19 Airborne Aerosol Transmission Risk in Schools", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250791", - "rel_abs": "Ventilation rate plays a significant role in preventing the airborne transmission of diseases in indoor spaces. Classrooms are a considerable challenge during the COVID-19 pandemic because of large occupancy density and mainly poor ventilation conditions. The indoor CO2 level may be used as an index for estimating the ventilation rate and airborne infection risk. In this work, we analyzed a one-day measurement of CO2 levels in three schools to estimate the ventilation rate and airborne infection risk. Sensitivity analysis and Bayesian calibration methods were applied to identify uncertainties and calibrate key parameters. The outdoor ventilation rate with a 95% confidence was 1.96 {+/-} 0.31ACH for Room 1 with mechanical ventilation and fully open window, 0.40 {+/-} 0.08 ACH for Rooms 2, and 0.79 {+/-} 0.06 ACH for Room 3 with only windows open. A time-averaged CO2 level < 450 ppm is equivalent to a ventilation rate > 10 ACH in all three rooms. We also defined the probability of the COVID-19 airborne infection risk associated with ventilation uncertainties. The outdoor ventilation threshold to prevent classroom COVID-19 aerosol spreading is between 3 - 8 ACH, and the CO2 threshold is around 500 ppm of a school day (< 8 hr) for the three schools.\n\nPractical ImplicationsThe actual outdoor ventilation rate in a room cannot be easily measured, but it can be calculated by measuring the transient indoor CO2 level. Uncertainty in input parameters can result in uncertainty in the calculated ventilation rate. Our three classrooms study shows that the estimated ventilation rate considering various input parameters uncertainties is between {+/-} 8-20 %. As a result, the uncertainty of the ventilation rate contributes to the estimated COVID-19 airborne aerosol infection risks uncertainty up to {+/-} 10 %. Other studies can apply the proposed Bayesian and MCMC method to estimating building ventilation rates and airborne aerosol infection risks based on actual measurement data such as CO2 levels with uncertainties and sensitivity of input parameters identified. The outdoor ventilation rate and CO2 threshold values as functions of exposure times could be used as the baseline models to develop correlations to be implemented by cheap/portable sensors to be applied in similar situations to monitor ventilation conditions and airborne risk levels.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Danlin Hou", - "author_inst": "Concordia University, Montreal, Canada" - }, - { - "author_name": "Ali Katal", - "author_inst": "Concordia University, Montreal, Canada" - }, - { - "author_name": "Liangzhu (Leon) Wang", - "author_inst": "Concordia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.01.21250537", "rel_title": "Towards a COVID-19 symptom triad: The importance of symptom constellations in the SARS-CoV-2 pandemic", @@ -926805,6 +924007,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.01.21250769", + "rel_title": "Sarilumab treatment of hospitalised patients with severe or critical COVID-19: a multinational, randomised, adaptive, phase 3, double-blind, placebo-controlled trial", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250769", + "rel_abs": "BackgroundElevated proinflammatory cytokines have been associated with 2019 coronavirus disease (COVID-19) severity. We assessed efficacy and safety of sarilumab, an interleukin-6 receptor inhibitor, in severe (requiring supplemental oxygen by nasal canula or face mask) or critical (requiring greater supplemental oxygen, mechanical ventilation, or extracorporeal support) COVID-19.\n\nMethodsThis was a 60-day, randomised, double-blind, placebo-controlled, multinational trial in patients hospitalised with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pneumonia, who required oxygen supplementation or intensive care. Patients were randomised 2:2:1 to intravenous sarilumab 400 mg, sarilumab 200 mg, or placebo. The primary endpoint was time to [≥]2-point clinical improvement (7-point scale; range: 1 [death] to 7 [not hospitalised]). The key secondary endpoint was proportion of patients alive at day 29. Safety outcomes included adverse events and laboratory assessments. This trial is registered with ClinicalTrials.gov (NCT04327388).\n\nFindingsBetween March 28 and July 3, 2020, 420 patients were randomised; 416 received treatment (placebo, n=84; sarilumab 200 mg, n=159; sarilumab 400 mg, n=173). At day 29, there were no significant differences in median (95% CI) time to [≥]2-point improvement between placebo (12{middle dot}0 [9{middle dot}0-15{middle dot}0] days) and sarilumab groups (200 mg: 10{middle dot}0 [9{middle dot}0-12{middle dot}0] days, p=0.96, log-rank test; 400 mg: 10{middle dot}0 [9{middle dot}0-13{middle dot}0] days, p=0.34) or in proportions of patients alive (placebo, 91{middle dot}7%; sarilumab 200 mg, 89{middle dot}9%, p=0{middle dot}63; sarilumab 400 mg, 91{middle dot}9%, p=0{middle dot}85). At day 29, there were numerical, nonsignificant survival differences between sarilumab 400 mg (88%) and placebo (79%; difference +9%, 95% CI -7{middle dot}7 to 25{middle dot}5, p=0{middle dot}25) for critical patients. There were no unexpected safety signals.\n\nInterpretationThis trial did not demonstrate efficacy of sarilumab in patients hospitalised with COVID-19 and receiving supplemental oxygen. Adequately powered trials of targeted immunomodulatory therapies assessing survival as a primary endpoint are suggested in patients with critical COVID-19.\n\nFundingSanofi and Regeneron Pharmaceuticals, Inc.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Francois-Xavier Lescure", + "author_inst": "Assistance Publique - Hopitaux de Paris, Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, APHP.7, INSERM, IAME, UMR 1137, Univ of Pa" + }, + { + "author_name": "Hitoshi Honda", + "author_inst": "Division of Infectious Diseases, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan" + }, + { + "author_name": "Robert A Fowler", + "author_inst": "Sunnybrook Health Sciences Centre, Toronto, ON, Canada" + }, + { + "author_name": "Jennifer Sloane Lazar", + "author_inst": "Sanofi, Bridgewater, NJ, USA" + }, + { + "author_name": "Genming Shi", + "author_inst": "Sanofi, Bridgewater, NJ, USA" + }, + { + "author_name": "Peter Wung", + "author_inst": "Sanofi, Bridgewater, NJ, USA" + }, + { + "author_name": "Naimish Patel", + "author_inst": "Sanofi, Cambridge, MA, USA" + }, + { + "author_name": "Owen Hagino", + "author_inst": "Sanofi, Bridgewater, NJ, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.01.21250493", "rel_title": "Sex disparities and neutralizing antibody durability to SARS-CoV-2 infection in convalescent individuals", @@ -927920,61 +925169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.01.21250846", - "rel_title": "Deleterious effects of SARS-CoV-2 infection on human pancreatic cells", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250846", - "rel_abs": "COVID-19 pandemic has infected more than 46 million people worldwide and caused more than 1.2 million deaths. It is transmitted by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and affects the respiratory tract as well as extra-pulmonary systems, including the pancreas, that express the virus entry receptor, Angiotensin-Converting Enzyme 2 (ACE2) receptor. Importantly, the endocrine and exocrine pancreas, the latter composed of ductal and acinar cells, express high levels of ACE2, which correlates to impaired functionality characterized as acute pancreatitis observed in some cases presenting with COVID-19. Since acute pancreatitis is already one of the most frequent gastrointestinal causes of hospitalization in the U.S. and the majority of studies investigating the effects of SARS-CoV-2 on the pancreas are clinical and observational, we utilized human iPSC technology to investigate the potential deleterious effects of SARS-CoV-2 infection on iPSC-derived pancreatic cultures containing endocrine and exocrine cells. Interestingly, SARS-CoV-2 is capable of infecting iPSC-derived pancreatic cells, thus perturbing their normal molecular and cellular phenotypes. The infection increased a key inflammatory cytokine, CXCL12, known to be involved in pancreas dysfunction. Transcriptome analysis of infected pancreatic cultures confirmed that SARS-CoV-2 hijacks the ribosomal machinery in these cells. Notably, the SARS-CoV-2 infectivity of the pancreas is confirmed in post-mortem tissues from COVID-19 patients, which showed co-localization of SARS-CoV-2 in pancreatic endocrine and exocrine cells and increased the expression of some pancreatic ductal stress response genes. Thus, we demonstrate for the first time that SARS-CoV-2 can directly infect human iPSC-derived pancreatic cells with supporting evidence of presence of the virus in post-mortem pancreatic tissue of confirmed COVID-19 human cases. This novel model of iPSC-derived pancreatic cultures will open new avenues for the comprehension of the SARS-CoV-2 infection and potentially establish a platform for endocrine and exocrine pancreas-specific antiviral drug screening.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Syairah Hanan Shaharuddin", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Victoria L Wang", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Roberta DeSouza Santos", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Yizhou Wang", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Harneet Jawanda", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Wohaib Hasan", - "author_inst": "Takeda Pharmaceuticals" - }, - { - "author_name": "Gustavo L Garcia", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Vaithilingaraja Arumugaswami", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Dhruv Sareen", - "author_inst": "Cedars-Sinai Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.02.21250910", "rel_title": "Elevated mucosal antibody responses against SARS-CoV-2 are correlated with lower viral load and faster decrease in systemic COVID-19 symptoms", @@ -928543,6 +925737,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2021.01.31.21250867", + "rel_title": "Standard and anomalous second waves in the COVID-19 pandemic", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.31.21250867", + "rel_abs": "We apply a generalised logistic growth model, with time dependent parameters, to describe the fatality curves of the COVID-19 disease for several countries that exhibit a second wave of infections. The model parameters vary as a function of time according to a logistic function, whose two extreme values, i.e., for early and late times, characterise the first and second waves, respectively. We show that the theoretical curves are in excellent agreement with the empirical data for all cases considered. The model also allows for predictions about the time of occurrence and relative severity of the second wave, in comparison to the first wave. It is shown furthermore that the COVID-19 second waves can be generically classified in two main types, namely, standard and anomalous second waves, according as to whether the second wave starts well after or still during the first wave, respectively. We have also observed that the standard second waves tend, in their majority, to be more severe than the corresponding first wave, whereas for anomalous second waves the opposite occurs.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Giovani L. Vasconcelos", + "author_inst": "Departamento de F\u00edsica, Universidade Federal do Paran\u00e1,Curitiba, Paran\u00e1, Brazil" + }, + { + "author_name": "Arthur A. Brum", + "author_inst": "Departamento de F\u00edsica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil" + }, + { + "author_name": "Francisco A. G. Almeida", + "author_inst": "Departamento de F\u00edsica, Universidade Federal de Sergipe, Sergipe, Brazil" + }, + { + "author_name": "Ant\u00f4nio M.S. M\u00e2cedo", + "author_inst": "Departamento de F\u00edsica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil" + }, + { + "author_name": "Gerson C. Duarte-Filho", + "author_inst": "Departamento de F\u00edsica, Universidade Federal de Sergipe, Sergipe, Brazil" + }, + { + "author_name": "Raydonal Ospina", + "author_inst": "Departamento de Estat\u00edstica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.02.21250909", "rel_title": "Muscle strength is associated with COVID-19 hospitalization in adults 50 years of age and older", @@ -929954,153 +927187,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.02.02.21250989", - "rel_title": "Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250989", - "rel_abs": "Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent \"second wave\" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@987a5org.highwire.dtl.DTLVardef@1a8a141org.highwire.dtl.DTLVardef@1f2de56org.highwire.dtl.DTLVardef@1e2f9b8org.highwire.dtl.DTLVardef@78bfcc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONAssociation between ethnicity and COVID-19 death 1st Sept - 9th Nov 2020\n\nC_TABLECAPTION C_TBL", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "William J Hulme", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Brian McKenna", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Harriet J Forbes", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Chris J Bates", - "author_inst": "TPP, TPP House, Horsforth, Leeds" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Nichola J DeVito", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Henry Drysdale", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, TPP House, Horsforth, Leeds" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, Horsforth, Leeds" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, TPP House, Horsforth, Leeds" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, TPP House, Horsforth, Leeds" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Richard Grieve", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.03.429522", "rel_title": "Knowledge and Awareness of coronavirus disease 2019 (COVID-19) among Chinese dental students----a comparison study.", @@ -930617,6 +927703,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.01.31.21250868", + "rel_title": "Molecular epidemiology of SARS-CoV-2 in Greece reveals low rates of onward virus transmission after lifting of travel restrictions based on risk assessment during summer 2020", + "rel_date": "2021-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.31.21250868", + "rel_abs": "Molecular epidemiology has provided an additive value to traditional public health tools by identifying SARS-CoV-2 clusters, or providing evidence that clusters based on virus sequences and contact tracing are highly concordant. Our aim was to infer the levels of virus importation and to estimate the impact of public health measures related to travel restrictions to local transmission in Greece. Our phylogenetic and phylogeographic analyses included 389 SARS-CoV-2 sequences collected during the first 7 months of the pandemic in Greece and a random collection in 5 replicates of 3,000 sequences sampled globally, as well as the best hits to our dataset identified by BLAST. Phylogenetic analyses revealed the presence of 70 genetically distinct viruses identified as independent introductions into Greece. The proportion of imported strains was 41%, 11.5%, and 8.8% during the three periods of sampling, namely, March (no travel restrictions), April to June (strict travel restrictions), and July to September (lifting of travel restrictions based on a thorough risk assessment), respectively. These findings reveal low levels of onward transmission from imported cases during summer and underscore the importance of targeted public health measures that can increase the safety of international travel during a pandemic.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Evangelia Georgia Kostaki", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Georgios A. Pavlopoulos", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece, Institute for Fundamental" + }, + { + "author_name": "Kleio-Maria Verrou", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Giannis Ampatziadis-Michailidis", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Vaggelis Harokopos", + "author_inst": "Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece" + }, + { + "author_name": "Pantelis Hatzis", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece, Institute for Fundamental B" + }, + { + "author_name": "Panagiotis Moulos", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece, Institute for Fundamental Bi" + }, + { + "author_name": "Nikolaos Siafakas", + "author_inst": "Laboratory of Clinical Microbioloy, ATTIKON University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Spyridon Pournaras", + "author_inst": "Laboratory of Clinical Microbioloy, ATTIKON University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Christos Hadjichristodoulou", + "author_inst": "Laboratory of Hygiene and Epidemiology, Faculty of Medicine, Larisa, Greece" + }, + { + "author_name": "Fani Chatzopoulou", + "author_inst": "Labnet, Laboratories, Thessaloniki, Greece" + }, + { + "author_name": "Dimitrios Chatzidimitriou", + "author_inst": "Labnet, Laboratories, Thessaloniki, Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece" + }, + { + "author_name": "Periklis Panagopoulos", + "author_inst": "2nd Department of Internal Medicine, General Hospital of Alexandroupoli, Democritus University of Thrace, Alexandroupoli, Greece" + }, + { + "author_name": "Panagiota Lourida", + "author_inst": "Infectious Diseases Clinic A, Thoracic Diseases General Hospital Sotiria, Athens, Greece" + }, + { + "author_name": "Aikaterini Argyraki", + "author_inst": "Infectious Diseases Clinic A, Thoracic Diseases General Hospital Sotiria, Athens, Greece" + }, + { + "author_name": "Theodoros Lytras", + "author_inst": "School of Medicine, European University Cyprus, Nicosia, Cyprus" + }, + { + "author_name": "Spyros Sapounas", + "author_inst": "National Public Health Organization, Athens, Greece" + }, + { + "author_name": "Gerasimos Gerolymatos", + "author_inst": "National Public Health Organization, Athens, Greece" + }, + { + "author_name": "Georgios Panagiotakopoulos", + "author_inst": "National Public Health Organization, Athens, Greece" + }, + { + "author_name": "Panagiotis Prezerakos", + "author_inst": "Department of Nursing, University of Peloponnese, Tripoli, Greece" + }, + { + "author_name": "Sotirios Tsiodras", + "author_inst": "4th Department of Internal Medicine, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Vana Sypsa", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Angelos Hatzakis", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Cleo Anastassopoulou", + "author_inst": "Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Nikolaos Spanakis", + "author_inst": "Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Athanasios Tsakris", + "author_inst": "Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Meletios Athanasios Dimopoulos", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece, Department of Therapeutics, " + }, + { + "author_name": "Anastasia Kotanidou", + "author_inst": "1st Intensive Care Unit, General Hospital Evangelismos, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Petros Sfikakis", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece, 1st Department of Prop. Inte" + }, + { + "author_name": "Georgios Kollias", + "author_inst": "Center of New Biotechnologies & Precision Medicine, Medical School, University of Athens, Institute for Bioinnovation, Biomedical Sciences Research Center 'Alex" + }, + { + "author_name": "Gkikas Magiorkinis", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Dimitrios Paraskevis", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.31.21250167", "rel_title": "Dynamics of SARS-CoV-2-specific antibodies during and after COVID19: Lessons from a biobank in Argentina", @@ -931628,45 +928857,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.31.426979", - "rel_title": "In vitro inactivation of SARS-CoV-2 with 0.5% povidone iodine nasal spray (Nasodine) at clinically relevant concentrations and timeframes using tissue culture and PCR based assays", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.426979", - "rel_abs": "BACKGROUNDThere has been considerable speculation regarding the potential of PVP-I nasal disinfection as an adjunct to other countermeasures during the ongoing SARS-CoV-2 pandemic. Nasodine is a commercial formulation of 0.5% PVP-I that has been evaluated for safety and efficacy in human trials as a treatment for the common cold, including a Phase III trial (ANZCTR: ACTRN12619000764134). This study presents the first report of the in vitro efficacy of this formulation against SARS-CoV-2.\n\nMETHODSWe conducted in vitro experiments to determine if the PVP-I formulation inactivated SARS-CoV-2 using two independent assays and virus isolates, and incorporating both PCR-based detection and cell culture methods to assess residual virus after exposure to the formulation.\n\nRESULTSBased on cell culture results, the PVP-I formulation was found to rapidly inactivate SARS-CoV-2 isolates in vitro in short timeframes (15 seconds to 15 minutes) consistent with the minimum and maximum potential residence time in the nose. The Nasodine formula was found to be more effective than 0.5% PVP-I in saline. Importantly, it was found that the formulation inactivated culturable virus but had no effect on PCR-detectable viral RNA.\n\nCONCLUSIONSThe PVP-I formulation eliminated the viability of SARS-CoV-2 virus with short exposure times consistent with nasal use. PCR alone may not be adequate for viral quantification in nasal PVP-I studies; future studies should incorporate cell culture to assess viral viability. Nasal disinfection with PVP-I may be a useful intervention for newly-diagnosed COVID-19 patients to reduce transmission risk and disease progression to the lower respiratory tract.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Simon P Tucker", - "author_inst": "Firebrick Pharma Limited" - }, - { - "author_name": "Stephen Goodall", - "author_inst": "Firebrick Pharma Limited" - }, - { - "author_name": "Peter Molloy", - "author_inst": "Firebrick Pharma Limited" - }, - { - "author_name": "Justin Julander", - "author_inst": "Utah State University" - }, - { - "author_name": "Michelle Mendenhall", - "author_inst": "Utah State University" - }, - { - "author_name": "Peter Friedland", - "author_inst": "Sir Charles Gairdner Hospital, Perth, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.01.429176", "rel_title": "Host PDZ-containing proteins targeted by SARS-Cov-2", @@ -932227,6 +929417,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.28.20181040", + "rel_title": "Modeling the potential impact of indirect transmission on COVID-19 epidemic", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.20181040", + "rel_abs": "The spread of SARS-CoV-2 through direct transmission (person-to-person) has been the focus of most studies on the dynamics of COVID-19. The efficacy of social distancing and mask usage at reducing the risk of direct transmission of COVID-19 has been studied by many researchers. Little or no attention is given to indirect transmission of the virus through shared items, commonly touch surfaces and door handles. The impact of the persistence of SARS-CoV-2 on hard surfaces and in the environment, on the dynamics of COVID-19 remain largely unknown. Also, the current increase in the number of cases despite the strict non-pharmaceutical interventions suggests a need to study the indirect transmission of COVID-19 while incorporating testing of infected individuals as a preventive measure. Assessing the impact of indirect transmission of the virus may improve our understanding of the overall dynamics of COVID-19. We developed a novel deterministic susceptible-exposed-infected-removed-virus-death compartmental model to study the impact of indirect transmission pathway on the spread of COVID-19, the sources of infection, and prevention/control. We fitted the model to the cumulative number of confirmed cases at episode date in Toronto, Canada using a Markov Chain Monte Carlo optimization algorithm. We studied the effect of indirect transmission on the epidemic peak, peak time, epidemic final size and the effective reproduction number, based on different initial conditions and at different stages. Our findings revealed an increase in cases with indirect transmission. Our work highlights the importance of implementing additional preventive and control measures involving cleaning of surfaces, fumigation, and disinfection to lower the spread of COVID-19, especially in public areas like the grocery stores, malls and so on. We conclude that indirect transmission of SARS-CoV-2 has a significant effect on the dynamics of COVID-19, and there is need to consider this transmission route for effective mitigation, prevention and control of COVID-19 epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jummy Funke David", + "author_inst": "York University" + }, + { + "author_name": "Sarafa Adewale Iyaniwura", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Pei Yuan", + "author_inst": "York University" + }, + { + "author_name": "Yi Tan", + "author_inst": "York University" + }, + { + "author_name": "Jude Dzevela Kong", + "author_inst": "York University" + }, + { + "author_name": "Huaiping Zhu", + "author_inst": "York University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.28.21250421", "rel_title": "Viral sequencing reveals US healthcare personnel rarely become infected with SARS-CoV-2 through patient contact", @@ -933278,105 +930507,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.29.21250730", - "rel_title": "How best do we engage the general population in testing for COVID-19?", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250730", - "rel_abs": "The UK Scientific Advisory Group for Emergencies (SAGE) emphasises the need for high levels of engagement with communities and individuals to ensure the effectiveness of any COVID-19 testing programme. A novel pilot health surveillance programme to assess the feasibility of weekly mass RT-LAMP testing for the SARS-CoV-2 virus using saliva samples collected at home was developed and piloted by the University of Southampton and Southampton City Council. Rapid qualitative evaluation was conducted to explore experiences of those who took part in the programme, of those who declined and of those in the educational and healthcare organisations involved in the pilot testing who were responsible for roll-out. This included 77 interviews and 20 focus groups with 223 staff, students, pupils and household members from four schools, one university, and one community healthcare NHS trust. Conversations revealed that high levels of communication, trust and convenience were necessary to ensure peoples engagement with the programme. This suggests community leaders and stakeholder organisations should be involved throughout programme development and implementation to optimise these features of the testing. Participants and stakeholders motivations, challenges and concerns need to be understood and these insights used to modify the programme in a continuous, real-time process to ensure and sustain engagement with testing over the extended period necessary.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Daniella Watson", - "author_inst": "University of Southampton" - }, - { - "author_name": "Natalia Laverty Baralle", - "author_inst": "University of Southampton" - }, - { - "author_name": "Jawahr Alagil", - "author_inst": "University of Southampton" - }, - { - "author_name": "Krithika Anil", - "author_inst": "University of Plymouth" - }, - { - "author_name": "Sandy Ciccognani", - "author_inst": "University of Southampton" - }, - { - "author_name": "Rachel Dewar-Haggart", - "author_inst": "University of Southampton" - }, - { - "author_name": "Sarah Fearn", - "author_inst": "University of Southampton" - }, - { - "author_name": "Julia Groot", - "author_inst": "University of Bath" - }, - { - "author_name": "Kathryn Knowles", - "author_inst": "University of Southampton" - }, - { - "author_name": "Claire Meagher", - "author_inst": "University of Southampton" - }, - { - "author_name": "Carmel McGrath", - "author_inst": "University of Southampton" - }, - { - "author_name": "Sarah Muir", - "author_inst": "University of Southampton" - }, - { - "author_name": "Jo Musgrove", - "author_inst": "University of Southampton" - }, - { - "author_name": "Kate Glyn-Owen", - "author_inst": "University of Southampton" - }, - { - "author_name": "Kath Woods-Townsend", - "author_inst": "University of Southampton" - }, - { - "author_name": "Andrew Mortimore", - "author_inst": "University of Southampton" - }, - { - "author_name": "Paul Roderick", - "author_inst": "University of Southampton" - }, - { - "author_name": "Janis Baird", - "author_inst": "University of Southampton" - }, - { - "author_name": "Hazel Inskip", - "author_inst": "University of Southampton" - }, - { - "author_name": "Keith Godfrey", - "author_inst": "University of Southampton" - }, - { - "author_name": "Mary Barker", - "author_inst": "University of Southampton" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.28.21250163", "rel_title": "Ultra-short-wave diathermy shortens the course of moderate and severe COVID-19: a randomized controlled trial", @@ -933985,6 +931115,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250759", + "rel_title": "Genetically predicted serum vitamin D and COVID-19: a Mendelian randomization study", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250759", + "rel_abs": "ObjectivesTo investigate causality of the association of serum vitamin D with the risk and severity of COVID-19 infection.\n\nDesignTwo-sample Mendelian randomization study.\n\nSettingSummary data from genome-wide analyses in the population-based UK Biobank and SUNLIGHT Consortium, applied to meta-analyzed results of genome-wide analyses in the COVID-19 Host Genetics Initiative.\n\nParticipants17,965 COVID-19 cases including 11,085 laboratory or physician confirmed cases, 7,885 hospitalized cases, and 4,336 severe respiratory cases, and 1,370,547 controls, primarily of European ancestry.\n\nExposuresGenetically predicted variation in serum vitamin D status, based on genome-wide significant single nucleotide polymorphisms (SNPs) associated with serum vitamin D or risk of vitamin D deficiency/insufficiency.\n\nMain outcome measuresSusceptibility to and severity of COVID-19 infection, including severe respiratory infection and hospitalization.\n\nResultsMendelian randomization analysis, powered to detect moderate effects comparable to those seen in observational studies, provided little to no evidence for an effect of genetically predicted serum vitamin D on susceptibility to or severity of COVID-19 infection. Using SNPs in loci related to vitamin D metabolism as proxies for serum vitamin D concentration, the odds ratio for a standard deviation increase in serum vitamin D was 1.04 (95% confidence interval 0.92 to 1.18) for any COVID-19 infection versus population controls, 1.05 (0.84-1.31) for hospitalized COVID-19 versus population controls, 0.96 (0.64 to 1.43) for severe respiratory COVID-19 versus population controls, 1.15 (0.99 to 1.35) for COVID-19 positive versus COVID-19 negative, and 1.44 (0.75 to 2.78) for hospitalized COVID-19 versus non-hospitalized COVID-19. Results were similar in analyses that used all SNPs with genome-wide significant associations with serum vitamin D (i.e., including SNPs in loci with no known relationship to vitamin D metabolism) and in analyses using SNPs with genome-wide significant associations with risk of vitamin D deficiency or insufficiency.\n\nConclusionsThese findings suggest that genetically predicted differences in long-term vitamin D nutritional status do not causally affect susceptibility to and severity of COVID-19 infection, and that associations observed in previous studies may have been driven by confounding. These results do not exclude the possibility of low-magnitude causal effects, nor do they preclude potential causal effects of acute responses to therapeutic doses of vitamin D. Future directions include extension of this work to non-European ancestry populations, and high-risk populations, for example persons with comorbid disease.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Bonnie K Patchen", + "author_inst": "Cornell University" + }, + { + "author_name": "Andrew G Clark", + "author_inst": "Cornell University" + }, + { + "author_name": "Nathan M Gaddis", + "author_inst": "Research Triangle Institute International" + }, + { + "author_name": "Dana B Hancock", + "author_inst": "Research Triangle Institute International" + }, + { + "author_name": "Patricia A Cassano", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.21250798", "rel_title": "Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C", @@ -934872,25 +932037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.30.21250834", - "rel_title": "Minimizing loss of life in Covid-19 in a 100 day period in the U.S.A. by age-tailored dosing and distribution of a limited vaccine supply", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250834", - "rel_abs": "BackgroundWe aimed at minimizing loss of lives in the Covid-19 pandemic in the USA by identifying optimal vaccination strategies during a 100-day period with limited vaccine supplies. While lethality is highest in the elderly, transmission and case numbers are highest in the younger. A strategy of first vaccinating the elderly is widely used, thought to protect the vulnerable, elderly best. Despite lower immunogenicity in the elderly, mRNA vaccines retain high efficacy, implying that in the younger, reduced vaccine doses might suffice, thereby increasing vaccination counts with a given vaccine supply.\n\nMethodsUsing published immunogenicity data of the Moderna mRNA-1273 vaccine, we examined the value of personalized-dose vaccination strategies, using a modeling approach incorporating age-related vaccine immunogenicity, social contact patterns, population structure, Covid-19 case and death rates in the USA in late January 2021. An increase if the number of persons that can be vaccinated and a potential reduction of the individual protective efficacy was accounted for.\n\nResultsAge-personalized dosing strategies reduced cases faster, shortening the pandemic, reducing the delay to reaching <100000 cases/day from 64 to 30 days and avoiding 25000 deaths within 100 days in the USA. In an \"elderly first\" vaccination strategy, mortality is higher even in the elderly. Findings were robust with transmission blocking efficacies of reduced dose vaccination between 30% to 90%, and with a vaccine supply from 1 to 3 million full dose vaccinations per day.\n\nConclusionRapid reduction of Covid-19 case and death rate in the USA in 100 days with a limited vaccine supply is best achieved when personalized, age-tailored dosing for highly effective vaccines is used, according to this vaccination strategy model parameterized to U.S. demographics, Covid-19 transmission and vaccine characteristics. Protecting the vulnerable is most effectively achieved by personalized-dose vaccination of all population segments, while an \"elderly first\" approach costs more lives, even in the elderly.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Patrick Hunziker", - "author_inst": "University Hospital Basel; University of Basel, Switzerland; CLINAM Foundation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.29.21250643", "rel_title": "Emergence of first strains of Sars-CoV-2 lineage B.1.1.7 in Romania", @@ -935487,6 +932633,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.27.21250570", + "rel_title": "Mapping a Pandemic: SARS-CoV-2 Seropositivity in the United States", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250570", + "rel_abs": "Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population (n = 11,382) and who had not previously been diagnosed with COVID-19 were selected by quota sampling from 241,424 volunteers (ClinicalTrials.gov NCT04334954). Enrolled participants provided medical, geographic, demographic, and socioeconomic information and 9,028 blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. Samples were analyzed via ELISA for anti-Spike and anti-RBD antibodies. Estimation of seroprevalence was performed by using a weighted analysis to reflect the US population. We detected an undiagnosed seropositivity rate of 4.6% (95% CI: 2.6 - 6.5%). There was distinct regional variability, with heightened seropositivity in locations of early outbreaks. Subgroup analysis demonstrated that the highest estimated undiagnosed seropositivity within groups was detected in younger participants (ages 18-45, 5.9%), females (5.5%), Black/African American (14.2%), Hispanic (6.1%), and Urban residents (5.3%), and lower undiagnosed seropositivity in those with chronic diseases. During the first wave of infection over the spring/summer of 2020 an estimate of 4.6% of adults had a prior undiagnosed SARS-CoV-2 infection. These data indicate that there were 4.8 (95% CI: 2.8-6.8) undiagnosed cases for every diagnosed case of COVID-19 during this same time period in the United States, and an estimated 16.8 million undiagnosed cases by mid-July 2020.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Heather Kalish", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Carleen Klumpp-Thomas", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sally Hunsberger", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Holly Ann Baus", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Michael P Fay", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nalyn Siripong", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Jing Wang", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Jennifer Hicks", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jennifer Mehalko", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Jameson Travers", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Matthew Drew", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Kyle Pauly", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jacquelyn Spathies", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tran Ngo", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Kenneth M Adusei", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Maria Karkanitsa", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jennifer A Croker", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Yan Li", + "author_inst": "University of Maryland at College Park" + }, + { + "author_name": "Barry I Graubard", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Lindsay Czajkowski", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Olivia Belliveau", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Cheryl Chairez", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Kelly Snead", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Peter Frank", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Anandakumar Shunmugavel", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Alison Han", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Luca T Giurgea", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Luz Angela Rosas", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Rachel Bean", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Rani Athota", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Adriana Cervantes-Medina", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Monica Gouzoulis", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Brittany Heffelfinger", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Shannon Valenti", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Rocco Caldararo", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Michelle M Kolberg", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Andrew Kelly", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Reid Simon", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Saifullah Shafiq", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Vanessa Wall", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Susan Reed", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Eric W Ford", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Ravi Lokwani", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "John-Paul Denson", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Simon Messing", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Sam G Michael", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "William Gillette", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Robert P Kimberly", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Steven E Reis", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Matthew D Hall", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Matthew J Memoli", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Kaitlyn Sadtler", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250564", "rel_title": "Point-of-Care CRISPR-Cas-Assisted SARS-CoV-2 Detection in an Automated and Mobile Droplet Magnetofluidic Device", @@ -936754,145 +934127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.01.27.21250593", - "rel_title": "Post-Mendelian genetic model in COVID-19", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250593", - "rel_abs": "Host genetics is an emerging theme in COVID-19 and few common polymorphisms and some rare variants have been identified, either by GWAS or candidate gene approach, respectively. However, an organic model is still missing. Here, we propose a new model that takes into account common and rare germline variants applied in a cohort of 1,300 Italian SARS-CoV-2 positive individuals. Ordered logistic regression of clinical WHO grading on sex and age was used to obtain a binary phenotypic classification. Genetic variability from WES was synthesized in several boolean representations differentiated according to allele frequencies and genotype effect. LASSO logistic regression was used for extracting relevant genes. We defined about 100 common driver polymorphisms corresponding to classical \"threshold model\". Extracted genes were demonstrated to be gender specific. Stochastic rare more penetrant events on about additional 100 extracted genes, when occurred in a medium or severe background (common within the family), simulate Mendelian inheritance in 14% of subjects (having only 1 mutation) or oligogenic inheritance (in 10% having 2 mutations, in 11% having 3 mutations, etc).\n\nThe combined effect of common and rare results can be described as an integrated polygenic score computed as: (nseverity - nmildness) + F (mseverity - mmildness)\n\nwhere n is the number of common driver genes, m is the number of driver rare variants and F is a factor for appropriately weighing the more powerful rare variants. We called the model \"post-Mendelian\". The model well describes the cohort, and patients are clustered in severe or mild by the integrated polygenic scores, the F factor being calibrated around 2, with a prediction capacity of 65% in males and 70% in females. In conclusion, this is the first comprehensive model interpreting host genetics in a holistic post-Mendelian manner. Further validations are needed in order to consolidate and refine the model which however holds true in thousands of SARS-CoV-2 Italian subjects.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Nicola Picchiotti", - "author_inst": "University of Siena, DIISM-SAILAB, Siena, Italy; Department of Mathematics, University of Pavia, Pavia, Italy" - }, - { - "author_name": "Elisa Benetti", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Chiara Fallerini", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Sergio Daga", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Margherita Baldassarri", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Francesca Fava", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy; Genetica" - }, - { - "author_name": "Kristina Zguro", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Floriana Valentino", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Gabriella Doddato", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Annarita Giliberti", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Rossella Tita", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Sara Amitrano", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Mirella Bruttini", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy; Genetica" - }, - { - "author_name": "Laura Di Sarno", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Nicola Iuso", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Diana Alaverdian", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Giada Beligni", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Susanna Croci", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Ilaria Meloni", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Anna Maria Pinto", - "author_inst": "Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy" - }, - { - "author_name": "Chiara Gabbi", - "author_inst": "Independent Medical Scientist, Milan, Italy" - }, - { - "author_name": "Stefano Ceri", - "author_inst": "Politecnico di Milano, DEIB, Milano, Italy" - }, - { - "author_name": "Antonio Esposito", - "author_inst": "Politecnico di Milano, DEIB, Milano, Italy" - }, - { - "author_name": "Pietro Pinoli", - "author_inst": "Politecnico di Milano, DEIB, Milano, Italy" - }, - { - "author_name": "Francis P. Crawley", - "author_inst": "Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review-Europe (SIDCER), Leuven, Belgium." - }, - { - "author_name": "Elisa Frullanti", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy" - }, - { - "author_name": "Francesca Mari", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy; Genetica" - }, - { - "author_name": "- GEN-COVID Multicenter Study", - "author_inst": "" - }, - { - "author_name": "Marco Gori", - "author_inst": "University of Siena, DIISM-SAILAB, Siena, Italy; Universite Cote d Azur, Inria, CNRS, I3S, Maasai" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Medical Genetics, University of Siena, Italy; Genetica" - }, - { - "author_name": "Simone Furini", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.01.27.21250238", "rel_title": "Disentangling the association of hydroxychloroquine treatment with mortality in Covid-19 hospitalized patients through Hierarchical Clustering", @@ -937553,6 +934787,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.27.21249817", + "rel_title": "Multinational Prevalence of Neurological Phenotypes in Patients Hospitalized with COVID-19", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21249817", + "rel_abs": "OBJECTIVENeurological complications can worsen outcomes in COVID-19. We defined the prevalence of a wide range of neurological conditions among patients hospitalized with COVID-19 in geographically diverse multinational populations.\n\nMETHODSUsing electronic health record (EHR) data from 348 participating hospitals across 6 countries and 3 continents between January and September 2020, we performed a cross-sectional study of hospitalized adult and pediatric patients with a positive SARS-CoV-2 reverse transcription polymerase chain reaction test, both with and without severe COVID-19. We assessed the frequency of each disease category and 3-character International Classification of Disease (ICD) code of neurological diseases by countries, sites, time before and after admission for COVID-19, and COVID-19 severity.\n\nRESULTSAmong the 35,177 hospitalized patients with SARS-CoV-2 infection, there was increased prevalence of disorders of consciousness (5.8%, 95% confidence interval [CI]: 3.7%-7.8%, pFDR<.001) and unspecified disorders of the brain (8.1%, 95%CI: 5.7%-10.5%, pFDR<.001), compared to pre-admission prevalence. During hospitalization, patients who experienced severe COVID-19 status had 22% (95%CI: 19%-25%) increase in the relative risk (RR) of disorders of consciousness, 24% (95%CI: 13%-35%) increase in other cerebrovascular diseases, 34% (95%CI: 20%-50%) increase in nontraumatic intracranial hemorrhage, 37% (95%CI: 17%-60%) increase in encephalitis and/or myelitis, and 72% (95%CI: 67%-77%) increase in myopathy compared to those who never experienced severe disease.\n\nINTERPRETATIONUsing an international network and common EHR data elements, we highlight an increase in the prevalence of central and peripheral neurological phenotypes in patients hospitalized with SARS-CoV-2 infection, particularly among those with severe disease.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Trang T Le", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Alba Guti\u00e9rrez-Sacrist\u00e1n", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jiyeon Son", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Chuan Hong", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Andrew M South", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Brett K Beaulieu-Jones", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Ne Hooi Will Loh", + "author_inst": "National University Health Systems Singapore" + }, + { + "author_name": "Yuan Luo", + "author_inst": "Northwestern University" + }, + { + "author_name": "Michele Morris", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kee Yuan Ngiam", + "author_inst": "National University Health Systems Singapore" + }, + { + "author_name": "Lav P Patel", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Malarkodi J Samayamuthu", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Emily Schriver", + "author_inst": "University of Pennsylvania Health System" + }, + { + "author_name": "Amelia LM Tan", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jason Moore", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Tianxi Cai", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Gilbert S. Omenn", + "author_inst": "University of Michigan" + }, + { + "author_name": "Paul Avillach", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Isaac S Kohane", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "- The Consortium for Clinical Characterization of COVID-19 by EHR (4CE)", + "author_inst": "" + }, + { + "author_name": "Shyam Visweswaran", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Danielle L Mowery", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Zongqi Xia", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.01.28.21250673", "rel_title": "Is vitamin D deficiency associated with the COVID-19 epidemic in Europe?", @@ -938280,41 +935621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.26.21250065", - "rel_title": "The Experience of Two Independent Schools with In-Person Learning During the COVID-19 Pandemic", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250065", - "rel_abs": "BACKGROUNDIn 2020, U.S schools closed due to SARS-CoV-2 but their role in transmission was unknown. In fall 2020, national guidance for reopening omitted testing or screening recommendations. We report the experience of 2 large independent K-12 schools (School-A and School-B) that implemented an array of SARS-CoV-2 mitigation strategies that included periodic universal testing.\n\nMETHODSSARS-CoV-2 was identified through periodic universal PCR testing, self-reporting of tests conducted outside school, and contact tracing. Schools implemented behavioral and structural mitigation measures, including mandatory masks, classroom disinfecting, and social distancing.\n\nRESULTSOver the fall semester, School-A identified 112 cases in 2320 students and staff; School-B identified 25 cases (2.0%) in 1200 students and staff. Most cases were asymptomatic and none required hospitalization. Of 69 traceable introductions, 63(91%) were not associated with school-based transmission, 59 cases (54%) occurred in the 2 weeks post-Thanksgiving. In 6/7 clusters, clear noncompliance with mitigation protocols was found. The largest outbreak had 28 identified cases and was traced to an off-campus party. There was no transmission from students to staff.\n\nCONCLUSIONSAlthough school-age children can contract and transmit SARS-CoV-2, rates of COVID-19 infection related to in-person education were significantly lower than those in the surrounding community. However, social activities among students outside of school undermined those measures and should be discouraged, perhaps with behavioral contracts, to ensure the safety of school communities. In addition, introduction risks were highest following extended school breaks. These risks may be mitigated with voluntary quarantines and surveillance testing prior to re-opening.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Darria Long Gillespie", - "author_inst": "University of Tennessee at Erlanger Hospital Chattanooga" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "Santa Fe Institute" - }, - { - "author_name": "Stephen C Redd", - "author_inst": "Private Citizen" - }, - { - "author_name": "Jonathan M Zenilman", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.27.21250521", "rel_title": "Induction of labour during the COVID-19 pandemic: a national survey of impact on practice in the UK", @@ -938987,6 +936293,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.28.428743", + "rel_title": "Development of spike receptor-binding domain nanoparticle as a vaccine candidate against SARS-CoV-2 infection in ferrets", + "rel_date": "2021-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.28.428743", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of COVID-19 pandemic, enters host cells via the interaction of its Receptor-Binding Domain (RBD) of Spike protein with host Angiotensin-Converting Enzyme 2 (ACE2). Therefore, RBD is a promising vaccine target to induce protective immunity against SARS-CoV-2 infection. In this study, we report the development of RBD protein-based vaccine candidate against SARS-CoV-2 using self-assembling H. pylori-bullfrog ferritin nanoparticles as an antigen delivery. RBD-ferritin protein purified from mammalian cells efficiently assembled into 24-mer nanoparticles. 16-20 months-old ferrets were vaccinated with RBD-ferritin nanoparticles (RBD-nanoparticles) by intramuscular or intranasal inoculation. All vaccinated ferrets with RBD-nanoparticles produced potent neutralizing antibodies against SARS-CoV-2. Strikingly, vaccinated ferrets demonstrated efficient protection from SARS-CoV-2 challenge, showing no fever, body weight loss and clinical symptoms. Furthermore, vaccinated ferrets showed rapid clearance of infectious viruses in nasal washes and lungs as well as viral RNA in respiratory organs. This study demonstrates the Spike RBD-nanoparticle as an effective protein vaccine candidate against SARS-CoV-2.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Young-Il Kim", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Dokyun Kim", + "author_inst": "Cleveland Clinic Lerner Research Institute" + }, + { + "author_name": "Kwang-Min Yu", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Hogyu David Seo", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Shin-Ae Lee", + "author_inst": "Cleveland Clinic Lerner College of Medicine" + }, + { + "author_name": "Mark Anthony B. Casel", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Seung-Gyu Jang", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Stephanie Kim", + "author_inst": "Cleveland Clinic Lerner Research Institute" + }, + { + "author_name": "WooRam Jung", + "author_inst": "Cleveland Clinic Lerner Research Institute" + }, + { + "author_name": "Chih-Jen Lai", + "author_inst": "Cleveland Clinic Lerner Research Institute" + }, + { + "author_name": "Young Ki Choi", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Jae U. Jung", + "author_inst": "Lerner Research Institute, Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.29.428535", "rel_title": "Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility", @@ -940134,69 +937503,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.20.21249279", - "rel_title": "A flexible, pan-species, multi-antigen platform for the detection and monitoring of SARS-CoV-2-specific antibody responses", - "rel_date": "2021-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21249279", - "rel_abs": "The SARS-CoV-2 pandemic and the vaccination effort that is ongoing has created an unmet need for accessible, affordable, flexible and precise platforms for monitoring the induction, specificity and maintenance of virus-specific immune responses. Herein we validate a multiplex (Luminex-based) assay capable of detecting SARS-CoV-2-specific antibodies irrespective of host species, antibody isotype, and specimen type (e.g. plasma, serum, saliva or blood spots). The well-established precision of Luminex-based assays provides the ability to follow changes in antibody levels over time to many antigens, including multiple permutations of the most common SARS-CoV-2 antigens. This platform can easily measure antibodies known to correlate with neutralization activity as well as multiple non-SARS-CoV-2 antigens such as vaccines (e.g. Tetanus toxoid) or those from frequently encountered agents (influenza), which serve as stable reference points for quantifying the changing SARS-specific responses. All of the antigens utilized in our study can be made in-house, many in E. coli using readily available plasmids. Commercially sourced antigens may also be incorporated and newly available antigen variants can be rapidly produced and integrated, making the platform adaptable to the evolving viral strains in this pandemic.\n\nBrief SummaryA multi-antigen assay for monitoring SARS-CoV-2-specific antibodies irrespective of host species, antibody isotype, and specimen type was developed.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Huifeng Shen", - "author_inst": "University of Georgia" - }, - { - "author_name": "David Forgacs", - "author_inst": "University of Georgia" - }, - { - "author_name": "Digantkumar Chapla", - "author_inst": "University of Georgia" - }, - { - "author_name": "Kelley W Moreman", - "author_inst": "University of Georgia" - }, - { - "author_name": "Lance Wells", - "author_inst": "University of Georgia" - }, - { - "author_name": "Sarah A Hamer", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Stephen M Tompkins", - "author_inst": "University of Georgia" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University of Georgia" - }, - { - "author_name": "Nadine Rouphael", - "author_inst": "Emory University" - }, - { - "author_name": "Srilatha Edupuganti", - "author_inst": "Emory University" - }, - { - "author_name": "Matthew H Collins", - "author_inst": "Emory University" - }, - { - "author_name": "Rick Tarleton", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.26.21250506", "rel_title": "The Association Between Hypoglycemic Agents and Clinical Outcomes of COVID-19 in Patients with Diabetes: A Systematic Review and Meta-Analysis", @@ -941017,6 +938323,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.27.428428", + "rel_title": "Efficacy of GC-376 against SARS-CoV-2 virus infection in the K18 hACE2 transgenic mouse model", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428428", + "rel_abs": "The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the defining global health emergency of this century. GC-376 is a Mpro inhibitor with antiviral activity against SARS-CoV-2 in vitro. Using the K18-hACE2 mouse model, the in vivo antiviral efficacy of GC-376 against SARS-CoV-2 was evaluated. GC-376 treatment was not toxic in K18-hACE2 mice and produced milder tissue lesions, reduced viral loads, fewer presence of viral antigen, and reduced inflammation in comparison to vehicle-treated controls, most notably in the brain in mice challenged with a low virus dose. Although GC-376 was not sufficient to improve neither clinical symptoms nor survival, it did show a positive effect against SARS-CoV-2 in vivo. This study supports the notion that the K18-hACE2 mouse model is suitable to study antiviral therapies against SARS-CoV-2, and GC-376 represents a promising lead candidate for further development to treat SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "C. Joaquin Caceres", + "author_inst": "University of Georgia" + }, + { + "author_name": "Stivalis Cardenas-Garcia", + "author_inst": "University of Georgia" + }, + { + "author_name": "Silvia Carnaccini", + "author_inst": "University of Georgia" + }, + { + "author_name": "Brittany Seibert", + "author_inst": "University of Georgia" + }, + { + "author_name": "Daniela S Rajao", + "author_inst": "University of Georgia" + }, + { + "author_name": "Jun Wang", + "author_inst": "The University of Arizona" + }, + { + "author_name": "Daniel R Perez", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.26.428356", "rel_title": "Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain", @@ -941904,33 +939253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21250215", - "rel_title": "Data Driven High Resolution Modeling and Spatial Analyses of the COVID-19 Pandemic in Germany", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250215", - "rel_abs": "The SARS-CoV-2 virus has spread around the world with over 90 million infections to date, and currently many countries are fighting the second wave of infections. With neither sufficient vaccination capacity nor effective medication, non-pharmaceutical interventions (NPIs) remain the measure of choice. However, NPIs place a great burden on society, the mental health of individuals, and economics. Therefore the cost/benefit ratio must be carefully balanced and a target-oriented small-scale implementation of these NPIs could help achieve this balance. To this end, we introduce a modified SEIR-class compartment model and parametrize it locally for all 412 districts of Germany. The NPIs are modeled at district level by time varying contact rates. This high spatial resolution makes it possible to apply geostatistical methods to analyse the spatial patterns of the pandemic in Germany and to compare the results of different spatial resolutions. We find that the modified SEIR model can successfully be fitted to the COVID-19 cases in German districts, states, and also nationwide. We propose the correlation length as a further measure, besides the weekly incidence rates, to describe the current situation of the epidemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lennart Sch\u00fcler", - "author_inst": "University Potsdam" - }, - { - "author_name": "Justin M. Calabrese", - "author_inst": "Center for Advanced Systems Understanding" - }, - { - "author_name": "Sabine Attinger", - "author_inst": "Helmholtz Centre for Environmental Research -- UFZ" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.21.21249496", "rel_title": "Management of conductive deafness from Otitis Media with Effusion (known as glue ear) in children using bone conduction headsets when grommet operations were unavailable during COVID-19.", @@ -942555,6 +939877,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.22.21250308", + "rel_title": "Projected spread of COVID-19's second wave in South Africa under different levels of lockdown", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250308", + "rel_abs": "South Africa is currently experiencing a second wave of resurgence in COVID-19 infection. In this modelling study, we use a Bayesian compartmental model to project possible spread of the second wave of COVID-19 in South Africa under various levels of lockdown restrictions. Our model suggests that strict lockdown restrictions will have to be in place up to the end of March 2021 before cases can drop to levels observed, in September to early November 2020, after the first wave. On the one hand, extended lockdown restrictions have negative consequences - albeit effective, they are not sustainable over extended periods. On the other hand, short lockdown restrictions over a few weeks will not have a lasting effect on the spread of the disease. Lockdown restrictions need to be supplemented with increased rapid testing, palliative support for the vulnerable, and implementations of other non-pharmaceutical interventions (NPIs) such as mask mandate. These multifaceted approaches could help keep cases under control until vaccines are widely available.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Elisha B Are", + "author_inst": "Stellenbosch University" + }, + { + "author_name": "Caroline B Colijn", + "author_inst": "Simon Fraser University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.22.21250120", "rel_title": "Estimating COVID-19 Cases on University Campuses Prior To Semester", @@ -943742,101 +941087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.22.21250321", - "rel_title": "Factors influencing nursing students' intention to accept COVID-19 vaccination - A pooled analysis of seven countries", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250321", - "rel_abs": "Experiencing the second wave of COVID-19 pandemic, high vaccination coverage by a safe and effective vaccine globally would be a great achievement. Acceptance of vaccination by healthcare students is an important issue as they have a key role as future professionals in educating patients, informing and guiding them to the right clinical decision. The aim of this study was to explore the intention of nursing students to get vaccinated for SARS-CoV-2 infection and the factors acting either as motivators or barriers towards vaccination. A multicenter cross-sectional study was conducted in 7 countries (Greece, Albania, Cyprus, Spain, Italy, Czech Republic and Kosovo) through a web survey. In total 2249 undergraduate nursing students participated. Forty three point eight percent of students agreed to accept a safe and effective COVID-19 vaccine, while the acceptance was higher among Italian students. The factors for intention to get vaccinated were male gender (p=0.008), no working experience in healthcare facilities during the pandemic (p=0.001), vaccination for influenza in 2019 and 2020 (p<0.001), trust in doctors (p<0.001), governments and experts (p=0.012), high level of knowledge (p<0.001) and fear of COVID-19 (p<0.001). Understanding of factors that influence students decision to accept COVID-19 vaccination could increase the acceptance rate contributing to a management of the pandemic.\n\nHighlightsO_LILess than half of the sample intended to accept COVID-19 vaccination\nC_LIO_LIFactors that influenced nursing students to get vaccinated against COVID-19 were male gender, no working experience in healthcare facilities during the pandemic, vaccination for influenza in 2019 and 2020, trust in doctors, governments and experts, high level of knowledge and fear of COVID-19.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Evridiki Patelarou", - "author_inst": "Hellenic Mediterranean University" - }, - { - "author_name": "Petros Galanis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Enkeleint A Mechili", - "author_inst": "University of Vlora" - }, - { - "author_name": "Agathi Argyriadi", - "author_inst": "Frederick University" - }, - { - "author_name": "Alexandros Argyriadis", - "author_inst": "Frederick University" - }, - { - "author_name": "Evanthia Asimakopoulou", - "author_inst": "Frederick University" - }, - { - "author_name": "Stiliana Brokaj", - "author_inst": "University of Vlora" - }, - { - "author_name": "Jorgjia Bucaj", - "author_inst": "University of Vlora" - }, - { - "author_name": "Juan Manuel Carmona-Torres", - "author_inst": "University of Castilla-La Mancha" - }, - { - "author_name": "Ana Isabel Cobo-Cuenca", - "author_inst": "University of Castilla-La Mancha" - }, - { - "author_name": "Jakub Dolezel", - "author_inst": "University of Ostrava" - }, - { - "author_name": "Stefano Finotto", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Darja Jarosov", - "author_inst": "University of Ostrava" - }, - { - "author_name": "Athina Kalokairinou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Daniela Mecugni", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Velide Pulomenaj", - "author_inst": "AAB College" - }, - { - "author_name": "Aurela Saliaj", - "author_inst": "University of Vlora" - }, - { - "author_name": "Idriz Sopjani", - "author_inst": "AAB College" - }, - { - "author_name": "Majlinda Zahaj", - "author_inst": "University of Vlora" - }, - { - "author_name": "Athina Patelarou", - "author_inst": "Hellenic Mediterranean University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.23.21250370", "rel_title": "Patients with Asthma and Chronic Obstructive Pulmonary Disease (COPD) have increased levels of plasma inflammatory mediators upregulated in severe COVID-19", @@ -944633,6 +941883,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.24.21250074", + "rel_title": "Adaptive immunity to human coronaviruses is widespread but low in magnitude", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250074", + "rel_abs": "Endemic human coronaviruses (hCoV) circulate worldwide but cause minimal mortality. Although seroconversion to hCoV is near ubiquitous during childhood, little is known about hCoV-specific T cell memory in adults. We quantified CD4 T cell and antibody responses to hCoV spike antigens in 42 SARS-CoV-2 uninfected individuals. T cell responses were widespread within conventional memory and cTFH compartments but did not correlate with IgG titres. SARS-CoV-2 cross-reactive T cells were observed in 48% of participants and correlated with HKU1 memory. hCoV-specific T cells exhibited a CCR6+ central memory phenotype in the blood, but were enriched for frequency and CXCR3 expression in human lung draining lymph nodes. Overall, hCoV-specific humoral and cellular memory are independently maintained, with a shared phenotype existing among coronavirus-specific CD4 T cells. This understanding of endemic coronavirus immunity provides insight into the homeostatic maintenance of immune responses that are likely to be critical components of protection against SARS-CoV-2.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Hyon-Xhi Tan", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Wen Shi Lee", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Kathleen M Wragg", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Christina Nelson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Robyn Esterbauer", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Hannah G Kelly", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Thakshila Amarasena", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Robert M Jones", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "Graham Starkey", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "Bao Zhong Wang", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "Osamu Yoshino", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "Thomas Tiang", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "M Lindsay Grayson", + "author_inst": "Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "Helen Opdam", + "author_inst": "Department of Intensive Care Medicine, Austin Health, Melbourne, VIC, Australia" + }, + { + "author_name": "Angela Vago", + "author_inst": "Department of Surgery, Austin Health, Heidelberg, VIC, Australia." + }, + { + "author_name": "- The Austin Liver Transplant Perfusionist Group", + "author_inst": "" + }, + { + "author_name": "Laura K Mackay", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Claire L Gordon", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Adam K Wheatley", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Stephen J Kent", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + }, + { + "author_name": "Jennifer A Juno", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty institute for Infection and Immunity, Melbourne, VIC, Australia." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.25.20230094", "rel_title": "Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data", @@ -945520,85 +942869,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.26.428212", - "rel_title": "A novel SARS-CoV-2 related coronavirus in bats from Cambodia", - "rel_date": "2021-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428212", - "rel_abs": "Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Vibol Hul", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - }, - { - "author_name": "Deborah Delaune", - "author_inst": "Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France." - }, - { - "author_name": "Erik A. Karlsson", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - }, - { - "author_name": "Alexandre Hassanin", - "author_inst": "Institut de Systematique, evolution, Biodiversite, Sorbonne Universite, MNHN, CNRS, EPHE, UA, Paris, France." - }, - { - "author_name": "Putita Ou Tey", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - }, - { - "author_name": "Artem Baidaliuk", - "author_inst": "Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France." - }, - { - "author_name": "Fabiana Gambaro", - "author_inst": "Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France." - }, - { - "author_name": "Vuong Tan Tu", - "author_inst": "Institut de Systematique, evolution, Biodiversite, Sorbonne Universite, MNHN, CNRS, EPHE, UA, Paris, France." - }, - { - "author_name": "Lucy Keatts", - "author_inst": "Wildlife Conservation Society, Health Program, Bronx, NY, USA." - }, - { - "author_name": "Jonna Mazet", - "author_inst": "One Health Institute, School of Veterinary Medicine, University of California, Davis, USA" - }, - { - "author_name": "Christine Johnson", - "author_inst": "One Health Institute, School of Veterinary Medicine, University of California, Davis, USA" - }, - { - "author_name": "Philippe Buchy", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - }, - { - "author_name": "Philippe Dussart", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - }, - { - "author_name": "Tracey Goldstein", - "author_inst": "One Health Institute, School of Veterinary Medicine, University of California, Davis, USA" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France." - }, - { - "author_name": "Veasna Duong", - "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.25.428191", "rel_title": "Variant and mutation analysis of SARS-CoV-2 genomes isolated from the Kingdom of Bahrain", @@ -946263,6 +943533,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.19.21250097", + "rel_title": "Contact patterns before and during the UK's Autumn 2020 COVID-19 lockdown among university students and staff", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250097", + "rel_abs": "IntroductionUK universities re-opened in September 2020, despite the on-going coronavirus epidemic. During the first term, various national social distancing measures were introduced, including banning groups of >6 people and the second lockdown in November. COVID-19 can spread rapidly in university-settings, and students adherence to social distancing measures is critical for controlling transmission.\n\nMethodsWe measured university staff and student contact patterns via an online, longitudinal survey capturing self-reported contacts on the previous day. We investigated the change in contacts associated with COVID-19 guidance periods: post-first lockdown (23/06/2020-03/07/2020), relaxed guidance period (04/07/2020-13/09/2020), \"rule-of-six\" period (14/09/2020-04/11/2020), and the second lockdown (05/11/2020-25/11/2020).\n\nResults722 staff (4199 responses) (mean household size: 2.6) and 738 students (1906 responses) (mean household size: 4.5) were included in the study. Contact number decreased with age. Staff in single-person households reported fewer contacts than individuals in 2-and 3-person households, and individuals in 4-and 5-person households reported more contacts.\n\nFor staff, daily contacts were higher in the relaxed guidance and \"rule-of-six\" periods (means: 3.2 and 3.5, respectively; medians: 3) than the post-first lockdown and second lockdown periods (means: 4.5 and 5.4, respectively; medians: 2). Few students responded until 05/10/2020, after which the median student contacts was 2 and the mean was 5.7, until the second lockdown when it dropped to 3.1.\n\nDiscussionUniversity staff and students responded to national guidance by altering their social contacts. The response in staff and students was similar, suggesting that students are able to adhere to social distancing guidance while at university.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Finn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Caroline Relton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Clara Montgomery", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gibran Hemani", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jane Metz", + "author_inst": "University of Bristol" + }, + { + "author_name": "Josephine G Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Katy Turner", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachel Kwiatkowska", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Sauchelli", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "University of Exeter" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.20.21250195", "rel_title": "Integrating Operant and Cognitive Behavioral Economics to Inform Infectious Disease Response: Prevention, Testing, and Vaccination in the COVID-19 Pandemic", @@ -947330,41 +944675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.23.21250376", - "rel_title": "Predictive power of SARS-CoV-2 wastewater surveillance for diverse populations across a large geographical range", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250376", - "rel_abs": "The COVID-19 pandemic has exacerbated the disparities in healthcare delivery in the US. Many communities had, and continue to have, limited access to COVID-19 testing, making it difficult to track the spread and impact of COVID-19 in early days of the outbreak. To address this issue we monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA at the population-level using municipal wastewater influent from 19 cities across the state of Minnesota during the COVID-19 outbreak in Summer 2020. Viral RNA was detected in wastewater continually for 20-weeks for cities ranging in populations from 500 to >1, 000, 000. Using a novel indexing method, we were able to compare the relative levels of SARS-CoV-2 RNA for each city during this sampling period. Our data showed that viral RNA trends appeared to precede clinically confirmed cases across the state by several days. Lag analysis of statewide trends confirmed that wastewater SARS-CoV-2 RNA levels preceded new clinical cases by 15-17 days. At the regional level, new clinical cases lagged behind wastewater viral RNA anywhere from 4-20 days. Our data illustrates the advantages of monitoring at the population-level to detect outbreaks. Additionally, by tracking infections with this unbiased approach, resources can be directed to the most impacted communities before the need outpaces the capacity of local healthcare systems.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Richard G Melvin", - "author_inst": "University of Minnesota Medical School, Duluth Campus" - }, - { - "author_name": "Nabiha Chaudhry", - "author_inst": "University of Minnesota Medical School, Duluth Campus" - }, - { - "author_name": "Onimitein Georgewill", - "author_inst": "University of Maryland, College Park" - }, - { - "author_name": "Rebecca Freese", - "author_inst": "University of Minnesota Clinical and Translational Science Institute" - }, - { - "author_name": "Glenn E Simmons Jr.", - "author_inst": "University of Minnesota Medical School, Duluth Campus" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.21.21250226", "rel_title": "Determinants of the incidence and mortality rates of COVID-19 during the first six months of the pandemic; A cross-country study", @@ -948313,6 +945623,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.23.21249978", + "rel_title": "Do Not Attempt Resuscitation (DNAR) status in people with suspected COVID-19: Secondary analysis of the PRIEST observational cohort study", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21249978", + "rel_abs": "BackgroundCardiac arrest is common in people admitted with suspected COVID-19 and has a poor prognosis. Do Not Attempt Resuscitation (DNAR) orders can reduce the risk of futile resuscitation attempts but have raised ethical concerns.\n\nObjectivesWe aimed to describe the characteristics and outcomes of adults admitted to hospital with suspected COVID-19 according to their DNAR status and identify factors associated with an early DNAR decision.\n\nMethodsWe undertook a secondary analysis of 13977 adults admitted to hospital with suspected COVID-19 and included in the Pandemic Respiratory Infection Emergency System Triage (PRIEST) study. We recorded presenting characteristics and outcomes (death or organ support) up to 30 days. We categorised patients as early DNAR (occurring before or on the day of admission) or late/no DNAR (no DNAR or occurring after the day of admission). We undertook descriptive analysis comparing these groups and multivariable analysis to identify independent predictors of early DNAR.\n\nResultsWe excluded 1249 with missing DNAR data, and identified 3929/12748 (31%) with an early DNAR decision. They had higher mortality (40.7% v 13.1%) and lower use of any organ support (11.6% v 15.7%), but received a range of organ support interventions, with some being used at rates comparable to those with late or no DNAR (e.g. non-invasive ventilation 4.4% v 3.5%). On multivariable analysis, older age (p<0.001), active malignancy (p<0.001), chronic lung disease (p<0.001), limited performance status (p<0.001), and abnormal physiological variables were associated with increased recording of early DNAR. Asian ethnicity was associated with reduced recording of early DNAR (p=0.001).\n\nConclusionsEarly DNAR decisions were associated with recognised predictors of adverse outcome, and were inversely associated with Asian ethnicity. Most people with an early DNAR decision survived to 30 days and many received potentially life-saving interventions.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laura Sutton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Benjamin Thomas", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sarah Connelly", + "author_inst": "University of Sheffield" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.01.22.21250346", "rel_title": "Prevalent comorbidities among young and underprivileged: Death portrait of COVID-19 among 235 555 hospitalized patients in Brazil", @@ -949248,37 +946589,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.01.24.427939", - "rel_title": "In silico investigation of the new UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 variants with a focus at the ACE2-Spike RBD interface", - "rel_date": "2021-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.24.427939", - "rel_abs": "SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor and several in silico methods to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both UK and South African strains) should be favorable for the interaction with ACE2 while the K417N and E484K substitutions (South African) would seem unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the predicted less favorable (regarding binding) K417N and E484K Spike replacements. Our finding suggests that, if indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions outside the direct Spike-ACE2 interface.\n\nHihglightsO_LITransmission of the UK and possibly South African SARS-CoV-2 strains appears substantially increased compared to other variants\nC_LIO_LIThis could be due, in part, to increased affinity between the variant Spike proteins and ACE2\nC_LIO_LIWe investigated in silico the 3D structure of the Spike-ACE2 complex with a focus on Spike K417N, E484K and N501Y\nC_LIO_LIThe N501Y substitution is predicted to increase the affinity toward ACE2 (UK strain) with subsequent enhanced transmissibility and possibly pathogenicity\nC_LIO_LIAdditional substitutions at positions 417 and 484 (South African strain) may pertub the interaction with ACE2 raising questions about transmissibility and pathogenicity\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Bruno Villoutreix", - "author_inst": "Inserm" - }, - { - "author_name": "Vincent Calvez", - "author_inst": "APHP, Pitie Salpetriere Hospital" - }, - { - "author_name": "Anne-Genevieve Marcelin", - "author_inst": "Pitie-Salpetriere hospital" - }, - { - "author_name": "Abdel-Majid Khatib", - "author_inst": "INSERM, LAMC, UMR 1029, Allee Geoffroy St Hilaire, Pessac, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.23.427885", "rel_title": "Variation analysis of SARS-CoV-2 complete sequences from Iran", @@ -949919,6 +947229,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.01.16.21249956", + "rel_title": "Clinical effectiveness of convalescent plasma in hospitalized patients with COVID-19: a systematic review and meta-analysis", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.16.21249956", + "rel_abs": "Given the variability of previously reported results, this systematic review aims to determine the clinical effectiveness of convalescent plasma employed in the treatment of hospitalized patients with diagnosis of COVID-19.\n\nWe conducted a systematic review of controlled clinical trials assessing treatment with convalescent plasma for hospitalized patients with a diagnosis of SARS-CoV-2 infection. The outcomes were mortality, clinical improvement, and ventilation requirement.\n\nA total of 50 studies were retrieved from the databases. Four articles were finally included in the data extraction, qualitative and quantitative synthesis of results. The meta-analysis suggests that there is no benefit of convalescent plasma compared to standard care or placebo in the reduction of the overall mortality and in the ventilation requirement; but there could be a benefit for the clinical improvement in patients treated with plasma.\n\nWe can conclude that the convalescent plasma transfusion cannot reduce the mortality or ventilation requirement in hospitalized patients diagnosed with SARS-CoV-2 infection. More controlled clinical trials conducted with methodologies that ensure a low risk of bias are still needed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Roberto Ariel Abeldano Zuniga", + "author_inst": "University of Sierra Sur" + }, + { + "author_name": "Ruth Ana Maria Gonzalez Villoria", + "author_inst": "University of Sierra Sur" + }, + { + "author_name": "Maria Vanesa Elizondo", + "author_inst": "Catholic University of Cuyo" + }, + { + "author_name": "Anel Yaneli Nicolas Osorio", + "author_inst": "University of Sierra Sur" + }, + { + "author_name": "Silvia Mercedes Coca", + "author_inst": "University of Sierra Sur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.21.20245795", "rel_title": "Longitudinal trends and risk factors for depressed mood among Canadian adults during the first wave of COVID-19", @@ -950646,121 +947991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.22.427775", - "rel_title": "Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh", - "rel_date": "2021-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427775", - "rel_abs": "Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Pallavali Roja Rani", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Mohamed Imran", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "J. Vijaya Lakshmi", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Bani Jolly", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "S. Afsar", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Abhinav Jain", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Mohit Kumar Divakar", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Panyam Suresh", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Disha Sharma", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Nambi Rajesh", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Rahul C Bhoyar", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Dasari Ankaiah", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Sanaga Shanthi Kumari", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Gyan Ranjan", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Valluri Anitha Lavanya", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Mercy Rophina", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "S. Umadevi", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Paras Sehgal", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Avula Renuka Devi", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "A. Surekha", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Pulala Chandra", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Rajamadugu Hymavathy", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "P R Vanaja", - "author_inst": "Kurnool Medical College, Kurnool, Andhra Pradesh, India" - }, - { - "author_name": "Vinod Scaria", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - }, - { - "author_name": "Sridhar Sivasubbu", - "author_inst": "CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.01.21.427315", "rel_title": "DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins", @@ -951553,6 +948783,37 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.01.21.427574", + "rel_title": "Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients", + "rel_date": "2021-01-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427574", + "rel_abs": "We present an updated version of our automated computational pipeline, Infection Pathogen Detector IPD 2.0 with a SARS-CoV-2 module, to perform genomic analysis to understand the pathogenesis and virulence of the virus. Analysing the currently available 208911 SARS-CoV2 genome sequences (as accessed on 28 Dec 2020), we generate an extensive database of sample- wise variants and clade annotation, which forms the core of the SARS-CoV-2 analysis module of the analysis pipeline. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil along with data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Thus, the persistence of pandemic may lead to the emergence of newer regional strains with improved fitness. IPD 2.0 also adopts the recent dynamic clade nomenclature and shows improvement in accuracy of clade assignment, processing time and portability, to its predecessor and thus could be a vital tool to help facilitate genomic surveillance in a population to identify variants involved in breakthrough infections.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sanket Shashikant Desai", + "author_inst": "Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre" + }, + { + "author_name": "Aishwarya Rane", + "author_inst": "Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre" + }, + { + "author_name": "Asim Joshi", + "author_inst": "Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre" + }, + { + "author_name": "Amit Dutt", + "author_inst": "Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.01.20.427541", "rel_title": "In vitro infection of human lung tissue with SARS-CoV-2: Heterogeneity in host defense and therapeutic response", @@ -952312,33 +949573,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.01.17.21249988", - "rel_title": "Population-scale patient safety data reveal inequalities in adverse events before and during COVID-19 pandemic", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249988", - "rel_abs": "Adverse patient safety events were associated with 110 thousand deaths in the U.S. alone in 2019. The COVID-19 pandemic has further challenged the ability of healthcare systems to ensure safe medication use, and its effects on patient safety remain unknown. Here, we investigate negative outcomes associated with medication use before and during the pandemic. Using a dataset of 10,443,476 reports involving 3,624 drugs and 19,193 adverse events, we develop an algorithmic approach to analyze the pandemics impact on the incidence of drug safety events by evaluating disproportional reporting relative to the pre-pandemic time, quantifying unexpected trends in clinical outcomes, and adjusting for drug interference. Among 64 adverse events identified by our analyses, we find 54 have increased incidence rates during the pandemic, even though adverse event reporting decreased by 4.4% overall. We find clinically relevant differences in drug safety outcomes between demographic groups. Compared to male patients, women report 47.0% more distinct adverse events whose occurrence significantly increased during the pandemic relative to pre-pandemic levels. Out of 53 adverse events with a pre-pandemic gender gap, 33 have an increased gender gap during the pandemic. While musculoskeletal and metabolic side effects are disproportionately enriched in women during the pandemic, immune-related adverse events are enriched only in men. We also find the number of adverse events with an increased reporting ratio is higher in adults (by 16.8%) than in older patients (adjusted for population size). Our findings have implications for safe medication use and tie the variation in adverse events to patients that may be disproportionately affected by preventable inequities during a public health emergency.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xiang Zhang", - "author_inst": "Harvard University" - }, - { - "author_name": "Marissa Sumathipala", - "author_inst": "Harvard University" - }, - { - "author_name": "Marinka Zitnik", - "author_inst": "Harvard Unviersity; Broad Institute of MIT and Harvard; Harvard Data Science Initiative" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.01.16.21249935", "rel_title": "The Socioeconomic Impact of COVID-19 in Urban Informal Settlements", @@ -952863,6 +950097,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.17.21249878", + "rel_title": "NEWS2 and laboratory predictors correlated with clinical deterioration in hospitalised patients with COVID-19", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249878", + "rel_abs": "BackgroundWe aimed to determine prognostic values of NEWS2 and laboratory parameters during the first week of COVID-19.\n\nMethodsAll adult patients who were hospitalized for a confirmed COVID-19 between the 11th of March and the 11th of May 2020 were retrospectively included. To evaluate the factors in prognosis which are admission to intensive care unit (ICU) and in-hospital death, univariate logistic regression analysis was performed at admission (D0), at day-3 (D3), day-5 (D5), and day-7 (D7). Additionally, receiver operating characteristic (ROC) analyses were performed.\n\nResultsOverall, 611 patients were included. Clinical deterioration was observed in 79 (12.9%) patients during hospitalisation, 36 (5.9%) during the first three days, 54 (8.8%) during the first five days, and 62 (10.1%) during the first week of hospitalisation. Our results showed that NEWS2, procalcitonin, neutrophil/lymphocyte ratio (NLR), and albumin were the best predictors for clinical deterioration at D0, D3, D5, and D7. Procalcitonin had the highest odds ratio for clinical deterioration on all days in univariate analysis. ROC analyses showed that NEWS2 at D7, procalcitonin at D5, albumin at D7, and NLR at D5 had highest AUC values. Additionally, we detected a strong correlation between NEWS2 and laboratory parameters including neutrophil, lymphocyte, NLR, platelet/lymphocyte ratio, CRP, procalcitonin, ferritin, and urea on all days.\n\nConclusionThis study provides a list of several laboratory parameters correlated with NEWS2 and potential predictors for ICU admission or in-hospital death during the clinical course of COVID-19. Dynamic monitoring of NEWS2 and laboratory parameters is vital for improving clinical outcomes.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Gulsah Tuncer", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Serkan Surme", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Osman Faruk Bayramlar", + "author_inst": "Department of Public Health, Bakirkoy District Health Directorate" + }, + { + "author_name": "Hatice Kubra Karanalbant", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Betul Copur", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Meltem Yazla", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Esra Zerdali", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Inci Yilmaz-Nakir", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Ayse Ruhkar Kurt-Cinar", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Ahmet Buyukyazgan", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Hatice Balli", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Yesim Kurekci", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Serap Simsek-Yavuz", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Istanbul Faculty of Medicine, Istanbul University" + }, + { + "author_name": "Mehmet Mesut Sonmez", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Gonul Sengoz", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + }, + { + "author_name": "Filiz Pehlivanoglu", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.18.21250041", "rel_title": "Endothelial cell-activating antibodies in COVID-19", @@ -953706,29 +951019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.19.21249936", - "rel_title": "The COVID-19 Infodemic: The complex task of elevating signal and eliminating noise.", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21249936", - "rel_abs": "In Situation Report #3 and 39 days before declaring COVID-19 a pandemic, the WHO declared a -19 infodemic. The volume of coronavirus tweets was far too great for one to find accurate or reliable information. Healthcare workers were flooded with which drowned the of valuable COVID-19 information. To combat the infodemic, physicians created healthcare-specific micro-communities to share scientific information with other providers. We analyzed the content of eight physician-created communities and categorized each message in one of five domains. We coded 1) an application programming interface to download tweets and their metadata in JavaScript Object Notation and 2) a reading algorithm using visual basic application in Excel to categorize the content. We superimposed the publication date of each tweet into a timeline of key pandemic events. Finally, we created NephTwitterArchive.com to help healthcare workers find COVID-19-related signal tweets when treating patients. We collected 21071 tweets from the eight hashtags studied. Only 9051 tweets were considered signal: tweets categorized into both a domain and subdomain. There was a trend towards fewer signal tweets as the pandemic progressed, with a daily median of 22% (IQR 0-42%. The most popular subdomain in Prevention was PPE (2448 signal tweets). In Therapeutics, Hydroxychloroquine/chloroquine wwo Azithromycin and Mechanical Ventilation were the most popular subdomains. During the active Infodemic phase (Days 0 to 49), a total of 2021 searches were completed in NephTwitterArchive.com, which was a 26% increase from the same time period before the pandemic was declared (Days -50 to -1). The COVID-19 Infodemic indicates that future endeavors must be undertaken to eliminate noise and elevate signal in all aspects of scientific discourse on Twitter. In the absence of any algorithm-based strategy, healthcare providers will be left with the nearly impossible task of manually finding high-quality tweets from amongst a tidal wave of noise.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "TEJAS DESAI", - "author_inst": "NOD Analytics" - }, - { - "author_name": "Arvind Conjeevaram", - "author_inst": "Trustwell Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.01.18.21249414", "rel_title": "Temporal Trends in COVID-19 associated AKI from March to December 2020 in New York City", @@ -954857,6 +952147,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.19.21250085", + "rel_title": "Incidence and Relative Risk of infection with SARS-CoV-2 virus (Covid-19) in European Soccer Players.", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250085", + "rel_abs": "The purpose of the present study was to investigate the incidence and relative risk of infection Covid-virus in soccer players. Data from five leagues was used and compared to data from the normal population in each country. Our results revealed that the relative risk was higher in soccer players in three countries when correcting for the estimated true number of infected people in the populations. We discuss that the reason for the higher incidence in soccer players is caused by the virus entering a group of players that work closely together.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Thomas Bull Andersen", + "author_inst": "Department of Public Health - Sport Science, Aarhus University, Denmark" + }, + { + "author_name": "Andreas Busk Dahl", + "author_inst": "Department of Public Health - Sport Science, Aarhus University, Denmark" + }, + { + "author_name": "Jeppe Bjerregaard Carstensen", + "author_inst": "Department of Public Health - Sport Science, Aarhus University, Denmark" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.19.427373", "rel_title": "Inactivated rabies virus vectored SARS-CoV-2 vaccine prevents disease in a Syrian hamster model.", @@ -955728,49 +953045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.19.21250115", - "rel_title": "Excessive matrix metalloproteinase-1 and hyperactivation of endothelial cells occurred in COVID-19 patients and were associated with the severity of COVID-19", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250115", - "rel_abs": "COVID-19 starts as a respiratory disease that can progress to pneumonia, severe acute respiratory syndrome (SARS), and multi-organ failure. Growing evidence suggests that COVID-19 is a systemic illness that primarily injures the vascular endothelium, yet the underlying mechanisms remain unknown. SARS-CoV-2 infection is believed to trigger a cytokine storm that plays a critical role in the pathogenesis of endothelialitis and vascular injury, eventually leading to respiratory and multi-organ failure in COVID-19 patients. We used a multiplex immunoassay to systematically profile and compare 65 inflammatory cytokines/chemokines/growth factors in plasma samples from 24 hospitalized (severe/critical) COVID-19 patients, 14 mild/moderate cases, and 13 healthy controls (HCs). Patients with severe/critical and mild/moderate COVID-19 had significantly higher plasma levels of 20 analytes than HCs. Surprisingly, only one cytokine (MIF) was among these altered analytes, while the rest were chemokines and growth factors. In addition, only MMP-1 and VEGF-A were significantly elevated in hospitalized COVID-19 patients when compared to mild/moderate cases. Given that excessive MMP-1 plays a central role in tissue destruction in a wide variety of vascular diseases and that elevated VEGF-A, an EC activation marker, increases vascular permeability, we further studied MMP-1 enzymatic activity and other EC activation markers such as soluble forms of CD146, ICAM-1, and VCAM-1. We found that plasma MMP-1 enzymatic activity and plasma levels of MMP-1 and EC activation markers were highly dysregulated in COVID-19 patients. Some dysregulations were associated with patients age or gender, but not with race. Our results demonstrate that COVID-19 patients have distinct inflammatory profiles that are distinguished from the cytokine storms in other human diseases. Excessive MMP-1 and hyperactivation of ECs occur in COVID-19 patients and are associated with the severity of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fahim Syed", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Wei Li", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Ryan F Relich", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Patrick M Russell", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Shanxiang Zhang", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Michelle K Zimmerman", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Qigui Yu", - "author_inst": "Indiana University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21250139", "rel_title": "Overcrowding and Exposure to Secondhand Smoke Increase Risk for COVID-19 Infection Among Latinx Families in Greater San Francisco Bay Area", @@ -956399,6 +953673,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.15.426463", + "rel_title": "Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426463", + "rel_abs": "Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Yasunori Watanabe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luiza Mendon\u00e7a", + "author_inst": "University of Oxford" + }, + { + "author_name": "Elizabeth R. Allen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew Howe", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Mercede Lee", + "author_inst": "University of Oxford" + }, + { + "author_name": "Joel D Allen", + "author_inst": "University Of Southampton" + }, + { + "author_name": "Himanshi Chawla", + "author_inst": "University of Southampton" + }, + { + "author_name": "David Pulido", + "author_inst": "University of Oxford" + }, + { + "author_name": "Francesca Donnellan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Hannah Davies", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marta Ulaszewska", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sandra Belij-Rammerstorfer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susan Morris", + "author_inst": "University of Oxford" + }, + { + "author_name": "Wanwisa Dejnirattisai", + "author_inst": "University of Oxford" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "University of Oxford" + }, + { + "author_name": "Piyada Supasa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Gavin R. Screaton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Catherine M. Green", + "author_inst": "University of Oxford" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peijun Zhang", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah C Gilbert", + "author_inst": "University of Oxford" + }, + { + "author_name": "Max Crispin", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.17.427000", "rel_title": "Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions", @@ -957426,249 +954803,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.01.17.426875", - "rel_title": "From COVID-19 to the Common Cold: Novel Host-Targeted, Pan-Respiratory Antiviral Small Molecule Therapeutics", - "rel_date": "2021-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.17.426875", - "rel_abs": "We present a small molecule chemotype, identified by an orthogonal drug screen, exhibiting nanomolar activity against members of all the six viral families causing most human respiratory viral disease, with a demonstrated barrier to resistance development. Antiviral activity is shown in mammalian cells, including human primary bronchial epithelial cells cultured to an air-liquid interface and infected with SARS-CoV-2. In animals, efficacy of early compounds in the lead series is shown by survival (for a coronavirus) and viral load (for a paramyxovirus). The drug target is shown to include a subset of the protein 14-3-3 within a transient host multi-protein complex containing components implicated in viral lifecycles and in innate immunity. This multi-protein complex is modified upon viral infection and largely restored by drug treatment. Our findings suggest a new clinical therapeutic strategy for early treatment upon upper respiratory viral infection to prevent progression to lower respiratory tract or systemic disease.\n\nOne Sentence SummaryA host-targeted drug to treat all respiratory viruses without viral resistance development.", - "rel_num_authors": 57, - "rel_authors": [ - { - "author_name": "Andreas Mueller-Schiffmann", - "author_inst": "Institute of Neuropathology, Heinrich Heine University, Duesseldorf, Germany" - }, - { - "author_name": "Maya Michon", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Anuradha F. Lingappa", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Shao Feng Yu", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Li Du", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Fred Deiter", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Suguna Mallesh", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Jackelyn Crabtree", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Usha F. Lingappa", - "author_inst": "Prosetta Biosciences Inc" - }, - { - "author_name": "Amanda Macieik", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Lisa Mueller", - "author_inst": "Institute of Virology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine-Universitat" - }, - { - "author_name": "Philipp Niklas Ostermann", - "author_inst": "Institute of Virology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine-Universitat" - }, - { - "author_name": "Marcel Andree", - "author_inst": "Institute of Virology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine-Universitat" - }, - { - "author_name": "Ortwin Adams", - "author_inst": "Institute of Virology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine-Universitat" - }, - { - "author_name": "Heiner Schaal", - "author_inst": "Institute of Virology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine-Universitat" - }, - { - "author_name": "Robert J. Hogan", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Ralph A. Tripp", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Umesh Appiah", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Sanjeev K. Anand", - "author_inst": "Santo Biotech, LLC" - }, - { - "author_name": "Thomas W. Campi", - "author_inst": "Santo Biotech, LLC" - }, - { - "author_name": "Michael J. Ford", - "author_inst": "MS Bioworks" - }, - { - "author_name": "Jonathan C. Reed", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Jim Lin", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Olayemi Akintunde", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Kiel Copeland", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Christine Nichols", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Emma Petrouski", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "A. Raquel Moreira", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "I-ting Jiang", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Nicholas DeYarman", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Sean Broce", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Ian Brown", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Ilana Segal", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Danielle Goldsmith", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Sharon Lau", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Shi Hong", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Vinod Asundi", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Erica M Briggs", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Ngwe Sin Phyo", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Markus Froehlich", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Bruce Onisko", - "author_inst": "Onipro, LLC" - }, - { - "author_name": "Kent Matlack", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Debendranath Dey", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Jaisri R. Lingappa", - "author_inst": "University of Washington" - }, - { - "author_name": "M. Dharma Prasad", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Carsten Korth", - "author_inst": "Institute of Neuropathology, Heinrich Heine University, Duesseldorf, Germany" - }, - { - "author_name": "Anatoliy Kitaygorodskyy", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Dennis Solas", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Homer Boushey", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "John Greenland", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Satish Pillai", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Michael K. Lo", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Christina F. Spiropoulou", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Joel M. Montgomery", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Suganya Selvarajah", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Kumar Paulvannan", - "author_inst": "Prosetta Biosciences, Inc" - }, - { - "author_name": "Vishwanath R. Lingappa", - "author_inst": "Prosetta Biosciences Inc" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.01.17.425424", "rel_title": "Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China.", @@ -959217,6 +956351,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.14.21249829", + "rel_title": "Direct Simulation of the CoVid-19 epidemic", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249829", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWWe introduce an agent-based model to simulate the epidemiological dynamics of COVID-19. Most computational models proposed to study this epidemic do no take into account human mobility. We present a direct simulation model where mobility plays a key role and propose as well four quarantine strategies. The results show that the no-quarantine strategy does lead to a high peak of contagions with no rebound. Quarantined strategies, for their part, show a re-emergence of the epidemic with smaller and softer peaks.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Augusto Cabrera-Becerril", + "author_inst": "UNAM, School of Sciences" + }, + { + "author_name": "Raul Peralta", + "author_inst": "Centro de Investigacion en Dinamica Celular" + }, + { + "author_name": "Pedro Miramontes", + "author_inst": "Facultad de Ciencias, Universidad Nacional Autonoma de Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.14.21249386", "rel_title": "Epidemiological Investigation of New SARS-CoV-2 Variant of Concern 202012/01 in England", @@ -960215,37 +957376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.14.21249803", - "rel_title": "The impact of high dose oral cotrimoxazole in patients with COVID-19 with hypoxic respiratory failure requiring non-invasive ventilation: A Case Control Study", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249803", - "rel_abs": "BackgroundCOVID-19 can be fatal in a significant proportion of people who develop critical illness, resulting in hypoxic respiratory failure secondary to Acute Respiratory Distress Syndrome (ARDS) which is thought to be mediated by a cytokine storm syndrome. Steroids have been shown to be of some benefit, but the mainstay of treatment remains supportive.\n\nMethodsThe data was collected retrospectively from consecutive, newly diagnosed patients presenting to the critical care facility of I Q City Medical College Hospital, Durgapur, India between June and November 2020 with critical COVID-19 on non-invasive ventilation treated with high dose oral cotrimoxazole (CTX) in addition to standard therapy (ST) and compared with patients with critical COVID-19 receiving standard therapy alone.\n\nResults201 patients were identified. Of which 151 patients received CTX in addition to ST (mean age {+/-} SD 59 {+/-} 13 years, 81% male and mean BMI {+/-} SD 28 {+/-} 2) and 50 patients received ST alone (mean age {+/-} SD 63 {+/-} 12, 64% male and mean BMI {+/-} SD 27 {+/-} 2). We observed that the patients with critical COVID-19 receiving CTX in addition to ST had significantly better outcomes including reduced in-patient mortality (13% versus 40%, p <0.001), length of hospital and critical care unit stay (mean, 11 versus 15 days (p <0.001) and 6 versus 11 days (p <0.001) respectively), and the need for mechanical ventilation (16% versus 42%, p <0.001) with improved CRP at day 7 (mean, 38mg/L versus 62mg/L, p = 0.001).\n\nConclusionThese results may be due to the antibiotic and anti-cytokine effects of CTX. Clinical trials are currently underway to test our observations.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Saurabh Singh", - "author_inst": "Department of Respiratory Medicine, IQ City Medical College Hospital, Durgapur, West Bengal, India" - }, - { - "author_name": "Thomas John", - "author_inst": "Epsom & St Helier University Hospitals NHS Trust" - }, - { - "author_name": "Prashant Kumar", - "author_inst": "Department of Respiratory Medicine, IQ City Medical College Hospital, Durgapur, West Bengal, India" - }, - { - "author_name": "Syed Rehan Quadery", - "author_inst": "Department of Respiratory Medicine, Epsom and St Helier University Hospitals NHS Trust, London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.13.20249064", "rel_title": "Optimising SARS-CoV-2 pooled testing strategies on social networks for low-resource settings", @@ -960890,6 +958020,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.12.21249654", + "rel_title": "From SARS and MERS to COVID-19: a review of the quality and responsiveness of clinical management guidelines in outbreak settings", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249654", + "rel_abs": "ObjectiveTo assess the responsiveness and quality of clinical management guidelines (CMGs) in SARS, MERS and COVID-19 and determine whether this has improved over time.\n\nDesignRapid literature review, quality assessment and focus group consultation.\n\nData Sources- Google and Google Scholar were systematically searched from inception to 6th June 2020.This was supplemented with hand searches of national and international public health agency and infectious disease society websites as well as directly approaching clinical networks in regions where few CMGs had been identified via the primary search.\n\nEligibility CriteriaCMGs for the treatment of COVID-19/SARS/MERS providing recommendations on supportive care and/or specific treatment.\n\nMethodsData extraction was performed using a standardised form. The Appraisal of Guidelines for Research and Evaluation (AGREE-II) tool was used to evaluate the quality of the CMGs. Six COVID-19 treatments were selected to assess the responsiveness of a subset of guidelines and their updates to 20th November 2020. We ran two sessions of focus groups with patient advocates to elicit their views on guideline development.\n\nResultsWe included 37 COVID-19, six SARS, and four MERS CMGs. Evidence appraisals in CMGs generally focused on novel drugs rather than basic supportive care; where evidence for the latter was provided it was generally of a low quality. Most CMGs had major methodological flaws (only two MERS-CoV and four COVID-19 CMGs were recommended for use by both reviewers without modification) and there was no evidence of improvement in quality over time. CMGs scored lowest in the following AGREE-II domains: scope and purpose, editorial independence, stakeholder engagement, and rigour of development. Of the COVID-19 CMGs, only eight included specific guidance for the management of elderly patients and only ten for high-risk groups; a further eight did not specify the target patient group at all. Early in the pandemic, multiple guidelines recommended unproven treatments and whilst in general findings of major clinical trials were eventually adopted, this was not universally the case. Eight guidelines recommended that use of unproven agents should be considered on a case-by-case basis. Patient representatives expressed concern about the lack of engagement with them in CMG development and that these documents are not accessible to non-experts.\n\nConclusionThe quality of most CMGs produced in coronaviridae outbreaks is poor and we have found no evidence of improvement over time, highlighting that current development frameworks must be improved. There is an need to strengthen the evidence base surrounding basic supportive care and develop methods to engage patients in CMG development from the beginning in outbreak settings.\n\nSystematic review registrationPROSPERO CRD42020167361", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Samuel Lipworth", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ishmeala Rigby", + "author_inst": "Brighton and Sussex Medical School" + }, + { + "author_name": "Vincent Cheng", + "author_inst": "University of Bristol" + }, + { + "author_name": "Peter Bannister", + "author_inst": "Brighton and Sussex Medical School" + }, + { + "author_name": "Eli Harriss", + "author_inst": "University of Oxford" + }, + { + "author_name": "Karen Cook", + "author_inst": "Not affiliated" + }, + { + "author_name": "Erhui Cai", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mais Tattan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Terrence Epie", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lakshmi Manoharan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kate Lambe", + "author_inst": "Brighton and Sussex School of Medicine" + }, + { + "author_name": "Melina Michelen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anna Gilibets", + "author_inst": "Brighton and Sussex School of Medicine" + }, + { + "author_name": "Andrew Dagens", + "author_inst": "University of Oxford" + }, + { + "author_name": "Louise Sigfrid", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Horby", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.13.21249721", "rel_title": "Increased infections, but not viral burden, with a new SARS-CoV-2 variant", @@ -962145,49 +959354,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.01.12.21249692", - "rel_title": "Impact of COVID-19 on Migrants' Access to Primary Care:A National Qualitative Study", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249692", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to considerable changes in the delivery of primary care in the UK, including rapid digitalisation, yet the extent to which these have impacted on marginalised migrant groups - already facing existing barriers to NHS care - is unknown. Understanding the perspectives and experiences of health professionals and migrants will support initiatives to deliver more effective health services, including delivery of the COVID-19 vaccine, to marginalised groups.\n\nAimTo understand the impact of the COVID-19 pandemic on migrants and their access to primary healthcare, and implications for COVID-19 vaccine roll out.\n\nDesign and SettingPrimary care professionals, administrative staff, and migrants (foreign born; >18 years; <10 years in UK), were recruited in three phases using purposive, convenience and snowball sampling from urban, suburban and rural settings.\n\nMethodsIn-depth semi-structured interviews were conducted by telephone. Data were analysed iteratively, informed by thematic analysis.\n\nResults64 clinicians were recruited in Phase 1 (25 GPs, 15 nurses, 7 HCAs, 1 Pharmacists); Phase 2 comprised administrative staff (11 PMs and 5 receptionists); and in Phase 3 we recruited 17 migrants (88% asylum seekers; 65% female; mean time in UK 4 years). We found that digitalisation and virtual consultations (telephone, video, and online form-based) have amplified existing inequalities in access to healthcare for many migrants due to lack of digital literacy and access to technology, compounded by language barriers. Use of virtual consultations has resulted in concerns around building trust and the risk of missing safeguarding cues. Participants highlighted challenges around registering and accessing healthcare due to the physical closure of surgeries. Participants reported indirect discrimination, language and communication barriers, and lack of access to targeted and tailored COVID-19 information or interventions. In addition, migrants reported a range of specific beliefs around COVID-19 and on potential COVID-19 vaccines, from acceptance to mistrust, often influenced by misinformation. PCPs raised concerns that migrants may have increased risk factors for poor general health and to severe illness from COVID-19, in part due to their social and economic situation. Innovative opportunities were suggested to engage migrant groups through translated digital health advice using text templates and YouTube which merit further exploration.\n\nConclusionPandemic-related changes in primary care delivery may be here to stay, and some migrant groups are at risk of digital exclusion and may need targeted additional support to access services. As primary care networks operationalise the delivery of the COVID-19 vaccine, these findings provide critical information on specific strategies required to support migrant population to access primary care and overcome misinformation around COVID-19 and the COVID-19 vaccine.\n\nHow this fits inThe impact of pandemic-related shifts in primary care delivery on marginalised migrant groups, who may already face major disparities in accessing primary care, is poorly elucidated. We found that the rapid digitalisation of primary care services and physical closure of surgeries during the pandemic have amplified disparities in access to healthcare for specific migrant groups, with many lacking access to and capacity to use technology, compounded by language barriers. Migrants may be at increased risk of misinformation about COVID-19, which merits further consideration as COVID-19 vaccine roll out begins. Improved outreach to local migrant community organisations and places of worship, alongside co-designing with migrants more inclusive delivery approaches and creative integration of migrant ambassadors into information-sharing campaigns are needed. Primary care can maximise the opportunities of digitalisation for migrants through flexible engagement by multiple modalities (e.g. text, email, letter and YouTube videos) to provide targeted, translated advice and information, virtual group consultations for patients with a specific condition, and working with local leaders and NGOs to access and disseminate information through informal communication channels.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Felicity Knights", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Jessica Carter", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Anna Deal", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Alison F Crawshaw", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Sally E Hayward", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Lucinda Jones", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - }, - { - "author_name": "Sally Hargreaves", - "author_inst": "The Migrant Health Research Group, Institute for Infection and Immunity, St George's, University of London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2021.01.13.21249460", "rel_title": "Physicians' Reactions to COVID-19: The Results of an International Internet Survey", @@ -962648,6 +959814,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.14.21249848", + "rel_title": "Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249848", + "rel_abs": "ObjectiveCOVID-19 appears to have caused less severe outbreaks in many low- and middle-income countries (LMIC) compared with high-income countries, possibly because of differing demographics, socio-economics, surveillance, and policy responses. Here, we investigate the role of multiple factors on COVID-19 dynamics in the Philippines, a LMIC that has had a relatively severe COVID-19 outbreak.\n\nMethodsWe applied an age-structured compartmental model that incorporated time-varying mobility, testing, and personal protective behaviors (through a \"Minimum Health Standards\" policy, MHS) to represent the Philippines COVID-19 epidemic nationally and for three highly affected regions (Calabarzon, Central Visayas, and the National Capital Region). We estimated effects of control measures, key epidemiological parameters, and interventions.\n\nFindingsPopulation age structure, contact rates, mobility, testing, and MHS were sufficient to explain the Philippines epidemic based on the good fit between modelled and reported cases, hospitalisations, and deaths. Several of the fitted epidemiological parameters were consistent with those reported in high-income settings. The model indicated that MHS reduced the probability of transmission per contact by 15-26%. The February 2021 case detection rate was estimated at [~]9%, population recovered at [~]12%, and scenario projections indicated high sensitivity to MHS adherence.\n\nConclusionsCOVID-19 dynamics in the Philippines are driven by age, contact structure, mobility, and MHS adherence, and the epidemic can be understood within a similar framework as for high-income settings. Continued compliance with low-cost MHS should allow the Philippines to maintain epidemic control until vaccines are widely distributed, but disease resurgence could occur due to low population immunity and detection rates.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jamie M Caldwell", + "author_inst": "University of Hawaii at Manoa" + }, + { + "author_name": "Elvira de Lara-Tuprio", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Timothy Robin Y Teng", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Maria Regina Justina E Estuar", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Raymond Francis Sarmiento", + "author_inst": "University of the Philippines" + }, + { + "author_name": "Milinda Abayawardana", + "author_inst": "Monash University" + }, + { + "author_name": "Robert Neil F Leong", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Richard T Gray", + "author_inst": "University of New South Wales" + }, + { + "author_name": "James G Wood", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Emma McBryde", + "author_inst": "James Cook University" + }, + { + "author_name": "Romain Ragonnet", + "author_inst": "Monash University" + }, + { + "author_name": "James M Trauer", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.13.21249725", "rel_title": "The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres", @@ -963911,29 +961140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.15.21249870", - "rel_title": "Variability of Individual Infectiousness Derived from Aggregate Statistics of COVID-19", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249870", - "rel_abs": "The quantification of spreading heterogeneity in the COVID-19 epidemic is crucial as it affects the choice of efficient mitigating strategies irrespective of whether its origin is biological or social. We present a method to deduce temporal and individual variations in the basic reproduction number R directly from epidemic trajectories at a community level. Using epidemic data from the 98 districts in Denmark we estimate an overdispersion factor k for COVID-19 to be about 0.11 (95% confidence interval 0.08 - 0.18), implying that 10 % of the infected cause between 70 % to 87 % of all infections.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Julius B Kirkegaard", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Kim Sneppen", - "author_inst": "University of Copenhagen" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.14.426652", "rel_title": "Natural SARS-CoV-2 infection in kept ferrets, Spain", @@ -964730,6 +961936,61 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.01.14.426695", + "rel_title": "SARS-CoV-2 spike protein arrested in the closed state induces potent neutralizing responses", + "rel_date": "2021-01-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426695", + "rel_abs": "The majority of SARS-CoV-2 vaccines in use or in advanced clinical development are based on the viral spike protein (S) as their immunogen. S is present on virions as pre-fusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described that act against both open and closed conformations. The long-term success of vaccination strategies will depend upon inducing antibodies that provide long-lasting broad immunity against evolving, circulating SARS-CoV-2 strains, while avoiding the risk of antibody dependent enhancement as observed with other Coronavirus vaccines. Here we have assessed the results of immunization in a mouse model using an S protein trimer that is arrested in the closed state to prevent exposure of the receptor binding site and therefore interaction with the receptor. We compared this with a range of other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induce a long-lived, strongly neutralizing antibody response as well as T-cell responses. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralising responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, virus-inhibiting immune responses than open spikes, and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. Together with their improved stability and storage properties we suggest that closed spikes may be a valuable component of refined, next-generation vaccines.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "George W Carnell", + "author_inst": "Department of Veterinary Medicine, University of Cambridge" + }, + { + "author_name": "Katarzyna A Ciazynska", + "author_inst": "Medical Research Council Laboratory of Molecular Biology" + }, + { + "author_name": "David A Wells", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Xiaoli Xiong", + "author_inst": "Medical Research Council Laboratory of Molecular Biology" + }, + { + "author_name": "Ernest T Aguinam", + "author_inst": "Department of Veterinary Medicine, University of Cambridge" + }, + { + "author_name": "Stephen H McLaughlin", + "author_inst": "Medical Research Council Laboratory of Molecular Biology" + }, + { + "author_name": "Donna Mallery", + "author_inst": "Medical Research Council Laboratory of Molecular Biology" + }, + { + "author_name": "Leo C James", + "author_inst": "Medical Research Council Laboratory of Molecular Biology" + }, + { + "author_name": "Jonathan Luke Heeney", + "author_inst": "University of Cambridge" + }, + { + "author_name": "John A. G. Briggs", + "author_inst": "MRC Laboratory of Molecular Biology" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.12.21249511", "rel_title": "The National COVID Cohort Collaborative: Clinical Characterization and Early Severity Prediction", @@ -965881,37 +963142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.12.21249661", - "rel_title": "Based Analysis Framework for identifying COVID-19 Incidence and Fatality Determinants at National Level Case study: Africa", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249661", - "rel_abs": "BackgroundCOVID-19 pandemic is an extraordinary threat with significant implications in all aspects of human life, therefore, it represents the most immediate challenges for all countries all over the world.\n\nObjectivesThis study is intended to develop a GIS-based analysis model to explore, quantify and model the relationships between COVID-19 morbidity and mortality and their potential predictor variables.\n\nMethodFor this purpose, a model was developed to estimate COVID-19 incidence and fatality rates in Africa up to 16th of August 2020 at the national level. The model involved Ordinary Least Squares (OLS) and Geographically Weighted Regression (GWR) analysis through ArcGIS was applied.\n\nResultSpatial Autocorrelation Analysis revealed that there was positive spatial autocorrelation in COVID-19 incidence (Moran index 0.16. P value <0.1), and fatality (Moran index 0.0.35, P value<0.01) rates within different African countries. At continental level, OLS revealed that COVID-19 incidence rate was found to be positively associated with overcrowding, health expenditure, HIV infections and air pollution and negatively associated with BCG vaccine ({beta}=2.97,1.45, 0.01, 3.29, -47.65 respectively, P< 0.05) At the same time, COVID-19 fatality was found to be positively related to asthma prevalence and tobacco use. Yet, certain level of inconsistency was noted in the case of COVID-19 fatality, which was negatively related to elder population, poverty, and cardiovascular mortality (P<0.05). This model showed convenient level of validity in modeling the relationship between COVID-19 incidence as well as fatality and their key predictors using GWR. In this respect, the model explained about 58% and 55% of the variance in COVID-19 incidence and fatality rates, respectively, as a function of considered predictors.\n\nConclusionApplication of the suggested model can assist in guiding intervention strategies, particularly in case of local and community level whenever the data on COVID-19 cases and predictors variables are available.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mahmoud A Hassaan", - "author_inst": "Institute of Graduate Studies & Research (" - }, - { - "author_name": "Ramy M Ghazy", - "author_inst": "High Institute of Public Health" - }, - { - "author_name": "Rofida G. Abdelwahab Abdelwahab", - "author_inst": "Institute of Graduate Studies & Research" - }, - { - "author_name": "Toka A Elbarky", - "author_inst": "Institute of Graduate Studies & Research (" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.11.21249547", "rel_title": "Impact of the Coronavirus Disease (COVID-19) on the Mental Health and Physical Activity of Pharmacy Students at the University of Zambia: A Cross-Sectional Study", @@ -966628,6 +963858,37 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.01.12.426373", + "rel_title": "Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution", + "rel_date": "2021-01-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.12.426373", + "rel_abs": "The emergence of new variants of SARS-CoV-2 herald a new phase of the pandemic. This study used state-of-the-art phylodynamic methods to ascertain that the rapid rise of B.1.1.7 \"Variant of Concern\" most likely occurred by global dispersal rather than convergent evolution from multiple sources.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Bram Vrancken", + "author_inst": "Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven" + }, + { + "author_name": "Simon Dellicour", + "author_inst": "KULeuven - University of Leuven" + }, + { + "author_name": "Davey M Smith", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Antoine Chaillon", + "author_inst": "University of California San Diego" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.01.13.426558", "rel_title": "Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant", @@ -967463,53 +964724,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.04.20248661", - "rel_title": "Association of homelessness with COVID-19 positivity among individuals visiting a testing center", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.20248661", - "rel_abs": "We conducted a chart audit of all patients attending an inner-city COVID-19 testing centre in Toronto, Canada between March and April 2020. Of the 2050 unique individuals tested, 214 (10.4%) were homeless. People experiencing homelessness were more likely to test positive for COVID-19 compared to those not experiencing homelessness even after adjustment for age, sex, and the presence of any medical co-morbidity (15.4% vs. 6.7%, p<0.001; OR 2.41, 95% CI 1.51 to 3.76, p<0.001).", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tara Kiran", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Amy Craig-Neil", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Paul Das", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Joel Lockwood", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Ri Wang", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Nikki Nathanielsz", - "author_inst": "University of Toronto" - }, - { - "author_name": "Esther Rosenthal", - "author_inst": "St. Michael's Hospital" - }, - { - "author_name": "Stephen Hwang", - "author_inst": "St. Michael's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.09.21249515", "rel_title": "Impact of Residential Neighborhood and Race/Ethnicity on Outcomes of Hospitalized Patients with COVID-19 in the Bronx", @@ -968218,6 +965432,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.10.20249014", + "rel_title": "Cerebrospinal fluid in COVID-19 neurological complications: no cytokine storm or neuroinflammation.", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.20249014", + "rel_abs": "BACKGROUNDNeurological complications occur in COVID-19. We aimed to examine cerebrospinal fluid (CSF) of COVID-19 subjects with neurological complications and determine presence of neuroinflammatory changes implicated in pathogenesis.\n\nMETHODSCross-sectional study of CSF neuroinflammatory profiles from 18 COVID-19 subjects with neurological complications categorized by diagnosis (stroke, encephalopathy, headache) and illness severity (critical, severe, moderate, mild). COVID-19 CSF was compared with CSF from healthy, infectious and neuroinflammatory disorders and stroke controls (n=82). Cytokines (IL-6, TNF, IFN{gamma}, IL-10, IL-12p70, IL-17A), inflammation and coagulation markers (high-sensitivity-C Reactive Protein [hsCRP], ferritin, fibrinogen, D-dimer, Factor VIII) and neurofilament light chain (NF-L), were quantified. SARS-CoV2 RNA and SARS-CoV2 IgG and IgA antibodies in CSF were tested with RT-PCR and ELISA.\n\nRESULTSCSF from COVID-19 subjects showed a paucity of neuroinflammatory changes, absence of pleocytosis or specific increases in pro-inflammatory markers or cytokines (IL-6, ferritin, or D-dimer). Anti-SARS-CoV2 antibodies in CSF of COVID-19 subjects (77%) were observed despite no evidence of SARS-CoV2 viral RNA. A similar increase of pro-inflammatory cytokines (IL-6, TNF, IL-12p70) and IL-10 in CSF of COVID-19 and non-COVID-19 stroke subjects was observed compared to controls. CSF-NF-L was elevated in subjects with stroke and critical COVID-19. CSF-hsCRP was present almost exclusively in COVID-19 cases.\n\nCONCLUSIONThe paucity of neuroinflammatory changes in CSF of COVID-19 subjects and lack of SARS-CoV2 RNA do not support the presumed neurovirulence of SARS-CoV2 or neuroinflammation in pathogenesis of neurological complications in COVID-19. Elevated CSF-NF-L indicates neuroaxonal injury in COVID-19 cases. The role of CSF SARS-CoV2 IgG antibodies is still undetermined.\n\nFUNDINGThis work was supported by NIH R01-NS110122 and The Bart McLean Fund for Neuroimmunology Research.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Maria A. Garcia", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Paula V. Barreras", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Allie Lewis", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Gabriel Pinilla", + "author_inst": "Fundacion Valle del Lili" + }, + { + "author_name": "Lori J. Sokoll", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thomas Kickler", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba Mostafa", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Mario Caturegli", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Abhay Moghekar", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kathryn C. Fitzgerald", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "- Hopkins Neuro-COVID-19 Group", + "author_inst": "" + }, + { + "author_name": "Carlos A Pardo", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.01.12.426388", "rel_title": "Inhibitor Binding Modulates Protonation States in the Active Site of SARS-CoV-2 Main Protease", @@ -969289,89 +966566,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.01.08.425974", - "rel_title": "Immunogenicity and Protective Efficacy of an Intranasal Live-attenuated Vaccine Against SARS-CoV-2 in Preclinical Animal Models", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.08.425974", - "rel_abs": "The global deployment of an effective and safe vaccine is currently a public health priority to curtail the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we evaluated a Newcastle disease virus (NDV)-based intranasal vectored-vaccine in mice and hamsters for its immunogenicity, safety and protective efficacy in challenge studies with SARS-CoV-2. The recombinant (r)NDV-S vaccine expressing spike (S) protein of SARS-CoV-2 administrated via intranasal route in mice induced high levels of SARS-CoV-2-specific neutralizing immunoglobulin A (IgA) and IgG2a antibodies and T cell-mediated immunity. Hamsters vaccinated with two doses of vaccine showed complete protection from clinical disease including lung infection, inflammation, and pathological lesions after SARS-CoV-2 challenge. Importantly, a single or double dose of intranasal rNDV-S vaccine completely blocked SARS-CoV-2 shedding in nasal turbinate and lungs within 4 days of vaccine administration in hamsters. Taken together, intranasal administration of rNDV-S has the potential to control infection at the site of inoculation, which should prevent both the clinical disease and transmission to halt the spread of the COVID-19 pandemic.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Jun-Guy Park", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "Fatai S. Oladunni", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "Mohammed A. Rohaim", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - }, - { - "author_name": "Jayde Whittingham-Dowd", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - }, - { - "author_name": "James Tollitt", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - }, - { - "author_name": "Bakri M Assas", - "author_inst": "Faculty of Applied Medical Sciences, Department of Medical Laboratory Technology, Immunology Group, King Abdul Aziz University, Jeddah, Saudi Arabia" - }, - { - "author_name": "Wafaa Alhazmi", - "author_inst": "Faculty of Applied Medical Sciences, Department of Medical Laboratory Technology, Microbiology Group, King Abdul Aziz University, Jeddah, Saudi Arabia" - }, - { - "author_name": "Abdullah Almilaibary", - "author_inst": "Faculty of Medicine, Al Baha University, Al Baha, Saudi Arabia" - }, - { - "author_name": "Munir Iqbal", - "author_inst": "The Pirbright Institute, UK" - }, - { - "author_name": "Pengxiang Chang", - "author_inst": "The Pirbright Institute, UK" - }, - { - "author_name": "Renee Escalona", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "Vinay Shivanna", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "Jordi B. Torrelles", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "John J Worthington", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - }, - { - "author_name": "Lucy H. Jackson-Jones", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Texas Biomedical Research Institute, Host-Pathogen Interactions and Population Health Programs, San Antonio, TX, 78227, USA" - }, - { - "author_name": "Muhammad Munir", - "author_inst": "Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.11.426218", "rel_title": "Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class", @@ -970512,6 +967706,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.05.21249310", + "rel_title": "Ivermectin as a potential treatment for mild to moderate COVID-19: A double blind randomized placebo-controlled trial", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249310", + "rel_abs": "ObjectiveIvermectin has been suggested as a treatment for COVID-19.This randomised control trial was conducted to test the efficacy of Ivermectin in the treatment of mild and moderate COVID-19.\n\nDesignParallel, double blind, randomised, placebo controlled trial Setting: A tertiary care dedicated COVID-19 hospital in Bihar, India\n\nParticipantsAdult patients (> 18 years) admitted with mild to moderate COVID 19 disease (saturation > 90% on room air, respiratory rate < 30 and no features of shock) with no contraindications to ivermectin and willing to participate in the study\n\nInterventionPatients in the intervention arm were given ivermectin 12 mg on day 1 and day 2 of admission. Patients in the placebo arm were given identical looking placebo tablets. Rest of the treatment was continued as per the existing protocol and the clinical judgment of the treating teams.\n\nOutcome MeasuresThe primary outcome measure was a negative RT-PCR test for SARS-CoV-2 on day 6 of admission. The secondary outcome measures were symptom status on day 6, discharge status on day 10, admission to ICU, need for invasive mechanical ventilation and in-hospital mortality.\n\nResultsA total of 115 patients were enrolled for the study of which 112 were included in the final analysis. Of them, 55 were randomised to the intervention arm while 57 were randomised to the placebo arm. There was no significant difference in the baseline characteristics of the two arms. There was no significant difference in the primary outcome, i.e. negative RT-PCR status on day 6 between the two groups. Similarly, there was no significant difference between the two groups in most of the secondary outcome measures, viz. symptom status on day 6, discharge status on day 10, admission to ICU, and need for invasive mechanical ventilation. However, while there was no in-hospital mortality in the intervention arm, there were 4 deaths in the placebo arm. As a result, all patients in the intervention arm (n=56) were successfully discharged as compared to 93.1% (n=54/58) in the placebo arm (RR 1.1, 95% CI 1.0 to 1.2, p=0.019).\n\nConclusionThere was no difference in the primary outcome i.e. negative RT-PCR status on day 6 of admission with the use of ivermectin. However, a significantly higher proportion of patients were discharged alive from the hospital when they received ivermectin.\n\nStrengths and Limitations of the StudyO_LIThis study was randomised and double blind, thereby minimizing the chance of bias.\nC_LIO_LIAll outcome measures except symptom status on day 6 were objective and placebo control was used for comparison.\nC_LIO_LIOnly single repeat RT-PCR was done. So median time to viral clearance in the two groups could not be calculated.\nC_LIO_LISevere cases were not included in the study.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ravi Kirti", + "author_inst": "All India Institute of Medical Sciences, patna" + }, + { + "author_name": "Ranjini Roy", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Chandrima Pattadar", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Rishav Raj", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Neeraj Agarwal", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Bibinagar, India" + }, + { + "author_name": "Bijit Biswas", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Pramod Kumar Manjhi", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Deependra kumar Rai", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Shyama Shyama", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Anjani Kumar", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + }, + { + "author_name": "Asim Sarfaraz", + "author_inst": "All India Institute of Medical Sciences (AIIMS), Patna, India" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.08.20249017", "rel_title": "MassMark: A Highly Scalable Multiplex NGS-based Method for High-Throughput, Accurate and Sensitive Detection of SARS-CoV-2 for Mass Testing", @@ -971571,81 +968824,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.04.20248897", - "rel_title": "IL-2 and IFN- are biomarkers of SARS-CoV-2 specific cellular response in whole blood stimulation assays", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.20248897", - "rel_abs": "A proper description of the immune response to SARS-CoV-2 will be critical for the assessment of protection elicited after both infection and vaccination. Uncoupled T and B cell responses have been described in acute and convalescent patients and exposed individuals. We assessed the potential usefulness of whole blood stimulation assays to identify functional cellular immune responses to SARS-CoV-2. Blood from COVID-19 recovered individuals (5 months after infection) and negative subjects was stimulated for 24 hours with HLA predicted peptide \"megapools\" of the Spike and Nucleoprotein, or the mixture of them. After stimulation, cytokines were quantified using a beads-based multiplex assay. Interleukin-2 and IFN-{gamma} were found to be specific biomarkers of SARS-CoV-2 cellular response. Using the Spike and Nucleoprotein mixture, 91.3% of COVID-19 recovered individuals presented an IL-2 stimulation index over the cut-off, while 82.6% showed IFN-{gamma}. All the negative individuals presented an IL-2 response under the cut-off, while 5.3% of these subjects presented positive IFN-{gamma} stimulation indexes. Moreover, IL-2 production correlated with IgG levels for Spike 1, RBD, and Nucleocapsid. In conclusion, we demonstrate the potential of whole blood stimulation assays and the quantification of IL-2 and IFN-{gamma} for the analysis of SARS-CoV-2 functional cellular responses.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Begona Perez-Cabezas", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Ricardo Ribeiro", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Ines Costa", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Sofia Esteves", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Ana Rafaela Teixeira", - "author_inst": "i3S, University of Porto, Portugal." - }, - { - "author_name": "Teresa Reis", - "author_inst": "Department of Clinical Pathology, Centro Hospitalar e Universitario de Coimbra, Portugal" - }, - { - "author_name": "Ricardo Monteiro", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Alexandre Afonso", - "author_inst": "Department of Occupational Health, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal" - }, - { - "author_name": "Vitor Pinheiro", - "author_inst": "Department of Occupational Health, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal" - }, - { - "author_name": "Maria Isabel Antunes", - "author_inst": "Department of Occupational Health, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal" - }, - { - "author_name": "Maria Lucilia Araujo", - "author_inst": "Department of Clinical Pathology, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal" - }, - { - "author_name": "Joao Niza Ribeiro", - "author_inst": "Instituto Superior de Saude Publica, University of Porto, Portugal" - }, - { - "author_name": "Anabela Cordeiro-da-Silva", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Nuno Santarem", - "author_inst": "i3S, University of Porto, Portugal" - }, - { - "author_name": "Joana Tavares", - "author_inst": "i3S, University of Porto, Portugal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.06.21249272", "rel_title": "Integrated Vaccination and Non-Pharmaceutical Interventions based Strategies in Ontario, Canada, as a Case Study: a Mathematical Modeling Study", @@ -972282,6 +969460,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.06.20248960", + "rel_title": "Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.20248960", + "rel_abs": "In 579 COVID patients samples collected between March and July of 2020, we examined the effects of non-synonymous mutations harbored by the circulating B.1.1.7 strain on linear antibody epitope signal for spike glycoprotein and nucleoprotein. At the antigen level, the mutations only substantially reduced signal in 0.5% of the population. Although some epitope mutations reduce measured signal in up to 6% of the population, these are not the dominant epitopes for their antigens. Given dominant epitope patterns observed, our data suggest that the mutations would not result in immune evasion of linear epitopes for a large majority of these COVID patients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Winston A. Haynes", + "author_inst": "Serimmune, Inc." + }, + { + "author_name": "Kathy Kamath", + "author_inst": "Serimmune, Inc." + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "John Shon", + "author_inst": "Serimmune, Inc." + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.06.20249091", "rel_title": "Epidemiological and Clinical Characteristics, and Virologic Features of COVID-19 Patients in Kazakhstan: a Nation-Wide, Retrospective, Cohort Study.", @@ -973272,41 +970485,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.01.07.425806", - "rel_title": "Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a nai\u0308ve human antibody library", - "rel_date": "2021-01-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425806", - "rel_abs": "Infection with SARS-CoV-2 elicits robust antibody responses in some patients, with a majority of the response directed at the receptor binding domain (RBD) of the spike surface glycoprotein. Remarkably, many patient-derived antibodies that potently inhibit viral infection harbor few to no mutations from the germline, suggesting that naive antibody libraries are a viable means for discovery of novel SARS-CoV-2 neutralizing antibodies. Here, we used a yeast surface-display library of human naive antibodies to isolate and characterize three novel neutralizing antibodies that target the RBD: one that blocks interaction with angiotensin-converting enzyme 2 (ACE2), the human receptor for SARS-CoV-2, and two that target other epitopes on the RBD. These three antibodies neutralized SARS-CoV-2 spike-pseudotyped lentivirus with IC50 values as low as 60 ng/mL in vitro. Using a biolayer interferometry-based binding competition assay, we determined that these antibodies have distinct but overlapping epitopes with antibodies elicited during natural COVID-19 infection. Taken together, these analyses highlight how in vitro selection of naive antibodies can mimic the humoral response in vivo, yielding neutralizing antibodies and various epitopes that can be effectively targeted on the SARS-CoV-2 RBD.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Benjamin Nikola Bell", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Abigail E. Powell", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Carlos Rodriguez", - "author_inst": "xCella Biosciences" - }, - { - "author_name": "Jennifer R Cochran", - "author_inst": "Stanford University" - }, - { - "author_name": "Peter S. Kim", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.08.425825", "rel_title": "Artemisia annua L. extracts prevent in vitro replication of SARS-CoV-2", @@ -973955,6 +971133,29 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.07.425724", + "rel_title": "Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population.", + "rel_date": "2021-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425724", + "rel_abs": "The whole world is drastically affected by the current pandemic due to severe virus, SARS-CoV-2 and scientists are rigorously looking for the efficient vaccine against it that become an emergent issue. Reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell / B-cell response to antigen. In the present study, we conducted population coverage analysis referring to the diverse Indian population. By using tools from Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Selection of these epitopes have been conducted based on their binding affinity with the maximum number of HLA alleles belong to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting that this protein has adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 221 selected epitopes are considered that shows the projected population coverage as 83.08% with 19.29 average hit (average number of epitope hits/HLA combinations recognized by the population) and 5.91 pc90 (minimum number of epitope hits/HLA combinations recognized by 90% of the population). 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Docking analysis of each epitope with their respective allele suggests that the epitope NSFTRGVYY represents highest binding affinity with docking score -7.6 kcal/mol with its allele HLA-C*07:01 among all the epitopes. Since the Covid-19 cases are still in progress and seem to remain like this until we find an effective vaccine, moreover in countries like India, vast diversity in the population may present a hindrance to particular vaccine efficiency. Outcomes from this study could be critical to design vaccine against SARS-CoV-2 for a different set of the population within the country.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sreevidya S. Devi", + "author_inst": "Mar Athanasios College for Advanced Studies, India" + }, + { + "author_name": "Manish Dwivedi", + "author_inst": "Amity University Uttar Pradesh, Lucknow-226028" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.07.425740", "rel_title": "Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera", @@ -975022,81 +972223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.05.21249240", - "rel_title": "Fever, Diarrhea, and Severe Disease Correlate with High Persistent Antibody Levels against SARS-CoV-2", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249240", - "rel_abs": "Lasting immunity will be critical for overcoming the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, factors that drive the development of high titers of anti-SARS-CoV-2 antibodies and how long those antibodies persist remain unclear. Our objective was to comprehensively evaluate anti-SARS-CoV-2 antibodies in a clinically diverse COVID-19 convalescent cohort at defined time points to determine if anti-SARS-CoV-2 antibodies persist and to identify clinical and demographic factors that correlate with high titers. Using a novel multiplex assay to quantify IgG against four SARS-CoV-2 antigens, a receptor binding domain-angiotensin converting enzyme 2 inhibition assay, and a SARS-CoV-2 neutralization assay, we found that 98% of COVID-19 convalescent subjects had anti-SARS-CoV-2 antibodies five weeks after symptom resolution (n=113). Further, antibody levels did not decline three months after symptom resolution (n=79). As expected, greater disease severity, older age, male sex, obesity, and higher Charlson Comorbidity Index score correlated with increased anti-SARS-CoV-2 antibody levels. We demonstrated for the first time that COVID-19 symptoms, namely fever, abdominal pain, diarrhea and low appetite, correlated consistently with higher anti-SARS-CoV-2 antibody levels. Our results provide new insights into the development and persistence of anti-SARS-CoV-2 antibodies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Maya F Amjadi", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Tammy Armbrust", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Aisha M Mergaert", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Sandeep R Narpala", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Peter J Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "S Janna Bashar", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Christopher R Glover", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Anna S Heffron", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Alison Taylor", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Britta Flach", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "David H O'Connor", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Adrian B McDermott", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Ajay K Sethi", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Miriam A Shelef", - "author_inst": "University of Wisconsin-Madison" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.06.21249314", "rel_title": "Impaired performance of SARS-CoV-2 antigen-detecting rapid tests at elevated temperatures", @@ -975697,6 +972823,81 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.06.425396", + "rel_title": "SARS-CoV-2 spike downregulates tetherin to enhance viral spread", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.06.425396", + "rel_abs": "The antiviral restriction factor, tetherin, blocks the release of several different families of enveloped viruses, including the Coronaviridae. Tetherin is an interferon-induced protein that forms parallel homodimers between the host cell and viral particles, linking viruses to the surface of infected cells and inhibiting their release. We demonstrated that SARS-CoV-2 infection causes tetherin downregulation, and that tetherin depletion from cells enhances SARS-CoV-2 viral titres. We investigated the potential viral proteins involved in abrogating tetherin function and found that SARS- CoV-2 ORF3a reduces tetherin localisation within biosynthetic organelles via reduced retrograde recycling and increases tetherin localisation to late endocytic organelles. By removing tetherin from the Coronavirus budding compartments, ORF3a enhances virus release. We also found expression of Spike protein caused a reduction in cellular tetherin levels. Our results confirm that tetherin acts as a host restriction factor for SARS-CoV-2 and highlight the multiple distinct mechanisms by which SARS-CoV-2 subverts tetherin function.\n\nAuthor SummarySince it was identified in 2019, SARS-CoV-2 has displayed voracious transmissibility which has resulted in rapid spread of the virus and a global pandemic. SARS-CoV-2 is a member of the Coronaviridae family whose members are encapsulated by a host-derived protective membrane shell. Whilst the viral envelope may provide protection for the virus, it also provides an opportunity for the host cell to restrict the virus and stop it spreading. The anti-viral restriction factor, tetherin, acts to crosslink viruses to the surface of infected cells and prevent their spread to uninfected cells. Here, we demonstrate that SARS-CoV-2 undergoes viral restriction by tetherin, and that SARS-CoV-2 moves tetherin away from the site of Coronavirus budding to enhance its ability to escape and infect naive cells. Tetherin depletion from cells enhanced SARS-CoV-2 viral release and increased propagation of the virus. We found that the SARS-CoV-2 protein, ORF3a, redirects tetherin away from the biosynthetic organelles where tetherin would become incorporated to newly forming SARS-CoV-2 virions - and instead relocalises tetherin to late endocytic organelles. We also found that SARS-CoV-2 Spike downregulates tetherin. These two mechanisms, in addition to the well described antagonism of interferon and subsequent ISGs highlight the multiple mechanisms by which SARS-CoV-2 abrogates tetherin function. Our study provides new insights into how SARS-CoV-2 subverts human antiviral responses and escapes from infected cells.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Hazel Stewart", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Roberta Palmulli", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kristoffer H Johansen", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Naomi McGovern", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ola M Shehata", + "author_inst": "University of Sheffield" + }, + { + "author_name": "George W Carnell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Hannah K Jackson", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jin S Lee", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jonathan C Brown", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas C Burgoyne", + "author_inst": "University College London" + }, + { + "author_name": "Jonathan Luke Heeney", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Klaus Okkenhaug", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew Firth", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew A Peden", + "author_inst": "University of Sheffield" + }, + { + "author_name": "James R Edgar", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.01.06.425622", "rel_title": "Self-organized stem cell-derived human lung buds with proximo-distal patterning and novel targets of SARS-CoV-2", @@ -976472,41 +973673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.04.21249218", - "rel_title": "State-level COVID-19 Trend Forecasting Using Mobility and Policy Data", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249218", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe importance of pandemic forecast cannot be overemphasized. We propose an interpretable machine learning approach for forecasting pandemic transmission rates by utilizing local mobility statistics and government policies. A calibration step is introduced to deal with time-varying relationships between transmission rates and predictors. Experimental results demonstrate that our approach is able to make accurate two-week ahead predictions of the state-level COVID-19 infection trends in the US. Moreover, the models trained by our approach offer insights into the spread of COVID-19, such as the association between the baseline transmission rate and the state-level demographics, the effectiveness of local policies in reducing COVID-19 infections, and so on. This work provides a good understanding of COVID-19 evolution with respect to state-level characteristics and can potentially inform local policymakers in devising customized response strategies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yifei Wang", - "author_inst": "Brandeis University" - }, - { - "author_name": "Hao Peng", - "author_inst": "Andover High School" - }, - { - "author_name": "Long Sha", - "author_inst": "Brandeis University" - }, - { - "author_name": "Zheyuan Liu", - "author_inst": "Brandeis University" - }, - { - "author_name": "Pengyu Hong", - "author_inst": "Brandeis University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.30.20249062", "rel_title": "Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in an end stage renal disease facility", @@ -977043,6 +974209,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.30.20249051", + "rel_title": "The social experience of participation in a COVID-19 vaccine trial: Subjects' motivations, others' concerns, and insights for vaccine promotion", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249051", + "rel_abs": "BackgroundVaccine hesitancy could undermine the effectiveness of COVID-19 vaccination programs. Knowledge about peoples lived experiences regarding COVID-19 vaccination can enhance vaccine promotion and increase uptake.\n\nAimTo use COVID-19 vaccine trial participants experiences to identify key themes in the lived experience of vaccination early in the vaccine approval and distribution process.\n\nMethodsWe interviewed 31 participants in the Iowa City, Iowa US site of the Pfizer/BioNTech COVID-19 vaccine phase 3 clinical trial. While trial participation differs from clinical receipt of an approved vaccine in key ways, it offers the first view of peoples lived experiences of potentially receiving a COVID-19 vaccine. The trial context is also useful since decision-making about vaccination and medical research participation often involve similar hopes and concerns, and because the public appears to view even approved COVID-19 vaccines as experimental given their novelty. Semi-structured interviews addressed subjects experiences, including decision-making and telling others about their trial participation. We analyzed verbatim transcripts of these interviews thematically and identified common themes relevant for vaccination decision-making.\n\nResultsParticipants across demographic groups, including age, sex/gender, race/ethnicity, and political affiliation, described largely similar experiences. Key motivations for participation included ending the pandemic/restoring normalcy, protecting oneself and others, doing ones duty, promoting/modeling vaccination, and expressing aspects of identity like being a helper, career-related motivations, and support of science/vaccines. Participants often felt uniquely qualified to help via trial participation due to personal attributes like health, sex/gender or race/ethnicity. They reported hearing concerns about side effects and the speed and politicization of vaccine development. Participants responded by normalizing and contextualizing side effects, de-politicizing vaccine development, and explaining how the rapid development process was nevertheless safe.\n\nConclusionThese findings regarding participants reported motivations for trial participation and interactions with concerned others can be incorporated into COVID-19 vaccine promotion messaging aimed at similar populations.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Emily Wentzell", + "author_inst": "University of Iowa" + }, + { + "author_name": "Ana-Monica Racila", + "author_inst": "University of Iowa Hospitals and Clinics" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.03.20237602", "rel_title": "Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations", @@ -977946,29 +975135,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.01.05.424956", - "rel_title": "In-Vitro Fluorescence Microscopy Studies Show Retention of Spike-Protein (SARS-Cov-2) on Cell Membrane in the Presence of Amodiaquin Dihydrochloride Dihydrate Drug", - "rel_date": "2021-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.424956", - "rel_abs": "The ability of S-glycoprotein (S-protein) in SARS-Cov-2 to bind to the host cell receptor protein (angiotensin-converting enzyme 2 (ACE2)) leading to its entry in the cellular system determines its contagious index and global spread. Three available drugs (Riboflavin, Amodiaquin dihydrochloride dihydrate (ADD), and Remidesivir) were investigated to understand the kinetics of S-protein and its entry inside a cellular environment. Optical microscopy and fluorescence-based assays on 293T cells (transfected with ACE2 plasmid) were used as the preamble for assessing the behavior of S-protein in the presence of these drugs for the first 12 hours post-S-protein - ACE2 binding. Preliminary results suggest relatively long retention of S-protein on the cell membrane in the presence of ADD drug. Evident from the %-overlap and colocalization of S-protein with endosome studies, a significant fraction of S-protein entering the cell escape endosomal degradation process, suggesting S-protein takes non-endocytic mediated entry in the presence of ADD. In contrast, in the presence of Riboflavin, S-protein carries out a normal endocytic pathway, comparable to the control (no drug) group. Therefore, the present study indicates ADD potentially affects S-proteins entry mechanism (endocytic pathway) in addition to its reported target action mechanism. Hence, ADD substantially interferes with S-protein cellular entrance mechanism. This is further strengthened by 24 hrs study. However, detailed studies at the molecular scale are necessary to clarify our understanding of exact intermediate molecular processes. The present study (based on limited data) reveals ADD could be a potential candidate to manage Covid-19 functions through the yet unknown molecular mechanism.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Partha Pratim Mondal", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Subhra Mandal", - "author_inst": "Creighton University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.12.29.20248869", "rel_title": "High levels of plasminogen activator inhibitor-1, tissue plasminogen activator and fibrinogen in patients with severe COVID-19", @@ -978553,6 +975719,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.29.20248969", + "rel_title": "Reliability of Google Trends: Analysis of the Limits and Potential of Web Infoveillance During COVID-19 Pandemic and for Future Research", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248969", + "rel_abs": "BackgroundAlongside the COVID-19 pandemic, government authorities around the world have had to face a growing infodemic capable of causing serious damages to public health and economy. In this context, the use of infoveillance tools has become a primary necessity.\n\nObjectiveThe aim of this study is to test the reliability of a widely used infoveillance tool which is Google Trends. In particular, the paper focuses on the analysis of relative search volumes (RSVs) quantifying their dependence on the day they are collected.\n\nMethodsRSVs of the query coronavirus + covid during February 1 - December 4, 2020 (period 1), and February 20 - May 18, 2020 (period 2), were collected daily by Google Trends from December 8 to 27, 2020. The survey covered Italian regions and cities, and countries and cities worldwide. The search category was set to all categories. Each dataset was analyzed to observe any dependencies of RSVs from the day they were gathered. To do this, by calling i the country, region, or city under investigation and j the day its RSV was collected, a Gaussian distribution [Formula] was used to represent the trend of daily variations of xij = RSVsij. When a missing value was revealed (anomaly), the affected country, region or city was excluded from the analysis. When the anomalies exceeded 20% of the sample size, the whole sample was excluded from the statistical analysis. Pearson and Spearman correlations between RSVs and the number of COVID-19 cases were calculated day by day thus to highlight any variations related to the day RSVs were collected. Student t-test was used to assess the statistical significance of the differences between the average RSVs of the various countries, regions, or cities of a given dataset. Two RSVs were considered statistical confident when t < 1.5. A dataset was deemed unreliable if the confident data exceeded 20% (confidence threshold). The percentage increase{Delta} was used to quantify the difference between two values.\n\nResultsGoogle Trends has been subject to an acceptable quantity of anomalies only as regards the RSVs of Italian regions (0% in both period 1 and period 2) and countries worldwide (9.7% during period 1 and 10.9% during period 2). However, the correlations between RSVs and COVID-19 cases underwent significant variations even in these two datasets (Max |{Delta}| = + 625% for Italian regions, and Max |{Delta}| = +175% for countries worldwide). Furthermore, only RSVs of countries worldwide did not exceed confidence threshold. Finally, the large amount of anomalies registered in Italian and international cities RSVs made these datasets unusable for any kind of statistical inference.\n\nConclusionsIn the considered timespans, Google Trends has proved to be reliable only for surveys concerning RSVs of countries worldwide. Since RSVs values showed a high dependence on the day they were gathered, it is essential for future research that the authors collect queries data for several consecutive days and work with their RSVs averages instead of daily RSVs, trying to minimize the standard errors until an established confidence threshold is respected.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alessandro Rovetta", + "author_inst": "Mensana srls; Redeev srl" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.28.20248957", "rel_title": "Comparative Study - The Impact and Profile of COVID-19 Patients Who Are Indicated for Neuroimaging: Vascular Phenomena Are Been Found in the Brain and Olfactory Bulbs", @@ -979488,29 +976673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.30.20248889", - "rel_title": "Cardiometabolic risks of SARS-CoV-2 hospitalization using Mendelian Randomization", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248889", - "rel_abs": "IntroMany cardiometabolic conditions have demonstrated associative evidence with COVID-19 hospitalization risk. However, the observational designs of the studies in which these associations are observed preclude causal inferences of hospitalization risk. Mendelian Randomization (MR) is an alternative risk estimation method more robust to these limitations that allows for causal inferences.\n\nMethods & materialsWe applied four MR methods (MRMix, IMRP, IVW, MREgger) to publicly available GWAS summary statistics from European (COVID-19 GWAS n=2,956) and multi-ethnic populations (COVID-19 GWAS n=10,808) to better understand extant causal associations between Type II Diabetes (GWAS n=659,316), BMI (n=681,275), diastolic and systolic blood pressure, and pulse pressure (n=757,601 for each) and COVID-19 hospitalization risk across populations.\n\nResultsAlthough no significant causal effect evidence was observed, our data suggested a trend of increasing hospitalization risk for Type II diabetes (IMRP OR, 95% CI: 1.67, 0.96-2.92) and pulse pressure (OR, 95% CI: 1.27, 0.97-1.66) in the multi-ethnic sample.\n\nConclusionsType II diabetes and Pulse pressure demonstrates a potential causal association with COVID-19 hospitalization risk, the proper treatment of which may work to reduce the risk of a severe COVID-19 illness requiring hospitalization. However, GWAS of COVID-19 with large sample size is warranted to confirm the causality.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Noah J Lorincz-Comi", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Xiaofeng Zhu", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.28.20248936", "rel_title": "Lockdown Effects on Sars-CoV-2 Transmission - The evidence from Northern Jutland", @@ -979979,6 +977141,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.03.21249157", + "rel_title": "Implications in the quantitation of SARS-CoV2 copies in concurrent nasopharyngeal swabs, whole mouth fluid and respiratory droplets", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249157", + "rel_abs": "ImportanceThe nasopharyngeal swab (NPS) is considered the ideal diagnostic specimen for Covid-19, while WMF is recently promoted due to collection simplicity and importance in disease transmission. There is limited knowledge on the relative viral load in these samples - NPS, whole mouth fluid (WMF) and respiratory droplets (RD; another important source in transmission), on how the loads vary with disease severity and on how much virus is shed.\n\nObjectiveTo quantify and compare SARS-CoV2 copies in the NPS, WMF and RD samples, and correlate with disease severity.\n\nDesignCross sectional study.\n\nSettingTertiary care multi-speciality hospital with limited resources in a low-to-middle income country.\n\nParticipantsEighty suspected COVID-19 patients were recruited from the COVID-19 out-patient clinic and hospital isolation wards.\n\nInterventionConcurrent NPS, WMF and RD samples were collected from all the recruited patients and tested for SARS-CoV2 copies by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR).\n\nMain outcomes and measuresThe main outcome was COVID-19 measured by SARS-CoV2 quantitative RT-PCR in NPS samples. COVID-19 disease severity was determined according to NIH criteria. Virus shedding was defined as the presence of SARS-CoV2 copies in the WMF and RD samples.\n\nResultsSARS-CoV2 was detected in 55/80 (69%) of the NPS samples. Of these 55, WMF and RD samples were positive in 44 (80%) and 17 (31%), respectively. The concordance of WMF with NPS was 84% (p=0.02). SARS-CoV2 copy numbers were comparable in the NPS (median: 8.74x10^5) and WMF (median: 3.07x10^4), but lower in RD samples (median: 3.60x10^2). Patients with mild disease had higher copies in the NPS (median: 3.46x10^6), while patients with severe disease had higher copies in the WMF (median: 1.34x10^6) and RD samples (median: 4.29x10^4). The 25-75% interquartile range of NPS SARS-CoV2 copies was significantly higher in the WMF (p=0.0001) and RD (p=0.01) positive patients.\n\nConclusion and relevanceSARS-CoV2 copies are highest in NPS samples. WMF is a reliable surrogate sample for diagnosis. High copy numbers in the NPS imply initial virological phase and higher risk of virus shedding via WMF and RD.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSHow the numbers of SARS-CoV2 copies in nasopharyngeal swab (NPS) samples might reflectvirus shedding from the whole upper aerodigestive tract and indicatedisease severity?\n\nFindingsIn this cross-sectional study involving 80 suspected COVID-19 patients, the data indicate higher SARS-CoV2 copies in NPS samples of patients with mild disease,and in the whole mouth fluid (WMF) and respiratory droplet (RD) samples of patients with severe disease. Patients with higher SARS-CoV2 copies in the NPS shed the virus in the WMF and RD samples at statistically higher levels.\n\nMeaningHigh SARS-CoV2 copies in NPS samples imply initial virological phase withhigh levels of shedding through both WMF and RD.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Priya Kannian", + "author_inst": "The Voluntary Health Services Hospital" + }, + { + "author_name": "Bagavad Gita Jayaraman", + "author_inst": "Chennai Dental Research Foundation, Chennai, India" + }, + { + "author_name": "Swarna Alamelu", + "author_inst": "Ragas Dental College and Hospital, Chennai, India" + }, + { + "author_name": "Chandra Lavanya", + "author_inst": "Ragas Dental College and Hospital, Chennai, India" + }, + { + "author_name": "Nagalingeswaran Kumarasamy", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Gunaseelan Rajan", + "author_inst": "Chennai Dental Research Foundation, Chennai, India" + }, + { + "author_name": "Kannan Ranganathan", + "author_inst": "Ragas Dental College and Hospital, Chennai, India" + }, + { + "author_name": "Pasuvaraj Mahanathi", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Veeraraghavan Ashwini", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Stephen J Challacombe", + "author_inst": "King's College, London, UK" + }, + { + "author_name": "Jennifer Webster-Cyriaque", + "author_inst": "University of North Carolina, Chapel Hill, USA" + }, + { + "author_name": "Newell W Johnson", + "author_inst": "Griffith University, Queensland, Australia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.31.20248236", "rel_title": "Sub-5-minute Detection of SARS-CoV-2 RNA using a Reverse Transcriptase-Free Exponential Amplification Reaction, RTF-EXPAR", @@ -980790,29 +978015,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.02.21249126", - "rel_title": "Burden of predominant psychological reactions among the healthcare workers and general during COVID-19 pandemic phase: a systematic review and meta-analysis", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.21249126", - "rel_abs": "AimPresent systematic review and meta-analysis examined the burden of psychological reactions predominantly anxiety, depression, stress and insomnia during novel COVID-19 pandemic phase among the frontline healthcare, non-frontline healthcare and general.\n\nMethodologyPubMed, EMBASE and SCOPUS were searched for studies between Jan 1, 2020 to May 25, 2020. Brief protocol of the systematic review was registered with the PROSPERO database, (CRD42020186229).Any study that reported the burden of at least one of psychological reactions including anxiety or depression or stress or insomnia was eligible. Heterogeneity was assessed using I2 statistic and results were synthesized using random effect meta-analysis.\n\nResultsOut of 52eligible studies, 43 reported anxiety, 43 reported depression, 20 reported stress and 11 reported insomnia. Overall prevalence for anxiety, depression, stress and insomnia were 26.6%, 26.2%,26.2% and 34.4% respectively. Anxiety and depression were found highest among the COVID-19 patients (43.3% and 51.75 respectively). Apart from COVID-19 patients, prevalence of anxiety, depression, stress and insomnia were found highest among the frontline healthcare (27.2%, 32.1%,55.6% and 34.4% respectively) as compared to general healthcare workers (26.9%, 15.7%, 7.0% and 34.0% respectively) and general population (25.9%, 25.9%,25.4% and 29.4% respectively).\n\nConclusionAnxiety and depression were found highest among the COVID-19 patients. Apart from COVID-19 patients, the anxiety, depression, stress and insomnia were more prevalent among frontline healthcare workers compared to general. Such increased prevalence is prompting towards the global mental health emergency. Therefore a call of urgent attention and pan-region effective mental-health intervention are required to mitigate these psychological reactions.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Bhaskar Thakur", - "author_inst": "Division of Biostatistics & Epidemiology, Texas Tech Health Science Center, El Paso, TX, USA" - }, - { - "author_name": "Mona Pathak", - "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.02.20248940", "rel_title": "Brazilian model estimation for SARS-CoV-2 peak contagion (BMESPC): first and second wave", @@ -981533,6 +978735,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.29.20248976", + "rel_title": "Laboratory Biomarkers of COVID-19 Disease Severity and Outcome: Findings from a Developing Country", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248976", + "rel_abs": "AimTo identify laboratory biomarkers that predict disease severity and outcome among COVID-19 patients admitted to the Millennium COVID-19 Care Center in Ethiopia.\n\nMethodsA retrospective cohort study was conducted among 429 RT-PCR confirmed COVID- 19 patients who were on follow up from July to October 2020 and with complete clinical and laboratory data. Data was described using frequency tables. Robust Poisson regression model was used to identify predictors of COVID-19 disease severity where adjusted relative risk (RR), P-value and 95% CI for RR were used to test significance and interpretation of results. Binary Logistic regression model was used to assess the presence of statistically significant association between the explanatory variables and COVID-19 disease outcome where adjusted odds ratio, P- value and 95% CI for adjusted odds ratio were used for testing significance and interpretation of results\n\nResultsAmong the 429 patients studied, 182 (42.4%) had Severe disease at admission and the rest 247 (57.6%) had Non-severe disease (15.6% mild and 42.0% moderate). Regarding disease outcome, 45 (10.5%) died and 384 (89.5%) were discharged alive. Age group (ARR= 1.779, 95% CI= 1.405- 2.252, p-value < 0.0001), Neutrophil to Lymphocyte ratio (NLR) (ARR= 4.769, 95% CI= 2.419 - 9.402 p-value <0.0001), Serum glutamic oxaloacetic transaminase (SGOT) (ARR= 1.358, 95% CI= 1.109- 1.662 p-value=0.003), Sodium (ARR= 1.321, 95% CI= 1.091- 1.600 p-value=0.004) and Potassium (ARR= 1.269, 95% CI= 1.059-1.521 p-value=0.010) were found to be significant predictors of COVID-19 disease severity.\n\nThe following factors were significantly associated with COVID-19 disease outcome; age group (AOR= 2.767, 95% CI= 1.099 - 6.067, p-value=0.031), white blood cell count (AOR= 4.253, 95% CI= 1.918 - 9.429, p-value=0.0001) and sodium level (AOR= 3.435, 95% CI= 1.439, 8.198, p-value=0.005).\n\nConclusionsThe laboratory markers of NLR of above three, raised SGOT and deranged sodium and potassium levels (both hypo- and hyper-states) were found to be significant predictors of developing severe COVID-19 disease. In addition, deranged values of white blood cell count and sodium levels were significantly associated with worse outcome of the disease. Therefore, assessing and monitoring these laboratory markers at the earliest stage of the disease could have a considerable impact in halting disease progression and death.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Tigist W. Leulseged", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Ishmael S. Hassen", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Birhanu T. Ayele", + "author_inst": "Divison of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" + }, + { + "author_name": "Yakob G. Tsegay", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Daniel S. Abebe", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Mesay G. Edo", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Endalkachew H. Maru", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Wuletaw C. Zewde", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Lydia K. Naylor", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Dejen F. Semane", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Menayit T. Deresse", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + }, + { + "author_name": "Bereket B. Tezera", + "author_inst": "Millennium COVID-19 Care Center, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.01.425028", "rel_title": "Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant", @@ -982672,33 +979937,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.12.26.20248858", - "rel_title": "Public Search Interests related to COVID-19: Insights from Google Search Trends in Bangladesh", - "rel_date": "2021-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248858", - "rel_abs": "ObjectivePublic response monitoring is critical to reducing COVID-19 infections and developing effective public health strategies. This study explored Google search trends to understand public responses to COVID-19 concerns in Bangladesh.\n\nMethodsWe used country-level Google search trends data to examine the association between Google search terms related to COVID-19 deaths, face masks, and COVID-19 vaccines and the actual and one-week lagged actual COVID-19 death counts from February 2, 2020, to December 19, 2020, in Bangladesh. Results: Search terms related to COVID-19 deaths, face masks, and COVID-19 vaccines increased and peaked during March and April, but then began declining gradually after June 2020. The mean relative search volume for face masks (35 points) was higher than for death information (8 points) and vaccines (16 points) throughout the study period, and searching for masks peaked (100 points) during the third week of March. Search interests for death information and face masks were negatively correlated with the actual and one-week lagged actual COVID-19 death counts.\n\nConclusionIn response to declining trends in COVID-19-related google search terms, policymakers should strengthen ongoing risk communication and preventive information dissemination programs to control and prevent COVID-19 cases and deaths.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mazbahul G Ahamad", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Monir U Ahmed", - "author_inst": "Shahjalal University of Science and Technology" - }, - { - "author_name": "Daniel R Uden", - "author_inst": "University of Nebraska-Lincoln" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.12.28.20248920", "rel_title": "Determinants of in-hospital mortality in COVID-19; a prospective cohort study from Pakistan", @@ -983243,6 +980481,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.12.28.20248922", + "rel_title": "The Ugandan Severe Acute Respiratory Syndrome -Coronavirus 2 (SARS-CoV-2) Model: A Data Driven Approach to Estimate Risk", + "rel_date": "2021-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248922", + "rel_abs": "ObjectivesThe first case of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) was identified on March 21, 2020, in Uganda. The number of cases increased to 8,287 by September 30, 2020. By May throughout June, most of the cases were predominantly imported cases of truck drivers from neighbouring countries. Uganda responded with various restrictions and interventions including lockdown, physical distancing, hand hygiene, and use of face masks in public, to control the growth rate of the outbreak. By end of September 2020, Uganda had transitioned into community transmissions and most of the reported cases were locals contacts and alerts. This study assessed risks associated with SARS-CoV-2 in Uganda, and presents estimates of the reproduction ratio in real time. An optimal control analysis was performed to determine how long the current mitigation measures such as controlling the exposure in communities, rapid detection, confirmation and contact tracing, partial lockdown of the vulnerable groups and control at the porous boarders, could be implemented and at what cost.\n\nMethodsThe daily confirmed cases of SARS-CoV-2 in Uganda were extracted from publicly available sources. Using the data, relative risks for age, gender, and geographical location were determined. Four approaches were used to forecast SARS-CoV-2 in Uganda namely linear exponential, nonlinear exponential, logistic and a deterministic model. The discrete logistic model and the next generation matrix method were used to estimate the effective reproduction number.\n\nResultsResults showed that women were at a higher risk of acquiring SARS-CoV-2 than the men, and the population attributable risk of SARS-CoV-2 to women was 42.22%. Most of the women affected by SARS-CoV-2 were likely contacts of cargo truck drivers at the boarders, where high infection rates were reported. Although most deaths in Uganda were in the age group of 60-69, the highest case fatality rate per 1000 was attributable the age group of 80-89, followed by 70-79. Geographically, Amuru had the highest relative risk compared to the national risk to SARS-CoV-2. For the case of mitigation scenarios, washing hands with 70% com pliance and regular hand washing of 6 times a day, was the most effective and sustainable to reduce SARS- CoV-2 exposure. This was followed by public wearing of face masks if at least 60% of the population complied, and physical distancing by 60% of the population. If schools, bars and churches were opened without compliance, i.e., no distancing, no handwashing and no public wearing of face masks, to mitigation measures, the highest incidence was observed, leading to a big replacement number. If mitigation measures are not followed by the population, then there will be high incidences and prevalence of the virus in the population.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Betty K Nannyonga", + "author_inst": "Makerere University" + }, + { + "author_name": "Henry Kyobe Bosa", + "author_inst": "Uganda Peoples Defense Forces" + }, + { + "author_name": "Yonas Tegegn Wodermariam", + "author_inst": "WHO" + }, + { + "author_name": "Pontiano Kaleebu", + "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit, Uganda Virus Research Institute" + }, + { + "author_name": "John Ssenkusu", + "author_inst": "School of Public Health, College of Health Sciences, Makerere University" + }, + { + "author_name": "Tom Lutalo", + "author_inst": "School of Public Health, College of Health Sciences, Makerere University" + }, + { + "author_name": "Willford Kirungi", + "author_inst": "Ministry of Health, Uganda" + }, + { + "author_name": "Fredrick Edward Makumbi", + "author_inst": "Ministry of Health, Uganda" + }, + { + "author_name": "Vincent Aloysius Ssembatya", + "author_inst": "Makerere University" + }, + { + "author_name": "Henry G Mwebesa", + "author_inst": "Ministry of Health, Uganda" + }, + { + "author_name": "Diana Atwine", + "author_inst": "Ministry of Health, Uganda" + }, + { + "author_name": "Jane Ruth Aceng", + "author_inst": "Ministry of Health, Uganda" + }, + { + "author_name": "Rhoda K Wanyenze", + "author_inst": "School of Public Health, College of Health Sciences, Makerere University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.27.20248876", "rel_title": "The evaluation of a newly developed antigen test (QuickNavi\u2122-COVID19 Ag) for SARS-CoV-2: A prospective observational study in Japan", @@ -984006,65 +981311,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.24.20248633", - "rel_title": "Unraveling COVID-19-related hospital costs: The impact of clinical and demographic conditions", - "rel_date": "2020-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248633", - "rel_abs": "IntroductionAlthough patients clinical conditions were previously shown to be associated with coronavirus disease 2019 (COVID-19) severity and outcomes, their impact on hospital costs is not known. The economic evaluation of COVID-19 admissions allows the assessment of hospital costs associated with the treatment of these patients, including the main cost components and costs driven by demographic and clinical conditions. The aim of this study was to determine the COVID-19 hospitalization-related costs and their association with clinical conditions.\n\nMethodsProspective observational cohort study of the hospitalization costs of patients with COVID-19 admitted between March 30 and June 30, 2020, who were followed until discharge, death, or external transfer, using micro-costing methodology. The study was carried out in the Central Institute of the Hospital das Clinicas, affiliated with the Faculty of Medicine of the University of Sao Paulo, Brazil, which is the largest hospital complex in Latin America and was designated to exclusively admit COVID-19 patients during the pandemic response.\n\nResultsThe average cost of the 3,254 admissions (51.7% of which involved intensive care unit (ICU) stays) was US$12,637.42. Overhead cost was the main cost component, followed by daily fixed costs and drugs. Sex, age and underlying hypertension (US$14,746.77), diabetes (US$15,002.12), obesity (US$18,941.55), cancer (US$10,315.06), chronic renal failure (US$15,377.84), and rheumatic (US$17,764.61), hematologic (US$15,908.25) and neurologic diseases (US$15,257.95) were significantly associated with higher costs. Age >69 years, RT-PCR-confirmed COVID-19, comorbidities, the use of mechanical ventilation, dialysis, or surgery, and poor outcomes remained significantly associated with higher costs after model adjustment.\n\nConclusionKnowledge of COVID-19-associated hospital costs and their impact across different populations can aid in the development of a generalizable and comprehensive approach to hospital preparedness, decision-making and planning for future risk management. Determining the disease-associated costs is the first step in evaluating the cost-effectiveness of treatments and vaccination programs.\n\nSUMMARY BOXO_ST_ABSQuestionC_ST_ABSWhat are the COVID-19 hospitalization-related costs?\n\nFindingsIn this prospective cohort that was carried out in a single reference quaternary center designated for the treatment of severe cases of COVID-19, more than three thousand patients were included, and their costs of hospitalization were found to be directly related to the age and comorbidities. The costs were more than 50% higher in older patients, 10-24% higher in patients with comorbidities, and 24-200% higher when additional therapeutic procedures were required.\n\nMeaningDetermining the disease-associated costs is the first step in conducting future evaluations of the cost-effectiveness of treatments and vaccination programs, supporting their implementation with a comprehensive population-based approach.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Anna Anna Miethke-Morais", - "author_inst": "Clinical Director's Office, Hospital das Clinicas, Faculty of Medicine, University of Sao Paulo, SP, Brazil" - }, - { - "author_name": "Alex Cassenote", - "author_inst": "Department of Gastroenterology, Faculty of Medicine, University of Sao Paulo, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Heloisa Piva", - "author_inst": "Executive Director's Office, Instituto Central, Hospital das Clinicas, Faculty of Medicine, University of Sao Paulo, SP, Brazil" - }, - { - "author_name": "Eric Tokunaga", - "author_inst": "Strategy and Operations Department, Hospital das Clinicas, University of Sao Paulo Medical School - FMUSP, Sao Paulo, Brazil" - }, - { - "author_name": "Vilson Cobello", - "author_inst": "Information Technology Department, University of Sao Paulo School of Medicine FM-USP, Sao Paulo, Brazil" - }, - { - "author_name": "Fabio Augusto Rodrigues Alves", - "author_inst": "Affiliated Researcher, Health Technology Assessment Center of the Clinical Hospital (HC-FMUSP), Sao Paulo University Medical School (FMUSP), Sao Paulo, Brazil." - }, - { - "author_name": "Renata Aparecida dos Santos Lobo", - "author_inst": "Health Technology Assessment Center of the Clinics Hospital of the Sao Paulo University Medical School, NATS-HCFMUSP" - }, - { - "author_name": "Evelinda Trindade", - "author_inst": "Health Technology Assessment Center of the Clinics Hospital of the Sao Paulo University Medical School, NATS-HCFMUSP" - }, - { - "author_name": "Luiz Augusto Carneiro D'Albuquerque", - "author_inst": "Digestive Organs Transplant Division, Gastroenterology Department, University of Sao Paulo School of Medicine FM-USP, Sao Paulo, Brazil" - }, - { - "author_name": "- HCFMUSP Covid-19 Study Group", - "author_inst": "" - }, - { - "author_name": "Luciana Haddad", - "author_inst": "Digestive Organs Transplant Division, Gastroenterology Department, University of Sao Paulo School of Medicine FM-USP, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.12.24.20248842", "rel_title": "Simulating Retarded SEIRS model for COVID-19: will the second epidemic happen?", @@ -984812,6 +982058,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.29.424644", + "rel_title": "Defective NETs Clearance contributes to sustained FXII Activation in COVID-19-associated Pulmonary Thrombo-Inflammation", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424644", + "rel_abs": "BackgroundCoagulopathy and inflammation are hallmarks of Coronavirus disease 2019 (COVID-19) and are associated with increased mortality. Clinical and experimental data have revealed a role for neutrophil extracellular traps (NETs) in COVID-19 disease. The mechanisms that drive thrombo-inflammation in COVID-19 are poorly understood.\n\nMethodsWe performed proteomic analysis and immunostaining of postmortem lung tissues from COVID-19 patients and patients with other lung pathologies. We further compared coagulation factor XII (FXII) and DNase activities in plasma samples from COVID-19 patients and healthy control donors and determined NET-induced Factor XIII (FXII) activation using a chromogenic substrate assay.\n\nFindingsFXII expression and activity were increased in the lung parenchyma, within the pulmonary vasculature and in fibrin-rich alveolar spaces of postmortem lung tissues from COVID-19 patients. In agreement with this, plasma FXII activation (FXIIa) was increased in samples from COVID-19 patients. Furthermore, FXIIa colocalized with NETs in COVID-19 lung tissue indicating that NETs accumulation leads to FXII contact activation in COVID-19. We further showed that an accumulation of NETs is partially due to impaired NET clearance by extracellular DNases as DNase substitution improved NET dissolution and reduced FXII activation in vitro.\n\nInterpretationCollectively, our study supports that the NETs/FXII axis contributes to the pathogenic chain of procoagulant and proinflammatory responses in COVID-19. Targeting both, NETs and FXIIa, could provide a strategy to mitigate COVID-19-induced thrombo-inflammation.\n\nFundingThis study was supported by the European Union (840189), the Werner Otto Medical Foundation Hamburg (8/95) and the German Research Foundation (FR4239/1-1, A11/SFB877, B08/SFB841 and P06/KFO306).", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hanna Englert", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Chandini Rangaswamy", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Carsten Deppermann", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Jan-Peter Sperhake", + "author_inst": "University Medical Center Hamburg (UKE), Department of Legal Medicine" + }, + { + "author_name": "Christoph Krisp", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Danny Schreier", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine, Vascular Biology Laboratory" + }, + { + "author_name": "Emma Gordon", + "author_inst": "The University of Queensland, UQ Centre for Cardiac and Vascular Biology, Institute for Molecular Bioscience" + }, + { + "author_name": "Sandra Konrath", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine, Vascular Biology Laboratory" + }, + { + "author_name": "Munif Haddad", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Giordano Pula", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Reiner Mailer", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Hartmut Schlueter", + "author_inst": "Universitatsklinikum Hamburg-Eppendorf" + }, + { + "author_name": "Stefan Kluge", + "author_inst": "University Medical Center Hamburg-Eppendorf, Department of Intensive Care Medicine, Hamburg, Germany" + }, + { + "author_name": "Florian Langer", + "author_inst": "University Medical Center Hamburg (UKE), II. Medical Clinic and Polyclinic" + }, + { + "author_name": "Klaus Pueschel", + "author_inst": "University Medical Center Hamburg (UKE), Department of Legal Medicine" + }, + { + "author_name": "Kosta Panousis", + "author_inst": "CSL Limited, BIO21 Institute" + }, + { + "author_name": "Evi Stavrou", + "author_inst": "Case Western Reserve University School of Medicine, Department of Medicine" + }, + { + "author_name": "Coen Maas", + "author_inst": "University Medical Center Utrecht, Department of Clinical Chemistry and Haematology" + }, + { + "author_name": "Thomas Renne", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine" + }, + { + "author_name": "Maike Frye", + "author_inst": "University Medical Center Hamburg (UKE), Institute for Clinical Chemistry and Laboratory Medicine, Vascular Biology Laboratory" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.12.29.424530", "rel_title": "Host Specific SARS-CoV-2 Mutations: Insertion of the Phenylalanine in the NSP6 Linked to the United Kingdome and Premature Termination of the ORF-8 Associated with the European and the United States of America Derived Samples.", @@ -985703,20 +983044,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.28.424582", - "rel_title": "Emerging SARS-CoV-2 diversity revealed by rapid whole genome sequence typing.", - "rel_date": "2020-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424582", - "rel_abs": "BackgroundDiscrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events.\n\nMethodsWe developed a tool (GNUVID) that integrates whole genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to each of 69,686 SARS-CoV-2 complete, high-quality genomes available from GISAID as of October 20th 2020. STs were then clustered into clonal complexes (CCs), and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events, and to estimate effective viral diversity across locations and over time in 16 US states.\n\nResultsGNUVID is a scalable tool for viral genotype classification (available at https://github.com/ahmedmagds/GNUVID) that can be used to quickly process tens of thousands of genomes. Our genotyping ST/CC analysis uncovered dynamic local changes in ST/CC prevalence and diversity with multiple replacement events in different states. We detected an average of 20.6 putative introductions and 7.5 exportations for each state. Effective viral diversity dropped in all states as shelter-in-place travel-restrictions went into effect and increased as restrictions were lifted. Interestingly, our analysis showed correlation between effective diversity and the date that state-wide mask mandates were imposed.\n\nConclusionsOur classification tool uncovered multiple introduction and exportation events, as well as waves of expansion and replacement of SARS-CoV-2 genotypes in different states. Combined with future genomic sampling the GNUVID system could be used to track circulating viral diversity and identify emerging clones and hotspots.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.12.27.424507", "rel_title": "Losartan promotes cell survival following SARS-CoV-2 infection in vitro", @@ -986361,6 +983688,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.26.424450", + "rel_title": "The mechanism of SARS-CoV-2 nucleocapsid protein recognition by the human 14-3-3 proteins", + "rel_date": "2020-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.26.424450", + "rel_abs": "The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association can regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, while hijacking cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.\n\nHighlightsSARS-CoV-2 nucleocapsid protein (N) binds to all seven human 14-3-3 isoforms. This association with 14-3-3 strictly depends on phosphorylation of N. The two proteins interact in 2:2 stoichiometry and with the Kd in a M range. Affinity of interaction depends on the specific 14-3-3 isoform. Conserved Ser197-phosphopeptide of N is critical for the interaction.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kristina V Tugaeva", + "author_inst": "A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia" + }, + { + "author_name": "Dorothy E. D. P. Hawkins", + "author_inst": "York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom" + }, + { + "author_name": "Jake L. R. Smith", + "author_inst": "York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom" + }, + { + "author_name": "Oliver W Bayfield", + "author_inst": "University of York" + }, + { + "author_name": "De-Sheng Ker", + "author_inst": "York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom" + }, + { + "author_name": "Andrey A Sysoev", + "author_inst": "A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia" + }, + { + "author_name": "Oleg I Klychnikov", + "author_inst": "Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia" + }, + { + "author_name": "Alfred A Antson", + "author_inst": "York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom" + }, + { + "author_name": "Nikolai N. Sluchanko", + "author_inst": "A.N.Bach Institute of biochemistry, FRC of biotechnology of RAS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.12.26.424423", "rel_title": "The neutralization effect of Montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies", @@ -987504,33 +984882,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.24.424260", - "rel_title": "TCR meta-clonotypes for biomarker discovery with tcrdist3: quantification of public, HLA-restricted TCR biomarkers of SARS-CoV-2 infection", - "rel_date": "2020-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.24.424260", - "rel_abs": "As the mechanistic basis of adaptive cellular antigen recognition, T cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages antigen-enriched repertoires to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly identify and quantify functionally similar TCRs in bulk repertoires. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the 17 SARS-CoV-2 antigen-enriched repertoires with the strongest evidence of HLA-restriction. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (FDR < 0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Koshlan Mayer-Blackwell", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA" - }, - { - "author_name": "Philip Bradley", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew Fiore-Gartland", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.23.424231", "rel_title": "Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene", @@ -988139,6 +985490,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.24.20248519", + "rel_title": "Mental health, personality and lifetime psychedelic use during the COVID-19 pandemic", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248519", + "rel_abs": "BackgroundThe COVID-19 pandemic and its consequences represent a major challenge to the mental health and well-being of the general population. Some groups may be more vulnerable than others, depending on factors such as preexisting conditions, personality, and past life experiences. Building on previous work on the potential long-term benefits of psychedelics, we hypothesized that lifetime use of these drugs could be linked to better mental health indicators in the context of the ongoing pandemic.\n\nMethodsTwo anonymous online surveys were conducted between April 2020 and June 2020, including questions about lifetime experience with psychedelics and other psychoactive drugs, and psychometric scales designed to measure personality traits, anxiety, negative and positive affect, well-being and resilience. Principal component analysis was applied to divide the sample into groups of subjects based on their drug use reports.\n\nResults5618 participants (29.15 {+/-} 0.12 years, 71.97% female) completed both surveys and met the inclusion criteria, with 32.43% of the final sample reporting at least one use of a psychedelic drug. Lifetime psychedelic use was linked to increased openness and decreased conscientiousness, and with higher scores of positive affect. The reported number of past psychedelic experiences predicted higher scores of the secondary personality trait beta factor, which has been interpreted as a measure of plasticity. No significant associations between lifetime use of psychedelics and indicators of impaired mental health were observed.\n\nConclusionWe did not find evidence of an association between lifetime use of psychedelics and poor mental health indicators. Conversely, experience with psychedelic drugs was linked to increased positive affect and to personality traits that favor resilience and stability in the light of the ongoing crisis. Future studies should be conducted to investigate these results from a causal perspective.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Federico Cavanna", + "author_inst": "Departamento de F\u00edsica, Universidad de Buenos Aires and Instituto de F\u00edsica de Buenos Aires (IFIBA \u2212 CONICET), Pabell\u00f3n I, Ciudad Universitaria (1428), CABA, Bu" + }, + { + "author_name": "Carla Pallavicini", + "author_inst": "Departamento de F\u00edsica, Universidad de Buenos Aires and Instituto de F\u00edsica de Buenos Aires (IFIBA \u2212 CONICET), Pabell\u00f3n I, Ciudad Universitaria (1428), CABA, Bu" + }, + { + "author_name": "Virginia Milano", + "author_inst": "El Gato y La Caja" + }, + { + "author_name": "Juan Cuiule", + "author_inst": "El Gato y La Caja" + }, + { + "author_name": "Rocco Di Tella", + "author_inst": "El Gato y La Caja" + }, + { + "author_name": "Pablo Gonz\u00e1lez", + "author_inst": "El Gato y La Caja" + }, + { + "author_name": "Enzo Tagliazucchi", + "author_inst": "Departamento de F\u00edsica, Universidad de Buenos Aires and Instituto de F\u00edsica de Buenos Aires (IFIBA \u2212 CONICET), Pabell\u00f3n I, Ciudad Universitaria (1428), CABA, Bu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.24.20248802", "rel_title": "Characterizing Long COVID in an International Cohort: 7 Months of Symptoms and Their Impact", @@ -989310,49 +986704,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.18.20248480", - "rel_title": "Hospitalization for self-harm during the early months of the Covid-19 pandemic in France: a nationwide study", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248480", - "rel_abs": "IntroductionLittle is known to date about the impact of Covid-19 pandemic on self-harm incidence.\n\nMethodsThe number of hospitalizations for self-harm in France (mainland and overseas) from January to August 2020 (which includes the first confinement from March 17th to May 11th) was compared to the same period in 2019-2017. Hospital data with the ICD-10 codes X60-84 were extracted from the national administrative database (PMSI).\n\nResultsThere were 53,583 hospitalizations for self-harm in France between January and August 2020. Compared to the same period in 2019, this represents an overall 8.5% decrease. This decrease started the first week of the confinement and the number of hospitalizations remained at lower levels relative to 2019 until the end of August. The decrease was more marked in women (-9.8%) than men (-6.4%). However, an increase in hospitalizations was observed in individuals aged 75 and older (+5.3 to +11.6%). Moreover, the number of self-harm by firearm (+20.3%), jumping from height (+10.5%), and drowning (+4.7%) increased between 2019 and 2020, as well as the number of hospitalizations in intensive care (+3.5%) and deaths at discharge from hospital (+8.0%). No correlation was found between the evolution in the number of hospitalizations for self-harm and the number of severe cases of Covid-19 (hospitalization and mortality rates) across administrative departments.\n\nDiscussionDuring the early months of the Covid-19 pandemic in France - including the first confinement -, a general decrease in the number of hospitalizations for self-harm was observed. However, an increase was found among elderly, a population at higher Covid 19-related mortality risk, and in the number of more severe suicidal acts. These results, therefore, shed light on a complex relationship between the pandemic and self-harm occurrence. This situation may change with time, which requires active suicide prevention strategies.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fabrice Jollant", - "author_inst": "University de Paris" - }, - { - "author_name": "Adrien Roussot", - "author_inst": "CHU de Dijon" - }, - { - "author_name": "Emmanuelle Corruble", - "author_inst": "AP-HP" - }, - { - "author_name": "Jean-Christophe CHAUVET-GELINIER", - "author_inst": "CHU Dijon" - }, - { - "author_name": "Bruno Falissard", - "author_inst": "Inserm" - }, - { - "author_name": "Yann Mikaeloff", - "author_inst": "AP-HP" - }, - { - "author_name": "Catherine Quantin", - "author_inst": "CHU de Dijon" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.12.23.20248612", "rel_title": "Coronavirus GenBrowser for monitoring adaptive evolution and transmission of SARS-CoV-2", @@ -990097,6 +987448,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.23.20248794", + "rel_title": "How the COVID-19 pandemic affects transgender health care in upper-middle income and high income countries - A worldwide, cross-sectional survey", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248794", + "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic, access to medical care was restricted for nearly all non-acute medical conditions. Due to their status as a vulnerable social group and the inherent need for transition-related treatments (e.g., hormone treatment), transgender people are assumed to be affected particularly severely by the restrictions caused by the COVID-19 pandemic. This study aims to assess the impact of the COVID-19 pandemic on the health and health care of transgender people.\n\nMethods and findingsAs an ad hoc collaboration between researchers, clinicians, and 23 community organizations, we developed a web-based survey. The survey was translated into 26 languages, and participants were recruited via various social media and LGBTIQ-community sources. Recruitment started in May 2020. We assessed demographical data, physical and mental health problems (e.g., chronic physical conditions), risk factors (e.g., smoking), COVID-19 data (symptoms, contact history, knowledge and concerns about COVID-19), and the influence of the COVID-19 pandemic on access to transgender health care and health-related supplies. To identify factors associated with the experience of restrictions to transgender health care, we conducted multivariate logistic regression analysis.\n\n5267 transgender people from 63 higher-middle income and high-income countries participated in the study. Over 50% of the participants had risk factors for a severe course of a COVID-19 infection and were at a high risk of avoiding testing or treatment of a COVID-19 infection due to the fear of mistreatment or discrimination. Access to transgender health care services was restricted due to the COVID-19 pandemic for 50% of the participants. Male sex assigned at birth and a lower monthly income were significant predictors for the experience of restrictions to health care. 35.0% of the participants reported at least one mental health conditions. Every third participant had suicidal thoughts, and 3.2% have attempted suicide since the beginning of the COVID-19 pandemic. A limitation of the study is that we did not analyze data from low-income countries and access to the internet was necessary to participate.\n\nConclusionsTransgender people are assumed to suffer under the severity of the pandemic even more than the general population due to the intersections between their status as a vulnerable social group, their high amount of medical risk factors, and their need for ongoing medical treatment. The COVID-19 pandemic can potentiate these vulnerabilities, add new challenges for transgender individuals, and, therefore, can lead to devastating consequences, like severe physical or mental health issues, self-harming behaviour, and suicidality.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Andreas Koehler", + "author_inst": "University Medical Center Hamburg-Eppendorf, Institute for Sex Research, Sexual Medicine, and Forensic Psychiatry, Hamburg, Germany" + }, + { + "author_name": "Joz Motmans", + "author_inst": "Transgender Infopunt, Ghent University Hospital, Ghent, Belgium" + }, + { + "author_name": "Leo Mulio Alvarez", + "author_inst": "Transgender Europe, Berlin, Germany" + }, + { + "author_name": "David Azul", + "author_inst": "La Trobe University, La Trobe Rural Health School, Department of Community and Allied Health, Discipline of Speech Pathology, Melbourne, Australia" + }, + { + "author_name": "Karen Badalyan", + "author_inst": "Eurasian Key Populations Coalition, Warszawa, Poland" + }, + { + "author_name": "Koray Basar", + "author_inst": "Hacettepe University, Department of Psychiatry, Ankara, Turkey" + }, + { + "author_name": "Cecilia Dhejne", + "author_inst": "Karolinska University Hospital, Andrology, Sexual Medicine, Transgender Medicine, Stockholm, Sweden" + }, + { + "author_name": "Dragana Duisin", + "author_inst": "Clinical Centre of Serbia, Department of Psychiatry, Belgrade, Serbia" + }, + { + "author_name": "Bartosz Grabski", + "author_inst": "Jagiellonian University Medical College, Sexology Lab, Department of Psychiatry, Krakow, Poland" + }, + { + "author_name": "Aurore Dufrasne", + "author_inst": "Genres Pluriels, Brussels, Belgium" + }, + { + "author_name": "Natasa Jokic-Begic", + "author_inst": "University of Zagreb, Clinical and Health Psychology Unit, Department of Psychology, Faculty of Humanities and Social Sciences, Zagreb, Croatia" + }, + { + "author_name": "Antonio Prunas", + "author_inst": "University of Milan, Department of Psychology, Milan, Italy" + }, + { + "author_name": "Christina Richards", + "author_inst": "Tavistock and Portman NHS Foundation Trust & Regents University London, School of Psychotherapy and Psychology, London, United Kingdom" + }, + { + "author_name": "Kirill Sabir", + "author_inst": "FtM Phoenix Group, Moscow, Russia" + }, + { + "author_name": "Jaimie Vaele", + "author_inst": "University of Waikato, Faculty Arts & Social Sciences, New Zealand" + }, + { + "author_name": "Timo Ole Nieder", + "author_inst": "University Medical Center Hamburg-Eppendorf, Institute for Sex Research, Sexual Medicine, and Forensic Psychiatry, Hamburg, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.22.20248685", "rel_title": "Environmental scan of provincial and territorial planning for COVID-19 vaccination programs", @@ -990840,221 +988270,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.21.20248121", - "rel_title": "HLA-C* 04:01 is a Genetic Risk Allele for Severe Course of COVID-19", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248121", - "rel_abs": "BackgroundSince the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing demand to identify predictors of severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors. We sought to evaluate this hypothesis by conducting an international multicenter study using HLA sequencing with subsequent independent validation.\n\nMethodsWe analyzed a total of 332 samples. First, we enrolled 233 patients in Germany, Spain, and Switzerland for HLA and whole exome sequencing. Furthermore, we validated our results in a public data set (United States, n=99). Patients older than 18 years presenting with COVID-19 were included, representing the full spectrum of the disease. HLA candidate alleles were identified in the derivation cohort (n=92) and tested in two independent validation cohorts (n=240).\n\nResultsWe identified HLA-C* 04:01 as a novel genetic predictor for severe clinical course in COVID-19. Carriers of HLA-C* 04:01 had twice the risk of intubation when infected with SARS-CoV-2 (hazard ratio 2.1, adjusted p-value=0.0036). Importantly, these findings were successfully replicated in an independent data set. Furthermore, our findings are biologically plausible, as HLA-C* 04:01 has fewer predicted bindings sites with relevant SARS-CoV-2 peptides as compared to other HLA alleles. Exome sequencing confirmed findings from HLA analysis.\n\nConclusionsHLA-C* 04:01 carriage is associated with a twofold increased risk of intubation in patients infected with SARS-CoV-2. Testing for HLA-C* 04:01 could have clinical implications to identify high-risk patients and individualize management.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "January Weiner III", - "author_inst": "Berlin Institute of Health, Core Unit Bioinformatics, Berlin, DE 10178" - }, - { - "author_name": "Phillip Suwalski", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Manuel Holtgrewe", - "author_inst": "Berlin Institute of Health, Core Unit Genomics, Berlin" - }, - { - "author_name": "Charlotte Thibeault", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Berlin, DE 10117" - }, - { - "author_name": "Melina Mueller", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Dimitri Patriki", - "author_inst": "Kantonsspital Baden AG, Departement of Medicine Baden, CH 5404" - }, - { - "author_name": "Claudia Quedenau", - "author_inst": "Max Delbrueck Center for Molecular Medicine Berlin, DE 13125" - }, - { - "author_name": "Ulrike Krueger", - "author_inst": "Berlin Institute of Health, Core Unit Genomics Berlin, DE 10178" - }, - { - "author_name": "Elisa Theresa Helbig", - "author_inst": "Charite Universitaetsmedizin Berlin Berlin, DE 10117" - }, - { - "author_name": "Lena Lippert", - "author_inst": "Charite Universitaetsmedizin Berlin Berlin, DE 10117" - }, - { - "author_name": "Paula Stubbemann", - "author_inst": "Charite Universitaetsmedizin Berlin Berlin, DE 10117" - }, - { - "author_name": "Luis Miguel Real", - "author_inst": "Hospital Universitario de Valme, Unidad Clinica de Enfermedades Infecciosas y Microbiologia Sevilla, ES 41013" - }, - { - "author_name": "Juan Macias Sanchez", - "author_inst": "Hospital Universitario de Valme, Unidad Clinica de Enfermedades Infecciosas y Microbiologia Avenida de Bellavista s/n Sevilla, Sevilla, ES 41014" - }, - { - "author_name": "Juan A. Pineda", - "author_inst": "Hospital Universitario de Valme, Infectious Diseases Unit Sevilla, ES 41014" - }, - { - "author_name": "Marta Fernandez-Fuertes", - "author_inst": "Hospital Universitario de Valme" - }, - { - "author_name": "Xiaomin Wang", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Zehra Karadeniz", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Jacopo Saccomanno", - "author_inst": "Charite Universitaetsmedizin Berlin, Klinik m.S Infektiologie und Pneumologie Berlin, Berlin, DE 10117" - }, - { - "author_name": "Jan-Moritz Doehn", - "author_inst": "Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, Berlin, DE 10117" - }, - { - "author_name": "Ralf-Harto Hubner", - "author_inst": "Charite -Universitaetsmedizin Berlin, Department of Internal Medicine/Infectious Diseases and Respiratory Medicine Berlin, DE 13353" - }, - { - "author_name": "Bernd Hinzmann", - "author_inst": "Roche Sequencing Solutions Pleasanton, USA 94588" - }, - { - "author_name": "Mauricio Salvo", - "author_inst": "Roche Sequencing Solutions Pleasanton, USA 94588" - }, - { - "author_name": "Anja Blueher", - "author_inst": "Roche Sequencing Solutions Pleasanton, USA 94588" - }, - { - "author_name": "Sandra Siemann", - "author_inst": "Roche Sequencing Solutions Pleasanton, USA 94588" - }, - { - "author_name": "Stjepan Jurisic", - "author_inst": "Kantonsspital Baden AG Baden, CH 5404" - }, - { - "author_name": "Hansjuerg Beer", - "author_inst": "Kantonsspital Baden AG, Department of Internal Medicine Baden, CH 5404" - }, - { - "author_name": "Jonas Rutishauser", - "author_inst": "Kantonsspital Baden AG, Clinical Trials Unit Baden, CH 5404" - }, - { - "author_name": "Benedikt J. Wiggli", - "author_inst": "Kantonsspital Baden AG, Department of Infectious Diseases & Infection Control Baden, CH 5404" - }, - { - "author_name": "Hans Rudolf Schmid", - "author_inst": "Kantonsspital Baden AG Baden, CH 5404" - }, - { - "author_name": "Kathrin Danninger", - "author_inst": "Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria" - }, - { - "author_name": "Ronald Binder", - "author_inst": "Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria" - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz 1 D-10117 Berlin DE 10117" - }, - { - "author_name": "Barbara Muehlemann", - "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz 1 D-10117 Berlin DE 10117" - }, - { - "author_name": "Alice Braun", - "author_inst": "Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 D-10117 Berlin, DE 10117" - }, - { - "author_name": "Stephan Ripke", - "author_inst": "Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 D-10117 Berlin, DE 10117" - }, - { - "author_name": "Terry C. Jones", - "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz 1 D-10117 Berlin DE 10117" - }, - { - "author_name": "Norbert Suttorp", - "author_inst": "Charite Universitaetsmedizin Berlin, Department for Infectious Diseases and Respiratory Medicine Berlin, DE 10117" - }, - { - "author_name": "Martin Witzenrath", - "author_inst": "Charite Universitaetsmedizin Berlin, Department for Infectious Diseases and Respiratory Medicine Berlin, DE 10117" - }, - { - "author_name": "Stefan Hippenstiel", - "author_inst": "Charite Universitaetsmedizin Berlin, DE 10117" - }, - { - "author_name": "Tomasz Zemojtel", - "author_inst": "Berlin Institute of Health, Core Unit Genomics Berlin, DE 10178" - }, - { - "author_name": "Carsten Skurk", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Wolfgang Poller", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Tatiana Borodina", - "author_inst": "Max Delbrueck Center for Molecular Medicine Berlin, DE 13125" - }, - { - "author_name": "- Pa-COVID Study Group", - "author_inst": "-" - }, - { - "author_name": "Leif Erik Sander", - "author_inst": "Charite Universitaetsmedizin Berlin, Department for Infectious Diseases and Respiratory Medicine Berlin, DE 10117" - }, - { - "author_name": "Dieter Beule", - "author_inst": "Berlin Institute of Health, Core Unit Bioinformatics Berlin, DE 10178" - }, - { - "author_name": "Ulf Landmesser", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - }, - { - "author_name": "Toumy Guettouche", - "author_inst": "Roche Sequencing Solutions Pleasanton, USA 94588" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite Universitaetsmedizin Berlin, Department for Infectious Diseases and Respiratory Medicine Berlin, DE 10117" - }, - { - "author_name": "Bettina Heidecker", - "author_inst": "Department of Cardiology, Charite University Hospital Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.24.424322", "rel_title": "Inferring Toll-Like Receptor induced epitope subunit vaccine candidate against SARS-CoV-2: A Reverse Vaccinology approach", @@ -991650,6 +988865,77 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.12.22.423909", + "rel_title": "Platycodin D prevents both lysosome- and TMPRSS2-driven SARS-CoV-2 infection in vitro by hindering membrane fusion", + "rel_date": "2020-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423909", + "rel_abs": "An ongoing pandemic of coronavirus disease 2019 (COVID-19) is now the greatest threat to the global public health. Herbal medicines and their derived natural products have drawn much attention to treat COVID-19, but there has been no natural product showing inhibitory activity against SARS-CoV-2 infection with detailed mechanism. Here, we show that platycodin D (PD), a triterpenoid saponin abundant in Platycodon grandiflorum (PG), a dietary and medicinal herb commonly used in East Asia, effectively blocks the two main SARS-CoV-2 infection-routes via lysosome- and transmembrane protease, serine 2 (TMPRSS2)-driven entry. Mechanistically, PD prevents host-entry of SARS-CoV-2 by redistributing membrane cholesterol to prevent membrane fusion, which can be reinstated by treatment with a PD-encapsulating agent. Furthermore, the inhibitory effects of PD are recapitulated by a pharmacological inhibition or gene-silencing of NPC1, which is mutated in Niemann-Pick type C (NPC) patients displaying disrupted membrane cholesterol. Finally, readily available local foods or herbal medicines containing PG root show the similar inhibitory effects against SARS-CoV-2 infection. Our study proposes that PD is a potent natural product for preventing or treating COVID-19 and that a brief disruption of membrane cholesterol can be a novel therapeutic approach against SARS-CoV-2 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tai Young Kim", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Sangeun Jeon", + "author_inst": "Institut Pasteur Korea" + }, + { + "author_name": "Youngho Jang", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Lizaveta Gotina", + "author_inst": "Korea Institute of Science and Technology" + }, + { + "author_name": "Joungha Won", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Yeon Ha Ju", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Sunpil Kim", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Minwoo Wendy Jang", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Woojin Won", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Mingu Gordon Park", + "author_inst": "Institute for Basic Science" + }, + { + "author_name": "Ae Nim Pae", + "author_inst": "Korea Institute of Science and Technology" + }, + { + "author_name": "Sunkyu Han", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Seungtaek Kim", + "author_inst": "Institut Pasteur Korea" + }, + { + "author_name": "C. Justin Lee", + "author_inst": "Institute for Basic Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.12.23.424138", "rel_title": "mRNA vaccine CVnCoV protects non-human primates from SARS-CoV-2 challenge infection", @@ -992829,45 +990115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.18.20248490", - "rel_title": "Are college campuses superspreaders? A data-driven modeling study.", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248490", - "rel_abs": "The COVID-19 pandemic continues to present enormous challenges for colleges and universities and strategies for save reopening remain a topic of ongoing debate. Many institutions that reopened cautiously in the fall experienced a massive wave of infections and colleges were soon declared as the new hotspots of the pandemic. However, the precise effects of college outbreaks on their immediate neighborhood remain largely unknown. Here we show that the first two weeks of instruction present a high-risk period for campus outbreaks and that these outbreaks tend to spread into the neighboring communities. By integrating a classical mathematical epidemiology model and Bayesian learning, we learned the dynamic reproduction number for 30 colleges from their daily case reports. Of these 30 institutions, 14 displayed a spike of infections within the first two weeks of class, with peak seven-day incidences well above 1,000 per 100,000, an order of magnitude larger than the nation-wide peaks of 70 and 150 during the first and second waves of the pandemic. While most colleges were able to rapidly reduce the number of new infections, many failed to control the spread of the virus beyond their own campus: Within only two weeks, 17 campus outbreaks translated directly into peaks of infection within their home counties. These findings suggests that college campuses are at risk to develop an extreme incidence of COVID-19 and become superspreaders for neighboring communities. We anticipate that tight test-trace-quarantine strategies, flexible transition to online instruction, and-most importantly-compliance with local regulations will be critical to ensure a safe campus reopening after the winter break.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hannah Lu", - "author_inst": "Stanford University" - }, - { - "author_name": "Cortney Weintz", - "author_inst": "Stanford University" - }, - { - "author_name": "Joseph Pace", - "author_inst": "Stanford University" - }, - { - "author_name": "Dhiraj Indana", - "author_inst": "Stanford University" - }, - { - "author_name": "Kevin Linka", - "author_inst": "Stanford University" - }, - { - "author_name": "Ellen Kuhl", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.18.20248499", "rel_title": "Mental Disorder Prevalence Among Populations Impacted by Coronavirus Pandemics: A Multilevel Meta-Analytic Study of COVID-19, MERS & SARS", @@ -993600,6 +990847,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.21.20248610", + "rel_title": "Population risk factors for severe disease and mortality in COVID-19: A global systematic review and meta-analysis", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248610", + "rel_abs": "AimCOVID-19 clinical presentation is heterogeneous, ranging from asymptomatic to severe cases. While there are a number of early publications relating to risk factors for COVID-19 infection, low sample size and heterogeneity in study design impacted consolidation of early findings. There is a pressing need to identify the factors which predispose patients to severe cases of COVID-19. For rapid and widespread risk stratification, these factors should be easily obtainable, inexpensive, and avoid invasive clinical procedures. The aim of our study is to fill this knowledge gap by systematically mapping all the available evidence on the association of various clinical, demographic, and lifestyle variables with the risk of specific adverse outcomes in patients with COVID-19.\n\nMethodsThe systematic review was conducted using standardized methodology, searching three electronic databases (PubMed, Embase, and Web of Science) for relevant literature published between 1st January 2020 and 9th July 2020. Included studies reported characteristics of patients with COVID-19 while reporting outcomes relating to disease severity. In the case of sufficient comparable data, meta-analyses were conducted to estimate risk of each variable.\n\nResultsSeventy-six studies were identified, with a total of 17,860,001 patients across 14 countries. The studies were highly heterogeneous in terms of the sample under study, outcomes, and risk measures reported. A large number of risk factors were presented for COVID-19. Commonly reported variables for adverse outcome from COVID-19 comprised patient characteristics, including age >75 (OR = 2.65 (1.81-3.90)), male sex (OR = 2.05(1.39-3.04)) and severe obesity (OR = 2.57 (1.31-5.05)). Active cancer (OR = 1.46 (1.04-2.04)) was associated with increased risk of severe outcome. A number of common symptoms and vital measures (respiratory rate and SpO2) also suggested elevated risk profiles.\n\nConclusionsBased on the findings of this study, a range of easily assessed parameters are valuable to predict elevated risk of severe illness and mortality as a result of COVID-19, including patient characteristics and detailed comorbidities, alongside the novel inclusion of real-time symptoms and vital measurements.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Adam Booth", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "Angus Bruno Reed", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "Sonia Ponzo", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "Arrash Yassaee", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "Mert Aral", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "David Plans", + "author_inst": "Huma Therapeutics" + }, + { + "author_name": "Alain Labrique", + "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States." + }, + { + "author_name": "Diwakar Mohan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.20.20248580", "rel_title": "A New Extension of State-Space SIR Model to Account for Underreporting- An Application to the COVID-19 transmission in California and Florida", @@ -994367,57 +991661,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.20.20248420", - "rel_title": "SARS-CoV-2 infections in people with PCD: neither frequent, nor particularly severe", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248420", - "rel_abs": "People with pre-existing chronic health conditions are reportedly at high risk of getting the coronavirus disease (COVID-19) and of having a severe disease course but little data exist on rare diseases such as Primary Ciliary Dyskinesia (PCD). We studied risk and severity of SARS-CoV-2 infections among people with PCD using data from the COVID-PCD, a participatory study that collects data in real-time directly from people with PCD. Data was collected using online questionnaires. A baseline questionnaire collected information on demographic data, information about the PCD diagnosis and severity. A short weekly questionnaire collected information about current symptoms and incident SARS-CoV-2 infections. 578 people participated in the COVID-PCD by December 7, 2020, with a median number of follow-up weeks of 9 (interquartile range: 4-19 weeks). 256 (45%) of the participants had been tested for SARS-CoV-2 and 12 tested positive prior to study entry or during study follow up (2.1% of the total included population, 95% confidence interval (CI) 1.1-3.6%). 4 people tested positive during the study follow-up, corresponding to an incidence rate of 2.5 per 100 person-years (95% CI: 0.9-6.5). Overall, reported severity was mild with two reporting no symptoms, eight reporting mild symptoms, one reporting severe symptom without hospitalisation, and one reporting hospitalisation for 9 days. The study suggests that with careful personal protection, people with PCD do not seem to have an increased risk of infection with SARS-COV-2, nor an especially severe disease course.\n\nTake home messageIn this longitudinal study of people with PCD followed weekly via online questionnaires, the incidence rate of COVID-19 and the proportion of participants infected were low, and the observed severity mostly mild.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Eva Sophie Lunde Pedersen", - "author_inst": "University of Bern" - }, - { - "author_name": "Myrofora Goutaki", - "author_inst": "University of Bern" - }, - { - "author_name": "Amanda Harris", - "author_inst": "Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK" - }, - { - "author_name": "Lucy Dixon", - "author_inst": "PCD Family Support Group, London, UK" - }, - { - "author_name": "Michele Manion", - "author_inst": "PCD Foundation, Minneapolis, Minnesota" - }, - { - "author_name": "Bernhard Rindlisbacher", - "author_inst": "Selbsthilfegruppe Primaere Ciliaere Dyskinesie, Switzerland" - }, - { - "author_name": "- COVID-PCD patient advisory group", - "author_inst": "" - }, - { - "author_name": "Jane S Lucas", - "author_inst": "Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK; University of Southam" - }, - { - "author_name": "Claudia E Kuehni", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Paediatric Respiratory Medicine, Childrens University Hospital of Bern, Univ" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.21.20248605", "rel_title": "Modeling the flow of the COVID-19 in Germany: The cohort SEIR model based on the system dynamics approach", @@ -994918,6 +992161,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.22.423922", + "rel_title": "Active learning tools improve the learning outcomes, scientific attitude and critical thinking in higher education: Experiences in an online course during the COVID-19 pandemic", + "rel_date": "2020-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423922", + "rel_abs": "Active teaching methodologies have been placed as a hope for changing education at different levels, transiting from passive lecture-centered to student-centered learning. With the health measures of social distance, the COVID-19 pandemic forced a strong shift to remote education. With the challenge of delivering quality education through a computer screen, we validated and applied an online course model using active teaching tools for higher education. We incorporated published active-learning strategies into an online construct, with problem-based inquiry and design of inquiry research projects to serve as our core active-learning tool. The gains related to students science learning experiences and their attitudes towards science were assessed by applying questionnaires before, during and after the course. The course counted on the participation of 83 students, most of them (60,8%) from post-graduate students. Our results show that engagement provided by active learning methods can improve performance both in hard and soft skills. Students participation seems to be more relevant when activities require interaction of information, prediction and reasoning, such as open-ended questions and design of research projects. Therefore, our data shows that, in pandemic, active learning tools benefit students and improve their critical thinking and their motivation and positive positioning in science.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Izadora Volpato Rossi", + "author_inst": "Programa de Biologia Celular e Molecular, Universidade Federal de Parana, Brazil" + }, + { + "author_name": "Jordana Dinora de Lima", + "author_inst": "Programa de Biologia Celular e Molecular, Universidade Federal de Parana, Brazil" + }, + { + "author_name": "Bruna Sabatke", + "author_inst": "Programa de Biologia Celular e Molecular, Universidade Federal de Parana, Brazil" + }, + { + "author_name": "Maria Alice F Nunes", + "author_inst": "Programa de Biologia Celular e Molecular, Universidade Federal de Parana, Brazil" + }, + { + "author_name": "Graciela Evans Ramirez", + "author_inst": "SEPT, Universidade Federal de Parana, Brazil" + }, + { + "author_name": "Marcel I Ramirez", + "author_inst": "Instituto Oswaldo Cruz - Universidade Federal de Parana, Brazil" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2020.12.19.20248530", "rel_title": "LungAI: A Deep Learning Convolutional Neural Network for Automated Detection of COVID-19 from Posteroanterior Chest X-Rays", @@ -996501,29 +993783,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.19.20248544", - "rel_title": "From SARS-CoV-2 infection to COVID-19 disease: a proposed mechanism for viral spread to the lower airway based on in silico estimation of virion flow rates", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248544", - "rel_abs": "While the nasopharynx in the upper respiratory airway is the dominant initial infection site for SARS-CoV-2, the physiologic mechanism that launches the infection in the lower airway is still not well-understood. Based on the rapidity with which SARS-CoV-2 infection progresses to the lungs, it has been conjectured that the nasopharynx acts as the seeding zone for subsequent contamination of the lower airway via aspiration of virus-laden boluses of nasopharyngeal fluids. In this study, we examine the plausibility of this proposed mechanism. To this end, we have developed computational fluid mechanics models of the inhalation process in two medical imaging based airway reconstructions and have quantified the nasopharyngeal liquid volume ingested into the lower airspace during each aspiration. The numerical predictions are validated by comparing the number of projected aspirations (approximately 2 - 4) during an eight-hour sleep cycle with prior observational findings of 3 aspirations in human subjects. Extending the numerical trends on aspiration volume to earlier records on aspiration frequency for the entire day indicates a total aspirated nasopharyngeal liquid volume of 0.3 - 0.76 ml per day. We then used sputum assessment data from hospitalized COVID-19 patients to estimate the number of virions that are transmitted daily to the lungs via nasopharyngeal liquid boluses. For mean sputum viral load, our modeling projects that the number of virions penetrating to the lower airway per day will range over 2.1 x 106 - 5.3 x 106; for peak viral load, the corresponding number of penetrating virions hovers between 7.1 x 108 - 17.9 x 108. These findings fill in a key piece of the mechanistic puzzle of the progression from SARS-CoV-2 infection of the nasopharynx to the development of COVID-19 disease within a patient, and point to dysphagia as a potential underlying risk factor for COVID-19. The findings also have significant practical implications in the design of COVID-19 prophylactics and therapeutics that aim to constrain the pathogenic progress of the disease within the limits of the upper airway.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Saikat Basu", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Arijit Chakravarty", - "author_inst": "Fractal Therapeutics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.21.20248621", "rel_title": "A Systematic Review and Network Meta-Analysis for COVID-19 Treatments", @@ -997156,6 +994415,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.20.20248563", + "rel_title": "Development and external validation of a logistic regression derived formula based on repeated routine hematological measurements predicting survival of hospitalized Covid-19 patients", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248563", + "rel_abs": "BackgroundThe Covid-19 pandemic has become a global public health crisis and providing optimal patient care while preventing a collapse of the health care system is a principal objective worldwide.\n\nObjectiveTo develop and validate a prognostic model based on routine hematological parameters to predict uncomplicated disease progression to support the decision for an earlier discharge.\n\nDesignDevelopment and refinement of a multivariable logistic regression model with subsequent external validation. The time course of several hematological variables until four days after admission were used as predictors. Variables were first selected based on subject matter knowledge; their number was further reduced using likelihood ratio-based backward elimination in random bootstrap samples.\n\nSettingModel development based on three Austrian hospitals, validation cohorts from two Austrian and one Swedish hospital.\n\nParticipantsModel development based on 363 survivors and 78 non-survivors of Covid-19 hospitalized in Austria. External validation based on 492 survivors and 61 non-survivors hospitalized in Austria and Sweden.\n\nOutcomeIn-hospital death.\n\nMain ResultsThe final model includes age, fever upon admission, parameters derived from C-reactive protein (CRP) concentration, platelet count and creatinine concentration, approximating their baseline values (CRP, creatinine) and change over time (CRP, platelet count). In Austrian validation cohorts both discrimination and calibration of this model were good, with c indices of 0.93 (95% CI 0.90 - 0.96) in a cohort from Vienna and 0.93 (0.88 - 0.98) in one from Linz. The model performance seems independent of how long symptoms persisted before admission. In a small Swedish validation cohort, the model performance was poorer (p = 0.008) compared with Austrian cohorts with a c index of 0.77 (0.67 - 0.88), potentially due to substantial differences in patient demographics and clinical routine.\n\nConclusionsHere we describe a formula, requiring only variables routinely acquired in hospitals, which allows to estimate death probabilities of hospitalized patients with Covid-19. The model could be used as a decision support for earlier discharge of low-risk patients to reduce the burden on the health care system. The model could further be used to monitor whether patients should be admitted to hospital in countries with health care systems with emphasis on outpatient care (e.g. Sweden).", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Stefan Heber", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "David Pereyra", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Waltraud Schrottmaier", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Kerstin Kammerer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Jonas Santol", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Erich Pawelka", + "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital, Vienna, Austria" + }, + { + "author_name": "Markus Hana", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Alexander Scholz", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Markus Liu", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Agnes Hell", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Klara Heiplik", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Benno Lickefett", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Sebastian Haverall", + "author_inst": "Division of Internal Medicine, Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Marianna Traugott", + "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital, Vienna, Austria" + }, + { + "author_name": "Matthias Neuboeck", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Christian Schoergenhofer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Tamara Seitz", + "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital, Vienna, Austria" + }, + { + "author_name": "Christa Firbas", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Mario Karolyi", + "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital, Vienna, Austria" + }, + { + "author_name": "Guenter Weiss", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Bernd Jilma", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Rosa Bellmann-Weiler", + "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Helmut Salzer", + "author_inst": "Department of Pulmonology, Kepler University Hospital and Johannes Kepler University, Linz, Austria" + }, + { + "author_name": "Michael JM Fischer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Alexander Zoufaly", + "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital, Vienna, Austria" + }, + { + "author_name": "Alice Assinger", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.12.22.20248707", "rel_title": "How to coordinate vaccination and social distancing to mitigate SARS-CoV-2 outbreaks", @@ -998203,189 +995585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.423746", - "rel_title": "Immunological and pathological outcomes of SARS-CoV-2 challenge after formalin-inactivated vaccine immunisation of ferrets and rhesus macaques", - "rel_date": "2020-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.21.423746", - "rel_abs": "There is an urgent requirement for safe and effective vaccines to prevent novel coronavirus disease (COVID-19) caused by SARS-CoV-2. A concern for the development of new viral vaccines is the potential to induce vaccine-enhanced disease (VED). This was reported in several preclinical studies with both SARS-CoV-1 and MERS vaccines but has not been reported with SARS-CoV-2 vaccines. We have used ferret and rhesus macaques challenged with SARS-CoV-2 to assess the potential for VED in animals vaccinated with formaldehyde-inactivated SARS-CoV-2 (FIV) formulated with Alhydrogel, compared to a negative control vaccine in ferrets or unvaccinated macaques. We showed no evidence of enhanced disease in ferrets or rhesus macaques given FIV except for mild transient enhanced disease seen at seven days post infection in ferrets. This increased lung pathology was observed early in the infection (day 7) but was resolved by day 15. We also demonstrate that formaldehyde treatment of SARS-CoV-2 reduces exposure of the spike receptor binding domain providing a mechanistic explanation for suboptimal immunity.", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Kevin R Bewley", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Karen E R Gooch", - "author_inst": "Public Health England" - }, - { - "author_name": "Kelly M Thomas", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Stephanie R Longet", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Nathan Wiblin", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Laura Hunter", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Kin Chan", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Phillip Brown", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Rebecca A Russell", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Catherine Ho", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Gillian Slack", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Holly E Humphries", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Leonie Alden", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Lauren Allen", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Marilyn Aram", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Natalie Baker", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Emily Brunt", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Rebecca Cobb", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Susan Fotheringham", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Debbie Harris", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Chelsea Kennard", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Stephanie Leung", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Kathryn A Ryan", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Howard Tolley", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Nadina Wand", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Andrew White", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Laura Sibley", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Charlotte Sarfas", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Geoff Pearson", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Emma Rayner", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Xiaochao Xue", - "author_inst": "The Sir William Dunn School of Pathology, University of Oxford" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "The Jenner Institute, University of Oxford" - }, - { - "author_name": "Sue Charlton", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Sarah C Gilbert", - "author_inst": "University of Oxford" - }, - { - "author_name": "Quentin Sattentau", - "author_inst": "The Sire William Dunn School of Pathology, University of Oxford" - }, - { - "author_name": "Fergus Gleeson", - "author_inst": "Oxford Departments of Radiology and Nuclear Medicine, Oxford University Hospitals NHS Foundation Trust." - }, - { - "author_name": "Yper Hall", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Simon G. P. Funnell", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Sally Sharpe", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Francisco Javier Salguero", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Andrew R Gorringe", - "author_inst": "Public Health England, Porton Down" - }, - { - "author_name": "Miles Carroll", - "author_inst": "Public Health England, Porton Down" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.12.20.422693", "rel_title": "A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.", @@ -999054,6 +996253,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.20.423630", + "rel_title": "Mutation Landscape of SARS COV2 in Africa", + "rel_date": "2020-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.423630", + "rel_abs": "COVID-19 disease has had a relatively less severe impact in Africa. To understand the role of SARS CoV2 mutations on COVID-19 disease in Africa, we analysed 282 complete nucleotide sequences from African isolates deposited in the NCBI Virus Database. Sequences were aligned against the prototype Wuhan sequence (GenBank accession: NC_045512.2) in BWA v. 0.7.17. SAM and BAM files were created, sorted and indexed in SAMtools v. 1.10 and marked for duplicates using Picard v. 2.23.4. Variants were called with mpileup in BCFtools v. 1.11. Phylograms were created using Mr. Bayes v 3.2.6. A total of 2,349 single nucleotide polymorphism (SNP) profiles across 294 sites were identified. Clades associated with severe disease in the United States, France, Italy, and Brazil had low frequencies in Africa (L84S=2.5%, L3606F=1.4%, L3606F/V378I/=0.35, G251V=2%). Sub Saharan Africa (SSA) accounted for only 3% of P323L and 4% of Q57H mutations in Africa. Comparatively low infections in SSA were attributed to the low frequency of the D614G clade in earlier samples (25% vs 67% global). Higher disease burden occurred in countries with higher D614G frequencies (Egypt=98%, Morocco=90%, Tunisia=52%, South Africa) with D614G as the first confirmed case. V367F, D364Y, V483A and G476S mutations associated with efficient ACE2 receptor binding and severe disease were not observed in Africa. 95% of all RdRp mutations were deaminations leading to CpG depletion and possible attenuation of virulence. More genomic and experimental studies are needed to increase our understanding of the temporal evolution of the virus in Africa, clarify our findings, and reveal hot spots that may undermine successful therapeutic and vaccine interventions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Angus A Nassir", + "author_inst": "Bioinformatics Institute of Kenya" + }, + { + "author_name": "Clarisse Musanabaganwa", + "author_inst": "Rwanda Medical Research Center, Rwanda Biomedical Center" + }, + { + "author_name": "Ivan Mwikarago", + "author_inst": "National Reference Laboratory, Rwanda Biomedical Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.12.21.423761", "rel_title": "Predicting COVID-19 cases with unknown homogeneous or heterogeneous resistance to infectivity", @@ -1000148,105 +997374,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.12.18.20248470", - "rel_title": "Common variants at 21q22.3 locus influence MX1 gene expression and susceptibility to severe COVID-19", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248470", - "rel_abs": "The COVID-19 disease, caused by the SARS-Cov-2, presents a heterogeneous clinical spectrum. The risk factors do not fully explain the wide spectrum of disease manifestations, so it is possible that genetic factors could account for novel insights into its pathogenesis.\n\nIn our previous study, we hypothesized that common variants on chromosome 21, near TMPRSS2 and MX1 genes, may be genetic risk factors associated to the different clinical manifestations of COVID-19. Here, we performed an in-depth genetic analysis of chromosome 21 exploiting the genome-wide association study data including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry from COVID-19 Host Genetics Initiative. We found that five single nucleotide polymorphisms (SNPs) within TMPRSS2 and near MX1 gene show suggestive associations (P[≤]1x10-5) with severe COVID-19. All five SNPs replicated the association in two independent cohorts of Asian subjects while two and one out of the 5 SNPs replicated in African and Italian populations, respectively (P[≤]0.05). The minor alleles of these five SNPs correlated with a reduced risk of developing severe COVID-19 and increased level of MX1 expression in blood.\n\nOur findings provide further evidence that host genetic factors can contribute to determine the different clinical presentations of COVID-19 and that MX1, an antiviral effector of type I and III interferon pathway, may be a potential therapeutic target.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Immacolata Andolfo", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Roberta Russo", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Alessandro Vito Lasorsa", - "author_inst": "University of Naples, Federico II, CEINGE, biotecnologie avanzate" - }, - { - "author_name": "Sueva Cantalupo", - "author_inst": "University of Naples,Federico II, CEINGE biotecnologie avanzate" - }, - { - "author_name": "Barbara Eleni Rosato", - "author_inst": "University of Naples, Federico II, CEINGE, biotecnologie avanzate" - }, - { - "author_name": "Ferdinando Bonfiglio", - "author_inst": "Dipartimento di Ingegneria chimica, dei Materiali e della Produzione industriale, Universita' degli Studi di Napoli Federico II, Napoli, Italy" - }, - { - "author_name": "Giulia Frisso", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Pasquale Abete", - "author_inst": "COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy" - }, - { - "author_name": "Gian Marco Cassese", - "author_inst": "COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy" - }, - { - "author_name": "Giuseppe Servillo", - "author_inst": "Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Universita' degli Studi di Napoli Federico II, Napoli, Italy" - }, - { - "author_name": "Gabriella Esposito", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Ivan Gentile", - "author_inst": "Dipartimento di Medicina clinica e Chirurgia, Universita' degli Studi di Napoli Federico II, Napoli, Italy" - }, - { - "author_name": "Carmelo Piscopo", - "author_inst": "Medical and Laboratory Genetics Unit, A.O.R.N. Antonio Cardarelli, Napoli, Italy" - }, - { - "author_name": "Romolo Villani", - "author_inst": "Poison Centre, A.O.R.N. Antonio Cardarelli, Napoli, Italy" - }, - { - "author_name": "Giuseppe Fiorentino", - "author_inst": "AORN dei Colli Presidio Ospedaliero Cotugno, Napoli, Italy" - }, - { - "author_name": "Pellegrino Cerino", - "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy" - }, - { - "author_name": "Carlo Buonerba", - "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy" - }, - { - "author_name": "Biancamaria Pierri", - "author_inst": "Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy - Dipartimento di Medicina, Chirurgia e Odontoiatria Scuola Medica Salernitana, Universita'" - }, - { - "author_name": "Massimo Zollo", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Achille Iolascon", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - }, - { - "author_name": "Mario Capasso", - "author_inst": "Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universita' degli Studi di Napoli Federico II, Napoli, Italy - CEINGE Biotecnologie Avanzate, Napol" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.18.20248447", "rel_title": "Epidemiological feature, viral shedding, and antibody seroconversion among asymptomatic carriers and symptomatic/ presymptomatic COVID-19 patients", @@ -1001083,6 +998210,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.17.20248401", + "rel_title": "Longitudinal analysis of COVID-19 patients shows age-associated T cell changes independent of ongoing ill-health", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248401", + "rel_abs": "The trajectory of immunological and inflammatory changes following acute COVID-19 infection are unclear. We investigate immunological changes in convalescent COVID-19 and interrogate their potential relationships with persistent symptoms, termed long COVID.\n\nWe performed paired immunophenotyping at initial SARS-CoV-2 infection and convalescence (n=40, median 68 days) and validated findings in 71 further patients at median 101 days convalescence. Results were compared to 40 pre-pandemic controls. Fatigue and exercise tolerance were assessed and investigated their relationship with convalescent results.\n\nWe demonstrate persistent expansion of intermediate monocytes, effector CD8+, activated CD4+ and CD8+ T cells, and reduced naive CD4+ and CD8+ T cells at 68 days, with activated CD8+ T cells remaining increased at 101 days. Patients >60 years also demonstrate reduced naive CD4+ and CD8+ T cells and expanded activated CD4+ T cells at 101 days. Ill-health, fatigue, and reduced exercise tolerance were common but were not associated with immunological changes.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC=\"FIGDIR/small/20248401v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@26dd49org.highwire.dtl.DTLVardef@18a0aaeorg.highwire.dtl.DTLVardef@1c32b6dorg.highwire.dtl.DTLVardef@580b3d_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Liam Townsend", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Adam H Dyer", + "author_inst": "School of Medicine, Trinity Translational Medicine Institute" + }, + { + "author_name": "Aifric Naughton", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Rachel Kiersey", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Dean Holden", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Mary Gardiner", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Joanne Dowds", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Kate O'Brien", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Ciaran Bannan", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Parthiban Nadarajan", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Jean Dunne", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Ignacio Martin-Loeches", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Padraic Fallon", + "author_inst": "Trinity College Dublin" + }, + { + "author_name": "Colm Bergin", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Cliona O'Farrelly", + "author_inst": "Trinity Biomedical Sciences Institute, Trinity College Dublin" + }, + { + "author_name": "Cliona Ni Cheallaigh", + "author_inst": "St James's Hospital" + }, + { + "author_name": "Nollaig Bourke", + "author_inst": "Trinity College Dublin" + }, + { + "author_name": "Niall Conlon", + "author_inst": "St James's Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.17.20248396", "rel_title": "Negative vaccine attitudes and intentions to vaccinate against Covid-19 in relation to smoking status: a population survey of UK adults", @@ -1001922,33 +999136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.16.20248311", - "rel_title": "Household bubbles and COVID-19 transmission: insights from percolation theory", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248311", - "rel_abs": "BackgroundIn the era of social distancing to curb the spread of COVID-19, bubbling is the combining of two or more households to create an exclusive larger group. The impact of bubbling on COVID-19 transmission is challenging to quantify because of the complex social structures involved.\n\nMethodsWe developed a network description of households in the UK, using the configuration model to link households. We explored the impact of bubbling scenarios by joining together households of various sizes. For each bubbling scenario, we calculated the percolation threshold, that is, the number of connections per individual required for a giant component to form, numerically and theoretically. We related the percolation threshold to the household reproduction number.\n\nResultsWe find that bubbling scenarios in which single-person households join with another household has a minimal impact on network connectivity and transmission potential. Ubiquitous scenarios where all households form a bubble are likely to lead to extensive transmission that is hard to control. The impact of plausible scenarios, with variable uptake and heterogeneous bubble sizes, can be mitigated with reduced numbers of contacts outside the household.\n\nConclusionsBubbling of households comes at an increased risk of transmission, however under certain circumstances risks can be modest and could be balanced by other changes in behaviours.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Leon Danon", - "author_inst": "University of Exeter" - }, - { - "author_name": "Lucas Lacasa", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Ellen Brooks-Pollock", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.16.20248139", "rel_title": "The Persistence of Vaccine Hesitancy: COVID-19 Vaccination Intention", @@ -1002949,6 +1000136,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.18.423427", + "rel_title": "SARS-CoV-2 spike protein interacts with and activates TLR4", + "rel_date": "2020-12-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423427", + "rel_abs": "The onset of sepsis is an important feature of COVID19 and a main cause of death. It is unknown how SARS-CoV-2 infection results in viral sepsis in human. We recently found that SARS-CoV-2 provoked an anti-bacterial like response and activation of TLR4 pathway at the very early stage of infection in animal models. This abnormal immune response led to emergency granulopoiesis and sepsis. However, the original trigger of TLR4 signaling by SARS-CoV-2 is unknown. We here identified that the trimeric spike protein of SARS-CoV-2 could bind to TLR4 directly and robustly activate downstream signaling in monocytes and neutrophils. Moreover, specific TLR4 or NFKB inhibitor, or knockout of MyD88 could significantly block IL-1B induction by spike protein. We thus reveal that spike protein of SARS-CoV-2 functions as a potent stimulus causing TLR4 activation and sepsis related abnormal responses.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yingchi Zhao", + "author_inst": "Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China." + }, + { + "author_name": "Ming Kuang", + "author_inst": "Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China." + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "University of Chinese Academy of Sciences, CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese" + }, + { + "author_name": "Fuping You", + "author_inst": "Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.17.423313", "rel_title": "A human coronavirus evolves antigenically to escape antibody immunity", @@ -1003828,93 +1001046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.16.20248301", - "rel_title": "Optimality in COVID-19 vaccination strategies determined by heterogeneity in human-human interaction networks", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248301", - "rel_abs": "Reaching population immunity against COVID-19 is proving difficult even in countries with high vaccination levels. We demonstrate that this in part is due to heterogeneity and stochasticity resulting from community-specific human-human interaction and infection networks. We address this challenge by community-specific simulation of adaptive strategies. Analyzing the predicted effect of vaccination into an ongoing COVID-19 outbreak, we find that adaptive combinations of targeted vaccination and non-pharmaceutical interventions (NPIs) are required to reach population immunity. Importantly, the threshold for population immunity is not a unique number but strategy and community dependent. Furthermore, the dynamics of COVID-19 outbreaks is highly community-specific: in some communities vaccinating highly interactive people diminishes the risk for an infection wave, while vaccinating the elderly reduces fatalities when vaccinations are low due to supply or hesitancy. Similarly, while risk groups should be vaccinated first to minimize fatalities, optimality branching is observed with increasing population immunity. Bimodality emerges as the infection network gains complexity over time, which entails that NPIs generally need to be longer and stricter. Thus, we analyze and quantify the requirement for NPIs dependent on the chosen vaccination strategy. We validate our simulation platform on real-world epidemiological data and demonstrate that it can predict pathways to population immunity for diverse communities world-wide challenged by limited vaccination.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Bjoern Goldenbogen", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Stephan Oliver Adler", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Oliver Bodeit", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Judith Wodke", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Ximena Escalera-Fanjul", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Aviv Korman", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Maria Krantz", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Lasse Bonn", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Rafael Ubaldo Moran Torres", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Johanna EL Haffner", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Maxim Karnetzki", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Ivo Maintz", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Lisa Mallis", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Hannah Prawitz", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Patrick Steven Segelitz", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Martin Seeger", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Rune Linding", - "author_inst": "Humboldt-Universitaet zu Berlin" - }, - { - "author_name": "Edda Klipp", - "author_inst": "Humboldt-Universitaet zu Berlin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.16.20248166", "rel_title": "Using Administrative Data to Incorporate Age and Sex-Dependent Resource Use for COVID-19 Acute Care Resource Use Simulations in Ontario, Canada", @@ -1004659,6 +1001790,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.15.20248235", + "rel_title": "Exploring patient experiences of video consultations during Covid-19 in an outpatient care setting using routine feedback data from 955 contacts", + "rel_date": "2020-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248235", + "rel_abs": "BackgroundVideo consultations (VCs) were rapidly implemented in response to COVID-19, despite modest progress prior to the pandemic.\n\nObjectivesTo explore staff and patient experiences of VCs implemented during COVID-19, and use feedback insights to support quality improvement and service development.\n\nMethodsSecondary data analysis was conducted on 955 (22.6%) patient responses and 521 (12.3%) staff responses routinely collected following a VC between June-July 2020 in a rural, aging and outpatient care setting at a single NHS Trust. Patient and staff feedback were summarised using descriptive statistics and inductive thematic analysis and presented to Trust stakeholders.\n\nResultsMost (93.2%) patients reported having good (n=210, 22.0%), or very good (n=680, 71.2%) experience with VCs and felt listened to and understood (n=904, 94.7%). Most patients accessed their VC alone (n=806, 84.4%), except for those aged 71+ (n=23/58, 39.7%), with ease of joining VCs negatively associated with age (P<.001). Despite more difficulties joining, older people were most likely to be satisfied with the technology (n=46/58, 79.3%). Both patients and staff generally felt patients needs had been met (n=860, 90.1%, n=453, 86.9% respectively), although staff appeared to overestimate patient dissatisfaction with VC outcome (P=.021). Patients (n=848, 88.8%) and staff (n=419, 80.5%) generally felt able to communicate everything they wanted, although patients were significantly more positive than staff (P<.001). Patient satisfaction with communication was positively associated with technical performance satisfaction (P<.001). Most staff (89.8%) reported positive (n=185, 35.5%), or very positive (n=281, 54.3%) experiences of joining and managing a VC. Staff reported reductions in carbon footprint (n=380, 72.9%) and time (n=373, 71.6%). Most (n=880, 92.1%) patients would choose VCs again. Inductive thematic analysis of patient and staff responses identified three themes: i) barriers including technological difficulties, patient information and suitability concerns; ii) potential benefits including reduced stress, enhanced accessibility, cost and time savings; and iii) suggested improvements including trial calls, turning music off, photo uploads, expanding written character limit, supporting other internet browsers and shared interactive screen. This routine feedback, including evidence to suggest patients were more satisfied than clinicians had anticipated, was presented to relevant Trust stakeholders allowing improved processes and supporting development of a business case to inform the Trust decision on continuing VCs beyond COVID-19 restrictions.\n\nConclusionsFindings highlight the importance of regularly reviewing and responding to routine feedback following the implementation of a new digital service. Feedback helped the Trust improve the VC service, challenge clinician held assumptions about patient experience and inform future use of VCs. The feedback has focussed improvement efforts on patient information, technological improvements such as blurred backgrounds and interactive white boards, and responding to the needs of patients with dementia, communication or cognitive impairment or lack of appropriate technology. Findings have implications for other health providers.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hannah Louise Bradwell", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Rebecca Baines", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Katie J. Edwards", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Sebastian Stevens", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Kate Atkinson", + "author_inst": "Cornwall Partnership NHS Foundation Trust" + }, + { + "author_name": "Ellen Wilkinson", + "author_inst": "Cornwall Partnership NHS Foundation Trust" + }, + { + "author_name": "Arunangsu Chatterjee", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Ray B. Jones", + "author_inst": "University of Plymouth" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.15.20248285", "rel_title": "The Impact of COVID-19 Lockdowns on the Behavior of Italian Citizens and Particulate Matter 10 and 2.5 Emissions in Lombardy", @@ -1005330,113 +1002508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.15.20248096", - "rel_title": "Anosmia and other SARS-CoV-2 positive test-associated symptoms, across three national, digital surveillance platforms as the COVID-19 pandemic and response unfolded: an observation study", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248096", - "rel_abs": "BackgroundMultiple participatory surveillance platforms were developed across the world in response to the COVID-19 pandemic, providing a real-time understanding of community-wide COVID-19 epidemiology. During this time, testing criteria broadened and healthcare policies matured. We sought to test whether there were consistent associations of symptoms with SARS-CoV-2 test status across three national surveillance platforms, during periods of testing and policy changes, and whether inconsistencies could better inform our understanding and future studies as the COVID-19 pandemic progresses.\n\nMethodsFour months (1st April 2020 to 31st July 2020) of observation through three volunteer COVID-19 digital surveillance platforms targeting communities in three countries (Israel, United Kingdom, and United States). Logistic regression of self-reported symptom on self-reported SARS-CoV-2 test status (or test access), adjusted for age and sex, in each of the study cohorts. Odds ratios over time were compared to known changes in testing policies and fluctuations in COVID-19 incidence.\n\nFindingsAnosmia/ageusia was the strongest, most consistent symptom associated with a positive COVID-19 test, based on 658,325 tests (5% positive) from over 10 million respondents in three digital surveillance platforms using longitudinal and cross-sectional survey methodologies. During higher-incidence periods with broader testing criteria, core COVID-19 symptoms were more strongly associated with test status. Lower incidence periods had, overall, larger confidence intervals.\n\nInterpretationThe strong association of anosmia/ageusia with self-reported SARS-CoV-2 test positivity is omnipresent, supporting its validity as a reliable COVID-19 signal, regardless of the participatory surveillance platform or testing policy. This analysis highlights that precise effect estimates, as well as an understanding of test access patterns to interpret differences, are best done only when incidence is high. These findings strongly support the need for testing access to be as open as possible both for real-time epidemiologic investigation and public health utility.\n\nFundingNIH, NIHR, Alzheimers Society, Wellcome Trust\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAs the COVID-19 pandemic has evolved, testing capacity expanded and governmental guidelines adapted, generally encouraging testing with a broader set of symptoms, not just fever with respiratory symptoms. In parallel, multiple large-scale citizen science digital surveillance platforms launched to complement knowledge from laboratory and somewhat smaller clinical studies. Symptoms such as loss of sense of smell have been identified as strongly predictive of COVID-19 infection in both clinical and syndromic surveillance analyses, and have therefore been used to inform these testing policy changes and access expansion.\n\nAdded value of this studyThis study identifies symptoms that are or are not consistently associated with SARS-CoV-2 test positivity over time and across three country-based COVID-19 surveillance platforms in the United States, United Kingdom and Israel. These platforms are website and smartphone based, as well as cross-sectional and longitudinal. The study period of 4 months covers fluctuating COVID-19 prevalence during the fall of the first wave and, in some areas, rise of the second wave. In addition, the study period overlaps expansion of test access and test seeking. Importantly, these analyses track and highlight the value of individual symptoms to predict SARS-CoV-2 test positivity under a range of conditions.\n\nImplications of all the available evidenceDespite differences in surveillance methodology, access to SARS-CoV-2 testing and disease prevalence, loss of sense of smell or taste was consistently the strongest predictor of COVID-19 infection across all platforms over time. As access to testing broadened, the relevance of COVID-like symptoms and consistency of their predictive ability became apparent. However, confidence bounds generally widened with a fall in COVID-19 incidence. Therefore, for the most robust symptom-based COVID-19 prediction models should consider surveillance data during periods of higher incidence and improved test access, and effect estimates that replicate across different epidemiologic conditions and platforms.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Carole Helene Sudre", - "author_inst": "University College London" - }, - { - "author_name": "Ayya Keshet", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Mark S Graham", - "author_inst": "King's College London" - }, - { - "author_name": "Amit D Joshi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Smadar Shilo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Hagai Rossman", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Erika Molteni", - "author_inst": "King's College London" - }, - { - "author_name": "Kerstin Klaser", - "author_inst": "King's College London" - }, - { - "author_name": "Liane S Canas", - "author_inst": "King's College London" - }, - { - "author_name": "Michela Antonelli", - "author_inst": "King's College London" - }, - { - "author_name": "Marc Modat", - "author_inst": "King's College London" - }, - { - "author_name": "Joan Capdevila Pujol", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Sajaysurya Ganesh", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Tomer Meir", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Andrew T Chan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Claire Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "John S Brownstein", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Eran Segal", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - }, - { - "author_name": "Christina Astley", - "author_inst": "Boston Children's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.14.20247874", "rel_title": "Rapid detection of SARS-CoV-2 with Cas13", @@ -1006029,6 +1003100,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.14.20245266", + "rel_title": "Efficacy and Safety of Indomethacin in Covid -19 patients", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20245266", + "rel_abs": "BackgroundIndomethacin, a well-known non-steroidal anti-inflammatory drug (NSAID), has in addition broad spectrum anti-viral activity in the laboratory including on SARS-Cov-2 virus. This trial is to observe the likelihood of efficacy and safety of Indomethacin in treating RT-PCR positive Covid patients\n\nMaterials and MethodsThe study was done in two groups. In the first group of the study, where mild and moderate patients were involved, Propensity Score Matching was used as a methodology to compare Indomethacin and paracetamol based treatments in addition to the standard protocol for treating covid-19 patients.. Blood chemistry was collected before and after the treatment. The patients were monitored every day for clinical parameters. In this part, a patient developing hypoxia was the end point. In the second group, severe patients admitted with hypoxia were treated with Indomethacin in addition to Remdesivir, and the end point was the requirement of mechanical ventilation/admission to ICU.\n\nResultsIt was observed that patients treated with Indomethacin had a reduction in the number of days to become afebrile, reduction in cough and myalgia by half compared to the paracetamol set. Only one out of 72 patients in the Indomethacin arm of the first group required supplementary oxygen while 28 of the 72 patients required supplementary oxygen in the paracetamol arm. No one in the second group deteriorated enough to require mechanical ventilation. There wea no evidence of adverse reaction to indomethacin or deterioration of renal or liver function.\n\nConclusionIndomethacin, along with standard care, seems to provide faster symptomatic relief and prevent progression of pneumonia in Covid-19 patients. It should be considered to replace paracetamol when there is no contraindication for its use.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rajan Ravichandran", + "author_inst": "Department of Nephrology, MIOT International, Chennai" + }, + { + "author_name": "Prassana Purna", + "author_inst": "Department of Pulmonology, Narayana Medical College, Nellore, Andhra Pradesh, India" + }, + { + "author_name": "Sivakumar Vijayaragavan", + "author_inst": "Narayana Translational Research Centre, Narayana Medical College, Nellore, Andhra Pradesh, India" + }, + { + "author_name": "Ravi Teja Kalavakollu", + "author_inst": "Department of Pulmonology, Narayana Medical College, Nellore, Andhra Pradesh, India" + }, + { + "author_name": "Shilpa Gaidhane", + "author_inst": "Department of Medicine, Datta Meghe Institute of Medical Science, Wardha, Maharashtra, India" + }, + { + "author_name": "Ramarathnam Krishna Kumar", + "author_inst": "Department of Engineering Design, Indian Institute of Technology Madras, Chennai, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.14.20248184", "rel_title": "Uncertainty reduction in logistic regressions: a COVID-19 case-study using surrogate locations' asymptotic values", @@ -1007284,109 +1004394,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.16.422529", - "rel_title": "Niclosamide inhibits SARS-CoV2 entry by blocking internalization through pH-dependent CLIC/GEEC endocytic pathway", - "rel_date": "2020-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.422529", - "rel_abs": "Many viruses utilize the host endo-lysosomal network to infect cells. Tracing the endocytic itinerary of SARS-CoV2 can provide insights into viral trafficking and aid in designing new therapeutic targets. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV2 is internalized via the clathrin and dynamin-independent, pH-dependent CLIC/GEEC (CG) endocytic pathway. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, strongly block the uptake of RBD. Using transduction assays with SARS-CoV2 Spike-pseudovirus, we confirmed that these acidification inhibitors also impede viral infection. By contrast, Chloroquine neither affects RBD uptake nor extensively alters the endosomal pH, yet attenuates Spike-pseudovirus entry, indicating a pH-independent mechanism of intervention. We screened a subset of FDA-approved acidification inhibitors and found Niclosamide to be a potential SARS-CoV2 entry inhibitor. Niclosamide, thus, could provide broader applicability in subverting infection of similar category viruses entering host cells via this pH-dependent endocytic pathway.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Chaitra Prabhakara", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Rashmi Godbole", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Parijat Sil", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Sowmya Jahnavi", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Thomas S van Zanten", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Dhruv Sheth", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Neeraja Subhash", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Anchal Chandra", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Vijay Kumar Nuthakki", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Theja Parassini Puthiyapurayil", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine (inSTEM), Bengaluru, India" - }, - { - "author_name": "Riyaz Ahmed", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Ashaq Hussain Najar", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Sai Manoz Lingamallu", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine (inSTEM), Bengaluru, India" - }, - { - "author_name": "Snigdhadev Das", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Bhagyashri Mahajan", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Praveen Kumar Vemula", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine (inSTEM), Bengaluru, India" - }, - { - "author_name": "Sandip B Bharate", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Parvinder Pal Singh", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Ram Vishwakarma", - "author_inst": "CSIR - Indian Institute of Integrative Medicine, Jammu, India" - }, - { - "author_name": "Arjun Guha", - "author_inst": "Institute for Stem Cell Science and Regenerative Medicine (inSTEM), Bengaluru, India" - }, - { - "author_name": "Varadharajan Sundaramurthy", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - }, - { - "author_name": "Satyajit Mayor", - "author_inst": "National Centre for Biological Sciences (TIFR), Bengaluru, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.12.16.423002", "rel_title": "EXPERIMENTAL INVESTIGATION OF PULSE STERILIZATION OF VIRAL INFECTION", @@ -1007943,6 +1004950,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.12.10.20247080", + "rel_title": "Does Contact Tracing Work? Quasi-Experimental Evidence from an Excel Error in England", + "rel_date": "2020-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247080", + "rel_abs": "Contact tracing has been a central pillar of the public health response to the COVID-19 pandemic. Yet, contact tracing measures face substantive challenges in practice and well-identified evidence about their effectiveness remains scarce. This paper exploits quasi-random variation in COVID-19 contact tracing. Between September 25 and October 2, 2020, a total of 15,841 COVID-19 cases in England (around 15 to 20% of all cases) were not immediately referred to the contact tracing system due to a data processing error. Case information had been truncated from an Excel spreadsheet due to a row limit, which was discovered on October 3. There is substantial variation in the degree to which different parts of England areas were exposed - by chance - to delayed referrals of COVID-19 cases to to the contact tracing system. We show that more affected areas subsequently experienced a drastic rise in new COVID-19 infections and deaths alongside an increase in the positivity rate and the number of test performed, as well as a decline in the performance of the contact tracing system. Conservative estimates suggest that the failure of timely contact tracing due to the data glitch is associated with more than 125,000 additional infections and over 1,500 additional COVID-19-related deaths. Our findings provide strong quasi-experimental evidence for the effectiveness of contact tracing.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Thiemo Fetzer", + "author_inst": "University of Warwick" + }, + { + "author_name": "Thomas Graeber", + "author_inst": "Harvard Business School" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.10.20240689", "rel_title": "Foistar(Camostat mesylate) associated with the significant decrease in CRP levels compared to Kaletra(Lopinavir/Ritonavir) treatment in Korean mild COVID-19 pneumonic patients.", @@ -1008978,29 +1006008,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.11.20247825", - "rel_title": "Identifying Synergistic Interventions to Address COVID-19 Using a Large Scale Agent-Based Model", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247825", - "rel_abs": "There is a range of public health tools and interventions to address the global pandemic of COVID-19. Although it is essential for public health efforts to comprehensively identify which interventions have the largest impact on preventing new cases, most of the modeling studies that support such decision-making efforts have only considered a very small set of interventions. In addition, previous studies predominantly considered interventions as independent or examined a single scenario in which every possible intervention was applied. Reality has been more nuanced, as a subset of all possible interventions may be in effect for a given time period, in a given place. In this paper, we use cloud-based simulations and a previously published Agent-Based Model of COVID-19 (Covasim) to measure the individual and interacting contribution of interventions on reducing new infections in the US over 6 months. Simulated interventions include face masks, working remotely, stay-at-home orders, testing, contact tracing, and quarantining. Through a factorial design of experiments, we find that mask wearing together with transitioning to remote work/schooling has the largest impact. Having sufficient capacity to immediately and effectively perform contact tracing has a smaller contribution, primarily via interacting effects.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Philippe J. Giabbanelli", - "author_inst": "Miami University" - }, - { - "author_name": "Junjiang Li", - "author_inst": "Miami University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.14.20248152", "rel_title": "SARS-CoV-2 among migrants and forcibly displaced populations: a rapid systematic review", @@ -1009629,6 +1006636,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.11.20247437", + "rel_title": "Clinical and Demographic Characteristics of COVID-19 Patients Admitted in a Tertiary Care Hospital in the Dominican Republic", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247437", + "rel_abs": "To present clinical and demographic characteristics of COVID-19 patients admitted to Hospital Metropolitano de Santiago in Dominican Republic, we analyzed electronic medical records of all hospitalized patients clinically admitted as viral pneumonia through March - April, 2020. Of 374 patients, 150 (40.1%) laboratory confirmed, were included in this study. Most of the patients were men (104 / 69.3%) with a median (IQR 44 - 66) age of 54. Hypertension (83 / 55.3%) and diabetes mellitus (49 / 32.7%) were the most common comorbidities, whereas fever (120 / 80%), cough (79 / 52.7%) and fatigue (60 / 40%) were the most common presenting symptoms. 28 (18.7%) patients required admission to the intensive care unit, of them, 26 patients (17.3%) required mechanical ventilation. The overall mortality rate was 10.7% Higher levels of inflammatory markers were associated with longer length of stay (LOS). This findings indulge information that could contribute to stratify patients at higher risk of complications.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David De Luna", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Yori Roque", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Nicolas Batlle", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Brinia Cabrera", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Lissa Maria Cruz", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Katherine Gomez", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Miguelina Jaquez", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Rossy Belliard", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Osvaldo Tavarez", + "author_inst": "Hospital Metropolitano De Santiago (HOMS)" + }, + { + "author_name": "Jose Javier Sanchez", + "author_inst": "Pontificia Universidad Catolica Madre y Maestra" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.12.20247726", "rel_title": "Clinical and Virological Characteristics of Hospitalized COVID-19 Patients in a German Tertiary Care Center during the First Wave of the SARS-CoV-2 Pandemic", @@ -1010752,81 +1007814,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.13.20248120", - "rel_title": "Vaccines that prevent SARS-CoV-2 transmission may prevent or dampen a spring wave of COVID-19 cases and deaths in 2021", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20248120", - "rel_abs": "Ongoing SARS-CoV-2 vaccine trials assess vaccine efficacy against disease (VEDIS), the ability of a vaccine to block symptomatic COVID-19. They will only partially discriminate whether VEDIS is mediated by preventing infection as defined by the detection of virus in the airways (vaccine efficacy against infection defined as VESUSC), or by preventing symptoms despite breakthrough infection (vaccine efficacy against symptoms or VESYMP). Vaccine efficacy against infectiousness (VEINF), defined as the decrease in secondary transmissions from infected vaccine recipients versus from infected placebo recipients, is also not being measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna and Pfizer vaccines, which have observed VEDIS>90%, mediate VEDIS predominately by complete protection against infection, then prevention of a fourth epidemic wave in the spring of 2021, and associated reduction of subsequent cases and deaths by 60%, is likely to occur assuming rapid enough vaccine roll out. If high VEDIS is explained primarily by reduction in symptoms, then VEINF>50% will be necessary to prevent or limit the extent of this fourth epidemic wave. The potential added benefits of high VEINF would be evident regardless of vaccine allocation strategy and would be enhanced if vaccine roll out rate is low or if available vaccines demonstrate waning immunity. Finally, we demonstrate that a 1.0 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve VEINF=60% and that human challenge studies with 104 infected participants, or clinical trials in a university student population could estimate VESUSC, VESYMP and VEINF using viral load metrics.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "David A Swan", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Ashish Goyal", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Chloe Bracis", - "author_inst": "University Grenoble Alpes" - }, - { - "author_name": "Mia Moore", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elizabeth Krantz", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elizabeth R Brown", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Fabian Cardozo-Ojeda", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Daniel B Reeves", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Fei Gao", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Peter B Gilbert", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Lawrence Corey", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Myron S Cohen", - "author_inst": "UNC" - }, - { - "author_name": "Holly Janes", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Dobromir Dimitrov", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Joshua T Schiffer", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.13.422589", "rel_title": "Profiling of oral microbiota and cytokines in COVID-19 patients", @@ -1011451,6 +1008438,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.13.422548", + "rel_title": "Evaluation of in vitro activity of copper gluconate against SARS-CoV-2 using confocal microscopy-based high content screening", + "rel_date": "2020-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.13.422548", + "rel_abs": "ContextSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that emerged late in 2019 is the etiologic agent of coronavirus disease 2019 (Covid-19). There is an urgent need to develop curative and preventive therapeutics to limit the current pandemic and to prevent the re-emergence of Covid-19. This study aimed to assess the in vitro activity of copper gluconate against SRAS-CoV-2.\n\nMethodsVero E6 cells were treated with copper gluconate 18 hours before infection. Cells were infected with a recombinant GFP expressing SARS-CoV-2. Infected cells were maintained in fresh medium containing copper gluconate for an additional 48-hour period. The infection level was measured by the confocal microscopy-based high content screening method. The cell viability in presence of copper gluconate was assessed by XTT assay.\n\nResultsThe viability of Vero E6 cells treated with copper gluconate up to 200 M was found to be similar to that of untreated cells, but it dropped below 40% with 400 M of this agent. The infection rate was 23.8%, 18.9%, 20.6%, 6.9%, 5.3%,5.2% in cells treated with 0, 2, 10, 25, 50 and 100 M of copper gluconate respectively. As compared to untreated cells, the number of infected cells was reduced by 71%, 77%, and 78% with 25, 50, and 100 M of copper gluconate respectively (p < 0.05).\n\nConclusionCopper gluconate was found to mitigate SARS-CoV-2 infection in Vero E6 cells. Furthers studies are needed to determine whether copper homeostasis could play a role in SARS-CoV-2 infection.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC=\"FIGDIR/small/422548v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@1f99949org.highwire.dtl.DTLVardef@1bebae6org.highwire.dtl.DTLVardef@e05e37org.highwire.dtl.DTLVardef@49a3b2_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Killian Rodriguez", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Josselin Rigaill", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Estelle Audoux", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Florian Saunier", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Elisabeth Botelho-Nevers", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Amelie Prier", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Yann Dickerscheit", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Sylvie Pillet", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Bruno Pozzetto", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Thomas Bourlet", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + }, + { + "author_name": "Paul O Verhoeven", + "author_inst": "CIRI (Centre International de Recherche en Infectiologie), Equipe GIMAP (team 15), INSERM U1111, CNRS, ENS, UCBL1, Universite Jean Monnet, Universite de Lyon, S" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.13.422469", "rel_title": "A novel cell culture system modeling the SARS-CoV-2 life cycle", @@ -1012445,53 +1009491,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.06.20245019", - "rel_title": "AYUSH medicine as add-on therapy for mild category COVID-19; an open label randomised, controlled clinical trial.", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20245019", - "rel_abs": "BackgroundAYUSH formulations have a potential role in symptomatic treatment, preventing disease progression and improving quality of life in COVID-19 patients.\n\nObjectiveTo study the effect of AYUSH formulation (Kabasura Kudineer tablets, Shakti drops and Turmeric plus) as an add-on treatment in patients with mild COVID - 19\n\nMethodologySingle centre, two arms, open labelled randomized controlled trial with a total of 30 patients (15 in the intervention arm and 15 in the standard care arm). Intervention arm received a combination of 3 AYUSH formulation along with the standard of care treatment for 21 days. All patients were followed for 28 days. Symptom severity (using Modified Jackson scale), negative conversion of SARS-CoV-2 RNA (using RTPCR) and quality of life (WHOWOL BREF questionnaire) was assessed.\n\nResultsFifteen patients (93.8%) in the intervention group and twelve patients (92.3%) in the standard care arm had complete resolution of symptoms (P value= 0.36). Negative conversion for SARS-CoV-2 was seen in thirteen patients (92.9%) in intervention arm and eleven patients (100%) in standard care arm at day 28 (P value = 0.56). There was no difference in the quality of life scores between the 2 groups.\n\nConclusionThe use of Ayush interventions as add-on therapy did not negatively impact the clinical outcomes in COVID-19. This trial confirmed the safety and tolerability of Kabasura Kudineer tablets, Shakti drops and Turmeric plus tablets when used use among mild to moderate symptom category, of COVID-19. There were no serious adverse events in the treated group. There was no clinical progression of disease from baseline status and all trial participants recovered fully by day 28. A longer follow up and a larger sample size is recommended for future definitive trials with this alternative medicine (AYUSH) combination.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Anusha Rao", - "author_inst": "Narayana Health" - }, - { - "author_name": "Ranganatha R", - "author_inst": "Narayana Health, Bangalore, India" - }, - { - "author_name": "Vikneswaran G", - "author_inst": "Narayana Health, Bangalore, India" - }, - { - "author_name": "Sagar C", - "author_inst": "Narayana Health, Bangalore, India" - }, - { - "author_name": "Mathu Ruthra", - "author_inst": "Narayana Health, Bangalore, India" - }, - { - "author_name": "Sherin Manichen", - "author_inst": "Narayana Health, Bangalore, India" - }, - { - "author_name": "ALBEN SIGAMANI", - "author_inst": "NARAYANA HRUDAYALAYA LIMITED" - }, - { - "author_name": "Ravi kumar Reddy", - "author_inst": "Sriveda Sattva Private Limited, Bangalore, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.04.20243949", "rel_title": "The burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population: Results from a statewide survey in Karnataka, India", @@ -1013320,6 +1010319,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.09.20246421", + "rel_title": "Contacts and behaviours of university students during the COVID-19 pandemic at the start of the 2020/21 academic year", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246421", + "rel_abs": "CONQUEST (COroNavirus QUESTionnaire) is an online survey of contacts, behaviour, and COVID-19 symptoms for University of Bristol (UoB) staff/students. We analysed survey results from the start of the 2020/2021 academic year, prior to the second national lockdown (14/09/2020-01/11/2020), where COVID-19 outbreaks led to lockdown of some student halls of residence. The aim of these analyses was to enhance knowledge of student contact patterns to inform infection disease mathematical modelling approaches.\n\nResponses captured information on demographics, contacts on the previous day, symptoms and self-isolation during the prior week, and COVID-19 status.\n\n740 students provided 1261 unique records. Of 42 (3%) students testing positive in the prior fortnight, 99% had been self-isolating. The median number of contacts on the previous day was 2 (interquartile range: 1-5), mode: 1, mean: 6.1; 8% had [≥]20 contacts. 57% of student contacts were other UoB students/staff.\n\nMost students reported few daily contacts but there was heterogeneity, and some reported many. Around 40% of student contacts were with individuals not affiliated with UoB, indicating potential for transmission to non-students/staff.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Finn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Amy Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Caroline Relton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Clara Montgomery", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gibran Hemani", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jane Metz", + "author_inst": "University of Bristol" + }, + { + "author_name": "Josephine Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Katy Turner", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachel Kwiatkowska", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Sauchelli", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "University of Exeter" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.08.20246264", "rel_title": "Characterizing the Dynamic of COVID-19 with a New Epidemic Model: Susceptible-Exposed-Symptomatic-Asymptomatic-Active-Removed", @@ -1014339,33 +1011413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.10.20223990", - "rel_title": "Conundrum of re-positives COVID-19 cases: A Systematic review of Case reports and Case series", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20223990", - "rel_abs": "IntroductionThere have been case reports and case series published for RT PCR positive COVID - 19 cases that became RT PCR negative but subsequently became RT PCR positive after a symptom free interval following a negative RT PCR test. These cases may include re-positive, reactivated and re-infection cases. Hence, the systematic review to summarize and synthesize evidence from all available case series and case reports published was undertaken.\n\nMethodologyThe systematic review of case series and case reports was registered with Prospero with registration number CRD42020210446. PRISMA guidelines were followed for conducting the systematic review. Studies published in English language only were considered for the Systematic Review. Inclusion criteria for studies included case reports and case series which have documented cases of positive RT-PCR after a period of improvement or negative RT PCR. Reviews, opinions and animal studies were excluded. Case reports which described clinical presentation or manifestations of COVID-19 cases were also excluded from the studies. Methodological quality was assessed using modified Murad scale.\n\nResultsA total of 30 case reports/case series were included in the study, wherein a total of 219 cases were included. In re-positive cases, the age range varied from 10 months to 91 years. The pooled proportion using random effects was 12% with 95% CI from 09% to 15%. Among the re-positives, a total of 57 cases (26%) of the cases had co-morbidities. A total of 51 (23.3%) and 17 (7.8%) re-positive cases had been treated with antivirals and corticosteroids respectively. Among the symptomatic cases, the disease severity was lesser as compared to the initial episode of illness. Only a few studies have confirmed the presence of antibodies after the first episode. The few studies that had done contact tracing of re-positives did not find any positive cases among those in contact with re-positives.\n\nConclusionThis systematic review presents the review of all the case reports and case series on recurrence of COVID 19 disease. Although limited evidence has been generated due to paucity of such studies and shortcomings in the study designs of case reports and case-series, nonetheless, the evidence generated can still be used in making clinical decisions and framing policy guidelines", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Arun K Yadav", - "author_inst": "Armed Forces Medical College" - }, - { - "author_name": "Subhadeep Ghosh", - "author_inst": "ACMS" - }, - { - "author_name": "Sudhir Dubey", - "author_inst": "ACMS" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.09.20246629", "rel_title": "Optimal test allocation strategy for COVID-19", @@ -1014854,6 +1011901,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.10.20247346", + "rel_title": "What positives can be taken from the COVID-19 pandemic in Australia?", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247346", + "rel_abs": "ObjectiveTo investigate whether Australians have experienced any positive effects during the COVID-19 pandemic, despite the disruption to society and daily life.\n\nMethodsNational online longitudinal survey. As part of a June 2020 survey, participants (n=1370) were asked In your life, have you experienced any positive effects from the COVID-19 pandemic (yes/no), with a free-text explanation if yes, and also completed the WHO-Five well-being index. Differences were explored by demographic variables. Free-text responses were thematically coded.\n\nResults960 participants (70%) reported experiencing at least one positive effect during the COVID-19 pandemic. Living with others (p=.045) and employment situation (p<.001) at baseline (April), were associated with experiencing positive effects. Individuals working for pay from home were more likely to experience positive effects compared to those who were not working for pay (aOR=0.45, 95%CI: 0.32, 0.63, p<.001), or who were working for pay outside the home (aOR=0.40, 95%CI: 0.28, 0.58, p<.001). Age and education were not associated with positive effects when controlling for employment and household numbers. There was an overall effect of gender (p=.001), where those identifying as female were more likely than males (aOR=1.62, 95%CI: 1.25, 2.09) to report experiencing a positive effect. 54.2% of participants reported a sufficient level of wellbeing, 23.2% low wellbeing and a further 22.6% very low wellbeing. Of those experiencing positives, 945/960 (98%) provided an explanation. The three most common themes were Family time (33%), Work flexibility (29%), and Calmer life (19%).\n\nConclusionA large proportion of surveyed Australians reported positive effects resulting from changes to daily life due to the COVID-19 pandemic in Australia. Enhancing these aspects may build community resilience to cope with future pandemic responses. The needs of people living alone, and of those having to work outside the home or who are unemployed, should be considered by health policy makers and employers in future pandemic preparedness efforts, as these groups were least likely to report positive experiences and may be more vulnerable.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Samuel Cornell", + "author_inst": "University of Sydney" + }, + { + "author_name": "Brooke Nickel", + "author_inst": "University of Sydney" + }, + { + "author_name": "Erin Cvejic", + "author_inst": "University of Sydney" + }, + { + "author_name": "Carissa Bonner", + "author_inst": "University of Sydney" + }, + { + "author_name": "Kirsten J McCaffery", + "author_inst": "University of Sydney" + }, + { + "author_name": "Julie Ayre", + "author_inst": "University of Sydney" + }, + { + "author_name": "Tessa Copp", + "author_inst": "University of Sydney" + }, + { + "author_name": "Carys Batcup", + "author_inst": "University of Sydney" + }, + { + "author_name": "Jennifer MJ Isautier", + "author_inst": "University of Sydney" + }, + { + "author_name": "Thomas Dakin", + "author_inst": "University of Sydney" + }, + { + "author_name": "Rachael Dodd", + "author_inst": "University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.07.20245076", "rel_title": "COVID-19 Rapid Diagnostic test results and their associations with certain factors among the residents of Balochistan.", @@ -1016109,109 +1013215,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.12.10.20247338", - "rel_title": "IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247338", - "rel_abs": "Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- and N-gene targets and a sample control in a single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (NER). This combined, cost-effective test can be performed in 384-well plates with detection sensitivity suitable for clinical reporting, and will aid in future sample pooling efforts, thus improving throughput of SARS-CoV-2 detection.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC=\"FIGDIR/small/20247338v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@74929corg.highwire.dtl.DTLVardef@1457971org.highwire.dtl.DTLVardef@2825ddorg.highwire.dtl.DTLVardef@1cde2b6_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Elizabeth C. Stahl", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Connor A. Tsuchida", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Jennifer R. Hamilton", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Enrique Lin-Shiao", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Shana L. McDevitt", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Erica A. Moehle", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Lea B. Witkowsky", - "author_inst": "1University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "C. Kimberly Tsui", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Kathleen Pestal", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Holly K. Gildea", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Matthew McElroy", - "author_inst": "Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Amanda Keller", - "author_inst": "Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Iman Sylvain", - "author_inst": "Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Clara Williams", - "author_inst": "Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Ariana Hirsh", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Alison Ciling", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Alexander J. Ehrenberg", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "- SARS-CoV-2 consortium", - "author_inst": "-" - }, - { - "author_name": "Fyodor D. Urnov", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Bradley R. Ringeisen", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Petros Giannikopoulos", - "author_inst": "Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medica" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.10.417758", "rel_title": "EVs analysis in the COVID-19 era: insights on serum inactivation protocols towards downstream isolation and analysis", @@ -1017204,6 +1014207,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.10.419242", + "rel_title": "Molnupiravir (EIDD-2801) inhibits SARS-CoV2 replication in Syrian hamsters model", + "rel_date": "2020-12-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.419242", + "rel_abs": "Favipiravir and Molnupiravir, orally available antivirals, have been reported to exert antiviral activity against SARS-CoV2. In recent days preliminary efficacy data have been reported in COVID-19 patients. We here studied the combined antiviral effect of the drugs in the SARS-CoV2 hamster infection model. We first demonstrate that Molnupiravir can reduce infectious virus titers in lungs of infected animals in a dose-dependent manner by up to 3.5 log10 which is associated with a marked improvement of virus-induced lung pathology. When animals are treated with a combination of suboptimal doses of Molnupiravir and Favipiravir (that each alone result in respectively a 1.3 log10 and 1.1 log10 reduction of infectious virus titers in the lungs), a marked combined potency is observed. Infectious virus titers in the lungs of animals treated with the combo are on average reduced by 4.5 log10 and infectious virus are no longer detected in the lungs of 60% of treated infected animals. Both drugs result in an increased mutation frequency of the remaining viral RNA recovered from the lungs. In the combo-treated hamsters an increased frequency of C-to-T and G-to-A mutations in the viral RNA is observed as compared to the single treatment groups which may explain the pronounced antiviral potency of the combination. Our findings may lay the basis for the design of clinical studies to test the efficacy of the combination of Molnupiravir and Favipiravir in the treatment of COVID-19.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Rana Abdelnabi", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Caroline S. Foo", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Suzanne J. F. Kaptein", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Lana Langendries", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Laura Vangeel", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Judith Breuer", + "author_inst": "University College London" + }, + { + "author_name": "Juanita Pang", + "author_inst": "University College London" + }, + { + "author_name": "Rachel Williams", + "author_inst": "UCL" + }, + { + "author_name": "Valentijn Vergote", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Elisabeth Heylen", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Pieter Leyssen", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Kai Dallmeier", + "author_inst": "KU Leuven Rega Institute" + }, + { + "author_name": "Lotte Coelmont", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Dirk Jochmans", + "author_inst": "REGA Institute - KULeuven" + }, + { + "author_name": "Arnab K. Chatterjee", + "author_inst": "Calibr at Scripps Research" + }, + { + "author_name": "Steven De Jonghe", + "author_inst": "Rega Institute, KU Leuven" + }, + { + "author_name": "Birgit Weynand", + "author_inst": "KU Leuven" + }, + { + "author_name": "Johan Neyts", + "author_inst": "Rega Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.10.418996", "rel_title": "Betulonic acid derivatives inhibiting coronavirus replication in cell culture via the nsp15 endoribonuclease", @@ -1018035,93 +1015129,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.07.20245696", - "rel_title": "SARS Coronavirus-2 microneutralisation and commercial serological assays correlated closely for some but not all enzyme immunoassays", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245696", - "rel_abs": "BackgroundSerological testing for SARS-CoV-2 specific antibodies provides important research and diagnostic information relating to COVID-19 prevalence, incidence, and host immune response. A greater understanding of the relationship between functionally neutralising antibodies detected using microneutralisation assays and binding antibodies detected using scalable enzyme immunoassays (EIA) is needed in order to address protective immunity post-infection or vaccination, and assess EIA suitability as a surrogate test for screening of convalescent plasma donors. We assessed whether neutralising antibody titres correlated with signal cut-off ratios in five commercially available EIAs, and one in-house assay based on expressed spike protein targets.\n\nMethodsSera from individuals recovered from patients or convalescent plasma donors who reported laboratory-confirmed SARS-CoV-2 infection (n=200), and negative control sera collected prior to the COVID-19 pandemic (n=100) were assessed in parallel. Performance was assessed by calculating EIA sensitivity and specificity with reference to microneutralisation.\n\nResultsNeutralising antibodies were detected in 166 (83%) samples. Compared with this, the most sensitive EIAs were the Cobas Elecsys Anti-SARS-CoV-2 (98%) and Vitros Immunodiagnostic Anti-SARS-CoV-2 (100%), which detect total antibody targeting the N and S1 antigens, respectively. The assay with the best quantitative relationship with microneutralisation was the Euroimmun IgG.\n\nConclusionsThese results suggest the marker used (total Ab vs IgG vs IgA), and the target antigen are important determinants of assay performance. The strong correlation between microneutralisation and some commercially available assays demonstrate their potential for clinical and research use in assessing protection following infection or vaccination, and use as a surrogate test to assess donor suitability for convalescent plasma donation.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Gregory J Walker", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Zin Naing", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Alberto Ospina Stella", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Malinna Yeang", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Joanna Caguicla", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Vidiya Ramachandran", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Sonia R Isaacs", - "author_inst": "University of New South Wales" - }, - { - "author_name": "David Agapiou", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Rowena Bull", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Sacha Stelzer-Braid", - "author_inst": "University of New South Wales" - }, - { - "author_name": "James Daly", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "Iain B Gosbell", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "Veronica C Hoad", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "David O Irving", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "Joanne M Pink", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "Stuart Turville", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Anthony D Kelleher", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "William D Rawlinson", - "author_inst": "NSW Health Pathology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20245811", "rel_title": "Six-month antibody response to SARS-CoV-2 in healthcare workers assessed by virus neutralisation and commercial assays", @@ -1018810,6 +1015817,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.08.416297", + "rel_title": "Complete Protection of Nasal and Lung Airways Against SARS-CoV-2 Challenge by Antibody Plus Th1 Dominant N- and S-Specific T-Cell Responses to Subcutaneous Prime and Thermally-Stable Oral Boost Bivalent hAd5 Vaccination in an NHP Study", + "rel_date": "2020-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416297", + "rel_abs": "We have developed a dual-antigen COVID-19 vaccine incorporating genes for a modified SARS-CoV-2 spike (S-Fusion) protein and the viral nucleocapsid (N) protein with an Enhanced T-cell Stimulation Domain (N-ETSD) with the potential to increase MHC class I/II responses. The adenovirus serotype 5 platform used, hAd5 [E1-, E2b-, E3-], previously demonstrated to be effective in the presence of Ad immunity, can be delivered in an oral formulation that overcomes cold-chain limitations. The hAd5 S-Fusion + N-ETSD vaccine was evaluated in rhesus macaques showing that a subcutaneous prime followed by oral boosts elicited both humoral and Th1 dominant T-cell responses to both S and N that protected the upper and lower respiratory tracts from high titer (1 x 106 TCID50) SARS-CoV-2 challenge. Notably, viral replication was inhibited within 24 hours of challenge in both lung and nasal passages, becoming undetectable within 7 days post-challenge.\n\nONE SENTENCE SUMMARYhAd5 spike + nucleocapsid SC prime/oral boost vaccine elicits humoral and T-cell responses and protects rhesus macaques from SARS-CoV-2 challenge.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Elizabeth Gabitzsch", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Jeffrey T Safrit", + "author_inst": "NantKwest, Inc" + }, + { + "author_name": "Mohit Verma", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Adrian Rice", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Peter Sieling", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Lise Zakin", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Annie Shin", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Brett Morimoto", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Helty Adisetiyo", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Raymond Wong", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Ashish Bezawada", + "author_inst": "NantKwest Inc" + }, + { + "author_name": "Kyle Dinkins", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Joseph Balint", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Victor Peykov", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Hermes Garban", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Philip Liu", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Pete Bone", + "author_inst": "Iosbio, Inc." + }, + { + "author_name": "Andrew Bacon", + "author_inst": "IosBio,Inc" + }, + { + "author_name": "Jeff Drew", + "author_inst": "IsoBio, Inc" + }, + { + "author_name": "Daniel C Sanford", + "author_inst": "Battelle Biomedical ResearchCenter" + }, + { + "author_name": "Patricia Spilman", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Lennie Sender", + "author_inst": "NantKwest Inc" + }, + { + "author_name": "Shahrooz Rabizadeh", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Kayvan Niazi", + "author_inst": "ImmunityBio LLC" + }, + { + "author_name": "Patrick Soon-Shiong", + "author_inst": "NantWorks" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.09.416586", "rel_title": "Identification of a Novel Susceptibility Marker for SARS-CoV-2 Infection in Human Subjects and Risk Mitigation with a Clinically Approved JAK Inhibitor in Human/Mouse Cells", @@ -1019756,53 +1016878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.07.20245282", - "rel_title": "Effect of COVID-19 response policies on walking behavior in US cities", - "rel_date": "2020-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245282", - "rel_abs": "The COVID-19 pandemic has caused mass disruption to our daily lives. Mobility restrictions implemented to reduce the spread of COVID-19 have impacted walking behavior, but the magnitude and spatio-temporal aspects of these changes have yet to be explored. Walking is the most common form of physical activity and non-motorized transport, and so has an important role in our health and economy. Understanding how COVID-19 response measures have affected walking behavior of populations and distinct subgroups is paramount to help devise strategies to prevent the potential health and societal impacts of declining walking levels. In this study, we integrated mobility data from mobile devices and area-level data to study the walking patterns of 1.62 million anonymous users in 10 metropolitan areas in the United States (US). The data covers the period from mid-February 2020 (pre-lockdown) to late June 2020 (easing of lockdown restrictions). We detected when users were walking, measured distance walked and time of the walk, and classified each walk as recreational or utilitarian. Our results revealed dramatic declines in walking, especially utilitarian walking, while recreational walking has recovered and even surpassed the levels before the pandemic. However, our findings demonstrated important social patterns, widening existing inequalities in walking behavior across socio-demographic groups. COVID-19 response measures had a larger impact on walking behavior for those from low-income areas, of low education, and high use of public transportation. Provision of equal opportunities to support walking could be key to opening up our society and the economy.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ruth F Hunter", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "Leandro Garcia", - "author_inst": "Queen's University Belfast" - }, - { - "author_name": "Thiago Herick de Sa", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Belen Zapata-Diomedi", - "author_inst": "RMIT University" - }, - { - "author_name": "Christopher J Millett", - "author_inst": "Imperial College London" - }, - { - "author_name": "James Woodcock", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alex Pentland", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Esteban Moro", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.08.416339", "rel_title": "Natural SARS-CoV-2 infections, including virus isolation, among serially tested cats and dogs in households with confirmed human COVID-19 cases in Texas, USA", @@ -1020434,6 +1017509,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.04.20243972", + "rel_title": "Use of Public Data to Describe COVID-19 Contact Tracing in China during January 20-February 29, 2020", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243972", + "rel_abs": "ObjectiveAlthough contact tracing is generally not used to control influenza pandemics, China and several countries in the Western Pacific Region employed contact tracing as part of COVID-19 response activities. To improve understanding on the use of contact tracing for COVID-19 emergency public health response activities, we describe reported COVID-19 contacts traced and quarantined in China and a proxy for number of reported contacts traced per reported case.\n\nMethodsWe abstracted publicly available online aggregate data reported from Chinas National Health Commission and provincial health commissions COVID-19 daily situational reports for January 20-February 29, 2020. The number of new contacts traced by report date was computed as the difference between total contacts traced on consecutive reports. A proxy for the number of contacts traced per case was computed as the number of new contacts traced divided by the number of new cases.\n\nResultsDuring January 20-February 29, 2020, China reported 80,968 new COVID-19 cases (Hubei Province = 67,608 [83%]), and 659,899 contacts traced (Hubei Province = 265,617 [40%]). Non-Hubei provinces reported more contacts traced per case than Hubei Province; this difference increased over time.\n\nDiscussionAlong with other NPI used in China, contact tracing likely contributed to reducing SARS-CoV-2 transmission by quarantining a large number of potentially infected contacts. Despite reporting only 15% of total cases, non-Hubei provinces had 1.5 times more reported contacts traced compared to Hubei Province. Contract tracing may have been more complete in areas and periods with lower case counts.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Emilio Dirlikov", + "author_inst": "U.S. Centers for Disease Control and Prevention" + }, + { + "author_name": "Suizan Zhou", + "author_inst": "U.S. Centers for Disease Control and Prevention, China Country Office" + }, + { + "author_name": "Lifeng Han", + "author_inst": "U.S. Centers for Disease Control and Prevention, China Country Office" + }, + { + "author_name": "Zhijun Li", + "author_inst": "U.S. Centers for Disease Control and Prevention, China Country Office" + }, + { + "author_name": "Ling Hao", + "author_inst": "U.S. Centers for Disease Control and Prevention, China Country Office" + }, + { + "author_name": "Alexander J. Millman", + "author_inst": "U.S. Centers for Disease Control and Prevention, China Country Office" + }, + { + "author_name": "Barbara Marston", + "author_inst": "U.S. Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.04.412585", "rel_title": "Decontamination of Common Healthcare Facility Surfaces Contaminated with SARS-CoV-2 using Peracetic Acid Dry Fogging", @@ -1021117,69 +1018235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.07.20245167", - "rel_title": "A generic, scalable, and rapid TR-FRET -based assay for SARS-CoV-2 antigen detection", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245167", - "rel_abs": "The ongoing COVID-19 pandemic has seen an unprecedented increase in the demand for rapid and reliable diagnostic tools, leaving many laboratories scrambling for resources. We present a fast and simple method for the detection of SARS-CoV-2 in nasopharyngeal swabs. The method is based on the detection of SARS-CoV-2 nucleoprotein (NP) and S protein (SP) via time-resolved Forster resonance energy transfer (TR-FRET) with donor- and acceptor-labeled polyclonal anti-NP and -SP antibodies. Using recombinant proteins and cell culture-grown SARS-CoV-2 the limits of detection were established as 25 pg of NP or 20 infectious viral units (i.u.), and 875 pg of SP or 625 i.u. of SARS-CoV-2. Testing RT-PCR positive (n=48, with cycle threshold [Ct] values from 11 to 30) or negative (n=96) nasopharyngeal swabs, we showed that the assay yields positive results for all samples with Ct values of <25 and a single RT-PCR negative sample. We determined the presence of infectious virus in the RT-PCR-positive nasopharyngeal swabs by virus isolation, and observed a strong association between the presence of infectious virus and a positive antigen test result. The NP-based assay showed 97.4% (37/38) sensitivity and 100% (10/10) specificity in comparison with virus isolation, and 77.1% (37/48) and 99.0% (95/96) in comparison with SARS-CoV-2 RT-PCR. The assay is performed in a buffer that neutralizes SARS-CoV-2 infectivity and is relatively simple to set up as an \"in-house\" test. The assay principle as such is applicable to other viral infections, and could also be readily adapted to a massively high throughput testing format.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Juuso Rusanen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Lauri Kareinen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Leonora Szirovicza", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Hasan Ugurlu", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Lev Levanov", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Anu Elina Jaaskelainen", - "author_inst": "HUSLAB" - }, - { - "author_name": "Maarit Ahava", - "author_inst": "University of Helsinki and Helsinki University Hospital" - }, - { - "author_name": "Satu Kurkela", - "author_inst": "University of Helsinki and Helsinki University Hospital" - }, - { - "author_name": "Kalle Saksela", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Klaus Hedman", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Olli Vapalahti", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Jussi Hepojoki", - "author_inst": "University of Helsinki / Medicum" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.04.20243741", "rel_title": "SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection.", @@ -1021884,6 +1018939,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.06.20244780", + "rel_title": "Seasonality and Progression of COVID-19 among Countries With or Without Lock-downs.", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20244780", + "rel_abs": "Early predictions by computer simulation of 7 billion infections and 40 million deaths by COVID-19 during 2020 alone if lock-downs and other confining measures were not enforced may have justified restrictive policies mandated by governments of 165 countries. A main objective of the present study was to determine differences between the infection and death rate in countries that established early, nation-wide curfews, state-at-home orders, or lock-downs versus countries that did not mandate lock-downs to deal with the COVID-19 crisis.\n\nThe analyzed epidemiological data indicates that lock-downs, and other confining measures had no effect on the chances of healthy individuals becoming infected with- or dying of SARS-CoV-2.\n\nThe highest incidence of COVID-19 infection progressed from countries in northern latitudes, where it was winter at the beginning of the pandemic, to countries in the southern hemisphere in July 21, 2020 were winter was starting. This trend reversed again during the last quarter of 2020. A considerable (4-fold) increase in COVID-19 infection rate is observed between fall and beginning of winter in countries in the southern hemisphere. This seasonal progression correlates with the variation in the germicidal solar flux received by these countries, suggesting that infectious virus in the environment plays a role in the evolution of COVID-19. In addition, hypotheses are presented that could explain the recurrent new spikes of COVID-19 as well as the mortality of SARS-Co V-2 observed in some developed countries higher than the mortality rate reported in several developing countries.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Dr. Jose-Luis Sagripanti", + "author_inst": "Department of Defense" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.06.20244731", "rel_title": "Epidemic Progression and Vaccination in a Heterogeneous Population. Application to the Covid-19 epidemic", @@ -1022815,85 +1019889,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.05.409821", - "rel_title": "Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures", - "rel_date": "2020-12-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.05.409821", - "rel_abs": "The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, has rendered our understanding of coronavirus biology more essential than ever. Small molecule chemical probes offer to both reveal novel aspects of virus replication and to serve as leads for antiviral therapeutic development. The RNA-biased amiloride scaffold was recently tuned to target a viral RNA structure critical for translation in enterovirus 71, ultimately uncovering a novel mechanism to modulate positive-sense RNA viral translation and replication. Analysis of CoV RNA genomes reveal many conserved RNA structures in the 5-UTR and proximal region critical for viral translation and replication, including several containing bulge-like secondary structures suitable for small molecule targeting. Following phylogenetic conservation analysis of this region, we screened an amiloride-based small molecule library against a less virulent human coronavirus, OC43, to identify lead ligands. Amilorides inhibited OC43 replication as seen in viral plaque assays. Select amilorides also potently inhibited replication competent SARS-CoV-2 as evident in the decreased levels of cell free virions in cell culture supernatants of treated cells. Reporter screens confirmed the importance of RNA structures in the 5-end of the viral genome for small molecule activity. Finally, NMR chemical shift perturbation studies of the first six stem loops of the 5-end revealed specific amiloride interactions with stem loops 4, 5a, and 6, all of which contain bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Taken together, the use of multiple orthogonal approaches allowed us to identify the first small molecules aimed at targeting RNA structures within the 5-UTR and proximal region of the CoV genome. These molecules will serve as chemical probes to further understand CoV RNA biology and can pave the way for the development of specific CoV RNA-targeted antivirals.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Martina Zafferani", - "author_inst": "Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705" - }, - { - "author_name": "Christina Haddad", - "author_inst": "Department of Chemistry, Case Western Reserve University, Cleveland OH 441106" - }, - { - "author_name": "Le Luo", - "author_inst": "Department of Chemistry, Case Western Reserve University, Cleveland OH 441106" - }, - { - "author_name": "Jesse Davila-Calderon", - "author_inst": "Department of Chemistry, Case Western Reserve University, Cleveland OH 441106" - }, - { - "author_name": "Liang Yuan-Chiu", - "author_inst": "Department of Chemistry, Case Western Reserve University, Cleveland OH 441106" - }, - { - "author_name": "Christian Shema Mugisha", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA" - }, - { - "author_name": "Adeline G Monaghan", - "author_inst": "Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705" - }, - { - "author_name": "Andrew A Kennedy", - "author_inst": "Department of Internal Medicine, University of Michigan, 1150 W Medical Center Drive, Ann Arbor MI USA 48109" - }, - { - "author_name": "Joseph D Yesselman", - "author_inst": "Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588 USA" - }, - { - "author_name": "Robert R Gifford", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, UK, G61 1QH" - }, - { - "author_name": "Andrew W Tai", - "author_inst": "Department of Internal Medicine and Department of Microbiology & Immunology, University of Michigan, 1150 W Medical Center Dr, Ann Arbor MI 48109" - }, - { - "author_name": "Sebla B Kutluay", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA" - }, - { - "author_name": "Mei-Ling Li", - "author_inst": "Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ USA 08854" - }, - { - "author_name": "Gary Brewer", - "author_inst": "Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ USA 08854" - }, - { - "author_name": "Blanton S Tolbert", - "author_inst": "Department of Chemistry, Case Western Reserve University, Cleveland OH 441106" - }, - { - "author_name": "Amanda E Hargrove", - "author_inst": "Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.04.411736", "rel_title": "Genetic variability in COVID-19-related genes in the Brazilian population", @@ -1023622,6 +1020617,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20242750", + "rel_title": "Clinical Evaluation of a COVID-19 Antibody Lateral Flow Assay using Point of Care Samples", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242750", + "rel_abs": "IntroductionThe ongoing SARS-CoV-2 pandemic has spurred the development of numerous point of care (PoC) immunoassays. Assessments of performance of available kits are necessary to determine their clinical utility. Previous studies have mostly performed these assessments in a laboratory setting, which raises concerns of translating findings for PoC use. The aim of this study was to assess the performance of a lateral flow immunoassay for the detection of SARS-CoV-2 antibodies using samples collected at PoC.\n\nMethodOne lateral flow immunoassay (Humasis(R) COVID-19 IgG/IgM) was tested. In total, 50 PCR RT-PCR positive and 52 RT-PCR negative samples were collected at PoC. Fifty serum specimens from Dec 2018 to Feb 2019 were used as controls for specificity. Serum samples collected between Dec 2019 to Feb 2020 were used as additional comparators. Clinical data including symptom onset date was collected from patient history and the medical record.\n\nResultsThe overall sensitivity for the kit was 74% (95% CI: 59.7% -85.4%). The sensitivity for IgM and IgG detection >14 days after date of onset was 88% (95% CI: 68.8% -97.5%) and 84% (95% CI: 63.9% - 95.5%), with a negative predictive value (NPV) of 94% for IgM (95% CI: 83.5% - 98.8%) and 93% for IgG (95% CI: 81.8% - 97.9%). The overall specificity was 94% (95% CI: 83.5% - 98.8%). The Immunoglobulin specific specificity was 94% for IgM (95% CI: 83.5% - 98.8%) and 98% for IgG (95% CI: 89.4% - 100.0%), with a positive predictive value (PPV) of 88% for IgM (95% CI: 68.8% - 97.5%) and 95% for IgG (95% CI: 77.2% - 99.9%) respectively for samples collected from patients >14 days after date of onset. Specimen collected during early phase of COVID-19 pandemic (Dec 2019 to Feb 2020) showed 11.8% antibody positivity, and 11.3% of PCR-negative patients demonstrated antibody positivity.\n\nDiscussionHumasis(R) COVID-19 IgG/IgM LFA demonstrates greater than 90% PPV and NPV for samples collected 14 days after the onset of symptoms using samples collected at PoC. While not practical for the diagnosis of acute infection, the use of the lateral flow assays with high specificity may have utility for determining seroprevalence or seroconversion in longitudinal studies.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Won Lee", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Steven Straube", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Ryan Sincic", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jeanne A Noble", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Juan Carlos Montoy", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Aaron E Kornblith", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Arun Prakash", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Ralph Wang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Roland Bainton", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Philip Kurien", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242628", "rel_title": "McQ - An open-source multiplexed SARS-CoV-2 quantification platform", @@ -1024873,33 +1021923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.03.20243063", - "rel_title": "Why simple face masks are unexpectedly efficient in reducing viral aerosol transmissions", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243063", - "rel_abs": "During the current pandemic and in the past, shortages of high quality respirators have forced people to protect themselves with homemade face masks that filter poorly in comparison to N95 respirators 1-4 and are often designed in ways that makes them susceptible to leaks 5,6. Nevertheless, there is compelling epidemiological 7,8 and laboratory evidence 9-12 that face masks can be effective in impeding the spread of respiratory viruses such as influenza and SARS-CoV-2. Here we show that this apparent inconsistency can be resolved with a simple face mask model that combines our filtration efficiency measurements of various mask materials with existing data on exhaled aerosol characteristics. By reanalyzing these data we are able to reconcile the vastly different aerosol size distributions reported 13-19 and derive representative volume distributions for speech and breath aerosol. Multiplying filtration efficiency by those aerosol volumes, which are proportional to emitted viral load, shows that electrostatically charged materials perform the best but that even most uncharged fabrics remove > 85 % of breath and > 99 % of speech aerosol volume for exhaled particles < 10 {micro}m in diameter. A leak model we develop shows the best uncharged fabric masks are made of highly air-permeable and often thin materials reducing viral load by up to 45 % and 50 % for breath and speech, respectively. Less permeable materials provide reduced protection because unfiltered air is forced through the leak. This can even render some charged materials inferior to uncharged household materials. Our model also shows that thin fabric masks provide protection for the wearer from aerosols expelled by another person reducing inhaled viral load by up to 20 % and 50 % and if leaks are avoided up to 35 % and 90 % for breath and speech, respectively.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Steffen Freitag", - "author_inst": "University of Hawaii" - }, - { - "author_name": "Steven G. Howell", - "author_inst": "University of Hawaii" - }, - { - "author_name": "Kevin T. C. Jim", - "author_inst": "Oceanit Laboratories" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.03.20243352", "rel_title": "Association between Participation in Government Subsidy Program for Domestic Travel and Symptoms Indicative of COVID-19 Infection", @@ -1025540,6 +1022563,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.03.20243584", + "rel_title": "A Stochastic Compartmental Model for COVID-19", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243584", + "rel_abs": "We propose two stochastic models for the Coronavirus pandemic. The statistical properties of the models, in particular the correlation functions and the probability density function, have duly been computed. Our models, which generalises a model previously proposed and published in a specialised journal, take into account the adoption of the lockdown measures as well as the crucial role of the hospitals and Health Care Institutes. To accomplish this work we have analysed two scenarios: the SIS-model (Susceptible {Rightarrow} Infectious {Rightarrow} Susceptible) in presence of the lockdown measures and the SIS-model integrated with the action of the hospitals (always in presence of the lockdown measures). We show that in the case of the pure SIS-model, once the lockdown measures are removed, the Coronavirus will start growing again. However, in the second scenario, beyond a certain threshold of the hospital capacities, the Coronavirus is not only kept under control, but its capacity to spread tends to diminish in time. Therefore, the combined effect of the lockdown measures with the action of the hospitals and health Institutes is able to contain and dampen the spread of the SARS-CoV-2 epidemic. This result can be used during a period of time when the massive distribution of delivery of a limited number of vaccines in a given population is not yet feasible. By way of example, we analysed the data for USA and France where the intensities of the noise have been estimated by Statistical Mechanics. In particular, for USA we have analysed two possible hypotheses: USA is still subject to the first wave of infection by and USA is in the second (or third) wave of SARS-CoV-2 infection.The agreement between theoretical predictions and real data confirms the validity of our approach.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Giorgio Sonnino", + "author_inst": "Universite Libre de Bruxelles (ULB)" + }, + { + "author_name": "Fernando Mora", + "author_inst": "Universidad Adolfo Ibanez, Santiago, Chile" + }, + { + "author_name": "Pasquale Nardone", + "author_inst": "Universite Libre de Bruxelles (ULB)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.03.20243519", "rel_title": "A cross-national study of factors associated with perinatal mental health and wellbeing during the COVID-19 pandemic", @@ -1026415,73 +1023465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20190926", - "rel_title": "Clinical Characteristics and Risk Factors for Myocardial Injury and Arrhythmia in COVID-19 patients", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20190926", - "rel_abs": "The authors have withdrawn this manuscript because of a lack of novelty of results and, with that, a lack of intention to publish in a peer reviewed journal. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hong Gang Ren", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Xingyi Guo", - "author_inst": "Vanderbilt University School of Medicine" - }, - { - "author_name": "Lei Tu", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Qinyong Hu", - "author_inst": "Renmin Hospital of Wuhan University" - }, - { - "author_name": "Kevin Blighe", - "author_inst": "Clinical Bioinformatics Research Ltd." - }, - { - "author_name": "Luqman Bin Safdar", - "author_inst": "The Ministry of Agriculture and Rural Affairs" - }, - { - "author_name": "Justin Stebbing", - "author_inst": "Imperial College London" - }, - { - "author_name": "Shepard D Weiner", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Monte S Willis", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Frits R Rosendaal", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Guogang Xu", - "author_inst": "Chinese PLA General Hospital" - }, - { - "author_name": "Feng Cao", - "author_inst": "Chinese PLA General Hospital" - }, - { - "author_name": "Dao Weng Wang", - "author_inst": "Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.11.30.20241224", "rel_title": "COVID-19 Trends in Florida K-12 Schools, August 10 - November 14, 2020", @@ -1027014,6 +1023997,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.01.20241729", + "rel_title": "International estimates of intended uptake and refusal of COVID-19 vaccines: A rapid systematic review and meta-analysis of large nationally representative samples", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241729", + "rel_abs": "BackgroundWidespread uptake of COVID-19 vaccines will be essential to extinguishing the COVID-19 pandemic. Vaccines have been developed in unprecedented time and hesitancy towards vaccination among the general population is unclear.\n\nMethodsSystematic review and meta-analysis of studies using large nationally representative samples (n[≥]1000) to examine the percentage of the population intending to vaccinate, unsure, or intending to refuse a COVID-19 vaccine when available. Generic inverse meta-analysis and meta-regression were used to pool estimates and examine time trends. PubMed, Scopus and pre-printer servers were searched from January-November, 2020. Registered on PROSPERO (CRD42020223132).\n\nFindingsTwenty-eight nationally representative samples (n = 58,656) from 13 countries indicate that as the pandemic has progressed, the percentage of people intending to vaccinate and refuse vaccination have been decreasing and increasing respectively. Pooled data from surveys conducted during June-October suggest that 60% (95% CI: 49% to 69%) intend to vaccinate and 20% (95% CI: 13% to 29%) intend to refuse vaccination, although intentions vary substantially between samples and countries (I2 > 90%). Being female, younger, of lower income or education level and belonging to an ethnic minority group were consistently associated with being less likely to intend to vaccinate. Findings were consistent across higher vs. lower quality studies.\n\nInterpretationIntentions to be vaccinated when a COVID-19 vaccine becomes available have been declining globally and there is an urgent need to address social inequalities in vaccine hesitancy and promote widespread uptake of vaccines as they become available.\n\nFundingN/A\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Scopus and pre-print servers for manuscripts from January to November, 2020, reporting on studies examining intentions to be vaccinated against COVID-19 in large nationally representative samples (N[≥]1000). No language restrictions were applied. Search terms were [(COVID OR coronavirus OR SARS-COV-2) AND (Vaccine OR Vaccination) AND (Inten* OR willing* OR attitud* OR hypothetical)]. From 792 articles, we identified 20 eligible articles reporting on 28 nationally representative samples.\n\nAdded value of this studyThis is the first systematic study and meta-analysis to estimate the proportion of the global population willing to be vaccinated against vs. intending to refuse a vaccine when COVID-19 vaccines become available and how this trend has changed over time, using large and nationally representative samples. Results indicate that COVID-19 vaccination intentions vary substantially across countries, the percentage of the population intending to be vaccinated has declined across countries as the pandemic has progressed (March-May estimate: 79%, June-October estimate: 60%) and a growing number report intending to refuse a vaccine, when available (March-May estimate: 12%, June-October estimate: 20%). There is consistent socio-demographic patterning of vaccination intentions; being female, younger, of lower income or education level and belonging to an ethnic minority group are associated with a reduced likelihood of intending to be vaccinated when a vaccine become available.\n\nImplications of all the available evidenceIntentions to vaccinate against COVID-19 among the general public when a vaccine becomes available have been declining and this will limit the effectiveness of COVID-19 vaccination programmes. Findings highlight the need to improve public acceptability, trust and concern over the safety and benefit of COVID-19 vaccines and target vaccine uptake in disadvantaged groups who have already been disproportionately affected by the pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eric Robinson", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andrew Jones", + "author_inst": "University of Liverpool" + }, + { + "author_name": "India Lesser", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Michael Daly", + "author_inst": "Maynooth University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.01.20241596", "rel_title": "Correlation Between Adult Tobacco Smoking Prevalence and Mortality of Coronavirus Disease-19 Across The World", @@ -1027789,49 +1024803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.01.20242347", - "rel_title": "The impact of non-pharmaceutical interventions on the prevention and control of COVID-19 in New York City", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242347", - "rel_abs": "The emergence of coronavirus disease 2019 (COVID-19) has infected more than 37 million people worldwide. The control responses varied across countries with different outcomes in terms of epidemic size and social disruption. In this study, we presented an age-specific susceptible-exposed-infected-recovery-death model that considers the unique characteristics of COVID-19 to examine the effectiveness of various non-pharmaceutical interventions (NPIs) in New York City (NYC). Numerical experiments from our model show that the control policies implemented in NYC reduced the number of infections by 72% (IQR 53-95), and the number of deceased cases by 76% (IQR 58-96) by the end of 2020, respectively. Among all the NPIs, social distancing for the entire population and the protection for the elderly in the public facilities is the most effective control measure in reducing severe infections and deceased cases. School closure policy may not work as effectively as one might expect in terms of reducing the number of deceased cases. Our simulation results provide novel insights into the city-specific implementation of NPIs with minimal social disruption considering the locations and population characteristics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jiannan Yang", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Qingpeng Zhang", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "zhidong cao", - "author_inst": "Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Jianxi gao", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Dirk Pfeiffer", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Lu Zhong", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Daniel Dajun Zeng", - "author_inst": "Institute of Automation, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.02.408823", "rel_title": "A single intranasal or intramuscular immunization with chimpanzee adenovirus vectored SARS-CoV-2 vaccine protects against pneumonia in hamsters.", @@ -1028520,6 +1025491,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.11.23.20237404", + "rel_title": "A COVID-19 transmission model informing medication development and supply chain needs", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237404", + "rel_abs": "Accurate prediction of COVID-19 cases can optimize clinical trial recruitment, inform mitigation strategies and facilitate rapid medication development. Here we present a country-specific, modified Susceptible, Exposed, Infectious, Removed (SEIR) model of SARS-CoV-2 transmission using data from the Johns Hopkins University COVID-19 Dashboard. Inter-country differences in initial exposure, cultural/environmental factors, reporting requirements and stringency of mitigation strategies were incorporated. Asymptomatic patients and super-spreaders were also factored into our model. Using these data, our model estimated 65.8% of cases as asymptomatic; symptomatic and asymptomatic people were estimated to infect 2.12 and 5.83 other people, respectively. An estimated 9.55% of cases were super-spreaders with a 2.11-fold higher transmission rate than average. Our model estimated a mean maximum infection rate of 0.927 cases/day (inter-country range, 0.63-1.41) without mitigation strategies. Mitigation strategies with a stringency index value of [≥]60% were estimated to be required to reduce the reproduction ratio below 1. It was predicted that cases over the next 2 months would differ between countries, with certain countries likely to experience an accelerated accumulation of cases. Together, results from our model can guide distribution of diagnostic tests, impact clinical trial development, support medication development and distribution and inform mitigation strategies to reduce COVID-19 spread.\n\nKey FindingsO_LIPredicting COVID-19 cases can inform medication development and mitigation strategies\nC_LIO_LIWe created a modified SEIR model of SARS-CoV-2 transmission\nC_LIO_LIWe integrated asymptomatic cases, super-spreaders and hotspots that drive viral spread\nC_LIO_LIMitigation strategies with a stringency index of [≥]60% are required to reduce the RR below 1\nC_LIO_LISome countries may experience an accelerated accumulation of cases in the coming months\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Annabelle Lemenuel-Diot", + "author_inst": "Roche Innovation Center" + }, + { + "author_name": "Barry Clinch", + "author_inst": "Roche Products Ltd" + }, + { + "author_name": "Aeron C. Hurt", + "author_inst": "F. Hoffmann-La Roche Ltd" + }, + { + "author_name": "Paul Boutry", + "author_inst": "F. Hoffmann-La Roche Ltd" + }, + { + "author_name": "Johann Laurent", + "author_inst": "Roche Innovation Center" + }, + { + "author_name": "Mathias Leddin", + "author_inst": "Roche Innovation Center" + }, + { + "author_name": "Stefan Frings", + "author_inst": "F. Hoffmann-La Roche Ltd" + }, + { + "author_name": "Jean Eric Charoin", + "author_inst": "F. Hoffmann-La Roche Ltd" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.29.20235218", "rel_title": "Effective post-exposure prophylaxis of Covid-19 is associated with use of hydroxychloroquine: Prospective re-analysis of a public dataset incorporating novel data.", @@ -1029263,41 +1026281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20241273", - "rel_title": "Development and validation of automated computer aided-risk score for predicting the risk of in-hospital mortality using first electronically recorded blood test results and vital signs for COVID-19 hospital admissions: a retrospective development and validation study", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241273", - "rel_abs": "ObjectivesThere are no established mortality risk equations specifically for unplanned emergency medical admissions which include patients with the novel coronavirus SARS-19 (COVID-19). We aim to develop and validate a computer-aided risk score (CARMc19) for predicting mortality risk by combining COVID-19 status, the first electronically recorded blood test results and latest version of the National Early Warning Score (NEWS2).\n\nDesignLogistic regression model development and validation study using a cohort of unplanned emergency medical admissions to hospital.\n\nSettingYork Hospital (YH) as model development dataset and Scarborough Hospital (SH) as model validation dataset.\n\nParticipantsUnplanned adult medical admissions discharged over three months (11 March 2020 to 13 June 2020) from two hospitals (YH for model development; SH for external model validation) based on admission NEWS2 electronically recorded within {+/-}24 hours and/or blood test results within {+/-}96 hours of admission. We used logistic regression modelling to predict the risk of in-hospital mortality using two models: 1) CARMc19_N: age + sex + NEWS2 including subcomponents + COVID19; 2) CARMc19_NB: CARMc19_N in conjunction with seven blood test results and acute kidney injury score. Model performance was evaluated according to discrimination (c-statistic), calibration (graphically), and clinical usefulness at NEWS2 thresholds of 4+, 5+, 6+.\n\nResultsThe risk of in-hospital mortality following emergency medical admission was similar in development and validation datasets (8.4% vs 8.2%). The c-statistics for predicting mortality for Model CARMc19_NB is better than CARMc19_N in the validation dataset (CARMc19_NB = 0.88 (95%CI 0.86 to 0.90) vs CARMc19_N = 0.86 (95%CI 0.83 to 0.88)). Both models had good internal and external calibration (CARMc19_NB: 1.01 (95%CI 0.88 vs 1.14) & CARMc19_N: 0.95 (95%CI 0.83 to 1.06)). At all NEWS2 thresholds (4+, 5+, 6+) model CARMc19_NB had better sensitivity and similar specificity.\n\nConclusionsWe have developed a validated CARMc19 score with good performance characteristics for predicting the risk of in-hospital mortality following an emergency medical admission using the patients first, electronically recorded vital signs and blood tests results. Since the CARMc19 scores place no additional data collection burden on clinicians and is readily automated, it may now be carefully introduced and evaluated in hospitals with sufficient informatics infrastructure.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Muhammad Faisal", - "author_inst": "Faculty of Health Studies, University of Bradford, Bradford, UK Bradford Institute for Health Research Bradford, UK NIHR Yorkshire and Humber Patient Safety Tra" - }, - { - "author_name": "Mohammed Amin Mohammed", - "author_inst": "Faculty of Health Studies, University of Bradford, Bradford, UK NHS Midlands and Lancashire Commissioning Support Unit, The Strategy Unit, Kingston House, We" - }, - { - "author_name": "Donald Richardson", - "author_inst": "Department of Renal Medicine, York Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Massimo Fiori", - "author_inst": "York Teaching Hospitals NHS Foundation Trust, England UK" - }, - { - "author_name": "Kevin Beatson", - "author_inst": "York Teaching Hospitals NHS Foundation Trust, England UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.30.20241232", "rel_title": "Bridging the gaps in test interpretation of SARS-CoV-2 through Bayesian network modelling", @@ -1029906,6 +1026889,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.02.408229", + "rel_title": "Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics", + "rel_date": "2020-12-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408229", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the etiologic agent of Coronavirus Disease-2019 (COVID-19), is rapidly accumulating new mutations. Analysis of these mutations is necessary for gaining knowledge regarding different aspects of therapeutic development. Recently, we have reported a Sanger method based genome sequence of a viral isolate named SARS-CoV-2 NIB-1, circulating in Bangladesh. The genome has four novel mutations in V121D, V843F, A889V and G1691C positions. V121D substitution has the potential to destabilize the Non-Structural Protein (NSP-1) which inactivates the type-1 Interferon-induced antiviral system hence this mutant could be the basis of attenuated vaccines against SARS-CoV-V843F, A889V and G1691C are all located in NSP3. G1691C can decrease the flexibility of the protein while V843F and A889V changed the binding pattern of SARS-CoV-2 Papain-Like protease (PLPro) inhibitor GRL0617. V843F PLPro showed reduced affinity for Interferon Stimulating Gene-15 (ISG-15) protein whereas V843F+A889V double mutants exhibited the same binding affinity as wild type PLPro. Here, V843F is a conserved position of PLPro that damaged the structure but A889V, a less conserved residue, most probably neutralized that damage. Mutants of NSP1 could provide attenuated vaccines against coronavirus. Also, these mutations of PLPro could be targeted to develop anti-SARS therapeutics.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Mohammad Uzzal Hossain", + "author_inst": "Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Arittra Bhattacharjee", + "author_inst": "Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh; Department of Biochemistry and Microbiology, No" + }, + { + "author_name": "Md. Tabassum Hossain Emon", + "author_inst": "Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh" + }, + { + "author_name": "Zeshan Mahmud Chowdhury", + "author_inst": "Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh" + }, + { + "author_name": "Md. Golam Mosaib", + "author_inst": "Department of Biochemistry and Molecular Biology, Faculty of Health & Medical Sciences, Gono Bishwabidyaloy, Ashulia, Savar, Dhaka-1344, Bangladesh" + }, + { + "author_name": "Md. Moniruzzaman", + "author_inst": "Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Md. Hadisur Rahman", + "author_inst": "Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Md. Nazrul Islam", + "author_inst": "Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Irfan Ahmed", + "author_inst": "Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Md. Ruhul Amin", + "author_inst": "Center for Medical Biotechnology, MIS, Directorate General of Health Services, Dhaka, Bangladesh" + }, + { + "author_name": "Asif Rashed", + "author_inst": "Department of Microbiology, Mugda Medical College, Dhaka, Bangladesh" + }, + { + "author_name": "Keshob Chandra Das", + "author_inst": "Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + }, + { + "author_name": "Chaman Ara Keya", + "author_inst": "Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh" + }, + { + "author_name": "Md. Salimullah", + "author_inst": "Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.02.391664", "rel_title": "Lack of evidence of ACE2 expression and replicative infection by SARS-CoV-2 in human endothelial cells", @@ -1031205,277 +1028259,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.12.01.406637", - "rel_title": "Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.406637", - "rel_abs": "Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.", - "rel_num_authors": 64, - "rel_authors": [ - { - "author_name": "Joseph H. Lubin", - "author_inst": "Rutgers University" - }, - { - "author_name": "Christine Zardecki", - "author_inst": "Rutgers University" - }, - { - "author_name": "Elliott M. Dolan", - "author_inst": "Rutgers University" - }, - { - "author_name": "Changpeng Lu", - "author_inst": "Rutgers University" - }, - { - "author_name": "Zhuofan Shen", - "author_inst": "Rutgers University" - }, - { - "author_name": "Shuchismita Dutta", - "author_inst": "Rutgers University" - }, - { - "author_name": "John D. Westbrook", - "author_inst": "Rutgers University" - }, - { - "author_name": "Brian P. Hudson", - "author_inst": "Rutgers University" - }, - { - "author_name": "David S. Goodsell", - "author_inst": "Rutgers University" - }, - { - "author_name": "Jonathan K. Williams", - "author_inst": "Rutgers University" - }, - { - "author_name": "Maria Voigt", - "author_inst": "Rutgers University" - }, - { - "author_name": "Vidur Sarma", - "author_inst": "Rutgers University" - }, - { - "author_name": "Lingjun Xie", - "author_inst": "Rutgers University" - }, - { - "author_name": "Thejasvi Venkatachalam", - "author_inst": "Rutgers University" - }, - { - "author_name": "Steven Arnold", - "author_inst": "Rutgers University" - }, - { - "author_name": "Luz Helena Alfaro Alvarado", - "author_inst": "Grinnell College" - }, - { - "author_name": "Kevin Catalfano", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Aaliyah Khan", - "author_inst": "University of Maryland--Baltimore County" - }, - { - "author_name": "Erika McCarthy", - "author_inst": "Stevens Institute of Technology" - }, - { - "author_name": "Sophia Staggers", - "author_inst": "Frostburg State University" - }, - { - "author_name": "Brea Tinsley", - "author_inst": "Youngstown State University" - }, - { - "author_name": "Alan Trudeau", - "author_inst": "University of Central Florida" - }, - { - "author_name": "Jitendra Singh", - "author_inst": "New York City College of Technology" - }, - { - "author_name": "Lindsey Whitmore", - "author_inst": "Howard University" - }, - { - "author_name": "Helen Zheng", - "author_inst": "Watchung Hills Regional High School" - }, - { - "author_name": "Matthew Benedek", - "author_inst": "Xavier University" - }, - { - "author_name": "Jenna Currier", - "author_inst": "Hope College" - }, - { - "author_name": "Mark Dresel", - "author_inst": "Rutgers University" - }, - { - "author_name": "Ashish Duvvuru", - "author_inst": "Hope College" - }, - { - "author_name": "Britney Dyszel", - "author_inst": "Ursinus College" - }, - { - "author_name": "Emily Fingar", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Elizabeth M. Hennen", - "author_inst": "Roger Williams University" - }, - { - "author_name": "Michael Kirsch", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Ali A. Khan", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Charlotte Labrie-Cleary", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Stephanie Laporte", - "author_inst": "Brandeis University" - }, - { - "author_name": "Evan Lenkeit", - "author_inst": "Rutgers University" - }, - { - "author_name": "Kailey Martin", - "author_inst": "Ursinus College" - }, - { - "author_name": "Marilyn Orellana", - "author_inst": "Hope College" - }, - { - "author_name": "Melanie Ortiz-Alvarez de la Campa", - "author_inst": "University of Puerto Rico--Rio Piedras" - }, - { - "author_name": "Isaac Paredes", - "author_inst": "John Jay College" - }, - { - "author_name": "Baleigh Wheeler", - "author_inst": "Grand View University" - }, - { - "author_name": "Allison Rupert", - "author_inst": "Grand View University" - }, - { - "author_name": "Andrew Sam", - "author_inst": "Rutgers University" - }, - { - "author_name": "Katherine See", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Santiago Soto Zapata", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Paul A. Craig", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Bonnie L. Hall", - "author_inst": "Grand View University" - }, - { - "author_name": "Jennifer Jiang", - "author_inst": "Rutgers University" - }, - { - "author_name": "Julia R. Koeppe", - "author_inst": "State University of New York--Oswego" - }, - { - "author_name": "Stephen A. Mills", - "author_inst": "Xavier University" - }, - { - "author_name": "Michael J. Pikaart", - "author_inst": "Hope College" - }, - { - "author_name": "Rebecca Roberts", - "author_inst": "Ursinus College" - }, - { - "author_name": "Yana Bromberg", - "author_inst": "Rutgers University" - }, - { - "author_name": "J. Steen Hoyer", - "author_inst": "Rutgers University" - }, - { - "author_name": "Siobain Duffy", - "author_inst": "Rutgers University" - }, - { - "author_name": "Jay Tischfield", - "author_inst": "Rutgers University" - }, - { - "author_name": "Francesc X. Ruiz", - "author_inst": "Rutgers University" - }, - { - "author_name": "Eddy Arnold", - "author_inst": "Rutgers University" - }, - { - "author_name": "Jean Baum", - "author_inst": "Rutgers University" - }, - { - "author_name": "Jesse Sandberg", - "author_inst": "Rutgers University" - }, - { - "author_name": "Grace Brannigan", - "author_inst": "Rutgers University" - }, - { - "author_name": "Sagar D. Khare", - "author_inst": "Rutgers University" - }, - { - "author_name": "Stephen K. Burley", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.12.01.407148", "rel_title": "Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19", @@ -1032208,6 +1028991,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.11.25.20239038", + "rel_title": "COVID-19 Workplace Outbreaks by Industry Sector and their Associated Household Transmission, Ontario, Canada, January to June, 2020", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20239038", + "rel_abs": "IntroductionWorkplaces requiring in-person attendance of employees for ongoing operations may be susceptible to SARS-CoV-2 outbreaks that impact workers as well as their close contacts. To understand industry sectors impacted by workplace outbreaks in the first wave of the pandemic, and the additional burden of illness through household transmission, we analyzed public health declared workplace outbreaks between January 21 to June 30, 2020, and their associated cases from January 21 to July 28.\n\nMethodsNumber, size and duration of outbreaks were described by sector, and outbreak cases were compared to sporadic cases in the same time frame. Address matching identified household cases with onset [≥]2 days before, [≥]2 days after, or within 1 day of the workplace outbreak case.\n\nResultsThere were 199 outbreaks with 1245 cases, and 68% of outbreaks and 80% of cases belonged to i) Manufacturing, ii) Agriculture, Forestry, Fishing, Hunting, iii) Transportation and Warehousing. Median size of outbreaks was 3 cases (range: 1-140), and lasted median 7days (range: 0-119). Outbreak cases were significantly more likely to be male, younger, healthier, and have better outcomes. There were 608 household cases associated with 339 (31%) outbreak cases with valid addresses, increasing the burden of illness by 56%. The majority of household cases (368, 60%) occurred after the outbreak case.\n\nConclusionsWorkplace outbreaks primarily occurred in three sectors. COVID-19 prevention measures should target industry sectors at risk by preventing introduction from exposed employees, spread in the workplace, and spread outside of the workplace.\n\nWhat is already known about this topic?COVID-19 outbreaks occur within workplaces and can spread to the community\n\nWhat is added by this report?From January 21 - June 30, 2020, there were 199 workplace outbreaks in Ontario, Canada; 68% of outbreaks and 80% of outbreak-associated COVID-19 case were in three industry sectors: Manufacturing, Agriculture/Forestry/Fishing/Hunting, and Transportation/Warehousing. Household transmission occurred among 31% of outbreak cases, resulting in a 56% increase in workplace outbreak-associated cases when burden of household transmission is considered.\n\nWhat are the implications for public health practice?Workplace outbreak prevention measures should be targeted to industry sectors at risk by preventing introduction from exposed employees, spread in the workplace, and transmission to the greater community.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Michelle Murti", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Camille Achonu", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Brendan T. Smith", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jin Hee Kim", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "James Johnson", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Saranyah Ravindran", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.26.20239129", "rel_title": "Time trends in infectious and chronic disease consultations in Dakar, Senegal: Impact of Covid-19 Sanitary Measures", @@ -1033031,33 +1029861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.11.26.20239483", - "rel_title": "Risk exposures, risk perceptions, negative attitudes toward general vaccination, and COVID-19 vaccine acceptance among college students in South Carolina", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239483", - "rel_abs": "Growing attention has been paid to vaccination in control of the COVID-19 pandemic and young adults is one of the key populations for vaccination. Advanced understanding of young adults willingness to take a COVID-19 vaccine and the potential factors influencing their vaccine intention will contribute to the development and implementation of effective strategies to promote COVID-19 vaccine uptake among this group. The current study investigated how risk exposures and risk perceptions of COVID-19 (e.g., perceived susceptibility, severity, and fear of COVID-19) as well as negative attitudes toward general vaccination were related to COVID vaccine acceptance among college students based on online survey data from 1062 college students in South Carolina. Hierarchical linear regression was used to examine the association of these factors with COVID-19 vaccine acceptance controlling for key demographics. Results suggested that perceived severity and fear of COVID-19 were positively associated with vaccine acceptance, while higher level of risk exposures (work/study place exposure) and negative attitude toward general vaccination were associated with low vaccine acceptance. Our findings suggested that we need tailored education messages for college students to emphasize the severity of COVID-19, particularly potential long-term negative consequences on health, address the concerns of side effects of general vaccines by dispelling the misconception, and target the most vulnerable subgroups who reported high level of risk exposures while showed low intention to take the vaccine. Efforts are warranted to increase college students perceived susceptibility and severity and promote their self-efficacy in health management and encourage them to take protective behaviors including vaccine uptake.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina, Department of Health Promotion Education and Behavior, SC SmartState Center for Healthcare Quality" - }, - { - "author_name": "Cheuk Chi Tam", - "author_inst": "University of South Carolina, Department of Health Promotion Education and Behavior, SC SmartState Center for Healthcare Quality" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina, Department of Health Promotion Education and Behavior, SC SmartState Center for Healthcare Quality" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.26.20239434", "rel_title": "The evolving worldwide dynamic state of the COVID-19 outbreak", @@ -1033654,6 +1030457,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.28.20239848", + "rel_title": "Prevalence of IgG antibodies against SARS-CoV-2 among healthcare workers in a tertiary pediatric hospital in Poland", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20239848", + "rel_abs": "Data on prevalence of SARS-CoV-2 antibody in healthcare workers (HCWs) is scare, especially in pediatric settings. The purpose of this study was to evaluate the SARS-CoV-2 IgG-positivity among HCWs of a tertiary pediatric hospital. In addition, follow-up of serological response in the subgroup of seropositive HCWs was performed, to get some insight on persistence of IgG antibodies to SARS-CoV-2. Free, voluntary SARS-CoV-2 IgG testing was made available to HCWs of the Childrens Memorial Health Institute in Warsaw (Poland). Plasma samples were collected between July 1 and August 9, 2020 and tested using the Abbott SARS-CoV-2 IgG assay. Of 2282 eligible participants, 1879 (82.3%) HCWs volunteered to undergo testing. Sixteen HCWs tested positive for SARS-CoV-2 IgG, corresponding to the seroprevalence of 0.85%. Among seropositive HCWs, three had confirmed COVID-19. Of note, 8 (50%) seropositive HCWs reported neither symptoms nor unprotected contact with confirmed SARS-CoV-2 cases in the previous months. A decline in the IgG index was observed at median time of 86.5 days (range:84-128 days) after symptom onset or RT-PCR testing. The nationwide public health response measures together with infection prevention and control practices implemented at the hospital level, at the beginning of the COVID-19 pandemic, might explain a low seroprevalence. Further studies are warranted to elucidate the duration of anti-SARS-CoV-2 antibodies, as well as the correlation between seropositivity and protective immunity against reinfection. Regardless of the persistence of antibodies and their protective properties, such low prevalence indicates that this population is vulnerable to a second wave of the COVID-19 pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Beata Kasztelewicz", + "author_inst": "The Children's Memorial Health Institute" + }, + { + "author_name": "Katarzyna Janiszewska", + "author_inst": "The Children's Memorial Health Institute" + }, + { + "author_name": "Julia Burzy\u0144ska", + "author_inst": "The Children's Memorial Health Institute" + }, + { + "author_name": "Emilia Szyd\u0142owska", + "author_inst": "The Children's Memorial Health Institute" + }, + { + "author_name": "Marek Migda\u0142", + "author_inst": "The Children's Memorial Health Institute" + }, + { + "author_name": "Katarzyna Dzier\u017canowska-Fangrat", + "author_inst": "The Children's Memorial Health Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.27.20234997", "rel_title": "The possible beneficial role of the regular use of potent mouthwash solutions in the treatment of COVID-19", @@ -1034561,37 +1031403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.28.20240242", - "rel_title": "On the anti-correlation between COVID-19 infection rate and natural UV light in the UK", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240242", - "rel_abs": "While it is well established that the rate of COVID-19 infections can be suppressed by social distancing, environmental effects may also affect it. We consider the hypothesis that natural Ultra-Violet (UV) light is reducing COVID-19 infections by enhancing human immunity through increasing levels of Vitamin-D and Nitric Oxide or by suppressing the virus itself. We focus on the United Kingdom (UK), by examining daily COVID-19 infections (F) and UV Index (UVI) data from 23 March 2020 to 10 March 2021. We find an intriguing empirical anti-correlation between log10(F) and log10(UVI) with a correlation coefficient of -0.934 from 11 May 2020 (when the first UK lockdown ended) to 10 March 2021. The anti-correlation may reflect causation with other factors which are correlated with the UVI. We advocate that UVI should be added as a parameter in modelling the pattern of COVID-19 infections and deaths. We started quantifying such correlations in other countries and regions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arnon Blum", - "author_inst": "Bar Ilan University" - }, - { - "author_name": "Constantina Nicolaou", - "author_inst": "UCL" - }, - { - "author_name": "Ben Henghes", - "author_inst": "UCL" - }, - { - "author_name": "Ofer Lahav", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.27.20239970", "rel_title": "Willingness to vaccinate against COVID-19 in the US: Longitudinal evidence from a nationally representative sample of adults from April-October 2020", @@ -1035160,6 +1031971,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.29.20240408", + "rel_title": "A psychrometric model to predict the biological decay of the SARS-CoV-2 virus in aerosols", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20240408", + "rel_abs": "There is increasing evidence that the 2020 COVID-19 pandemic has been influenced by variations in air temperature and humidity. However, the impact that these environmental parameters have on survival of the SARS-CoV-2 virus has not been fully characterised. Therefore an analytical study was undertaken using published data to develop a psychrometric model to predict the biological decay rate of the virus in aerosols. This revealed that it is possible to predict with a high degree of accuracy (R2 = 0.718, p<0.001) the biological decay constant for SARS-CoV-2 using a regression model with enthalpy, vapour pressure and specific volume as predictors. Applying this to historical meteorological data from London, Paris and Milan over the pandemic period, produced results which indicate that the average half-life of the virus in aerosols was in the region 13-21 times longer in March 2020, when the outbreak was accelerating, than it was in August 2020 when epidemic in Europe was at its nadir. As such, this suggests that changes in virus survivability due the variations in the psychrometric qualities of the air might influence the transmission of COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Clive B Beggs", + "author_inst": "Leeds Beckett University" + }, + { + "author_name": "Eldad J Avital", + "author_inst": "Queen Mary University of London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.30.20240754", "rel_title": "The impact of COVID-19 disruption to cervical cancer screening in England on excess diagnoses.", @@ -1036207,53 +1033041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.11.25.20238030", - "rel_title": "Self-harm during the early period of the COVID-19 Pandemic in England: comparative trend analysis of hospital presentations", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238030", - "rel_abs": "BackgroundThe COVID-19 pandemic and public health measures necessary to address it may have major effects on mental health, including on self-harm. We have used well-established monitoring systems in two hospitals in England to investigate trends in self-harm presentations to hospitals during the early period of the pandemic.\n\nMethodData collected in Oxford and Derby on patients aged 18 years and over who received a psychosocial assessment after presenting to the emergency departments following self-harm were used to compare trends during the three-month period following lockdown in the UK (23rd March 2020) to the period preceding lockdown and the equivalent period in 2019.\n\nResultsDuring the 12 weeks following introduction of lockdown restrictions there was a large reduction in the number of self-harm presentations to hospitals by individuals aged 18 years and over compared to the pre-lockdown weeks in 2020 (mean weekly reduction of 13.5 (95% CI 5.6 - 21.4) and the equivalent period in 2019 (mean weekly reduction of 18.0 (95% CI 13.9 - 22.1). The reduction was greater in females than males, occurred in all age groups, with a larger reduction in presentations following self-poisoning than self-injury.\n\nConclusionsA substantial decline in hospital presentations for self-harm occurred during the three months following the introduction of lockdown restrictions. Reasons could include a reduction in self-harm at the community level and individuals avoiding presenting to hospital following self-harm. Longer-term monitoring of self-harm behaviour during the pandemic is essential, together with efforts to encourage help-seeking and the modification of care provision.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Keith Hawton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Deborah Casey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth Bale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fiona Brand", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jennifer Ness", - "author_inst": "Derbyshire Healthcare NHS Foundation Trust" - }, - { - "author_name": "Keith Waters", - "author_inst": "Derbyshire Healthcare NHS Foundation Trust" - }, - { - "author_name": "Samantha Kelly", - "author_inst": "Derbyshire Healthcare NHS Foundation Trust" - }, - { - "author_name": "Galit Guelayov", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.11.25.20238766", "rel_title": "The psychosocial impact on frontline health and social care professionals in the UK during the COVID-19 pandemic: a qualitative interview study.", @@ -1036778,6 +1033565,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.24.20237842", + "rel_title": "Positive rates predict death rates of Covid-19 locally and worldwide 13 days ahead", + "rel_date": "2020-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237842", + "rel_abs": "In the Covid-19-pandemic, the numbers of deceased do not consistently follow the number of new infections. The CFR mortality has declined in Germany from 5 % to 0.4 %. However, if we interpret the portion of positive tests as a positive rate, we find the positive rate and the numbers of deceased to run parallel with an offset of about 13 days. This has been observed worldwide in ten other countries and locally in Germany and North Rhine-Westphalia. In Germany the IFR mortality is about 29 per one million inhabitants, in the USA about 42, in Israel about 17, in the Netherlands 23, in Austria 27, in France 33, in Spain 36, in the UK 47 and Italy about 56 per million inhabitants. In Japan and South-Korea the mortality rate is only about 3 per million inhabitants, with an offset of about 25 days.\n\nThe daily positive ratio, which is reported by state health authorities, allows to estimate the number of deaths (and seriously ill people) about 13 days ahead. This gives local hospitals more time for detailed planning. The daily positive rate may be interpreted as a \"thermometer\" of the respective country. The positive rate gives a much better picture of the state of the pandemic and should be reported by the media in addition to infection numbers. In official guidelines a 7-day-positive-rate is a much better guideline than the 7-day-incidence.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Juergen Mimkes", + "author_inst": "Paderborn University, Germany" + }, + { + "author_name": "Rainer Janssen", + "author_inst": "Engineering Office, Paderborn, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.24.20237834", "rel_title": "Covid-19 vaccination intentions among Canadian parents of 9-12 year old children: results from the All Our Families longitudinal cohort", @@ -1037393,33 +1034203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.11.24.20237446", - "rel_title": "N95 respirators, disposable procedure masks and reusable cloth face coverings: total inward leakage and filtration efficiency of materials against aerosol", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237446", - "rel_abs": "Humans expel physiological particles continuously through normal respiratory activities such as breathing, talking, coughing and sneezing; a portion of these are aerosol in the size range <5.0 {micro}m. Misconceptions exist on how to best implement face coverings as an effective preventive health measure against potentially infectious respiratory generated aerosol. The aim of this study was to characterise the performance of face coverings against aerosol when worn by individuals, and to quantify the maximum aerosol penetration through the material used in the construction of each mask. The former addresses their use as a means of possible protection against aerosol present in the environment and the latter having relevance to filtration and reducing human generated aerosol from reaching the environment. Face covering performance was assessed by measuring the total inward leakage of aerosol through the mask material and face seal. Aerosol penetration was measured on swatches of material taken from the face covering. An inert polydisperse charge-neutralized NaCl aerosol, with a distribution ranging from 0.023 {micro}m to 5 m in diameter, was used for the experiments.\n\nTotal inward leakage tests were completed to assess the protection factor for nine variations of face coverings, including seven reusable cloth masks, of which six were homemade and one was commercially manufactured, and two styles of disposable procedure masks, one with ear loops and one with ties. Our results have shown that face coverings in general provide the wearer only limited protection against aerosol in the environment. All reusable cloth face coverings obtained a practical protection level of less than 2. The performance of the disposable procedure masks varied from 1.7 to 3.6. The mean practical protection level for the nine face coverings was 1.95 with a standard deviation of 0.89. Comparatively, a N95 respirator achieved a protection factor of 166. We have further shown that aerosol readily penetrates through most materials used in face coverings. Aerosol swatch penetration tests were completed on six different fabrics commonly available for reusable homemade face coverings, four different material systems comprised of multiple material types, eight different disposable procedure masks and the filtering material from three different N95 respirators. Maximum aerosol penetration through the six common fabrics varied from 39% to 91%; for systems comprised of multiple types of materials 4% to 23%; for materials used in disposable procedure masks 16% to 80%; and for filtering materials used in N95 respirators 1.0% to 1.9%. We also highlight that with the exception of some of the reusable cloth materials, penetration of particulates at 5 {micro}m diameter, representing the minimum filtration efficiency that could be achieved against droplets, was insignificant; the six common fabrics showed penetration from 1% to 44%; the fabric systems comprised of multiple types of materials <0.9%; the materials used in disposable procedure masks <0.9% to 6%; and the filtering materials used in three different N95 respirators <0.9%. The observations from this study directly demonstrate that face coverings may be optimized by incorporating high filtration efficiency materials in their construction. Face coverings with an enhanced level of filtration would be of benefit in circumstances where SARS-CoV-2 may be present in the aerosol of infected individuals to reduce aerosol emission from respiratory activities penetrating through into the environment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Scott Duncan", - "author_inst": "Defence Research and Development Canada- Suffield Research Centre" - }, - { - "author_name": "Paul A Bodurtha", - "author_inst": "Defence Research and Development Canada" - }, - { - "author_name": "Syed Naqvi", - "author_inst": "Defence Research and Development Canada- Suffield Research Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.11.24.20237040", "rel_title": "Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 health emergency", @@ -1038344,6 +1035127,205 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.24.20236802", + "rel_title": "Characteristics, outcomes, and mortality amongst 133,589 patients with prevalent autoimmune diseases diagnosed with, and 48,418 hospitalised for COVID-19: a multinational distributed network cohort analysis", + "rel_date": "2020-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20236802", + "rel_abs": "ObjectivePatients with autoimmune diseases were advised to shield to avoid COVID-19, but information on their prognosis is lacking. We characterised 30-day outcomes and mortality after hospitalisation with COVID-19 among patients with prevalent autoimmune diseases, and compared outcomes after hospital admissions among similar patients with seasonal influenza.\n\nDesignMultinational network cohort study\n\nSettingElectronic health records data from Columbia University Irving Medical Center (CUIMC) (NYC, United States [US]), Optum [US], Department of Veterans Affairs (VA) (US), Information System for Research in Primary Care-Hospitalisation Linked Data (SIDIAP-H) (Spain), and claims data from IQVIA Open Claims (US) and Health Insurance and Review Assessment (HIRA) (South Korea).\n\nParticipantsAll patients with prevalent autoimmune diseases, diagnosed and/or hospitalised between January and June 2020 with COVID-19, and similar patients hospitalised with influenza in 2017-2018 were included.\n\nMain outcome measures30-day complications during hospitalisation and death\n\nResultsWe studied 133,589 patients diagnosed and 48,418 hospitalised with COVID-19 with prevalent autoimmune diseases. The majority of participants were female (60.5% to 65.9%) and aged [≥]50 years. The most prevalent autoimmune conditions were psoriasis (3.5 to 32.5%), rheumatoid arthritis (3.9 to 18.9%), and vasculitis (3.3 to 17.6%). Amongst hospitalised patients, Type 1 diabetes was the most common autoimmune condition (4.8% to 7.5%) in US databases, rheumatoid arthritis in HIRA (18.9%), and psoriasis in SIDIAP-H (26.4%).\n\nCompared to 70,660 hospitalised with influenza, those admitted with COVID-19 had more respiratory complications including pneumonia and acute respiratory distress syndrome, and higher 30-day mortality (2.2% to 4.3% versus 6.3% to 24.6%).\n\nConclusionsPatients with autoimmune diseases had high rates of respiratory complications and 30-day mortality following a hospitalization with COVID-19. Compared to influenza, COVID-19 is a more severe disease, leading to more complications and higher mortality. Future studies should investigate predictors of poor outcomes in COVID-19 patients with autoimmune diseases.\n\nWhat is already known about this topicO_LIPatients with autoimmune conditions may be at increased risk of COVID-19 infection andcomplications.\nC_LIO_LIThere is a paucity of evidence characterising the outcomes of hospitalised COVID-19 patients with prevalent autoimmune conditions.\nC_LI\n\nWhat this study addsO_LIMost people with autoimmune diseases who required hospitalisation for COVID-19 were women, aged 50 years or older, and had substantial previous comorbidities.\nC_LIO_LIPatients who were hospitalised with COVID-19 and had prevalent autoimmune diseases had higher prevalence of hypertension, chronic kidney disease, heart disease, and Type 2 diabetes as compared to those with prevalent autoimmune diseases who were diagnosed with COVID-19.\nC_LIO_LIA variable proportion of 6% to 25% across data sources died within one month of hospitalisation with COVID-19 and prevalent autoimmune diseases.\nC_LIO_LIFor people with autoimmune diseases, COVID-19 hospitalisation was associated with worse outcomes and 30-day mortality compared to admission with influenza in the 2017-2018 season.\nC_LI", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Eng Hooi Tan", + "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, OX3 7LD, UK" + }, + { + "author_name": "Anthony G. Sena", + "author_inst": "1. Janssen Research and Development, Titusville, NJ USA, 2. Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Albert Prats-Uribe", + "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, OX3 7LD, UK" + }, + { + "author_name": "Seng Chan You", + "author_inst": "Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea" + }, + { + "author_name": "Waheed-Ul-Rahman Ahmed", + "author_inst": "1.Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, UK, 2.C" + }, + { + "author_name": "Kristin Kostka", + "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA" + }, + { + "author_name": "Christian Reich", + "author_inst": "Real World Solutions, IQVIA, Cambridge, MA USA" + }, + { + "author_name": "Scott L. Duvall", + "author_inst": "1. VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA, 2. Department of Internal Medicine, University " + }, + { + "author_name": "Kristine E. Lynch", + "author_inst": "1.VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA, 2. Department of Internal Medicine, University o" + }, + { + "author_name": "Michael E. Matheny", + "author_inst": "1.Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA , 2. Department of Biomedical Informatics, Vanderbilt University Medi" + }, + { + "author_name": "Talita Duarte-Salles", + "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina, Barcelona, Spain" + }, + { + "author_name": "Sergio Fernandez Bertolin", + "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" + }, + { + "author_name": "George Hripcsak", + "author_inst": "1.Department of Biomedical Informatics, Columbia University, New York, NY, US , 2. New York-Presbyterian Hospital, New York, NY, US" + }, + { + "author_name": "Karthik Natarajan", + "author_inst": "1. Department of Biomedical Informatics, Columbia University, New York, NY, US, 2. New York-Presbyterian Hospital, New York, NY, US" + }, + { + "author_name": "Thomas Falconer", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US" + }, + { + "author_name": "Matthew Spotnitz", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US" + }, + { + "author_name": "Anna Ostropolets", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, US" + }, + { + "author_name": "Clair Blacketer", + "author_inst": "1.Janssen Research and Development, Titusville, NJ USA, 2. Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Thamir M Alshammari", + "author_inst": "Medication Safety Research Chair, King Saud University" + }, + { + "author_name": "Heba Alghoul", + "author_inst": "Faculty of Medicine, Islamic University of Gaza, Palestine" + }, + { + "author_name": "Osaid Alser", + "author_inst": "Massachusetts General Hospital, Harvard Medical School, Boston, 02114, Massachusetts, USA" + }, + { + "author_name": "Jennifer C.E. Lane", + "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, OX3 7LD, UK" + }, + { + "author_name": "Dalia M Dawoud", + "author_inst": "Cairo University, Faculty of Pharmacy, Cairo, Egypt" + }, + { + "author_name": "Karishma Shah", + "author_inst": "Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, U" + }, + { + "author_name": "Yue Yang", + "author_inst": "DHC Technologies Co., LTD" + }, + { + "author_name": "Lin Zhang", + "author_inst": "1.School of Population Medicine and Public Health, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China, 2. Melbourne Scho" + }, + { + "author_name": "Carlos Areia", + "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU, UK" + }, + { + "author_name": "Asieh Golozar", + "author_inst": "1.Regeneron Pharmaceuticals, NY US, 2. Departament of Epidemiology, Johns Hopkins School of Public, Baltimore MD" + }, + { + "author_name": "Martina Recalde", + "author_inst": "1.Fundacio Institut Universitari per a la recerca a lAtencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain, 2. Universitat Autonoma de Bar" + }, + { + "author_name": "Paula Casajust", + "author_inst": "Real-World Evidence, Trial Form Support, Barcelona, Spain" + }, + { + "author_name": "Jitendra Jonnagaddala", + "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" + }, + { + "author_name": "Vignesh Subbian", + "author_inst": "College of Engineering, The University of Arizona Tucson, Arizona, USA" + }, + { + "author_name": "David Vizcaya", + "author_inst": "Bayer Pharmaceuticals, Sant Joan Despi, Spain" + }, + { + "author_name": "Lana YH Lai", + "author_inst": "School of Medical Sciences, University of Manchester, UK" + }, + { + "author_name": "Fredrik Nyberg", + "author_inst": "School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden" + }, + { + "author_name": "Daniel R. Morales", + "author_inst": "Division of Population Health Sciences, University of Dundee" + }, + { + "author_name": "Jose D. Posada", + "author_inst": "Stanford Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University" + }, + { + "author_name": "Nigam H. Shah", + "author_inst": "Stanford Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University" + }, + { + "author_name": "Mengchun Gong", + "author_inst": "Health Management Institute, Southern Medical University" + }, + { + "author_name": "Arani Vivekanantham", + "author_inst": "Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, U" + }, + { + "author_name": "Aaron Abend", + "author_inst": "Autoimmune Registry Inc., 125 West Lane, Guilford, CT 06437" + }, + { + "author_name": "Evan P Minty", + "author_inst": "O Brien School for Public Health, Faculty of Medicine, University of Calgary. 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada" + }, + { + "author_name": "Marc A. Suchard", + "author_inst": "Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA USA" + }, + { + "author_name": "Peter Rijnbeek", + "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Patrick B Ryan", + "author_inst": "1.Janssen Research and Development, Titusville, NJ USA, 2.Department of Biomedical Informatics, Columbia University, New York, NY, US" + }, + { + "author_name": "Daniel Prieto-Alhambra", + "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, OX3 7LD, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.26.400390", "rel_title": "A Novel Cell Therapy for COVID-19 and Potential Future Pandemics: Virus Induced Lymphocytes (VIL)", @@ -1039371,85 +1036353,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.25.398909", - "rel_title": "3D8, a nucleic acid-hydrolyzing scFv, confers antiviral activity against SARS-CoV-2 and multiple coronaviruses in vitro", - "rel_date": "2020-11-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.398909", - "rel_abs": "BackgroundThe current pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the etiology of Coronavirus-induced disease 19 (COVID-19) and poses a critical public health threat worldwide. Effective therapeutics and vaccines against multiple coronaviruses remain unavailable. Single chain variable fragment (scFv), a recombinant antibody exhibits broad-spectrum antiviral activity against DNA and RNA viruses owing to its nucleic acid-hydrolyzing property.\n\nObjectiveThis study is aimed to investigate an antiviral activity of 3D8 scFv against SARS-CoV-2 and other coronaviruses.\n\nMethods3D8, a recombinant scFv antibody was evaluated for antiviral activity against SARS-CoV-2, HCoV-OC43 and PEDV in Vero E6 cell cultures. Viral growth was quantified with quantitative RT-qPCR and plaque assay. Nucleic acid hydrolyzing activity of 3D8 was assessed through abzyme assays of in vitro viral transcripts and cell viability was determined by MTT assay.\n\nResults3D8 inhibited the replication of SARS-CoV-2, human coronavirus OC43 (HCoV-OC43), and porcine epidemic diarrhea virus (PEDV). Our results revealed the prophylactic and therapeutic effects of 3D8 scFv against SARS-CoV-2 in Vero E6 cells. Immunoblot and plaque assays showed the reduction of coronavirus nucleoproteins and infectious particles respectively in 3D8 scFv-treated cells.\n\nConclusionsThis data demonstrates the broad-spectrum antiviral activity of 3D8 against SARS-CoV-2 and other coronaviruses. Thus, it could be considered a potential antiviral countermeasure against SARS-CoV-2 and zoonotic coronaviruses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Gunsup Lee", - "author_inst": "Novelgen Co., Ltd." - }, - { - "author_name": "Shailesh Budhathoki", - "author_inst": "Department of Microbiology, College of Medicine, Hallym University" - }, - { - "author_name": "Geum-Young Lee", - "author_inst": "Department of Microbiology, Korea University College of Medicine" - }, - { - "author_name": "Kwang-ji Oh", - "author_inst": "Novelgen Co., Ltd." - }, - { - "author_name": "Yeon Kyoung Ham", - "author_inst": "Novelgen Co., Ltd." - }, - { - "author_name": "Young Jun Kim", - "author_inst": "Novelgen Co., Ltd." - }, - { - "author_name": "Ye Rin Lim", - "author_inst": "Institute of Medical Science, College of Medicine, Hallym University" - }, - { - "author_name": "Phuong Thi Hoang", - "author_inst": "College of Biotechnology and Bioengineering, Sungkyunkwan University" - }, - { - "author_name": "Yongjun Lee", - "author_inst": "College of Biotechnology and Bioengineering, Sungkyunkwan University" - }, - { - "author_name": "Seok-Won Lim", - "author_inst": "Animal Functional Genomics & Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University" - }, - { - "author_name": "Jun-Mo Kim", - "author_inst": "Animal Functional Genomics & Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University" - }, - { - "author_name": "Seungchan Cho", - "author_inst": "Department of Microbiology, Korea University College of Medicine" - }, - { - "author_name": "Tai-Hyun Kim", - "author_inst": "Novelgen Co., Ltd" - }, - { - "author_name": "Jin-Won Song", - "author_inst": "Department of Microbiology, Korea University College of Medicine" - }, - { - "author_name": "Sukchan Lee", - "author_inst": "College of Biotechnology and Bioengineering, Sungkyunkwan University" - }, - { - "author_name": "Won-Keun Kim", - "author_inst": "Department of Microbiology, College of Medicine, Hallym University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.25.398008", "rel_title": "Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection", @@ -1040110,6 +1037013,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.22.20236091", + "rel_title": "Comparing COVID-19 vaccine allocation strategies in India: a mathematical modelling study", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20236091", + "rel_abs": "BackgroundThe development and widespread use of an effective SARS-CoV-2 vaccine could help prevent substantial morbidity and mortality associated with COVID-19 infection and mitigate many of the secondary effects associated with non-pharmaceutical interventions. The limited availability of an effective and licensed vaccine will task policymakers around the world, including in India, with decisions regarding optimal vaccine allocation strategies. Using mathematical modelling we aimed to assess the impact of different age-specific COVID-19 vaccine allocation strategies within India on SARS CoV-2-related mortality and infection.\n\nMethodsWe used an age-structured, expanded SEIR model with social contact matrices to assess different age-specific vaccine allocation strategies in India. We used state-specific age structures and disease transmission coefficients estimated from confirmed Indian incident cases of COVID-19 between 28 January and 31 August 2020. Simulations were used to investigate the relative reduction in mortality and morbidity of vaccinate allocation strategies based on prioritizing different age groups, and the interactions of these strategies with several concurrent non-pharmacologic interventions (i.e., social distancing, mandated masks, lockdowns). Given the uncertainty associated with current COVID-19 vaccine development, we also varied several vaccine characteristics (i.e., efficacy, type of immunity conferred, and rollout speed) in the modelling simulations.\n\nResultsIn nearly all scenarios, prioritizing COVID-19 vaccine allocation for older populations (i.e., >60yrs old) led to the greatest relative reduction in deaths, regardless of vaccine efficacy, control measures, rollout speed, or immunity dynamics. However, preferential vaccination of this target group often produced higher total symptomatic infection counts and more pronounced estimates of peak incidence than strategies which targeted younger adults (i.e., 20-40yrs or 40-60yrs) or the general population irrespective of age. Vaccine efficacy, immunity type, target coverage and rollout speed all significantly influenced overall strategy effectiveness, with the time taken to reach target coverage significantly affecting the relative mortality benefit comparative to no vaccination.\n\nConclusionsOur findings support global recommendations to prioritize COVID-19 vaccine allocation for older age groups. Including younger adults in the prioritisation group can reduce overall infection rates, although this benefit was countered by the larger mortality rates in older populations. Ultimately an optimal vaccine allocation strategy will depend on vaccine characteristics, strength of concurrent non-pharmaceutical interventions, and region-specific goals such as reducing mortality, morbidity, or peak incidence.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Brody H Foy", + "author_inst": "Systems Biology Department, Harvard Medical School, Center for Systems Biology and Department of Pathology, Massachusetts General Hospital" + }, + { + "author_name": "Brian Wahl", + "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA, International Vaccine Access Center, Johns Hopkins Bloomber" + }, + { + "author_name": "Kayur Mehta", + "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA, International Vaccine Access Center, Johns Hopkins Bloomber" + }, + { + "author_name": "Anita Shet", + "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA, International Vaccine Access Center, Johns Hopkins Bloomber" + }, + { + "author_name": "Gautam I Menon", + "author_inst": "Departments of Physics and Biology, Ashoka University, Sonepat, India, Theoretical Physics and Computational Biology, The Institute of Mathematical Sciences, Ch" + }, + { + "author_name": "Carl D Britto", + "author_inst": "Department of Pediatrics, Boston Childrens Hospital, Boston, Massachusetts, United States of America, Division of Infectious Disease, St. Johns Research Instit" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.23.20236786", "rel_title": "Validating the RISE UP score for predicting prognosis in patients with COVID-19 in the emergency department, a retrospective study", @@ -1041037,69 +1037979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.23.20237206", - "rel_title": "The Contrasting Role of Nasopharyngeal Angiotensin Converting Enzyme 2 (ACE2) Expression in SARS-CoV-2 Infection: A Cross-Sectional Study of People Tested for COVID-19 in British Columbia", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237206", - "rel_abs": "BackgroundAngiotensin converting enzyme 2 (ACE2) serves as the host receptor for SARS-CoV-2, with a critical role in viral infection. We aim to understand population level variation of nasopharyngeal ACE2 expression in people tested for COVID-19 and the relationship between ACE2 expression and SARS-CoV-2 viral RNA load, while adjusting for expression of the complementary protease, Transmembrane serine protease 2 (TMPRSS2), soluble ACE2, age, and biological sex.\n\nMethodsA cross-sectional study of n=424 participants aged 1-104 years referred for COVID-19 testing was performed in British Columbia, Canada. Participants who tested negative or positive for COVID-19 were matched by age and biological sex. Viral and host gene expression was measured by quantitative reverse-transcriptase polymerase chain reaction. Bivariate analysis and multiple linear regression were performed to understand the role of nasopharyngeal ACE2 expression in SARS-CoV-2 infection. The ACE2 gene was targeted to measure expression of transmembrane and soluble transcripts.\n\nFindingsAnalysis shows no association between age and nasopharyngeal ACE2 expression in those who tested negative for COVID-19 (P=0{middle dot}092). Mean expression of transmembrane (P=1{middle dot}2e-4), soluble ACE2 (P<0{middle dot}0001) and TMPRSS2 (P<0{middle dot}0001) differed between COVID-19-negative and -positive groups. In bivariate analysis of COVID-19-positive participants, expression of transmembrane ACE2 positively correlated with SARS-CoV-2 RNA viral load (P<0{middle dot}0001), expression of soluble ACE2 negatively correlated (P<0{middle dot}0001), and no correlation was found with TMPRSS2 (P=0{middle dot}694). Multivariable analysis showed that the greatest viral RNA loads were observed in participants with high transmembrane ACE2 expression (B=0{middle dot}886, 95%CI:[0{middle dot}596 to 1{middle dot}18]), while expression of soluble ACE2 may protect against high viral RNA load in the upper respiratory tract (B= -0{middle dot}0990, 95%CI:[-0{middle dot}176 to -0{middle dot}0224]).\n\nInterpretationNasopharyngeal ACE2 expression plays a dual, contrasting role in SARS-CoV-2 infection of the upper respiratory tract. Transmembrane ACE2 positively correlates, while soluble ACE2 negatively correlates with viral RNA load after adjusting for age, biological sex and expression of TMPRSS2.\n\nFundingThis project (COV-55) was funded by Genome British Columbia as part of their COVID-19 rapid response initiative.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Aidan M Nikiforuk", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Kevin S Kuchinski", - "author_inst": "University of British Columbia" - }, - { - "author_name": "David D W Twa", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Christine D Lukac", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Hind Sbihi", - "author_inst": "University of British Columbia" - }, - { - "author_name": "C Andrew Basham", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Christian Steidl", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Natalie A Prystajecky", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Agatha N Jassem", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Mel Krajden", - "author_inst": "University of British Columbia" - }, - { - "author_name": "David M Patrick", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.24.20237644", "rel_title": "Excess mortality across regions of Europe during the first wave of the COVID-19 pandemic - impact of the winter holiday travelling and government responses", @@ -1041692,6 +1038571,49 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.11.23.393488", + "rel_title": "LinearTurboFold: Linear-Time RNA Structural Alignment and Conserved Structure Prediction with Applications to Coronaviruses", + "rel_date": "2020-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.393488", + "rel_abs": "The constant emergence of COVID-19 variants reduces the effectiveness of existing vaccines and test kits. Therefore, it is critical to identify conserved structures in SARS-CoV-2 genomes as potential targets for variant-proof diagnostics and therapeutics. However, the algorithms to predict these conserved structures, which simultaneously fold and align multiple RNA homologs, scale at best cubically with sequence length, and are thus infeasible for coronaviruses, which possess the longest genomes ([~]30,000 nt) among RNA viruses. As a result, existing efforts on modeling SARS-CoV-2 structures resort to single sequence folding as well as local folding methods with short window sizes, which inevitably neglect long-range interactions that are crucial in RNA functions. Here we present LinearTurboFold, an efficient algorithm for folding RNA homologs that scales linearly with sequence length, enabling unprecedented global structural analysis on SARS-CoV-2. Surprisingly, on a group of SARS-CoV-2 and SARS-related genomes, LinearTurbo-Folds purely in silico prediction not only is close to experimentally-guided models for local structures, but also goes far beyond them by capturing the end-to-end pairs between 5 and 3 UTRs ([~]29,800 nt apart) that match perfectly with a purely experimental work. Furthermore, LinearTurboFold identifies novel conserved structures and conserved accessible regions as potential targets for designing efficient and mutation-insensitive small-molecule drugs, antisense oligonucleotides, siRNAs, CRISPR-Cas13 guide RNAs and RT-PCR primers. LinearTurboFold is a general technique that can also be applied to other RNA viruses and full-length genome studies, and will be a useful tool in fighting the current and future pandemics.\n\nSignificance StatementConserved RNA structures are critical for designing diagnostic and therapeutic tools for many diseases including COVID-19. However, existing algorithms are much too slow to model the global structures of full-length RNA viral genomes. We present LinearTurboFold, a linear-time algorithm that is orders of magnitude faster, making it the first method to simultaneously fold and align whole genomes of SARS-CoV-2 variants, the longest known RNA virus ([~]30 kilobases). Our work enables unprecedented global structural analysis and captures long-range interactions that are out of reach for existing algorithms but crucial for RNA functions. LinearTurboFold is a general technique for full-length genome studies and can help fight the current and future pandemics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sizhen Li", + "author_inst": "Oregon State University" + }, + { + "author_name": "He Zhang", + "author_inst": "Baidu Research USA" + }, + { + "author_name": "Liang Zhang", + "author_inst": "Baidu Research USA" + }, + { + "author_name": "Kaibo Liu", + "author_inst": "Baidu Research USA" + }, + { + "author_name": "Boxiang Liu", + "author_inst": "Baidu Research USA" + }, + { + "author_name": "David H. Mathews", + "author_inst": "University of Rochester" + }, + { + "author_name": "Liang Huang", + "author_inst": "Oregon State University, Baidu Research USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.11.24.395079", "rel_title": "A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro", @@ -1042715,33 +1039637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.22.20236323", - "rel_title": "Duration of SARS-CoV-2 viral shedding in faeces as a parameter for wastewater-based epidemiology: Re-analysis of patient data using a shedding dynamics model", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20236323", - "rel_abs": "BackgroundWastewater-based epidemiology (WBE) is one of the most promising approaches to effectively monitor the spread of the novel coronavirus disease 2019 (COVID-19). The virus concentration in faeces and its temporal variations are essential information for WBE. While some clinical studies have reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) concentrations in faeces, the value varies amongst patients and changes over time.\n\nAimThe present study aimed to examine how the temporal variations in the concentration of virus in faeces affect the monitoring of disease incidence. We re-analysed the experimental findings of clinical studies to estimate the duration of virus shedding and the faecal virus concentration.\n\nMethodAvailable experimental data as of 23 October, 2020 were collected and patient data reported in Germany were included for further analysis. The viral shedding kinetics was modelled, and the dynamic model was fitted to the collected experimental data by a Bayesian framework. Using samples of posterior distributions, the duration of viral shedding and the concentration of virus copies in faeces over time were computed.\n\nResultsWe estimated the median concentration of SARS-CoV-2 in faeces as 2.6 (95% Credible Interval (CrI): 0.22-4.8) log copies per gram (g) of faeces over the shedding period, and our model implied that the duration of viral shedding was 23.2 days (95% CrI: 19.5-31.5), given the current standard quantification limit (Ct = 40). With simulated incidences, our results also indicated that a one-week delay between symptom onset and wastewater sampling increased the estimation of incidence by 13.5%.\n\nConclusionsOur results demonstrated that the temporal variation in virus concentration in faeces affects microbial monitoring systems such as WBE. The present study also implied the need for adjusting the estimates of virus concentration in faeces by incorporating the kinetics of unobserved concentrations. The method used in this study is easily implemented in further simulations; therefore, the results of this study might contribute to enhancing disease surveillance and risk assessments that require quantities of virus to be excreted into the environment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fuminari Miura", - "author_inst": "Ehime University" - }, - { - "author_name": "Masaaki Kitajima", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Ryosuke Omori", - "author_inst": "Hokkaido University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.21.20236117", "rel_title": "Antibody persistency and dynamic trend after SARS-CoV-2 infection over 8 months", @@ -1043390,6 +1040285,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.20.20235648", + "rel_title": "Distribution of Incubation Period of COVID-19 in the Canadian Context: Modeling and Computational Study", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235648", + "rel_abs": "We propose an original model based on a set of coupled delay differential equations with fourteen delays in order to accurately estimate the incubation period of COVID-19, employing publicly available data of confirmed corona cases. In this goal, we separate the total cases into fourteen groups for the corresponding fourteen incubation periods. The estimated mean incubation period we obtain is 6.74 days (95% Confidence Interval(CI): 6.35 to 7.13), and the 90th percentile is 11.64 days (95% CI: 11.22 to 12.17), corresponding to a good agreement with statistical supported studies. This model provides an almost zero-cost approach to estimate the incubation period.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Subhendu Paul", + "author_inst": "School of Mathematics and Statistics, Carleton University, Ottawa, Canada, K1S 5B6." + }, + { + "author_name": "Emmanuel Lorin", + "author_inst": "School of Mathematics and Statistics, Carleton University, Ottawa, Canada, K1S 5B6." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.21.20236109", "rel_title": "Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay", @@ -1044233,37 +1041151,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.11.23.394577", - "rel_title": "Publishing of COVID-19 Preprints in Peer-reviewed Journals, Preprinting Trends, Public Discussion and Quality Issues", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.394577", - "rel_abs": "IntroductionCOVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals. We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues.\n\nMethodsManuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data. The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints.\n\nResultsWith adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR=2.04, 95%CI 1.87-2.23) as well as over the entire observed period (OR=1.42, 95%CI 1.33-1.52). Submission-to-acceptance was by 38.67 days (95%CI 34.96-42.39) shorter for COVID-19 articles. Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020.\n\nConclusionCurrent data suggest a preference for publication of COVID-19-related preprints over the observed period.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ivan Kodvanj", - "author_inst": "University of Zagreb School of Medicine" - }, - { - "author_name": "Jan Homolak", - "author_inst": "University of Zagreb School of Medicine" - }, - { - "author_name": "Davor Virag", - "author_inst": "University of Zagreb School of Medicine" - }, - { - "author_name": "Vladimir Trkulja", - "author_inst": "University of Zagreb School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.11.23.393967", "rel_title": "Building a virtual summer research experience in cancer for high school and early undergraduate students: lessons from the COVID-19 pandemic", @@ -1045004,6 +1041891,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.20.20235291", + "rel_title": "Isolation thresholds for curbing SARS-CoV-2 resurgence", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235291", + "rel_abs": "Self-instigated isolation is heavily relied on to curb SARS-CoV-2 transmission. Accounting for uncertainty in the latent and prepatent periods, as well as the proportion of infections that remain asymptomatic, the limits of this intervention at different phases of infection resurgence are estimated. We show that by October 2020, SARS-CoV-2 transmission rates in England had already begun exceeding levels that could be interrupted using this intervention alone, lending support to the second national lockdown on November 5th 2020.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Laith Yakob", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.19.20234948", "rel_title": "A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic", @@ -1046415,233 +1043321,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.18.20231688", - "rel_title": "Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20231688", - "rel_abs": "Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by Reverse Transcription Polymerase Chain Reaction (RT-PCR). Although this is efficient, automatable and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using Mass Spectrometry (MS). We established the Cov-MS consortium, consisting of fifteen academic labs and several industrial partners to increase applicability, accessibility, sensitivity and robustness of this kind of SARS-CoV-2 detection. This in turn gave rise to the Cov-MS Digital Incubator that allows other labs to join the effort, navigate and share their optimizations, and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR, using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.", - "rel_num_authors": 53, - "rel_authors": [ - { - "author_name": "Bart Van Puyvelde", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University" - }, - { - "author_name": "Katleen Van Uytfanghe", - "author_inst": "Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Olivier Tytgat", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium | Department of Life Science Technologies, Imec, Leuven, Belgium" - }, - { - "author_name": "Laurence Van Oudenhove", - "author_inst": "Waters Corporation, Antwerp, Belgium" - }, - { - "author_name": "Ralf Gabriels", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Robbin Bouwmeester", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Simon Daled", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Tim Van Den Bossche", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Pathmanaban Ramasamy", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium | Interuniversity Institu" - }, - { - "author_name": "Sigrid Verhelst", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Laura De Clerck", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Laura Corveleyn", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Nathan Debunne", - "author_inst": "Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Evelien Wynendaele", - "author_inst": "Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Bart De Spiegeleer", - "author_inst": "Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Peter Judak", - "author_inst": "Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Kris Roels", - "author_inst": "Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Laurie De Wilde", - "author_inst": "Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Peter Van Eenoo", - "author_inst": "Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Tim Reyns", - "author_inst": "Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium" - }, - { - "author_name": "Marc Cherlet", - "author_inst": "Department of Pharmacology, Toxicology, and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Belgium" - }, - { - "author_name": "Emmie Dumont", - "author_inst": "Research Institute for Chromatography (RIC), Kortrijk, Belgium" - }, - { - "author_name": "Griet Debyser", - "author_inst": "Research Institute for Chromatography (RIC), Kortrijk, Belgium" - }, - { - "author_name": "Ruben t'Kindt", - "author_inst": "Research Institute for Chromatography (RIC), Kortrijk, Belgium" - }, - { - "author_name": "Koen Sandra", - "author_inst": "Research Institute for Chromatography (RIC), Kortrijk, Belgium" - }, - { - "author_name": "Surya Gupta", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Nicolas Drouin", - "author_inst": "Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands" - }, - { - "author_name": "Amy Harms", - "author_inst": "Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands" - }, - { - "author_name": "Thomas Hankemeier", - "author_inst": "Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands" - }, - { - "author_name": "Donald Jones", - "author_inst": "The Department of Chemical Pathology and Metabolic Diseases, Level 4, Sandringham Building, Leicester Royal Infirmary, Leicester, United Kingdom" - }, - { - "author_name": "Pankaj Gupta", - "author_inst": "Leicester Cancer Research Centre, RKCSB, University of Leicester, UK and John and Lucille van Geest biomarker facility, Cardiovascular Research Centre, Glenfiel" - }, - { - "author_name": "Cathy Lane", - "author_inst": "Sciex, Macclesfield, UK" - }, - { - "author_name": "Said El Ouadi", - "author_inst": "Sciex, Macclesfield, UK" - }, - { - "author_name": "Jean-Baptiste Vincendet", - "author_inst": "Sciex, Macclesfield, UK" - }, - { - "author_name": "Nick Morrice", - "author_inst": "Sciex, Macclesfield, UK" - }, - { - "author_name": "S. Oehrle", - "author_inst": "Waters Corporation, Milford, MA / Waters Corporation, Wilmslow, UK" - }, - { - "author_name": "Nikunj Tanna", - "author_inst": "Waters Corporation, Milford, MA / Waters Corporation, Wilmslow, UK" - }, - { - "author_name": "Steve Silvester", - "author_inst": "Alderley Analytical, Macclesfield, UK" - }, - { - "author_name": "Sally Hannam", - "author_inst": "Alderley Analytical, Macclesfield, UK" - }, - { - "author_name": "Florian Sigloch", - "author_inst": "Polyquant GmbH, Bad Abbach, Germany" - }, - { - "author_name": "Andrea Bhangu-Uhlmann", - "author_inst": "Polyquant GmbH, Bad Abbach, Germany" - }, - { - "author_name": "Jan Claereboudt", - "author_inst": "Waters Corporation, Antwerp, Belgium" - }, - { - "author_name": "Morteza Razavi", - "author_inst": "SISCAPA Assay Technologies, Inc., Washington DC USA and Victoria BC Canada" - }, - { - "author_name": "Norman Leigh Anderson", - "author_inst": "SISCAPA Assay Technologies, Inc." - }, - { - "author_name": "Sven Degroeve", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Lize Cuypers", - "author_inst": "Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Christophe Stove", - "author_inst": "Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Katrien Lagrou", - "author_inst": "Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Geert Antoine Martens", - "author_inst": "AZ Delta General Hospital" - }, - { - "author_name": "Dieter Deforce", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Lennart Martens", - "author_inst": "VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium | Department of Biomolecular Medicine, Ghent University, Ghent Belgium" - }, - { - "author_name": "Hans Vissers", - "author_inst": "Waters Corporation, Milford, MA / Waters Corporation, Wilmslow, UK" - }, - { - "author_name": "Maarten Dhaenens", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.18.20233932", "rel_title": "REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020", @@ -1047342,6 +1044021,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20234351", + "rel_title": "The potential impact of School Closure Relative to Community-based Non-pharmaceutical Interventions on COVID-19 Cases in Ontario, Canada", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234351", + "rel_abs": "ImportanceResurgent COVID-19 cases have resulted in the re-institution of nonpharmaceutical interventions, including school closure, which can have adverse effects on families. Understanding the impact of schools on the number of incident and cumulative COVID-19 cases is critical for decision-making.\n\nObjectiveTo determine the quantitative effect of schools being open or closed relative to community-based nonpharmaceutical interventions on the number of COVID-19 cases.\n\nDesignAn agent-based transmission model.\n\nSettingA synthetic population of one million individuals based on the characteristics of the population of Ontario, Canada.\n\nParticipantsMembers of the synthetic population clustered into households, neighborhoods or rural districts, cities or a rural region, day care facilities, classrooms - primary, elementary or high school, colleges or universities and workplaces.\n\nExposureSchool reopening on September 15, 2020, versus schools remaining closed under different scenarios for nonpharmaceutical interventions.\n\nMain Outcome and MeasuresIncident and cumulative COVID-19 cases between September 1, 2020 and October 31, 2020.\n\nResultsThe percentage of infections among students and teachers acquired within schools was less than 5% across modelled scenarios. Incident case numbers on October 31, 2020, were 4,414 (95% credible interval, CrI: 3,491, 5,382) and 4,740 (95% CrI 3,863, 5,691), for schools remaining closed versus reopening, respectively, with no other community-based nonpharmaceutical intervention; 714 (95%, CrI: 568, 908) and 780 (95% CrI 580, 993) for schools remaining closed versus reopening, respectively, with community-based nonpharmaceutical interventions implemented; 777 (95% credible CrI: 621, 993) and 803 (95% CrI 617, 990) for schools remaining closed versus reopening, respectively, applied to the observed case numbers in Ontario in early October 2020. Contrasting the scenarios with implementation of community-based interventions versus not doing so yielded a mean difference of 39,355 cumulative COVID-19 cases by October 31, 2020, while keeping schools closed versus reopening them yielded a mean difference of 2,040 cases.\n\nConclusions and relevanceOur simulations suggest that the majority of COVID-19 infections in schools were due to acquisition in the community rather than transmission within schools and that the effect of school reopening on COVID-19 case numbers is relatively small compared to the effects of community-based nonpharmaceutical interventions.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWith resurgence of COVID-19, reinstitution of school closure remains a possibility. Given the harm that closures can cause to children and families, the expected quantitative effect of school reopening or closure on incident and cumulative COVID-19 case numbers is an important consideration.\n\nFindingRelative to community-based nonpharmaceutical interventions, school closure resulted in a small change in COVID-19 incidence trajectories and cumulative case counts.\n\nMeaningCommunity-based interventions should take precedence over school closure.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "David MJ Naimark", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Kali Barrett", + "author_inst": "University Health Network" + }, + { + "author_name": "Yasin Khan", + "author_inst": "University Health Network" + }, + { + "author_name": "Stephen Mac", + "author_inst": "University of Toronto" + }, + { + "author_name": "Raphael Ximenes", + "author_inst": "University Health Network" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.20230375", "rel_title": "Multicenter evaluation of the Panbio COVID-19 Rapid Antigen-Detection Test for the diagnosis of SARS-CoV-2 infection", @@ -1048549,57 +1045271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.17.20232264", - "rel_title": "Early chains of transmission of COVID-19 in France", - "rel_date": "2020-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20232264", - "rel_abs": "IntroductionSARS-CoV-2, which causes COVID-19, has spread rapidly across the world. A dedicated surveillance system was implemented in France in January 2020 to improve early detection of cases and their contacts and limit secondary transmission. Our objective was to use contact-tracing data collected during this initial phase of the epidemic to better characterize SARS-CoV-2 transmission.\n\nMethodsWe analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterized the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.\n\nResultsOver the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95%CI 3.6-4.6) and increased with age of the index case and of the contact. Family contacts were at higher risk of becoming cases (adjusted odds ratio 2.1 (95%CI 1.4-3.0)) while nosocomial contacts were at lower risk (adjusted odds ratio 0.3 (95%CI 0.1-0.7)), compared to coworkers/friends. We identified 328 infector/infectee pairs, 49% of which were family members. The distribution of secondary cases was highly over-dispersed with 80% of secondary cases being caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range 2-8 days) in contact-tracing pairs where late transmission events may be censored, and 6.8 (3-8) days in pairs investigated retrospectively.\n\nConclusionThis study contributes to improving our knowledge of SARS-CoV-2 transmission, such as the importance of superspreading events. Contact-tracing data are challenging to collect but are key to better understand emerging pathogens.\n\nFunding statementThis work was supported by the LabEx \"Integrative Biology of Emerging Infectious Diseases (IBEID)\" (Grant Number ANR-10-LABX-62-IBEID), Sante Publique France, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Unions Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO).", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Juliette Paireau", - "author_inst": "Institut Pasteur/Sante publique France" - }, - { - "author_name": "Alexandra Mailles", - "author_inst": "Sante publique France" - }, - { - "author_name": "Catherine Eisenhauer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Franck de Laval", - "author_inst": "Service de Sante des Armees" - }, - { - "author_name": "Francois Delon", - "author_inst": "Service de Sante des Armees" - }, - { - "author_name": "Paolo Bosetti", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Henrik Salje", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Valerie Ponties", - "author_inst": "Sante publique France" - }, - { - "author_name": "Simon Cauchemez", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.18.20234088", "rel_title": "Knowledge and perceptions on COVID-19 among Senior High School students in Ghana: a cross-sectional study", @@ -1049248,6 +1045919,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.16.20232223", + "rel_title": "Clinical Profile of First 1000 COVID-19 Cases Admitted at Tertiary Care Hospitals and the Correlates of their Mortality: An Indian Experience", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232223", + "rel_abs": "ObjectiveTo describe the clinical profile and factors leading to increased mortality in coronavirus disease (COVID-19) patients admitted to a group of hospitals in India.\n\nDesignA records-based study of the first 1000 patients with a positive result on real-time reverse transcriptase-polymerase-chain-reaction assay for SARS-CoV-2 admitted to our facilities. Various factors such as demographics, presenting symptoms, co-morbidities, ICU admission, oxygen requirement and ventilator therapy were studied.\n\nResultsOf the 1000 patients, 24 patients were excluded due to lack of sufficient data. Of the remaining 976 in the early phase of the epidemic, males were admitted twice as much as females (67.1% and 32.9%, respectively). Mortality in this initial phase was 10.6% and slightly higher for males and steeply higher for older patients. More than 8% reported no symptoms and the most common presenting symptoms were fever (78.3%), productive cough (37.2%), and dyspnea (30.64%). More than one-half (53.6%) had no co-morbidity. The major co-morbidities were hypertension (23.7%), diabetes without (15.4%), and with complications (9.6%). The co-morbidities were associated with higher ICU admissions, greater use of ventilators as well as higher mortality. A total of 29.9% were admitted to the ICU, with a mortality rate of 32.2%. Mortality was steeply higher in those requiring ventilator support (55.4%) versus those who never required ventilation (1.4%). The total duration of hospital stay was just a day longer in patients admitted to the ICU than those who remained in wards.\n\nConclusionMale patients above the age of 60 and with co-morbidities faced the highest rates of mortality. They should be admitted to the hospital in early stage of the disease and given aggressive treatment to help reduce the morbidity and mortality associated with COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sandeep Budhiraja", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Aakriti Soni", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Vinitaa Jha", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Abhaya Indrayan", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Arun Dewan", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Omender Singh", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Yogendra Singh", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Indermohan Chugh", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Vijay Arora", + "author_inst": "Max Healthcare" + }, + { + "author_name": "Rajesh Pandey", + "author_inst": "BLK Hospital" + }, + { + "author_name": "Abdul Ansari", + "author_inst": "Nanavati Hospital" + }, + { + "author_name": "Sujeet Jha", + "author_inst": "Max Healthcare" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.16.20232447", "rel_title": "COVID-19 related outcomes for hospitalised older people at risk of frailty", @@ -1050123,85 +1046857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.16.20232678", - "rel_title": "RT-LAMP assay for ultra-sensitive detection of SARS-CoV-2 in saliva and VTM clinical samples", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232678", - "rel_abs": "The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostic platforms. Although several PCR-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid SARS-CoV-2 detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. There are limited reports of saliva as the sample source and some of these indicate inferior sensitivity when comparing RT-LAMP with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay to test saliva using a 2-step RT-LAMP assay, where a short 10-minute RT step is performed with only B3 and BIP primers before the final reaction. We show that while the 1-step RT-LAMP demonstrate satisfactory results, the optimized 2-step approach allows for single molecule sensitivity per reaction and performs significantly better than the 1-step RT-LAMP and conventional 2-step RT-LAMP approaches with all primers included in the RT Step. Importantly, we demonstrate RNA extraction-free RT-LAMP based assays for detection of SARS-CoV-2 from VTM and saliva clinical samples.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Anurup Ganguli", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Ariana Mostafa", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Jacob Berger", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Sarah A Stewart de Ramirez", - "author_inst": "Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, 61637" - }, - { - "author_name": "Ali Baltaji", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Kelly Roth", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Muhammad Aamir", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Surya Aedma", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Mohamed Mady", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Pranav Mahajan", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Sanjivani Sathe", - "author_inst": "Carle Foundation Hospital, Urbana, Illinois, USA" - }, - { - "author_name": "Mark Johnson", - "author_inst": "Carle Illinois College of Medicine" - }, - { - "author_name": "Karen White", - "author_inst": "Carle Illinois College of Medicine" - }, - { - "author_name": "James Kumar", - "author_inst": "Carle Illinois College of Medicine" - }, - { - "author_name": "Enrique Valera", - "author_inst": "University of Illinois at Urbana Champaign" - }, - { - "author_name": "Rashid Bashir", - "author_inst": "University of Illinois at Urbana Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.16.20232835", "rel_title": "Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation", @@ -1050714,6 +1047369,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.17.20228122", + "rel_title": "Delayed Stroke Treatment during COVID-19 Pandemic in China", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20228122", + "rel_abs": "BackgroundSocial distance, quarantine, pathogen testing and other preventive strategies implemented during COVID-19 pandemic may negatively influence the management of acute stroke.\n\nObjectiveThe current study aimed to evaluate the impacts of COVID-19 pandemic on treatment delay of acute stroke in China.\n\nMethodsThis study included patients with acute stroke admitted in two hospitals in Jiangsu, China. Patients admitted before and after the COVID-19 epidemic outbreak (January 31, 2020, as officially announced by Chinese government) were compared for pre- (measured as onset-to-door time) and post-hospital delay (measured as door-to-needle time). The influence factors for delayed treatment (indicated as onset-to-needle time >4.5 hours) were analyzed with multivariate logistic regression analysis.\n\nResultsOnset-to-door time increased from 202 min (IQR 65-492) before to 317 min (IQR 75-790) after the COVID-19 pandemic (P=0.001). Door-to-needle time increased from 50min (IQR 40-75) before to 65 min (IQR 48-84) after the COVID-19 pandemic (P=0.048). The proportion of patients with intravenous thrombolysis in those with acute ischemic stroke was decreased significantly after the pandemic (15.4% vs 20.1%; P=0.030). Multivariate logistic regression analysis indicated that patients after COVID-19 pandemic, lower educational level, rural residency, mild symptoms and transported by other means than ambulance were associated with delayed treatment.\n\nConclusionsCOVID-19 pandemic has remarkable impacts on the management of acute ischemic stroke. Both pre- and post-hospital delays were prolonged significantly, and proportion of patient arrived within the 4.5-hour time window for intravenous thrombolysis treatment was decreased. Given that anti-COVID-19 measures are becoming medical routines, efforts are warranted to shorten the delay so that the outcomes of stroke could be improved.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gelin Xu", + "author_inst": "Jinling Hospital" + }, + { + "author_name": "Shiyuan Gu", + "author_inst": "Department of Neurology, Jinling Clinical College of Nanjing Medical University, Nanjing 210002, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.11.18.20233700", "rel_title": "The impact of the coronavirus disease 2019 (COVID-19) outbreak on cancer practice in Japan: using an administrative database", @@ -1051481,45 +1048159,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.18.20233767", - "rel_title": "The impact of early public health interventions on SARS-CoV-2 transmission and evolution", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233767", - "rel_abs": "BackgroundMany countries have attempted to mitigate and control COVID-19 through the implementation of non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus.\n\nAimTo assess the duration of chains of virus transmission within individual countries and the extent to which countries export viruses to their geographic neighbours.\n\nMethodsTo address core questions in genomic epidemiology and public health we analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, within countries of northern Europe. To this end, we examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the pandemic.\n\nResultsThe Nordic countries differed markedly in the invasiveness of control strategies implemented. In particular, Sweden did not initially employ any strict population movement limitations and experienced markedly different transmission chain dynamics, which were more numerous and tended to have more cases, a set of features that increased with time during the first eight months of 2020.\n\nConclusionTogether with Denmark, Sweden was also characterised as a net exporter of SARS-CoV-2. Hence, Sweden effectively constituted an epidemiological and evolutionary refugia that enabled the virus to maintain active transmission and spread to other geographic localities. In sum, our analysis reveals the utility of genomic surveillance where active transmission chain monitoring is a key metric.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sebastian Duchene", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Leo Featherstone", - "author_inst": "Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia" - }, - { - "author_name": "Birgitte Freiesleben de Blasio", - "author_inst": "Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, No" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Jon Bohlin", - "author_inst": "Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, No" - }, - { - "author_name": "John H.-O. Pettersson", - "author_inst": "Uppsala university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.17.20210211", "rel_title": "The impacts of COVID-19 mitigation on dengue virus transmission: a modelling study", @@ -1052172,6 +1048811,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.17.387902", + "rel_title": "Sequential ER stress and inflammatory responses are induced by SARS-CoV-2 ORF3 through ERphagy", + "rel_date": "2020-11-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.17.387902", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have resulted in a number of severe cases of COVID-19 and deaths worldwide. However, knowledge of SARS-CoV-2 infection, diseases and therapy remains limited, underlining the urgency of fundamental studies and drug development. Studies have shown that induction of autophagy and hijacking of autophagic machinery are essential for infection and replication of SARS-CoV-2; however, the mechanism of this manipulation and function of autophagy during SARS-CoV-2 infection remain unclear. In the present study, we identified ORF3 as an inducer of autophagy and revealed that ORF3 localizes to the ER and induces FAM134B-related ERphagy through the HMGB1-Beclin1 pathway. As a consequence, ORF3 induces ER stress and inflammatory responses through ERphagy and sensitizes cells to ER stress-induced cell death, suggesting that SARS-CoV-2 ORF3 hijacks ERphagy and then harms ER homeostasis to induce inflammatory responses through excessive ER stress. These findings reveal a sequential induction of ERphagy, ER stress and acute inflammatory responses during SARS-CoV-2 infection and provide therapeutic potential for ERphagy and ER stress-related drugs for COVID-19 treatment and prevention.\n\nImportanceSARS-CoV-2 infection and replication require autophagosome-like double-membrane vacuoles. Inhibition of autophagy suppresses viral replication, indicating the essential role of autophagy in SARS-CoV-2 infection. However, how SARS-CoV-2 hijacks autophagy and the function of autophagy in the disease progression remain unknown. Here, we reveal that SARS-CoV-2 ORF3 induces ERphagy and consequently induces ER stress to trigger acute inflammatory responses and enhance sensitivity to ER stress-induced apoptosis. Our studies uncover ERphagy-induced inflammatory responses during SARS-CoV-2 infection and provide a promising therapeutic approach for treating SARS-CoV-2 infection and inflammatory responses in COVID-19 by manipulating autophagy and ER stress.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xiaolin Zhang", + "author_inst": "Institute of Human Virology,Zhongshan School of Medicine,Sun Yat-Sen University" + }, + { + "author_name": "Ziwei Yang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Xubing Long", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Qinqin Sun", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Fan Wang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Pei-hui Wang", + "author_inst": "Advanced Medical Research Institute, Shandong University" + }, + { + "author_name": "Xiaojuan Li", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + }, + { + "author_name": "Ersheng Kuang", + "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.17.377432", "rel_title": "An assessment of efficacy of Iodine complex (Renessans) against SARS-CoV-2 in non-human primates (Rhesus macaque)", @@ -1053167,77 +1049853,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.16.384917", - "rel_title": "Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck", - "rel_date": "2020-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.16.384917", - "rel_abs": "The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.\n\nAuthor summaryThrough ongoing human adaptation, spill-back events from other animal intermediates, or with the distribution of vaccines and therapeutics, the landscape of SARS-CoV-2 genetic variation is certain to change. The evolutionary mechanisms by which SARS-CoV-2 will continue to adapt to mammalian hosts depend on genetic variation generated within and between hosts. Here, using domestic cats as a model, we show that within-host SARS-CoV-2 genetic variation is predominantly influenced by genetic drift and purifying selection. Transmission of SARS-CoV-2 between hosts is defined by a narrow transmission bottleneck, involving 2-5 viruses. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which arises rapidly and is transmitted in cats. Spike H655Y has been previously shown to confer escape from human monoclonal antibodies and is currently found in over 1000 human sequences. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge, underscoring the importance of continued genomic surveillance in humans and non-human mammalian hosts.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Katarina M Braun", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Gage Kahl Moreno", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Peter J Halfmann", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Emma B Hodcroft", - "author_inst": "University of Bern" - }, - { - "author_name": "David A Baker", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Emma C Boehm", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Andrea M. Weiler", - "author_inst": "University of Wisconsin Madison" - }, - { - "author_name": "Amelia K Haj", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Masato Hatta", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Shiho Chiba", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Tadashi Maemura", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Katia Koelle", - "author_inst": "Emory University" - }, - { - "author_name": "Thomas Friedrich", - "author_inst": "University of Wisconsin Madison" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.17.386904", "rel_title": "Preclinical evaluation of Imatinib does not support its use as an antiviral drug against SARS-CoV-2", @@ -1054154,6 +1050769,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.12.20229658", + "rel_title": "Clinico-pathological features in fatal Covid-19 Infection: A Preliminary Experience of a Tertiary Care Centre in North India using Post-Mortem Minimally Invasive Tissue Biopsies", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20229658", + "rel_abs": "BackgroundThe Covid-19 pandemic began in China in December 2019. India is the second most affected country, as of November 2020 with more than 8.5million cases. Covid-19 infection primarily involves the lung with severity of illness varying from influenza-like illness to acute respiratory distress syndrome. Other organs have also found to be variably affected. Studies evaluating the histopathological changes of Covid-19 are critical in providing a better understanding of the disease pathophysiology and guiding treatment. Minimally invasive biopsy techniques (MITS/B) provide an easy and suitable alternative to complete autopsies. In this prospective single center study we present the histopathological examination of 37 patients who died with complications of Covid-19.\n\nMethodsThis was an observational study conducted in the Intensive Care Unit of JPN Trauma Centre AIIMS. A total of 37 patients who died of Covid-19 were enrolled in the study. Post-mortem percutaneous biopsies were taken by the help of surface landmarking/ultrasonography guidance from lung, heart, liver, and kidneys; after obtaining ethical consent. The biopsy samples were then stained with haematoxylin and eosin stain. Immunohistochemistry (IHC) was performed using CD61 and CD163 in all lung cores. SARS-CoV-2 virus was detected using IHC with primary antibodies in selected samples. Details regarding demographics, clinical parameters, hospital course, treatment details, and laboratory investigations were also collected for clinical correlation.\n\nResultsA total of 37 patients underwent post-mortem minimally invasive tissue sampling. Mean age of the patients was 48.7years and 59.5% of them were males. Respiratory failure was the most common complication seen in 97.3%. Lung histopathology showed acute lung injury and diffuse alveolar damage in 78% patients. Associated bronchopneumonia was seen in 37.5% patients and scattered microthrombi were visualised in 21% patients. Immunostaining with CD61 and CD163 highlighted megakaryocytes, and increased macrophages in all samples. Immunopositivity for SARS-CoV-2 was observed in Type II pneumocytes. Acute tubular injury with epithelial vacuolization was seen in 46% of the renal biopsies but none of them showed evidence of microvascular thrombosis. 71% of the liver tissue cores showed evidence of Kupfer cell hyperplasia. 27.5% had evidence of submassive hepatic necrosis and 14% had features of acute on chronic liver failure. All the heart biopsies showed non-specific features such as hypertrophy with nucleomegaly with no evidence of myocardial necrosis in any of the samples.\n\nConclusionsThe most common finding in this cohort is the diffuse alveolar damage with demonstration of SARS-CoV-2 protein in the acute phase of DAD. Microvascular thrombi were rarely identified in the lung, liver and kidney. Substantial hepatocyte necrosis, hepatocyte degeneration, Kupffer cell hypertrophy, micro, and macrovesicular steatosis unrelated to microvascular thrombi suggests that liver might be a primary target of Covid-19. This study highlights the importance of MITS/B in better understanding the pathological changes associated with Covid-19.", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Animesh Ray", + "author_inst": "All india institute medical sciences, New Delhi" + }, + { + "author_name": "Deepali Jain", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Shubham Agarwal", + "author_inst": "All india institute of medical sciences, New Delhi" + }, + { + "author_name": "Shekhar Swaroop", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Ayush Goel", + "author_inst": "All india Institute of medical sciences, new delhi" + }, + { + "author_name": "Prasenjit Das", + "author_inst": "All india Institute of medical sciences, New Delhi" + }, + { + "author_name": "Sudheer Kumar Arava", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Asit Ranjan Mridha", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Aruna Nambirajan", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Geetika Singh", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "S Arulselvi", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Purva Mathur", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Sanchit Kumar", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Shubham Sahni", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Jagbir Nehra", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Nazneen", + "author_inst": "All India Institute of medical sciences, New Delhi" + }, + { + "author_name": "Mouna BM", + "author_inst": "All India Institute of Medical sciences, New Delhi" + }, + { + "author_name": "Neha Rastogi", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Sandeep Mahato", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Chhavi Gupta", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "S Bharadhan", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Gaurav Dhital", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Pawan Goel", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Praful Pandey", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Santosh KN", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Shitij Chaudhary", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Vishakh C Keri", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Vishal Singh Chauhan", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Niranjan Mahishi", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Anand Shahi", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Ragu R", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Baidhnath Gupta", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Richa Aggarwal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Kapil Dev Soni", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Neeraj Nischal", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Manish Soneja", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Sanjeev Lalwani", + "author_inst": "All India institute of medical sciences, New delhi" + }, + { + "author_name": "Chitra Sarkar", + "author_inst": "All India institute of medical sciences, new Delhi" + }, + { + "author_name": "Randeep Guleria", + "author_inst": "All India institute of medical sciences, new delhi" + }, + { + "author_name": "Naveet Wig", + "author_inst": "All India institute of medical sciences, New Delhi" + }, + { + "author_name": "Anjan Trikha", + "author_inst": "All India institute of medical sciences, New Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.11.13.20231159", "rel_title": "Assessment of the Impacts of Pharmaceutical and Non-pharmaceutical Intervention on COVID-19 in South Africa Using Mathematical Model", @@ -1055181,49 +1051975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.11.13.20231555", - "rel_title": "Developing services for long Covid: lessons from a study of wounded healers", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231555", - "rel_abs": "Persistent symptoms lasting longer than 3 weeks are thought to affect 10-20% of patients following Covid 19 infection. No formal guidelines exist in the United Kingdom for treating long Covid patients and services are sporadic and variable, although additional funding is promised for their development.\n\nIn this study narrative interviews and focus groups are used to explore the lived experience of 43 healthcare professionals with long Covid. These individuals see the healthcare system from both professional and patient perspectives thus represent an important wealth of expertise to inform service design.\n\nWe present a set of co-designed quality standards highlighting equity and ease of access, minimal patient care burden, clinical responsibility, a multidisciplinary and evidence-based approach, and patient involvement and apply these to propose a potential care pathway model that could be adapted and translated to improve care of long Covid patients.\n\nSummary boxO_ST_ABSWhat is known?C_ST_ABS{blacksquare} Persistent symptoms (\"long Covid\") occur after Covid-19 in 10-20% of sufferers\n{blacksquare}Services to manage and rehabilitate patients with long Covid are not yet optimal\n{blacksquare}UK healthcare workers experience at least a threefold greater risk of Covid-19 infection and face significant occupational exposure\n{blacksquare}Healthcare workers with long Covid can offer important insights into service design and development\n\n\nWhat is the question?{blacksquare} What are the experiences of healthcare workers with long Covid and what are the implications from these for service development?\n\n\nWhat was found{blacksquare} Healthcare workers experienced a confusing novel condition that imposed high levels of uncertainty and a significant personal and professional impact.\n{blacksquare}Using professional contacts, patient- and professional Mindlines, support groups and Communities of Practice all helped to minimize this uncertainty and high quality therapeutic relationships were essential to cope with it.\n{blacksquare}Many experienced a lack of compassion during interactions with the healthcare system and were frustrated by challenges accessing, or absence of, appropriate services.\n{blacksquare}Suggestions for improvement included an integrated, multi-disciplinary assessment and rehabilitation service; a set of clinical quality standards; and co-created research and service development.\n\n\nWhat is the implication for practice now?{blacksquare} This study supports and extends the principles outlined in recently-developed NHS long Covid quality standards and will inform and support design of dedicated long Covid services.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Emma Ladds", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander Rushforth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sietse Wieringsa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sharon Taylor", - "author_inst": "Central and North West London NHS Foundation Trust and Division of Psychiatry Imperial College London, United Kingdom" - }, - { - "author_name": "Clare Rayner", - "author_inst": "Independent Occupational Physician, Manchester" - }, - { - "author_name": "Laiba Husain", - "author_inst": "University of Oxford" - }, - { - "author_name": "Trish Greenhalgh", - "author_inst": "University of Oxford, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.11.14.20231704", "rel_title": "Impact of the COVID-19 pandemic on Older Adults Mental Health Services: a mixed methods study", @@ -1055776,6 +1052527,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.13.20231209", + "rel_title": "Severe COVID-19 Is Fueled by Disrupted Gut Barrier Integrity", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231209", + "rel_abs": "A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Leila B Giron", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Harsh Dweep", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Xiangfan Yin", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Han Wang", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Mohammad Damra", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Aaron R Goldman", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Nicole Gorman", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Clovis S Palmer", + "author_inst": "The Burnet Institute" + }, + { + "author_name": "Hsin-Yao Tang", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Maliha W Shaikh", + "author_inst": "Rush University" + }, + { + "author_name": "Christopher B Forsyth", + "author_inst": "Rush University" + }, + { + "author_name": "Robert A Balk", + "author_inst": "Rush University" + }, + { + "author_name": "Netanel F Zilberstein", + "author_inst": "Rush University" + }, + { + "author_name": "Qin Liu", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Andrew Kossenkov", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Ali Keshavarzian", + "author_inst": "Rush University" + }, + { + "author_name": "Alan Landay", + "author_inst": "Rush University" + }, + { + "author_name": "Mohamed Abdel-Mohsen", + "author_inst": "The Wistar Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.15.20231993", "rel_title": "High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity", @@ -1056755,65 +1053593,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.14.383026", - "rel_title": "Effects of inactivation method on SARS-CoV-2 virion proteins and structure", - "rel_date": "2020-11-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.14.383026", - "rel_abs": "The risk posed by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) dictates that live-virus research is conducted in a biosafety level 3 (BSL3) facility. Working with SARS-CoV-2 at lower biosafety levels can expedite research yet requires the virus to be fully inactivated. In this study, we validated and compared two protocols for inactivating SARS-CoV-2: heat treatment and ultraviolet irradiation. The two methods were optimized to render the virus completely incapable of infection while limiting destructive effects of inactivation. We observed that 15 minutes of incubation at 65{degrees}C completely inactivates high titer viral stocks. Complete inactivation was also achieved with minimal amounts of UV power (70,000 J/cm2), which is 100-fold less power than comparable studies. Once validated, the two methods were then compared for viral RNA quantification, virion purification, and antibody recognition. We observed that UV irradiation resulted in a 2-log reduction of detectable genomes compared to heat inactivation. Protein yield following virion enrichment was equivalent for all inactivation conditions, but the resulting viral proteins and virions were negatively impacted by inactivation method and time. We outline the strengths and weaknesses of each method so that investigators might choose the one which best meets their research goals.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Emma K. Loveday", - "author_inst": "Montana State University" - }, - { - "author_name": "Kyle S. Hain", - "author_inst": "Montana State University" - }, - { - "author_name": "Irina Kochetkova", - "author_inst": "Montana State University" - }, - { - "author_name": "Jodi F. Hedges", - "author_inst": "Montana State University" - }, - { - "author_name": "Amanda Robison", - "author_inst": "Montana State University" - }, - { - "author_name": "Deann T. Snyder", - "author_inst": "Montana State University" - }, - { - "author_name": "Susan K. Brumfield", - "author_inst": "Montana State University" - }, - { - "author_name": "Mark J. Young", - "author_inst": "Montana State University" - }, - { - "author_name": "Mark A. Jutila", - "author_inst": "Montana State University" - }, - { - "author_name": "Connie B. Chang", - "author_inst": "Montana State University" - }, - { - "author_name": "Matthew P. Taylor", - "author_inst": "Montana State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.15.383463", "rel_title": "SARS-CoV-2-specific T cell memory is long-lasting in the majority of convalsecent COVID-19 individuals", @@ -1057394,6 +1054173,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.12.20230508", + "rel_title": "Asymptomatic and symptomatic SARS-CoV-2 infections elicit polyfunctional antibodies.", + "rel_date": "2020-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230508", + "rel_abs": "A large proportion of SARS-CoV-2 infected individuals remains asymptomatic. Little is known about the extent and quality of their antiviral humoral response. Here, we analyzed antibody functions in 52 asymptomatic infected individuals, 119 mild and 21 hospitalized COVID-19 patients. We measured anti-Spike antibody levels with the S-Flow assay and mapped SARS-CoV-2 Spike- and N-targeted regions by Luminex. Neutralization, complement deposition and Antibody-Dependent Cellular Cytotoxicity (ADCC) were evaluated using replication-competent SARS-CoV-2 or reporter cell systems. We show that COVID-19 sera mediate complement deposition and kill infected cells by ADCC. Sera from asymptomatic individuals neutralize the virus, activate ADCC and trigger complement deposition. Antibody levels and activities are slightly lower in asymptomatic individuals. The different functions of the antibodies are correlated, independently of disease severity. Longitudinal samplings show that antibody functions follow similar kinetics of induction and contraction, with minor variations. Overall, asymptomatic SARS-CoV-2 infection elicits polyfunctional antibodies neutralizing the virus and targeting infected cells.\n\n- Sera from convalescent COVID-19 patients activate the complement and kill infected cells by ADCC.\n- Asymptomatic and symptomatic SARS-CoV-2-infected individuals harbor polyfunctional antibodies.\n- Antibody levels and functions are slightly lower in asymptomatic individuals\n- The different antiviral activities of anti-Spike antibodies are correlated regardless of disease severity.\n- Functions of anti-Spike antibodies have similar kinetics of induction and contraction.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "J\u00e9r\u00e9my Dufloo", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Yoann Madec", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laura Tondeur", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francois Anna", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "St\u00e9phane Pelleau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Aurelie Wiedemann", + "author_inst": "Vaccine research Institute" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "R\u00e9my Robinot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marie-No\u00eblle Ungeheuer", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pierre Charneau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Michael White", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Yves L\u00e9vy", + "author_inst": "Vaccine Research Institute" + }, + { + "author_name": "Bruno Hoen", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Arnaud Fontanet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timoth\u00e9e Bruel", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.11.20229765", "rel_title": "SARS-CoV-2: Proof of recombination between strains and emergence of possibly more virulent ones", @@ -1058729,89 +1055603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.13.20231076", - "rel_title": "SARS-CoV-2 serological tests can generate false positive results for samples from patients with chronic inflammatory diseases", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231076", - "rel_abs": "ObjectivesPatients with chronic inflammatory diseases are often treated with immunosuppressants and therefore are of particular concern during the SARS-CoV-2 pandemic. Serological tests will improve our understanding of the infection and immunity in this population, unless the tests give false positive results. The aim of this study was to evaluate the specificity of SARS-Cov-2 serological assays with samples from patients with chronic inflammatory diseases collected before April 2019, thus defined as negative.\n\nMethodsSamples from patients with multiple sclerosis (MS, n=10), rheumatoid arthritis (RA, n=47) with or without rheumatoid factor (RF) and/or anti-cyclic citrullinated peptide antibodies (anti-CCP2) and RF +/- systemic lupus erythematosus (SLE, n=10), were tested with 17 commercially available lateral flow assays (LFA), two ELISA kits and one in-house developed multiplex bead-based assay.\n\nResultsSix LFA and the in-house IgG assay gave the correct negative results for all samples. However, the majority of assays (n=13), gave false positive signal with samples from patients with RA and SLE. This was most notable in RF positive RA samples. MS samples did not give any false positive in any of the assays.\n\nConclusionThe majority of the verified serological assays were sensitive to interfering antibodies in samples from patients with chronic inflammatory diseases and therefore may have poor specificity in this context. For these patients, the risk of false positivity should be considered when interpreting results of the SARS-CoV-2 serological assays.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nastya Kharlamova", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Nicky Dunn", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Sahl K Bedri", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Svante Jerling", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Malin Almgren", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Francesca Faustini", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Iva Gunnarsson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Johan Ronnelid", - "author_inst": "Uppsala University" - }, - { - "author_name": "Rille Pullerits", - "author_inst": "Sahlgrenska University Hospital" - }, - { - "author_name": "Inger Gjertsson", - "author_inst": "Sahlgrenska University Hospital" - }, - { - "author_name": "Karin Lundberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anna Manberg", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab" - }, - { - "author_name": "Elisa Pin", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab" - }, - { - "author_name": "Peter Nilsson", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab" - }, - { - "author_name": "Sophia Hober", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab" - }, - { - "author_name": "Katharina Fink", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anna Fogdell-Hahn", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.12.20230748", "rel_title": "Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis", @@ -1059344,6 +1056135,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.12.20230292", + "rel_title": "Comparison of seven commercial SARS-CoV-2 rapid Point-of-Care Antigen tests", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230292", + "rel_abs": "BackgroundAntigen point of care tests (AgPOCT) can accelerate SARS-CoV-2 testing. As first AgPOCT are becoming available, there is a growing interest in their utility and performance.\n\nMethodsHere we compare AgPOCT products by seven suppliers: the Abbott Panbio COVID-19 Ag Rapid Test; the RapiGEN BIOCREDIT COVID-19 Ag; the Healgen(R) Coronavirus Ag Rapid Test Cassette (Swab); the Coris Bioconcept Covid.19 Ag Respi-Strip; the R-Biopharm RIDA(R)QUICK SARS-CoV-2 Antigen; the NAL von minden NADAL COVID19-Ag Test; and the Roche/SD Biosensor SARS-CoV Rapid Antigen Test. Tests were evaluated on recombinant nucleoprotein, cultured endemic and emerging coronaviruses, stored clinical samples with known SARS-CoV-2 viral loads (n=138), stored samples from patients with respiratory agents other than SARS-CoV-2 (n=100), as well as self-sampled swabs from healthy volunteers (n=35).\n\nFindingsLimits of detection in six of seven tested products ranged between 2.08 x 106 and 2.88 x 107 copies per swab, the outlier at 1.58 x 1010 copies per swab. Specificities ranged between 98.53% and 100% in five products, with two outliers at 94.85% and 88.24%. False positive results were not associated with any specific respiratory agent. As some of the tested AgPOCT were early production lots, the observed issues with specificity are unlikely to persist.\n\nInterpretationThe sensitivity range of most AgPOCT overlaps with viral load figures typically observed during the first week of symptoms, which marks the infectious period in the majority patients. AgPOCTs with a limit of detection that approximates the virus concentration above which patients are infectious may enable shortcuts in decision-making in various areas of healthcare and public health.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Victor M Corman", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Verena C Haage", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Tobias Bleicker", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Marie Luisa Schmidt", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Barbara Muehlemann", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Marta Zuchowski", + "author_inst": "Labor Berlin GmbH" + }, + { + "author_name": "Wendy Karen Jo Lei", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Patricia Tscheak", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Elisabet Moencke-Buchner", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Marcel A Mueller", + "author_inst": "Charite Universitaetsmedizin" + }, + { + "author_name": "Andi Krumbholz", + "author_inst": "Christian-Albrecht University and University Medical Center Schleswig-Holstein" + }, + { + "author_name": "Jan Felix Drexler", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Charite Universitaetsmedizin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.13.381343", "rel_title": "ILRUN downregulates ACE2 expression and blocks infection of human cells by SARS-CoV-2", @@ -1060259,33 +1057117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.11.11.20229740", - "rel_title": "Impact of COVID-19 on the outreach strategy of cancer social service agencies in Singapore: A pre-post analysis with Facebook data", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229740", - "rel_abs": "The Singapore government implemented multiple restrictive measures as the novel coronavirus infection (COVID-19) spread through the community, thereby affecting the support service of cancer-related social service agencies (cancer-SSAs). We are interested to understand how Singapores cancer-SSAs utilized the social media platform Facebook to overcome the restrictions which were introduced due to COVID-19. Facebook posts from cancer-SSAs 365 Cancer Prevention Society (365CPS) and Singapore Cancer Society (SCS) between comparable periods in 2019 and 2020 were extracted. These posts were categorized using a classification scheme specifically developed for this study. Statistical analyses were performed to determine if there was a significant difference in the frequency of posts between 2019 and 2020, and across three specific periods in 2020. Results indicate that 365CPS appears to have adapted to the pandemic by increasing their posting frequency on Facebook in 2020, but the same was not evident for SCS. However, both SSAs tweaked their social media outreach strategy in line with social distancing measures, publishing posts detailing activities that beneficiaries can participate from home such as healthy recipes and virtual events. SSAs can scale up their efforts to achieve a higher level of health promotion and support for their beneficiaries.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kieran Ethan Tan", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Aravind Sesagiri Raamkumar", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Hwee Lin Wee", - "author_inst": "National University of Singapore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.11.11.20229526", "rel_title": "Universal Health Coverage and COVID-19 Pandemic: A Bangladesh Perspective", @@ -1061170,6 +1058001,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.11.10.20229237", + "rel_title": "Non-COVID-19 patients in times of pandemic: decreased emergency department visits and increased out-of-hospital mortality in Northern Italy", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229237", + "rel_abs": "ObjectiveThe aim of this was to assess the short-term impact of the pandemic on non-COVID-19 patients living in a one-million inhabitants area in Northern Italy (Bologna Metropolitan Area-BMA), analyzing time trends of Emergency Department (ED) visits, hospitalizations and mortality.\n\nMethodsWe conducted a retrospective observational study using data extracted from BMA healthcare informative systems. Weekly trends of ED visits, hospitalizations, in- and out-of-hospital, all-cause and cause-specific mortality between December 1st, 2019 to May 31st, 2020, were compared with those of the same period of the previous year, using Joinpoint regression models and incidence rate ratios.\n\nResultsNon-COVID-19 ED visits and hospitalizations showed a stable trend until the first Italian case of COVID-19 has been recorded, on February 19th, 2020, when they dropped simultaneously. The reduction of ED visits was observed in all age groups and across all severity and diagnosis groups. In the lockdown period a significant increase was found in overall out-of-hospital mortality (43.2%) and cause-specific out-of-hospital mortality related to neoplasms (76.7%), endocrine, nutritional and metabolic (79.5%) as well as cardiovascular (32.7%) diseases.\n\nConclusionsThe pandemic caused a sudden drop of ED visits and hospitalizations of non-COVID-19 patients during the lockdown period, and a concurrent increase in out-of-hospital mortality mainly driven by deaths for neoplasms, cardiovascular and endocrine diseases. The findings of this study might be useful to understand both the population reaction and the healthcare system response at the early phases of the pandemic in terms of reduced demand of care and systems capability in intercepting it.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Luca Santi", + "author_inst": "Policlinico S. Orsola Malpighi. Dipartimento dell Emergenza Urgenza. Unita operativa di Medicina d urgenza e Pronto Soccorso. Via Giuseppe Massarenti, 9, 40138," + }, + { + "author_name": "Davide Golinelli", + "author_inst": "University of Bologna" + }, + { + "author_name": "Andrea Tampieri", + "author_inst": "Ospedale S. Maria della Scaletta. Dipartimento di Emergenza urgenza e Accettazione. Unita Operativa di Pronto Soccorso e Medicina d Urgenza. Viale Amendola, 2, " + }, + { + "author_name": "Gabriele Farina", + "author_inst": "Policlinico S. Orsola-Malpighi. Dipartimento dell Emergenza Urgenza. Unita operativa di Medicina d urgenza e Pronto Soccorso. Via Giuseppe Massarenti, 9, 40138," + }, + { + "author_name": "Manfredi Greco", + "author_inst": "Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum University of Bologna. Via San Giacomo 12, 40126, Bologna, Italy." + }, + { + "author_name": "Simona Rosa", + "author_inst": "Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum. University of Bologna. Via San Giacomo 12, 40126, Bologna, Italy." + }, + { + "author_name": "Michelle Beleffi", + "author_inst": "Alma Mater Studiorum. University of Bologna. Via Zamboni, 33, 40126 Bologna, Italy." + }, + { + "author_name": "Bianca Biavati", + "author_inst": "Alma Mater Studiorum, University of Bologna. Via Zamboni, 33, 40126 Bologna, Italy." + }, + { + "author_name": "Francesca Campinoti", + "author_inst": "Alma Mater Studiorum, University of Bologna. Via Zamboni, 33, 40126 Bologna, Italy." + }, + { + "author_name": "Stefania Guerrini", + "author_inst": "Policlinico S. Orsola Malpighi. Dipartimento dell Emergenza Urgenza. Unita operativa di Medicina d urgenza e Pronto Soccorso. Via Giuseppe Massarenti, 9, 40138," + }, + { + "author_name": "Rodolfo Ferrari", + "author_inst": "Ospedale S. Maria della Scaletta. Dipartimento di Emergenza urgenza e Accettazione. Unita Operativa di Pronto Soccorso e Medicina d Urgenza. Viale Amendola, 2, " + }, + { + "author_name": "Paola Rucci", + "author_inst": "Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum, University of Bologna. Via San Giacomo 12, 40126, Bologna, Italy." + }, + { + "author_name": "Maria Pia Fantini", + "author_inst": "Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum, University of Bologna. Via San Giacomo 12, 40126, Bologna, Italy." + }, + { + "author_name": "Fabrizio Giostra", + "author_inst": "Policlinico S. Orsola-Malpighi. Dipartimento dell Emergenza Urgenza. Unita operativa di Medicina d urgenza e Pronto Soccorso. Via Giuseppe Massarenti, 9, 40138," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.11.10.20227710", "rel_title": "A room, a bar and a classroom: how the coronavirus is spread through the air depends on heavily mask filtration efficiency", @@ -1062061,137 +1058963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.08.20227876", - "rel_title": "Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227876", - "rel_abs": "BackgroundSafe and effective therapies for COVID-19 are urgently needed. In order to meet this need, the Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) public-private partnership initiated the Therapeutics for Inpatients with COVID-19 (TICO). TICO is a multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of novel candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. Four agents have so far entered the protocol, with rapid answers already provided for three of these. Other agents are expected to enter the protocol throughout 2021. This protocol contains a number of key design and implementation features that, along with challenges faced by the protocol team, are presented and discussed.\n\nProtocol Design and ImplementationThree clinical trial networks, encompassing a global network of clinical sites, participated in the protocol development and implementation. TICO utilizes a MAMS design with an agile and robust approach to futility and safety evaluation at 300 patients enrolled, with subsequent expansion to full sample size and an expanded target population if the agent shows an acceptable safety profile and evidence of efficacy. Rapid recruitment to multiple agents is enabled through the sharing of placebo as well as the confining of agent-specific information to protocol appendices, and modular consent forms. In collaboration with the Food and Drug Administration, a thorough safety data collection and DSMB schedule was developed for the study of agents with limited in-human data.\n\nChallengesChallenges included ensuring drug supply and reliable recruitment allowing for changing infection rates across the global network of sites, the need to balance the collection of data and samples without overburdening clinical staff, and obtaining regulatory approvals across a global network of sites.\n\nConclusionThrough a robust multi-network partnership, the TICO protocol has been successfully used across a global network of sites for rapid generation of efficacy data on multiple novel antiviral agents. The protocol design and implementation features used in this protocol, and the approaches to address challenges, will have broader applicability. Mechanisms to facilitate improved communication and harmonization among country-specific regulatory bodies are required.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Daniel D Murray", - "author_inst": "CHIP Centre of Excellence for Health, Immunity, and Infections, Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark" - }, - { - "author_name": "Abdel G Babiker", - "author_inst": "Medical Research Council Clinical Trials Unit at UCL, University College London, London, UK" - }, - { - "author_name": "Jason V Baker", - "author_inst": "Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA and University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Christina E Barkauskas", - "author_inst": "Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA." - }, - { - "author_name": "Samuel M Brown", - "author_inst": "Intermountain Medical Center, Murray, UT, USA and University of Utah School of Medicine, Salt Lake City, UT, USA" - }, - { - "author_name": "Christina Chang", - "author_inst": "The Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Victoria J Davey", - "author_inst": "U.S. Department of Veterans Affairs, Washington, D.C., USA" - }, - { - "author_name": "Annetine C Gelijns", - "author_inst": "Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Adit A Ginde", - "author_inst": "Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, CO, USA" - }, - { - "author_name": "Birgit Grund", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Elizabeth Higgs", - "author_inst": "National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA" - }, - { - "author_name": "Fleur Hudson", - "author_inst": "MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London" - }, - { - "author_name": "Virginia K Kan", - "author_inst": "Veteran Affairs Medical Center, Washington, D.C., USA and George Washington University School of Medicine and Health Sciences, Washington, D.C., USA" - }, - { - "author_name": "H Clifford Lane", - "author_inst": "National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA" - }, - { - "author_name": "Thomas A Murray", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Roger Paredes", - "author_inst": "Infectious Diseases Department & irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Catalonia, Spain" - }, - { - "author_name": "Mahesh K.B. Parmar", - "author_inst": "MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London" - }, - { - "author_name": "Sarah Pett", - "author_inst": "Medical Research Council Clinical Trials Unit at UCL, University College London, London, UK" - }, - { - "author_name": "Andrew N Phillips", - "author_inst": "Institute for Global Health, University College London, London, UK" - }, - { - "author_name": "Mark N Polizzotto", - "author_inst": "The Kirby Institute, University of New South Wales, Sydney, Australia and St Vincents Hospital, Sydney, Australia" - }, - { - "author_name": "Cavan Reilly", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Uriel Sandkovsky", - "author_inst": "Division of Infectious Diseases, Baylor University Medical Center, Dallas, TX, USA" - }, - { - "author_name": "Shweta Sharma", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Marc Teitelbaum", - "author_inst": "Leidos Biomedical Research, Inc., Frederick, MD, USA" - }, - { - "author_name": "B. Taylor Thompson", - "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA and Harvard Medical School Boston, MA, USA" - }, - { - "author_name": "Barnaby E Young", - "author_inst": "National Centre for Infectious Diseases, Singapore, Singapore and Tan Tock Seng Hospital, Singapore, Singapore and Lee Kong Chian School of Medicine, Nanyang Te" - }, - { - "author_name": "James D Neaton", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA" - }, - { - "author_name": "Jens D Lundgren", - "author_inst": "CHIP Centre of Excellence for Health, Immunity, and Infections, Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark" - }, - { - "author_name": "- TICO study group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.11.20230045", "rel_title": "Impacts of the COVID-19 Pandemic on Cardiac Rehabilitation Delivery around the World", @@ -1062872,6 +1059643,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.11.20229914", + "rel_title": "Comparative analysis of point-of-care lateral flow immunoassays for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in healthcare workers", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229914", + "rel_abs": "Since the Coronavirus Disease 2019 (COVID-19) pandemic, Brazil has the third-highest number of confirmed cases and the second-highest number of recovered patients. SARS-CoV-2 detection by real-time RT-PCR is the gold standard but requires a certified laboratory infrastructure with high-cost equipment and trained personnel. However, for large-scale testing, diagnostics should be fast, cost-effective, widely available, and deployed for the community, such as serological tests based on lateral flow immunoassay (LFIA) for IgM/IgG detection. We evaluated three different commercial point-of-care (POC) LFIAs for anti-SARS-CoV-2 IgM and IgG detection in capillary whole blood of 100 healthcare workers (HCW) from Sao Paulo university hospital previously tested by RT-PCR: 1) COVID-19 IgG/IgM BIO (Bioclin, Brazil), 2) Diagnostic kit for IgM/IgG Antibody to Coronavirus (SARS-CoV-2) (Livzon, China); and 3) SARS-CoV-2 Antibody Test (Wondfo, China). A total of 84 positives and 16 negatives HCW were tested. The data was also analyzed by the number of days post symptoms (DPS) in three groups: <30 (n=26), 30-59 (n=42), and >59 (n=16). The observed sensibility was 85.71%, 47.62%, and 44.05% for Bioclin, Wondfo, and Livzon, respectively, with a specificity of 100% for all LFIA. Bioclin was more sensitive (p<0.01), regardless of the DPS. Thus, the Bioclin may be used as a POC test to monitor SARS-CoV-2 seroconversion in HCW.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Danielle Dias Danielle Dias Conte", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Joseane M. A. Carvalho", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Luciano Kleber de Souza Luna", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Klinger Soares Faico-Filho", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Ana Helena Perosa", + "author_inst": "Universidade Federal de Sao Paulo, Hospital Sao Paulo" + }, + { + "author_name": "Nancy C. J. Bellei", + "author_inst": "Universidade Federal de Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.09.20228437", "rel_title": "Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples", @@ -1064215,29 +1061025,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.11.12.344424", - "rel_title": "Molecular Mimicry Map (3M) of SARS-CoV-2: Prediction of potentially immunopathogenic SARS-CoV-2 epitopes via a novel immunoinformatic approach", - "rel_date": "2020-11-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.12.344424", - "rel_abs": "Currently, more than 33 million peoples have been infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more than a million people died from coronavirus disease 2019 (COVID-19), a disease caused by the virus. There have been multiple reports of autoimmune and inflammatory diseases following SARS-CoV-2 infections. There are several suggested mechanisms involved in the development of autoimmune diseases, including cross-reactivity (molecular mimicry). A typical workflow for discovering cross-reactive epitopes (mimotopes) starts with a sequence similarity search between protein sequences of human and a pathogen. However, sequence similarity information alone is not enough to predict cross-reactivity between proteins since proteins can share highly similar conformational epitopes whose amino acid residues are situated far apart in the linear protein sequences. Therefore, we used a hidden Markov model-based tool to identify distant viral homologs of human proteins. Also, we utilized experimentally determined and modeled protein structures of SARS-CoV-2 and human proteins to find homologous protein structures between them. Next, we predicted binding affinity (IC50) of potentially cross-reactive T-cell epitopes to 34 MHC allelic variants that have been associated with autoimmune diseases using multiple prediction algorithms. Overall, from 8,138 SARS-CoV-2 genomes, we identified 3,238 potentially cross-reactive B-cell epitopes covering six human proteins and 1,224 potentially cross-reactive T-cell epitopes covering 285 human proteins. To visualize the predicted cross-reactive T-cell and B-cell epitopes, we developed a web-based application \"Molecular Mimicry Map (3M) of SARS-CoV-2\" (available at https://ahs2202.github.io/3M/). The web application enables researchers to explore potential cross-reactive SARS-CoV-2 epitopes alongside custom peptide vaccines, allowing researchers to identify potentially suboptimal peptide vaccine candidates or less ideal part of a whole virus vaccine to design a safer vaccine for people with genetic and environmental predispositions to autoimmune diseases. Together, the computational resources and the interactive web application provide a foundation for the investigation of molecular mimicry in the pathogenesis of autoimmune disease following COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hyunsu An", - "author_inst": "Gwangju Institute of Science and Technology" - }, - { - "author_name": "Jihwan Park", - "author_inst": "Gwangju Institute of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.11.12.379958", "rel_title": "Combined in silico docking and in vitro antiviral testing for drug repurposing identified lurasidone and elbasvir as SARS-CoV-2 and HCoV-OC43 inhibitors", @@ -1065378,6 +1062165,37 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.11.11.377713", + "rel_title": "In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human", + "rel_date": "2020-11-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.11.377713", + "rel_abs": "The worldwide outbreak of COVID-19 pandemic caused by SARS-CoV-2 leads to loss of mankind and global economic stability. The continuous spreading of the disease and its pathogenesis takes millions of lives of peoples and the unavailability of appropriate therapeutic strategy makes it much more severe. Toll-like receptors (TLRs) are the crucial mediators and regulators of host immunity. The role of several TLRs in immunomodulation of host by SARS-CoV-2 is recently demonstrated. However, the functionality of human intracellular TLRs including TLR3,7,8 and 9 is still being untested for sensing of viral RNA. This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Abhigyan Choudhury", + "author_inst": "Kazi Nazrul University, Asansol" + }, + { + "author_name": "Nabarun Chandra Das", + "author_inst": "Kazi Nazrul University, Asansol" + }, + { + "author_name": "Ritwik Patra", + "author_inst": "Kazi Nazrul University, Asansol" + }, + { + "author_name": "Suprabhat Mukherjee", + "author_inst": "Kazi Nazrul University, Asansol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "confirmatory results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.11.10.377606", "rel_title": "Recombinant ACE2 Expression is Required for SARS-CoV-2 to Infect Primary Human Endothelial Cells and Induce Inflammatory and Procoagulative Responses", @@ -1066285,25 +1063103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.07.20227603", - "rel_title": "COVID-19 case management: The policy model in Morocco context", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227603", - "rel_abs": "BackgroundBased on the updated scientific evidence around SARS-CoV-2 diagnostic, health policymakers had to consider that many decisions could enhance or limit the success of the overall COVID-19 control strategy. The purpose of this study is to share alternative COVID-19 case management based on the updated international knowledge.\n\nMethodsThis study presents the main information about COVID-19 case management in Morocco from March to October 2020. The NVivo qualitative model content analysis was used to compare and prioritize health decisions with updated scientific evidence.\n\nResultsThe lack of molecular diagnostic accuracy using the interpretation of cycles quantification values, was targeted only by allowing all private laboratories to do RT qPCR. However, there is an urgent need for standardisation with accurate molecular SARS-CoV-2 thermocyclers and kits that notify systematic cycles quantification and do more tests per days to control the spread effectively. A predictive tree of the cycles range is presented following three steps: 1) the initial clinical definition, 2) the molecular confirmation, 3) and the diagnostic follows up results of the RT qPCR up to 28 days after the onset. At the same time, the seasonal vaccination against influenza and pneumonia could help to reduce COVID-19 deaths.\n\nConclusionsUntil an available SARS-CoV-2 specific vaccine and/or curative effective treatment, updated control strategy in Morocco and similar context countries require to target population living in highly COVID-19 epidemic cities or areas by mass testing with the right interpretation of PCR values changes, associated to seasonal vaccination to foster the immunity.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Issam Bennis", - "author_inst": "Fez Regional Directorate of Ministry of Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.11.07.20226837", "rel_title": "Evaluating the Efficacy of Tocilizumab in Moderate to Severe COVID-19 with Progressive Illness despite Steroids: Identifying the Optimal Timing of its Administration in C3G study", @@ -1067036,6 +1063835,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.07.20227447", + "rel_title": "A fair efficacy formula for assessing the effectiveness of contact tracing applications", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227447", + "rel_abs": "Mobile contact tracing apps have been developed by many countries in response to the COVID-19 pandemic. Trials have focussed on unobserved population trials or staged scenarios aimed to simulate real life. No efficacy measure has been developed that assesses the fundamental ability of any proximity detection protocol to accurately detect, measure, and therefore assess the epidemiological risk that a mobile phone owner has been placed at. This paper provides a fair efficacy formula that can be applied to any mobile contact tracing app, using any technology, allowing its likely epidemiological effectiveness to be assessed. This paper defines such a formula and provides results for several simulated protocols as well as one real life protocol tested according to the standard methodology set out in this paper. The results presented show that protocols that use time windows greater than 30 seconds or that bucket their distance analogue (E.g. RSSI for Bluetooth) provide poor estimates of risk, showing an efficacy rating of less than 6%. The fair efficacy formula is shown in this paper to be able to be used to calculate the Efficacy of contact tracing variable value as used in two papers on using mobile applications for contact tracing [6]. The output from the formulae in this paper, therefore, can be used to directly assess the impact of technology on the spread of a disease outbreak. This formula can be used by nations developing contact tracing applications to assess the efficacy of their applications. This will allow them to reassure their populations and increase the uptake of contact tracing mobile apps, hopefully having an effect on slowing the spread of COVID-19 and future epidemics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Adam Fowler", + "author_inst": "VMware, Inc." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.07.20227595", "rel_title": "Balancing quarantine and self-distancing measures in adaptive epidemic networks", @@ -1067963,49 +1064781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.11.06.20227439", - "rel_title": "Changes of Humoral Immunity Response in SARS-CoV-2 Convalescent Patients over 8 months", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227439", - "rel_abs": "Many countries around the world have all seen a sharp rise in COVID-19 cases as the second wave since the beginning of October 2020. Decline of antibodies response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) that was reported exclusively in the early month increases the risk of reinfection for convalescent individuals. There is a current need to follow the maintenance of special antibodies against SARS-CoV-2. Here, we reported changes of antibodies against SARS-CoV-2 in convalescent patients over 8 months. Antibodies of all 20 participants targeting SARS-CoV-2 spike receptor binding-domain (RBD) had decreased from a mean OD450 value 1.78 to 0.38 over 8 months. The neutralizing antibody (NAb) titers decreased from the mean ID50 value 836 to 170. The NAb titers were significantly correlated with IgG level during 8 months (P<0.001). Furthermore, while RBD-specific IgG existence of 25% (5/20) convalescent plasma was undetectable, the NAb titers of 15% (3/20) convalescent plasma decreased below the threshold. In addition, compared to wild-type SARS-CoV-2 (S-D614), lower titers of neutralizing antibodies against its G614 variant were shown at 8 months after symptom onset. This study has important implications when considering antibody protection against SARS-CoV-2 reinfection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pai Peng", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Jie Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Hai-jun Deng", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Bei-zhong Liu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ni Tang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ai-Long Huang", - "author_inst": "Chongqing Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.07.20227512", "rel_title": "Vitamin D - contrary to vitamin K - does not associate with clinical outcome in hospitalized COVID-19 patients", @@ -1068538,6 +1065313,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.09.375139", + "rel_title": "Gain-of-function assay for SARS-CoV-2 Mpro inhibition in living cells", + "rel_date": "2020-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.375139", + "rel_abs": "The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here we demonstrate a quantitative reporter for Mpro function in living cells, in which protease inhibition by genetic or chemical methods results in strong eGFP fluorescence. This robust gain-of-function system readily distinguishes between inhibitor potencies and can be scaled-up to high-throughput platforms for drug testing.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Seyed Arad Moghadasi", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Jordan T Becker", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Christopher Belica", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Chloe Wick", + "author_inst": "University of Minnesota" + }, + { + "author_name": "William L Brown", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Reuben Harris", + "author_inst": "HHMI and University of Minnesota" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.08.373738", "rel_title": "Virucidal efficacy of different formulations for hand and surface disinfection targeting SARS CoV-2", @@ -1069960,33 +1066774,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.05.20226530", - "rel_title": "Medical Capacity Shortages Facilitated the Rapid Dissemination of COVID-19 in Wuhan, New York State, and Italy", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226530", - "rel_abs": "During the coronavirus disease 2019 (COVID-19) outbreak, every public health system faced the potential challenge of medical capacity shortages. Infections without timely diagnosis or treatment may facilitate the stealth transmission and spread of the virus. Using infection and medical capacity information reported in Wuhan in China, New York State in the United States, and Italy, we developed a dynamic susceptible-exposed-infected-recovered (SEIR) model to estimate the impact of medical capacity shortages during the COVID-19 outbreak at the city, state, and country levels. After accounting for the effects of travel restrictions and control measures, we find that the number of infections in Wuhan could have been 39% lower than the actual number if the medical capacity were doubled in this city. Similarly, we find the less shortages in medical capacity in both New York state and Italy, the faster decline in the daily infection numbers and the fewer deaths. This study provides a method for estimating potential shortages and explains how they may dynamically facilitate disease spreading during future pandemics such as COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yuehao Xu", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Cheng Zhang", - "author_inst": "Fudan University" - }, - { - "author_name": "Lixian Qian", - "author_inst": "Xi'an Jiaotong-Liverpool University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.05.20226605", "rel_title": "Alzheimer's and Parkinson's diseases predict different COVID-19 outcomes, a UK Biobank study", @@ -1070663,6 +1067450,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.04.20225920", + "rel_title": "Characterising heterogeneity and sero-reversion in antibody responses to mild SARS-CoV-2 infection: a cohort study using time series analysis and mechanistic modelling", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225920", + "rel_abs": "BackgroundSARS-CoV-2 serology is used to identify prior infection at individual and at population level. Extended longitudinal studies with multi-timepoint sampling to evaluate dynamic changes in antibody levels are required to identify the time horizon in which these applications of serology are valid, and to explore the longevity of protective humoral immunity.\n\nMethodsHealth-care workers were recruited to a prospective cohort study from the first SARS-CoV-2 epidemic peak in London, undergoing weekly symptom screen, viral PCR and blood sampling over 16-21 weeks. Serological analysis (n=12,990) was performed using semi-quantitative Euroimmun IgG to viral spike S1 domain and Roche total antibody to viral nucleocapsid protein (NP) assays. Comparisons were made to previously reported pseudovirus neutralising antibody measurements.\n\nFindingsA total of 157/729 (21.5%) participants developed positive SARS-CoV-2 serology by one or other assay, of whom 31.0% were asymptomatic and there were no deaths. Peak Euroimmun anti-S1 and Roche anti-NP measurements correlated (r=0.57, p<0.0001) but only anti-S1 measurements correlated with near-contemporary pseudovirus neutralising antibody titres (measured at 16-18 weeks, r=0.57, p<0.0001). By 21 weeks follow-up, 31/143 (21.7%) anti-S1 and 6/150 (4.0%) anti-NP measurements reverted to negative. Mathematical modelling suggested faster clearance of anti-S1 compared to anti-NP (median half-life of 2.5 weeks versus 4.0 weeks), earlier transition to lower levels of antibody production (median of 8 versus 13 weeks), and greater reductions in relative antibody production rate after the transition (median of 35% versus 50%).\n\nInterpretationMild SARS-CoV-2 infection is associated with heterogenous serological responses in Euroimmun anti-S1 and Roche anti-NP assays. Anti-S1 responses showed faster rates of clearance, more rapid transition from high to low level production rate and greater reduction in production rate after this transition. The application of individual assays for diagnostic and epidemiological serology requires validation in time series analysis.\n\nFundingCharitable donations via Barts Charity\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and bioRxiv for [\"antibody\" OR \"serology\"] AND [\"SARS-CoV-2\" OR \"COVID-19\"]. The available literature highlights widespread use of serology to detect recent SARS-CoV-2 infection in individual patients and in population epidemiological surveys. Antibody to virus spike protein S1 domain is widely reported to correlate with neutralising antibody titres. The existing assays have good sensitivity to detect seroconversion within 14 days of incident infection, but the available longitudinal studies have reported variable rates of decline in antibody levels and reversion to undetectable levels in some people over 3 months. High frequency multi-time point serology data for different antibody targets or assays in longitudinal cohorts from the time of incident infection to greater than 3 months follow up are lacking.\n\nAdded value of this studyWe combine detailed longitudinal serology using the Euroimmun anti-S1 and Roche anti-nucleocapsid protein (NP) assays in 731 health care workers from the time of the first SARS-CoV-2 epidemic peak in London, UK. In 157 seroconverters (using either assay) we show substantial heterogeneity in semiquantitative antibody measurements over time between individuals and between assays. Mathematical modelling of individual participant antibody production and clearance rates in individuals with at least 8 data points over 21 weeks showed anti-S1 antibodies to have a faster clearance rate, earlier transition from the initial antibody production rate to lower rates, and greater reduction in antibody production rate after this transition, compared to anti-NP antibodies as measured by these assays. As a result, Euroimmun anti-S1 measurements peaked earlier and then reduced more rapidly than Roche anti-NP measurements. In this study, these differences led to 21% anti-S1 sero-reversion, compared to 4% anti-NP sero-reversion over 4-5 months.\n\nImplications of all of the available evidenceThe rapid decline in anti-S1 antibodies measured by the Euroimmun assay following infection limits its application for diagnostic and epidemiological screening. If generalisable, these data are consistent with the hypothesis that anti-S1 mediated humoral immunity may not be sustained in some people beyond the initial post-infective period. Further work is required to understand the mechanisms behind the heterogeneity in antibody kinetics between individuals to SARS-CoV-2. Our data point to differential mechanisms regulating humoral immunity against these two viral targets.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Charlotte Manisty", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK and Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, " + }, + { + "author_name": "Thomas A Treibel", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK and Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, U" + }, + { + "author_name": "Melanie Jensen", + "author_inst": "Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK, London, UK" + }, + { + "author_name": "Amanda Semper", + "author_inst": "National Infection Service, Public Health England, Porton Down, UK" + }, + { + "author_name": "George Joy", + "author_inst": "Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK, London, UK" + }, + { + "author_name": "Rishi K Gupta", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Maria-Teresa Cutino-Moguel", + "author_inst": "Department of Virology, Barts Health NHS Trust, London, UK" + }, + { + "author_name": "Mervyn Andiapen", + "author_inst": "Centre for Cardiovascular Medicine and Devices, William Harvey Research Institute, Queen Mary University of London, London, UK" + }, + { + "author_name": "Jessica Jones", + "author_inst": "National Infection Service, Public Health England, Porton Down, UK" + }, + { + "author_name": "Stephen Taylor", + "author_inst": "National Infection Service, Public Health England, Porton Down, UK" + }, + { + "author_name": "Ashley Otter", + "author_inst": "National Infection Service, Public Health England, Porton Down, UK" + }, + { + "author_name": "Corinna Pade", + "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK" + }, + { + "author_name": "Joseph M Gibbons", + "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute" + }, + { + "author_name": "Wing Yiu J Lee", + "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK" + }, + { + "author_name": "Meleri Jones", + "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK" + }, + { + "author_name": "Dylan M Williams", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London, London, UK and Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, " + }, + { + "author_name": "Jonathan Lambourne", + "author_inst": "Department of Infection, Barts Health NHS Trust, London, UK" + }, + { + "author_name": "Marianna Fontana", + "author_inst": "Royal Free London NHS Foundation Trust, London, UK and Division of Medicine, University College London, London, UK" + }, + { + "author_name": "- COVIDsortium Investigators", + "author_inst": "" + }, + { + "author_name": "Daniel M Altmann", + "author_inst": "Department of Immunology and Inflammation, Imperial College London, London, UK" + }, + { + "author_name": "Rosemary Boyton", + "author_inst": "Department of Immunology and Inflammation, Imperial College London, London, UK" + }, + { + "author_name": "Mala K Maini", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Aine McKnight", + "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute" + }, + { + "author_name": "Timothy Brooks", + "author_inst": "National Infection Service, Public Health England, Porton Down, UK" + }, + { + "author_name": "Benny Chain", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "James C Moon", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK and Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, U" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.04.20225474", "rel_title": "COVID-19 Demographics, Acute Care Resource Use and Mortality by Age and Sex in Ontario, Canada: Population-based Retrospective Cohort Analysis", @@ -1071686,101 +1068596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.04.20225417", - "rel_title": "Th1 Dominant Nucleocapsid and Spike Antigen-Specific CD4+ and CD8+ Memory T Cell Recall Induced by hAd5 S-Fusion + N-ETSD Infection of Autologous Dendritic Cells from Patients Previously Infected with SARS-CoV-2", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225417", - "rel_abs": "To address the need for a safe, efficacious vaccine against SARS-CoV-2 infection with the critical properties of enabling both blocking viral entry into cells and clearing virus from cells already infected, we have developed a bivalent, human adenovirus serotype 5 (hAd5) SARS-CoV- 2 S-Fusion + N-ETSD vaccine that is currently in clinical testing. This vaccine uses the next- generation hAd5 [E1-, E2b-, E3-] platform previously used successfully in cancer patients with pre-existing adenovirus immunity, engineered to express both SARS-CoV-2 spike (S) protein modified to improve the generation of neutralizing antibodies to block entry of the virus, and nucleocapsid (N) protein with an Enhanced T cell Stimulation Domain (ETSD) to activate CD4+ and CD8+ T cells to clear the virus and block replication by killing infected cells. The targeting of N to endosomes and lysosomes to enhance CD4+ and CD8+ T-cell responses distinguishes our vaccine. In our previously reported pre-clinical studies we showed that in mice, the hAd5 S-Fusion + N-ETSD vaccine elicits both humoral and T-cell responses that are robust and T helper cell 1 (Th1) dominant. Here we report that the hAd5 S-Fusion + N-ETSD vaccine is recognized by anti-sera and T cells from previously SARS-CoV-2 infected patients, and that the presence of N is vital for T-cell recall. The findings presented herein: (i) demonstrate specific recognition of hAd5 S-Fusion + N-ETSD infected cells by plasma antibodies from previously SARS-CoV-2 infected patients, but not antibodies from virus-naive subjects; (ii) show enhanced binding of plasma SARS-CoV-2 antibodies from previously infected patients to monocyte-derived dendritic cells (MoDCs) expressing the hAd5 S-Fusion + N-ETSD vaccine as compared to hAd5 S-Fusion alone; (iii) reveal N-ETSD localizes to vesicles associated with MHC class II antigen presentation, including endosomes, lysosomes and autophagosomes in MoDCs; (iv) demonstrate endosome/lysosome-targeted N-ETSD elicits higher interferon-{gamma} T-cell responses than cytoplasm-localized N; and (v) N-ETSD alone or in the hAd5 S-Fusion + N-ETSD construct induces both CD4+ and CD8+ T cell memory recall. This recognition of hAd5 S-Fusion + N-ETSD vaccine antigens by T cells from previously SARS-CoV-2 infected patients, together with the ability of this vaccine candidate to elicit de novo immune responses in naive mice suggests that it re-capitulates the natural immune response to SARS-CoV-2 to activate both B and T cells towards viral neutralization and recognition of infected cells, critical for prevention of COVID-19 disease. Intriguingly, our hAd5 S-Fusion + N-ETSD T-cell biased vaccine has the potential to not only provide protection for uninfected individuals, but also to be utilized as a therapeutic for already infected patients to induce rapid clearance of the virus by activating T cells to kill the virus-infected cells, thereby reducing viral replication and lateral transmission.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Peter Sieling", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Lise Zakin", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Annie Shin", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Brett Morimoto", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Helty Adisetiyo", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Hermes Garban", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Philip Liu", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Adrian Rice", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Justin Taft", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Roosheel Patel", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Sofija Buta", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Marta Martin-Fernandez", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Dusan Bogunovic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Elizabeth Gabitzsch", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Jeffrey T. Safrit", - "author_inst": "NantKwest Inc." - }, - { - "author_name": "Lennie Sender", - "author_inst": "NantKwest Inc." - }, - { - "author_name": "Patricia Spilman", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Shahrooz Rabizadeh", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Kayvan Niazi", - "author_inst": "ImmunityBio LLC" - }, - { - "author_name": "Patrick Soon-Shiong", - "author_inst": "NantWorks" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.11.04.20226191", "rel_title": "Wastewater Analysis of SARS-CoV-2 as a Predictive Metric of Positivity Rate for a Major Metropolis", @@ -1072413,6 +1069228,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.05.20226522", + "rel_title": "What support do frontline workers want? A qualitative study of health and social care workers experiences and views of psychosocial support during the COVID-19 pandemic.", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226522", + "rel_abs": "BackgroundThe COVID-19 pandemic has placed a significant burden on the mental health and wellbeing of frontline health and social care workers. The need to support frontline staff has been recognised. However, there is to date little research specifically on how best to support the mental health needs of frontline workers, and none on their own experiences and views about what might be most helpful.\n\nAimsWe set out to redress this research gap by qualitatively exploring UK frontline health and social care workers own experiences and views of psychosocial support during the pandemic.\n\nMethodFrontline health and social care workers were recruited purposively through social media and by snowball sampling via healthcare colleagues. Workers who volunteered to take part in the study were interviewed remotely following a semi-structured interview guide. Transcripts of the interviews were analysed by the research team following the principles of Reflexive Thematic Analysis.\n\nResultsWe conducted 25 interviews with frontline workers from a variety of professional groups working in health and social care settings across the UK. Themes derived from our analysis showed that workers experiences and views about psychosocial support were complex. Peer support was many workers first line of support but could also be experienced as a burden. Workers were ambivalent about support shown by organisations, media and the public. Whilst workers valued psychological support services, there were many disparities in provision and barriers to access.\n\nConclusionsThe results of this study show that frontline health and social care workers are likely to need a flexible system of support including peer, organisational and professional support. More research is needed to fully unpack the structural, systemic and individual barriers to accessing psychosocial support. Greater collaboration, consultation and co-production of support services and their evaluation is warranted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jo Billings", + "author_inst": "University College London" + }, + { + "author_name": "Nada Abou Seif", + "author_inst": "University College London" + }, + { + "author_name": "Siobhan Hegarty", + "author_inst": "University College London" + }, + { + "author_name": "Tamara Ondruskova", + "author_inst": "University College London" + }, + { + "author_name": "Emilia Soulios", + "author_inst": "University College London" + }, + { + "author_name": "Michael A.P. Bloomfield", + "author_inst": "University College London" + }, + { + "author_name": "Talya Greene", + "author_inst": "University of Haifa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.05.20216606", "rel_title": "Community health worker knowledge, attitudes and practices towards COVID-19: learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique", @@ -1073716,20 +1070574,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.04.368092", - "rel_title": "High-level expression of the monomeric SARS-CoV-2 S-protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector.", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.368092", - "rel_abs": "The spike (S) protein is one of the three proteins forming the coronaviruses viral envelope. The S protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has a spatial structure similar to the S proteins of other mammalian coronaviruses, except for a unique receptor-binding domain (RBD), which is a significant inducer of host immune response. Recombinant SARS-CoV-2 RBD is widely used as a highly specific minimal antigen for serological tests. Correct exposure of antigenic determinants has a significant impact on the accuracy of such tests - the antigen has to be correctly folded, contain no potentially antigenic non-vertebrate glycans, and, preferably, should have a glycosylation pattern similar to the native S protein. Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. RBDv1 contained a native viral signal peptide, RBDv2 - human tPA signal peptide. We transfected a CHO DG44 cell line, selected stably transfected cells, and performed a few rounds of methotrexate-driven amplification of the genetic cassette in the genome. For the RBDv2 variant, a high-yield clonal producer cell line was obtained. We developed a simple purification scheme that consistently yielded up to 30 mg of RBD protein per liter of the simple shake flask cell culture. Purified proteins were analyzed by polyacrylamide gel electrophoresis in reducing and non-reducing conditions and gel filtration; for RBDv2 protein, the monomeric form content exceeded 90% for several series. Deglycosylation with PNGase F and mass spectrometry confirmed the presence of N-glycosylation. The antigen produced by the described technique is suitable for serological tests and similar applications.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.11.04.368449", "rel_title": "Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes", @@ -1074482,6 +1071326,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.04.20225706", + "rel_title": "Higher risk of mental health deterioration during the Covid-19 lockdown among students rather than non-students. The French Confins study", + "rel_date": "2020-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225706", + "rel_abs": "BackgroundCovid-19 pandemic and its consequences have raised fears of its psychological impact. The objective of this study was to estimate the effect of student status on mental health conditions during Covid-19 general lockdown among adults in France.\n\nMethodsUsing cross-sectional data of the Confins cohort, we estimated the effect of student status on depressive and anxiety symptoms, suicidal thoughts and perceived stress using multivariate logistic regression analyses. Stratified models for college students and non- students were performed to identify associated population-specific factors.\n\nResultsAmong the 2260 included participants, students represented 59% (n=1335 vs 925 non- students) and 78% of the total sample were female. Student status was more frequently associated with depressive symptoms (adjusted OR(aOR)=1.58; 95%CI 1.17;2.14), anxiety symptoms (aOR=1.51; 95%CI 1.10;2.07), perceived stress (n=1919, aOR=1.70, 95%CI 1.26;2.29) and frequent suicidal thoughts (n=1919, aOR=1.57, 95%CI 0.97;2.53). Lockdown conditions that could be potentially aggravating on mental health like isolation had a higher impact on students than non-students.\n\nLimitationsParticipants were volunteers, which could limit generalisation of the findings. The cross-sectional design did not allow determining if lockdown impacted directly mental health or if there is another cause. However, we adjusted analyses with the history of psychiatric disorders, and factors related to lockdown conditions were associated with mental health disturbances.\n\nConclusionsCollege students mental health is of great importance in the context of the general lockdown set up during the pandemic. Follow-up and interventions should be implemented especially for those at high-risk (younger people and those with history of psychiatric disorders).", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Julie Arsandaux", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Ilaria Montagni", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Melissa Macalli", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Nathalie Texier", + "author_inst": "Kappa Sante" + }, + { + "author_name": "Mathilde Pouriel", + "author_inst": "Kappa Sante" + }, + { + "author_name": "Raphael Germain", + "author_inst": "Kappa Sante" + }, + { + "author_name": "Adel Mebarki", + "author_inst": "KapCode" + }, + { + "author_name": "Sherazade Kinouani", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Marie Tournier", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Stephane Schuck", + "author_inst": "Kappa Sante" + }, + { + "author_name": "Christophe Tzourio", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.03.20225581", "rel_title": "COVID-19's U.S. Temperature Response Profile", @@ -1075945,41 +1072848,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.31.20223453", - "rel_title": "What is the efficacy and safety of rapid exercise tests for exertional desaturation in Covid-19: A rapid review protocol", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20223453", - "rel_abs": "BackgroundEven when resting pulse oximetry is normal in the patient with acute Covid-19, hypoxia can manifest on exertion. We sought to summarise the literature on the performance of different rapid tests for exertional desaturation.\n\nResearch questionWhat tests have been formally evaluated for the rapid assessment of exertional hypoxia? What is the evidence for their accuracy, practicability and safety in the context of suspected acute Covid-19? To what extent will these tests help identify patients with evidence of either silent or hidden hypoxia leading to earlier recognition of those at risk of severe outcomes?\n\nMethodWe aim to review three independent searches of AMED, CINAHL, EMBASE MEDLINE, Cochrane and PubMed using LitCovid, Scholar and Google databases until 24th September 2020. Screening, data abstraction, and quality appraisal of full-text papers will be completed independently by two reviewers including a topic expert and a review expert. Studies will be tabulated and assessed for risk of bias using QUADAS 2 tool.\n\nDiscussionThis rapid review aims to produce key findings relevant to the assessment of exertional desaturation in patients with suspected Covid-19. Establishing a validated tool to assess exertional desaturation will help to ensure that future research on this topic can be undertaken in a consistent way. An exertional desaturation test should be used in combination with a comprehensive clinical evaluation and only on patients whose resting oximetry reading is 96% or above unless in a supervised care setting. It should be terminated if the patient experiences adverse effects.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Asli kalin", - "author_inst": "Oxford University" - }, - { - "author_name": "Trish Greenhalgh", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Babak Javid", - "author_inst": "Division of Experimental Medicine, University of California" - }, - { - "author_name": "Matthew Knight", - "author_inst": "West Hertfordshire Hospitals NHS Trust" - }, - { - "author_name": "Matthew Inada-Kim", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.10.30.20223230", "rel_title": "SARS-CoV-2 Seroprevalence in a Cohort of Asymptomatic, RT-PCR Negative Croatian First League Football Players", @@ -1076640,6 +1073508,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.31.20220608", + "rel_title": "A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners.", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20220608", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in domestic and wild cats. However, little is known about natural viral infections of domestic cats, although their importance for modeling disease spread, informing strategies for managing positive human-animal relationships and disease prevention. Here, we describe the SARS-CoV-2 infection in a household of two human adults and sibling cats (one male and two females) using real-time RT-PCR, an ELISA test, viral sequencing, and virus isolation. On May 2020, the cat- owners tested positive for SARS-CoV-2. Two days later, the male cat showed mild respiratory symptoms and tested positive. Four days after the male cat, the two female cats became positive, asymptomatically. Also, one human and one cat showed antibodies against SARS-CoV-2. All cats excreted detectable SARS-CoV-2 RNA for a shorter duration than humans and viral sequences analysis confirmed human-to-cat transmission. We could not determine if cat-to-cat transmission also occurred.\n\nArticle Summary LineSARS-CoV-2 in naturally infected cats present a shorter shedding pattern compared to their owners.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Victor Neira Ramirez", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Barbara Brito", + "author_inst": "The ithree institute - University of Technology Sydney, Sydney, Australia" + }, + { + "author_name": "Belen Aguero", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Felipe Berrios", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Valentina Valdes", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Alberto Gutierrez", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Naomi Ariyama", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Patricio Espinoza", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Patricio Retamal", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Ana Gonzalez-reiche", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA" + }, + { + "author_name": "Zenab Khan", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA" + }, + { + "author_name": "Adriana Van de Guchte", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA" + }, + { + "author_name": "Jayeeta Dutta", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA" + }, + { + "author_name": "Lisa Miorin", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA." + }, + { + "author_name": "Thomas Kehrer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA." + }, + { + "author_name": "Nicolas Galarce", + "author_inst": "Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile." + }, + { + "author_name": "Leonardo Almonacid", + "author_inst": "Departamento de Enfermedades Infecciosas e Inmunologia Pediatrica, Escuela de Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Jorge Levican", + "author_inst": "Departamento de Enfermedades Infecciosas e Inmunologia Pediatrica, Escuela de Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile." + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rafael A. Medina", + "author_inst": "Pontificia Universidad Catolica de Chile" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.01.20224113", "rel_title": "Rapid homogeneous assay for detecting antibodies against SARS-CoV-2", @@ -1077387,45 +1074358,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.01.20223958", - "rel_title": "Low dose hydroxychloroquine is associated with lower mortality in COVID-19: a meta-analysis of 26 studies and 44,521 patients", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20223958", - "rel_abs": "BackgroundHydroxychloroquine (HCQ) was proposed as potential treatment for COVID-19, but its association with mortality is not well characterized. We conducted two meta-analyses to evaluate the association between HCQ (with or without azithromycin (AZM)) and total mortality in COVID-19 patients.\n\nMethodsArticles were retrieved until October 20th, 2020 by searching in seven databases. Data were combined using the general variance-based method on relative risk estimates.\n\nResultsA total of 26 articles were found (N=44,521 COVID-19 patients, including N=7,324 from 4 randomized clinical trials (RCTs)); 10 studies were valuable for analysing the association of HCQ+AZM. Overall, the use of HCQ was associated with 21% lower mortality risk (pooled risk ratio: 0.79, 95%CI: 0.67 to 0.93; high level of heterogeneity: I2=82%, random effects). This association vanished (1.10, 95%CI: 0.99 to 1.23 and 1.10, 95%CI: 0.99 to 1.23) when daily dose >400 mg or total dose >4,400 mg were used, respectively). HCQ+AZM was also associated with 25% lower mortality risk, but uncertainty was large (95%CI: 0.50 to 1.13; P=0.17). No association was apparent when only pooling the 4 RCTs (13.8% of the overall weight; pooled risk ratio: 1.11, 95%CI: 0.99 to 1.24).\n\nConclusionsHCQ use was not associated with either increased or decreased mortality in COVID-19 patients when 4 RCTs only were evaluated, while a 7% to 33% reduced mortality was observed when observational studies were also included. The association was mainly apparent when pooling studies using lower doses of HCQ. These findings can help disentangling the debate on HCQ use in COVID-19.\n\nKey-pointsLow dose hydroxychloroquine was associated with reduced mortality in COVID-19 patients, as seen in observational studies but not in randomised clinical trials, which used high doses of hydroxychloroquine. These findings can help disentangling the debate on hydroxychloroquine use in COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Augusto Di Castelnuovo", - "author_inst": "Mediterranea Cardiocentro, Naples, Italy" - }, - { - "author_name": "Simona Costanzo", - "author_inst": "Department of Epidemiology and Prevention, IRCCS Neuromed, Pozzilli, Italy" - }, - { - "author_name": "Antonio Cassone", - "author_inst": "Polo della genomica, genetica e biologia, University of Siena, Italy" - }, - { - "author_name": "Roberto Cauda", - "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS Cattolica S. Cuore University, Roma, Italy" - }, - { - "author_name": "Giovanni de Gaetano", - "author_inst": "Department of Epidemiology and Prevention, IRCCS Neuromed, Pozzilli, Italy" - }, - { - "author_name": "Licia Iacoviello", - "author_inst": "Department of Epidemiology and Prevention, IRCCS Neuromed, Pozzilli, Italy and Research Centre in Epidemiology and Preventive Medicine (EPIMED), Department of M" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.02.20224303", "rel_title": "Randomized controlled trial of convalescent plasma therapy against standard therapy in patients with severe COVID-19 disease", @@ -1078110,6 +1075042,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.03.20219121", + "rel_title": "SARS-CoV-2 antibody prevalence and symptoms in a local Austrian population", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20219121", + "rel_abs": "BackgroundSince December 2019 the novel coronavirus (SARS-CoV-2) is the center of global attention due to its rapid transmission and toll on health care systems and global economy. Population-based serosurveys measuring antibodies for SARS-CoV-2 provide one method for estimating infection rates and monitoring the progression of the epidemic.\n\nMethodsIn June 2020 we succeeded in testing almost half of the population of an Austrian township (n=835 of 1359 inhabitants) with a reported higher incidence for COVID-19 infections. We determined the level of prevalence for SARS-CoV-2 in this population, factors affecting, and symptoms correlated with prior infection.\n\nResultsWe found a high prevalence of 9% positive antibodies among the town population in comparison to 6% of the neighboring villages. Only 20% of SARS-CoV-2 cases self-declared being asymptomatic. In contrast, we identified six single major symptoms, including anosmia/ageusia, weight loss, anorexia, general debility, dyspnea, and fever, and especially their combination to be of high prognostic value for predicting SARS-CoV-2 infection in a patient. Our comparison of the gold standard lab-based ELISA test and the on-site antibody test demonstrated a lack of accuracy for the latter test form.\n\nConclusionsThis population study demonstrated a high prevalence of antibodies to SARS-CoV-2 as a marker of both active and past infections in an Austrian township. Several symptoms revealed a diagnostic value especially in combination. Results from self-administered antibody tests should be considered with caution.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dennis Ladage", + "author_inst": "Kliniken Maria Hilf" + }, + { + "author_name": "Yana Hoeglinger", + "author_inst": "Danube Private University" + }, + { + "author_name": "Dorothee Ladage", + "author_inst": "Danube Private University" + }, + { + "author_name": "Christoph Adler", + "author_inst": "University of Cologne" + }, + { + "author_name": "Israfil Yalcin", + "author_inst": "Danube Private University" + }, + { + "author_name": "Ralf Braun", + "author_inst": "Danube Private University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.11.02.20183236", "rel_title": "Factors Associated with COVID-19 Deaths and Infections: A Cross Country Evidence", @@ -1079121,57 +1076092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2020.11.01.20224022", - "rel_title": "The impact of keeping a religious beard in the COVID-19 pandemic: an online cross sectional survey study exploring experiences of male medical healthcare professionals", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20224022", - "rel_abs": "There has been a disproportionate effect on individuals from black Asian & Minority Ehnic (BAME) in the UK in Coronavirus disease (COVID-19) pandemic, especially in the NHS staff. Many of them have been asked to remove their beard to be eligible to do the fit test which can have negative implications on their spiritual, psychological & emotional wellbeing. This paper surveyed the responses of 469 healthcare professionals (HCPs) with beards regarding the challenges they face in regard to personal protective equipment (PPE), mask fit testing and attitude of employers & colleagues.\n\nProfessional discrimination through fit testing rejection, unavailability or inadequate PPE and the pressure to shave their beard are unpleasant outcomes of this pandemic for some of the NHS staff. NHS trusts & hospitals need to adjust their practices to include staff with beard in their COVID-19 arrangements.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Amer Hamed", - "author_inst": "Stepping Hill Hospital" - }, - { - "author_name": "Asam Latif", - "author_inst": "Faculty of Medicine & Health Sciences University of Nottingham, Nottingham" - }, - { - "author_name": "Mohammad Harris", - "author_inst": "Blackpool Victoria Hospital" - }, - { - "author_name": "Sufyan Patel", - "author_inst": "University Hospitals of Leicester" - }, - { - "author_name": "Muhammad Patel", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Syed Abdul Rahman Mustafa", - "author_inst": "University Hospitals of Leicester" - }, - { - "author_name": "Omeair Khan", - "author_inst": "The Princess Alexandra Hospital NHS Trust" - }, - { - "author_name": "Ahmad Shoaib", - "author_inst": "Keele University & Royal Stoke University Hospital" - }, - { - "author_name": "Salman Waqar", - "author_inst": "University of Oxford Department of Primary Care Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.11.03.20225227", "rel_title": "Space-Time Covid-19 Bayesian SIR modeling in South Carolina", @@ -1079788,6 +1076708,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.28.20219816", + "rel_title": "A Multi-Factor Risk Model for Severe Covid-19 for Vaccine Prioritization and Monitoring Based on a 15 Million Medicare Cohort", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20219816", + "rel_abs": "BackgroundRecommendations for prioritizing populations for COVID-19 vaccination have focused on front-line health care personnel and residents in long term care, followed by other individuals at higher risk for severe disease. Existing models for identifying higher risk individuals including those over age 65 lack the needed integration of socio-demographic and clinical risk factors to ensure equitable vaccine allocation.\n\nMethodsWe developed a predictive model for severe COVID-19 using clinical data from de-identified Medicare claims for 16 million Medicare fee-for-service beneficiaries, including 1 million COVID-19 cases, and socio-economic data from the CDC Social Vulnerability Index. To identify risk factors for severe COVID-19, we used multivariate logistic regression and random forest modeling. Predicted individual probabilities of COVID-19 hospitalization were then calculated for population risk stratification and COVID-19 vaccine prioritization, and for mapping of population risk levels at the county and zip code levels on a nationwide dashboard.\n\nResultsThe leading Covid-19 hospitalization risk factors driving the risk model were: Non-white ethnicity (particularly North American Native, Black, and Hispanic), end-stage renal disease, advanced age (particularly age over 85), prior hospitalization, leukemia, morbid obesity, chronic kidney disease, lung cancer, chronic liver disease, pulmonary fibrosis or pulmonary hypertension, and chemotherapy. However, previously reported risk factors such as chronic obstructive pulmonary disease and diabetes conferred modest hospitalization risk. Among all social vulnerability factors analyzed, residence in a low-income zip code was the only risk factor independently predicting Covid-19 hospitalization. The mapped hospitalization risk levels showed significant correlations with the cumulative COVID-19 case hospitalization rates at the zip code level in the fifteen most populous U.S. major metropolitan areas.\n\nConclusionThis multi-factor risk model which predicts severe Covid-19and its population risk dashboard can be used to optimize Covid-19 vaccine allocation in the higher risk Medicare population where socio-demographic and comorbidity risk factors need to be considered concurrently.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bettina Experton", + "author_inst": "Humetrix" + }, + { + "author_name": "Hassan Tetteh", + "author_inst": "Department of Defense Joint Artificial Intelligence Center" + }, + { + "author_name": "Nicole Lurie", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Peter Walker", + "author_inst": "Department of Defense Joint Artificial Intelligence Center" + }, + { + "author_name": "Colin Carroll", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Adrien Elena", + "author_inst": "Humetrix" + }, + { + "author_name": "Christopher Hein", + "author_inst": "Humetrix" + }, + { + "author_name": "Blake Schwendiman", + "author_inst": "Humetrix" + }, + { + "author_name": "Christopher Burrow", + "author_inst": "Humetrix" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.28.20221697", "rel_title": "U-shaped-aggressiveness of SARS-CoV-2: Period between onset of nonspecific-specific symptoms for COVID-19. A population-based cohort study", @@ -1080603,57 +1077574,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.29.20222190", - "rel_title": "Border Restriction as a Public Health Measureto Limit Outbreak of Coronavirus Disease 2019 (COVID-19)", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222190", - "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) led to pandemic that affected almost all countries in the world. Many countries have implemented border restriction as a public health measure to limit local outbreak. However, there is inadequate scientific data to support such a practice, especially in the presence of an established local transmission of the disease.\n\nMethodA novel metapopulation Susceptible-Exposed-Infectious-Recovered (SEIR) model with inspected migration was applied to investigate the effect of border restriction between Hong Kong and mainland China on the epidemiological characteristics of COVID-19 in Hong Kong. Isolation facilities occupancy was also studied.\n\nResultsAt R0 of 2{middle dot}2, the cumulative COVID-19 cases in Hong Kong can be reduced by 13{middle dot}99% (from 29,163 to 25,084) with complete border closure. At an in-patient mortality of 1{middle dot}4%, the number of deaths can be reduced from 408 to 351 (57 lives saved). However, border closure alone was insufficient to prevent full occupancy of isolation facilities in Hong Kong; effective public health measures to reduce local R0 to below 1{middle dot}6 was necessary.\n\nConclusionAs a public health measure to tackle COVID-19, border restriction is effective in reducing cumulative cases and mortality.\n\nArticle summaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIA novel metapopulation SEIR model with inspected migration was developed to investigate the epidemiological characteristics of COVID-19 in Hong Kong, Guangdong and the rest of China (excluding Hubei) in the presence or absence of border restriction.\nC_LIO_LIThe presented model is also suitable for further analysis of other emerging infectious diseases.\nC_LIO_LIBorder restriction is an effective public health measure in reducing cumulative cases and mortality for COVID-19.\nC_LIO_LIInteraction was assumed to be well-mixed within patch. The spatial effect in disease transmission within each patch is ignored, which can have a non-trivial effect on the dynamic of infectious disease.\nC_LIO_LIThe proposed model is deterministic in nature which ignores the randomness in migration and in the interactions among people; a stochastic model would be more realistic especially early in the disease.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Wang Chun Kwok", - "author_inst": "Queen Mary Hospital" - }, - { - "author_name": "Chun Ka Wong", - "author_inst": "Queen Mary Hospital" - }, - { - "author_name": "Ting Fung Ma", - "author_inst": "University of Wisconsin" - }, - { - "author_name": "Ka Wai Ho", - "author_inst": "University of Wisconsin" - }, - { - "author_name": "Wai Tong Louis Fan", - "author_inst": "Indiana University" - }, - { - "author_name": "King Pui Florence Chan", - "author_inst": "Queen Mary Hospital" - }, - { - "author_name": "Shung Kay Samuel Chan", - "author_inst": "Queen Mary Hospital" - }, - { - "author_name": "Chi Chun Terence Tam", - "author_inst": "Queen Mary Hospital" - }, - { - "author_name": "Pak Leung Ho", - "author_inst": "University of Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.29.20207167", "rel_title": "Gastroenterological and Hepatic Manifestations of Patients with COVID-19, Prevalence, Mortality by Country, and Intensive Care Admission Rate: Systematic Review and Meta-analysis.", @@ -1081238,6 +1078158,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20223198", + "rel_title": "Analytical and Clinical Performance of the Panbio COVID-19 Antigen-Detecting Rapid Diagnostic Test", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223198", + "rel_abs": "BackgroundThe current standard for COVID-19 diagnosis, RT-qPCR, has important drawbacks for its use as a tool for epidemiological control, including the need of laboratory-processing, high cost, and long turnaround from sampling to results release. Antigen-based rapid diagnostic tests (Ag-RDT) provide a promising alternative for this purpose.\n\nMethodsWe assessed the analytical and clinical performance of the Ag-RDT Panbio COVID-19 Ag Test (Abbott), using RT-qPCR as a reference test. The clinical performance was assessed using nasopharyngeal swabs, collected in routine practice for case confirmation and contact tracing, and nasal mid-turbinate swabs, collected in preventive screenings of asymptomatic individuals. Fresh samples were analysed by RT-q-PCR, stored at -80 {degrees}C, and analysed using the Ag-RDT according to the manufacturer instructions.\n\nFindingsThe Ag-RDT had a limit of detection of 6{middle dot}5x105 copies/reaction. The clinical performance was assessed on 1,406 frozen swabs with a PCR result available: 951 (67{middle dot}7%) positive and 455 (32{middle dot}4%) negative. The Ag-RDT identified the presence of SARS-CoV-2 in 872 of 951 PCR-positive samples (91{middle dot}7%; 95% CI 89{middle dot}8-93{middle dot}4 and ruled out its presence in 450 of 455 PCR-negative samples (specificity 98{middle dot}9%; 95% CI 97{middle dot}5- 99{middle dot}6). Sensitivity increased in samples with lower Ct values (Ct <25, 98{middle dot}2%; Ct<30, 94{middle dot}9%) and was higher among symptomatic cases (92{middle dot}6%) and their contacts (94{middle dot}2%) than among asymptomatic individuals (79{middle dot}5%). In the setting of asymptomatic screening, sensitivity also increased with lower Ct values (Ct <25, 100%; Ct<30, 98{middle dot}6%). Assuming a pre-test probability of 5%, the negative and positive predictive values were 99{middle dot}6% (99{middle dot}5 - 99{middle dot}6) and 81{middle dot}5% (65{middle dot}0 - 93{middle dot}2), respectively.\n\nInterpretationThe Panbio COVID-19 Ag-RDT has high sensitivity for detecting the presence of SARS-CoV-2 in nasal or nasopharyngeal swabs of both, symptomatic and asymptomatic individuals. The diagnostic performance of the test is particularly good in samples with viral loads associated with high risk of viral transmission (Ct <25), which show high positive and negative predictive values even when assuming a prevalence as low as 5%.\n\nFundingBlueberry diagnostics, Fundacio Institut dInvestigacio en Ciencies de la Salut Germans Trias i Pujol, and #YoMeCorono.org crowfunding campaing.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSOn October 6, 2020, we searched PubMed for articles containing \"Antigen\", \"test\", \"SARS-CoV-2\", \"COVID-19\" and \"performance\" in either the title or the abstract. We found five studies that showed the accuracy of point-of-care tests in identifying SARS-CoV-2 antigens for confirmation of clinically suspected COVID-19. We found high variability in the diagnostic accuracy of Ag-RDT. Most tests showed high specificity (i.e., 99% or higher), whereas sensitivity ranged from 11% to 92%; only one test reported sensitivity higher than 60%. We found no studies investigating the diagnostic accuracy of the Panbio COVID-19 Ag Test. We found no studies that assessed the performance of Ag-RDT for population-level screening of asymptomatic individuals.\n\nAdded value of this studyOur analysis provides information regarding the diagnostic accuracy of the Panbio COVID-19 Ag Test when tested on 1,406 frozen samples of nasopharyngeal and nasal swabs collected in routine practice for diagnostic confirmation of symptomatic individuals with suspected COVID-19 or contacts exposed to a positive case, and preventive screenings of unexposed asymptomatic individuals. Compared with RT-qPCR as reference test, the Ag-RDT showed a sensitivity and specificity of 91{middle dot}7% and 98{middle dot}9%. Test sensitivity increased in samples with viral load associated with high risk of transmission (Ct <25), reaching more than 98%, regardless of the presence of symptoms.\n\nImplications of all the available evidenceAvailable evidence show variability in the diagnostic performance of marketed Ag-RDT. Our results provide substantial evidence that the point-of-care Panbio COVID-19 Ag Test can accurately identify SARS-CoV-2 antigens in people with suspected clinical COVID-19 as well as in asymptomatic people with high viral load and therefore, associated with higher risk of transmission. This finding represents a potentially useful advance for mass screening of asymptomatic people at the point-of-care.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Oriol Mitja", + "author_inst": "Fundacio Lluita contra la Sida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.29.20222067", "rel_title": "Feasibility of collecting and processing of COVID-19 convalescent plasma for treatment of COVID-19 in Uganda", @@ -1082672,57 +1079611,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.30.20222984", - "rel_title": "Modeling COVID-19 Transmissions and Evaluation of Large Scale Social Restriction in Jakarta, Indonesia", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20222984", - "rel_abs": "This paper presents mathematical modeling and quantitative evaluation of Large Scale Social Restriction (LSSR) in Jakarta between 10 April and 4 June 2020. The special capital region of Jakarta is the only province among 34 provinces in Indonesia with an average Testing Positivity Rate (TPR) below 5% recommended by the World Health Organization (WHO). The transmission model is based on a discrete-time compartmental epidemiological model incorporating suspected cases. The quantitative evaluation is measured based on the estimation of the time-varying effective reproduction number ([R]t). Our results show the LSSR has been successfully suppressed the spread of COVID-19 in Jakarta, which was indicated by [R]t < 1. However, once the LSSR was relaxed, the effective reproduction number increased significantly. The model is further used for short-term forecasting to mitigate the course of the pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Agus Hasan", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Yuki Nasution", - "author_inst": "Universitas Mulawarman" - }, - { - "author_name": "Hadi Susanto", - "author_inst": "Khalifa University" - }, - { - "author_name": "Endah Putri", - "author_inst": "Institut Teknologi Sepuluh November" - }, - { - "author_name": "Venansius Tjahjono", - "author_inst": "Institut Teknologi Sepuluh Nopember" - }, - { - "author_name": "Dilla Puspita", - "author_inst": "Institut Teknologi Bandung" - }, - { - "author_name": "Kamal Sukandar", - "author_inst": "Institut Teknologi Bandung" - }, - { - "author_name": "Nuning Nuraini", - "author_inst": "Institut Teknologi Bandung" - }, - { - "author_name": "Widyastuti Widyastuti", - "author_inst": "Dinas Kesehatan Jakarta" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.10.30.20215301", "rel_title": "Remdesivir-based therapy improved recovery of patients with COVID-19 in the SARSTer multicentre, real-world study", @@ -1083483,6 +1080371,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20223123", + "rel_title": "High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223123", + "rel_abs": "BackgroundREACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive.\n\nMethodsREACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive.\n\nResultsOverall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%).\n\nConclusionThe co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Haowei Wang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christina J Atchison", + "author_inst": "Imperial College London" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "Lancaster University" + }, + { + "author_name": "Peter J Diggle", + "author_inst": "Lancaster University" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Imperial College" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Helen Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.30.20223305", "rel_title": "A New Approach to the Dynamic Modeling of an Infectious Disease", @@ -1084426,81 +1081389,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.31.363044", - "rel_title": "RAPPID: a platform of ratiometric bioluminescent sensors for homogeneous immunoassays", - "rel_date": "2020-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.31.363044", - "rel_abs": "Heterogeneous immunoassays such as ELISA have become indispensable in modern bioanalysis, yet translation into easy-to-use point-of-care assays is hindered by their dependence on external calibration and multiple washing and incubation steps. Here, we introduce RAPPID (Ratiometric Plug-and-Play Immunodiagnostics), a \"mix-and-measure\" homogeneous immunoassay platform that combines highly specific antibody-based detection with a ratiometric bioluminescent readout that can be detected using a basic digital camera. The concept entails analyte-induced complementation of split NanoLuc luciferase fragments, photoconjugated to an antibody sandwich pair via protein G adapters. We also introduce the use of a calibrator luciferase that provides a robust ratiometric signal, allowing direct in-sample calibration and quantitative measurements in complex media such as blood plasma. We developed RAPPID sensors that allow low-picomolar detection of several protein biomarkers, anti-drug antibodies, therapeutic antibodies, and both SARS-CoV-2 spike protein and anti-SARS-CoV-2 antibodies. RAPPID combines ratiometric bioluminescent detection with antibody-based target recognition into an easy-to-implement standardized workflow, and therefore represents an attractive, fast, and low-cost alternative to traditional immunoassays, both in an academic setting and in clinical laboratories for point-of-care applications.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yan Ni", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Bas J.H.M. Rosier", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Eva A. van Aalen", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Eva T.L. Hanckmann", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Lieuwe Biewenga", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Anna-Maria Makri Pistikou", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Bart Timmermans", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Chris Vu", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Sophie Roos", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Remco Arts", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Wentao Li", - "author_inst": "Utrecht University" - }, - { - "author_name": "Tom F.A. de Greef", - "author_inst": "Eindhoven University of Technology" - }, - { - "author_name": "Frank J.M. van Kuppeveld", - "author_inst": "Utrecht University" - }, - { - "author_name": "Berend-Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Maarten Merkx", - "author_inst": "Eindhoven University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.11.02.350439", "rel_title": "Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning", @@ -1085233,6 +1082121,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.02.363242", + "rel_title": "Ivermectin reduces coronavirus infection in vivo: a mouse experimental model", + "rel_date": "2020-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.02.363242", + "rel_abs": "SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). BALB/cJ female mice were infected with 6,000 PFU of MHV-A59 (Group Infected; n=20) and immediately treated with one single dose of 500 g/kg of ivermectin (Group Infected + IVM; n=20), or were not infected and treated with PBS (Control group; n=16). Five days after infection/treatment, mice were euthanized to obtain different tissues to check general health status and infection levels. Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). Furthermore, serum transaminase levels (aspartate aminotransferase and alanine aminotransferase) were significantly lower in treated mice compared to infected animals. In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ana Paula Arevalo", + "author_inst": "Transgenic and Experimental Animal Unit, Institut Pasteur de Montevideo" + }, + { + "author_name": "Romina Pagotto", + "author_inst": "Cell Biology Unit, Institut Pasteur de Montevideo" + }, + { + "author_name": "Jorge Porfido", + "author_inst": "Transgenic and Experimental Animal Unit, Institut Pasteur de Montevideo" + }, + { + "author_name": "Hellen Daghero", + "author_inst": "Cell Biology Unit, Institut Pasteur de Montevideo" + }, + { + "author_name": "Mercedes Segovia", + "author_inst": "Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo" + }, + { + "author_name": "Kanji Yamasaki", + "author_inst": "Pathobiology Department, Faculty of Veterinary" + }, + { + "author_name": "Belen Varela", + "author_inst": "Pathobiology Department, Faculty of Veterinary" + }, + { + "author_name": "Marcelo Hill", + "author_inst": "Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo" + }, + { + "author_name": "Jose Manuel Verdes", + "author_inst": "Pathobiology Department, Faculty of Veterinary" + }, + { + "author_name": "Maite Duhalde Vega", + "author_inst": "Institute of Biological Chemistry and Chemical Physics (UBA-CONICET). School of Pharmacy and Biochemistry, University of Buenos Aires, Argentina. Laboratory of " + }, + { + "author_name": "Mariela Bollati-Fogolin", + "author_inst": "Cell Biology Unit, Institut Pasteur de Montevideo" + }, + { + "author_name": "Martina Crispo", + "author_inst": "Transgenic and Experimental Animal Unit, Institut Pasteur de Montevideo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.11.02.364661", "rel_title": "Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses", @@ -1086080,25 +1083031,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2020.10.31.363176", - "rel_title": "A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium.", - "rel_date": "2020-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.31.363176", - "rel_abs": "SARS-CoV-2, causative agent of the COVID-19 pandemic, is thought to release its RNA genome at either the cell surface or within endosomes, the balance being dependent on spike protein stability, and the complement of receptors, co-receptors and proteases. To investigate possible mediators of pH-dependence, pKa calculations have been made on a set of structures for spike protein ectodomain and fragments from SARS-CoV-2 and other coronaviruses. Dominating a heat map of the aggregated predictions, 3 histidine residues in S2 are consistently predicted as destabilising in pre-fusion (all 3) and post-fusion (2 of 3) structures. Other predicted features include the more moderate energetics of surface salt-bridge interactions, and sidechain-mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290 - R273 and R355 - D398) have pKas that are calculated to be elevated and destabilising in more open forms of the spike trimer. These aspartic acids are most stabilised in a tightly closed conformation that has been observed when linoleic acid is bound, and which also affects the interactions of D614. The D614G mutation is known to modulate the balance of closed to open trimer. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. These observations are discussed in the context of SARS-CoV-2 infection, mutagenesis studies, and other human coronaviruses.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jim Warwicker", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.10.31.20223925", "rel_title": "Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context", @@ -1086683,6 +1083615,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221655", + "rel_title": "Pre-existing conditions are associated with long-COVID patients hospitalization, despite confirmed clearance of SARS-CoV-2 virus", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221655", + "rel_abs": "The current diagnostic gold-standard for SARS-CoV-2 clearance from infected patients is two consecutive negative PCR test results. However, there are anecdotal reports of hospitalization from protracted COVID complications despite such confirmed viral clearance, presenting a clinical conundrum. We conducted a retrospective analysis of 266 COVID patients to compare those that were admitted/re-admitted post-viral clearance (hospitalized post-clearance cohort, n=93) with those that were hospitalized pre-clearance but were not re-admitted post-viral clearance (non-hospitalized post-clearance cohort, n=173). In order to differentiate these two cohorts, we used neural network models for the augmented curation of comorbidities and complications with positive sentiment in the EHR physician notes. In the year preceding COVID onset, acute kidney injury (n=15 (16.1%), p-value: 0.03), anemia (n=20 (21.5%), p-value: 0.02), and cardiac arrhythmia (n=21 (22.6%), p-value: 0.05) were significantly enriched in the physician notes of the hospitalized post-clearance cohort. This study highlights that these specific pre-existing conditions are associated with amplified hospitalization risk in COVID patients, despite their successful SARS-CoV-2 viral clearance. Our finding that pre-COVID anemia amplifies risk of post-COVID hospitalization is particularly concerning given the high prevalence and endemic nature of anemia in many low- and middle-income countries (per the World Bank definition; e.g. India, Brazil), which are unfortunately also seeing high rates of SARS-CoV-2 infection and COVID-induced mortality. This study motivates follow-up prospective research into the specific risk factors we have identified that appear to predispose some patients towards the after effects of COVID-19.\n\nArticle summary - Strengths and limitations of this studyO_LIThis is the first study at a major healthcare center analyzing risk factors for post-viral clearance hospitalization of COVID-19 patients.\nC_LIO_LIThis analysis uses augmented curation methods to identify complications and comorbidities from the physician notes, rather than relying upon ICD codes.\nC_LIO_LIThe statistical analysis identifies specific comorbidities in the year preceding PCR diagnosis of SARS-CoV-2 which are associated with increased rates of post-viral clearance hospitalization.\nC_LIO_LIThe dataset used for this study is limited to a single healthcare system, so the underlying clinical characteristics of the study population are biased to reflect the clinical characteristics of individuals that receive medical treatment in certain regions of the United States (Arizona, Florida, Minnesota).\nC_LIO_LIIn this study, we use the first of two consecutive negative PCR tests to estimate the viral clearance date for each patient, however the true viral clearance date for each patient is unknown.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Colin Pawlowski", + "author_inst": "nference" + }, + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Eshwan Ramudu", + "author_inst": "nference" + }, + { + "author_name": "Christian Kirkup", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Nikhil Kayal", + "author_inst": "nference" + }, + { + "author_name": "Gabriela Berner", + "author_inst": "nference" + }, + { + "author_name": "Akash Anand", + "author_inst": "nference Labs" + }, + { + "author_name": "Rakesh Barve", + "author_inst": "nference Labs" + }, + { + "author_name": "John C O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221234", "rel_title": "Projected COVID-19 epidemic in the United States in the context of the effectiveness of a potential vaccine and implications for social distancing and face mask use", @@ -1087746,37 +1084741,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.29.361287", - "rel_title": "A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies", - "rel_date": "2020-10-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.29.361287", - "rel_abs": "Antibody engineering technologies face increasing demands for speed, reliability and scale. We developed CeVICA, a cell-free antibody engineering platform that integrates a novel generation method and design for camelid heavy-chain antibody VHH domain-based synthetic libraries, optimized in vitro selection based on ribosome display and a computational pipeline for binder prediction based on CDR-directed clustering. We applied CeVICA to engineer antibodies against the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike proteins and identified >800 predicted binder families. Among 14 experimentally-tested binders, 6 showed inhibition of pseudotyped virus infection. Antibody affinity maturation further increased binding affinity and potency of inhibition. Additionally, the unique capability of CeVICA for efficient and comprehensive binder prediction allowed retrospective validation of the fitness of our synthetic VHH library design and revealed direction for future refinement. CeVICA offers an integrated solution to rapid generation of divergent synthetic antibodies with tunable affinities in vitro and may serve as the basis for automated and highly parallel antibody generation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xun Chen", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Matteo Gentili", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Nir Hacohen", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Aviv Regev", - "author_inst": "MIT and Broad Inst. of MIT & Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.10.30.360115", "rel_title": "PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2", @@ -1089009,6 +1085973,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.29.361048", + "rel_title": "COVID-19 cytokines and the hyperactive immune response: Synergism of TNF-\u03b1 and IFN-\u03b3 in triggering inflammation, tissue damage, and death", + "rel_date": "2020-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.29.361048", + "rel_abs": "The COVID-19 pandemic has caused significant morbidity and mortality. Currently, there is a critical shortage of proven treatment options and an urgent need to understand the pathogenesis of multi-organ failure and lung damage. Cytokine storm is associated with severe inflammation and organ damage during COVID-19. However, a detailed molecular pathway defining this cytokine storm is lacking, and gaining mechanistic understanding of how SARS-CoV-2 elicits a hyperactive inflammatory response is critical to develop effective therapeutics. Of the multiple inflammatory cytokines produced by innate immune cells during SARS-CoV-2 infection, we found that the combined production of TNF- and IFN-{gamma} specifically induced inflammatory cell death, PANoptosis, characterized by gasdermin-mediated pyroptosis, caspase-8-mediated apoptosis, and MLKL-mediated necroptosis. Deletion of pyroptosis, apoptosis, or necroptosis mediators individually was not sufficient to protect against cell death. However, cells deficient in both RIPK3 and caspase-8 or RIPK3 and FADD were resistant to this cell death. Mechanistically, the JAK/STAT1/IRF1 axis activated by TNF- and IFN-{gamma} co-treatment induced iNOS for the production of nitric oxide. Pharmacological and genetic deletion of this pathway inhibited pyroptosis, apoptosis, and necroptosis in macrophages. Moreover, inhibition of PANoptosis protected mice from TNF- and IFN-{gamma}-induced lethal cytokine shock that mirrors the pathological symptoms of COVID-19. In vivo neutralization of both TNF- and IFN-{gamma} in multiple disease models associated with cytokine storm showed that this treatment provided substantial protection against not only SARS-CoV-2 infection, but also sepsis, hemophagocytic lymphohistiocytosis, and cytokine shock models, demonstrating the broad physiological relevance of this mechanism. Collectively, our findings suggest that blocking the cytokine-mediated inflammatory cell death signaling pathway identified here may benefit patients with COVID-19 or other cytokine storm-driven syndromes by limiting inflammation and tissue damage. The findings also provide a molecular and mechanistic description for the term cytokine storm. Additionally, these results open new avenues for the treatment of other infectious and autoinflammatory diseases and cancers where TNF- and IFN-{gamma} synergism play key pathological roles.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Evan Peter Williams", + "author_inst": "University of Tennessee Health Science Center" + }, + { + "author_name": "Lillian Zalduondo", + "author_inst": "University of Tennessee Health Science Center" + }, + { + "author_name": "Colleen Beth Jonsson", + "author_inst": "University of Tennessee Health Science Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.29.361261", "rel_title": "Modeling the Opening SARS-CoV-2 Spike: an Investigation of its Dynamic Electro-Geometric Properties", @@ -1090588,97 +1087579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.25.20219063", - "rel_title": "Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020", - "rel_date": "2020-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20219063", - "rel_abs": "Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of the virus to be tracked via phylogenetic analysis (Worobey et al., 2020; Hadfield et al., 2018; Pybus et al., 2020). While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced, allowing continent-specific variants to emerge. However, within Europe travel resumed in the summer of 2020, and the impact of this travel on the epidemic is not well understood. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread to multiple locations in Europe. We find no evidence of increased transmissibility of this variant, but instead demonstrate how rising incidence in Spain, resumption of travel across Europe, and lack of effective screening and containment may explain the variants success. Despite travel restrictions and quarantine requirements, we estimate 20E (EU1) was introduced hundreds of times to countries across Europe by summertime travellers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.\n\nSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the first pandemic where the spread of a viral pathogen has been globally tracked in near real-time using phylogenetic analysis of viral genome sequences (Worobey et al., 2020; Hadfield et al., 2018; Pybus et al., 2020). SARS-CoV-2 genomes continue to be generated at a rate far greater than for any other pathogen and more than 500,000 full genomes are available on GISAID as of February 2020 (Shu and McCauley, 2017).\n\nIn addition to tracking the viral spread, these genome sequences have been used to monitor mutations which might change the transmission, pathogenesis, or anti-genic properties of the virus. One mutation in particular, D614G in the spike protein, has received much attention. This variant (Nextstrain clade 20A) seeded large outbreaks in Europe in early 2020 and subsequently dominated the outbreaks in the Americas, thereby largely replacing previously circulating lineages. This rapid rise led to the suggestion that this variant is more transmissible, which has since been corroborated by phylogenetic (Korber et al., 2020; Volz et al., 2020) and experimental evidence (Plante et al., 2020; Yurkovetskiy et al., 2020).\n\nFollowing the global dissemination of SARS-CoV-2 in early 2020 (Worobey et al., 2020), intercontinental travel dropped dramatically. Within Europe, however, travel and in particular holiday travel resumed in summer (though at lower levels than in previous years) with largely uncharacterized effects on the pandemic. Here we report on a novel SARS-CoV-2 variant 20E (EU1) (S:A222V) that emerged in early summer 2020, presumably in Spain, and subsequently spread to multiple locations in Europe. Over the summer, it rose in frequency in parallel in multiple countries. As we report here, this variant, 20E (EU1), and a second variant 20A.EU2 with mutation S477N in the spike protein accounted for the majority of sequences in Europe in the autumn of 2020.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Emma B Hodcroft", - "author_inst": "University of Basel" - }, - { - "author_name": "Moira Zuber", - "author_inst": "University of Basel, Basel, Switzerland" - }, - { - "author_name": "Sarah Nadeau", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Timothy G Vaughan", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Katharine H. D. Crawford", - "author_inst": "Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA" - }, - { - "author_name": "Christian L Althaus", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Martina Reichmuth", - "author_inst": "University Bern" - }, - { - "author_name": "John E Bowen", - "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Alexandra C. Walls", - "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA, USA" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA" - }, - { - "author_name": "David Veesler", - "author_inst": "Department of Biochemistry, University of Washington, Seattle, Washington, USA" - }, - { - "author_name": "David Mateo", - "author_inst": "Kido Dynamics SA, Avenue de Sevelin 46, 1004 Lausanne, Switzerland" - }, - { - "author_name": "Alberto Hernando de Castro", - "author_inst": "Kido Dynamics SA, Avenue de Sevelin 46, 1004 Lausanne, Switzerland" - }, - { - "author_name": "I\u00f1aki Comas", - "author_inst": "Biomedicine Institute of Valencia (IBV-CSIC), Valencia, Spain" - }, - { - "author_name": "Fernando Gonzalez Candelas", - "author_inst": "FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain" - }, - { - "author_name": "- SeqCOVID-SPAIN consortium", - "author_inst": "" - }, - { - "author_name": "Tanja Stadler", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" - }, - { - "author_name": "Richard A Neher", - "author_inst": "University of Basel, Basel, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.25.20218735", "rel_title": "A multiagent coronavirus model with territorial vulnerability parameters", @@ -1091435,6 +1088335,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.10.22.20215277", + "rel_title": "The importance of the human factor during the evolution of SARS-CoV-2 pandemic: the successful case of the Italian strategy", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20215277", + "rel_abs": "In Italy, 311,364 cases and 35,851 deaths of people who tested positive for SARS-CoV-2 were registered as of September 29th, 2020. To avoid the spreading of the virus, mathematical models predicting the course of infections spread1 become the basis to plan stringent countermeasures. We applied a published algorithm to real data up to September 27th, modeling two scenarios where predicted and real data were compared: a conservative scenario with a lockdown still ongoing and a scenario reflecting what actually happened in Italy, where the lockdown has been removed. Results revealed that the number of individuals in life-threatening condition is much lower than predicted, as well as the number of symptomatic individuals. Contrarily, the number of asymptomatic individuals is much higher than predicted. This suggest that human beings are not passive victims, but active fighters able to change the course of the infection creating adaptive strategies against the infections spread.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cristina Scarpazza", + "author_inst": "University of Padova" + }, + { + "author_name": "Gianluca Musumeci", + "author_inst": "Ca Foscari University of Venice, Italy" + }, + { + "author_name": "Andrea Sigfrido Camperio Ciani", + "author_inst": "University of Padova" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.10.22.20218057", "rel_title": "Challenges for non-technical implementation of digital proximity tracing: early experiences from Switzerland", @@ -1092158,37 +1089085,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.23.20218214", - "rel_title": "The French Covid-19 contact tracing app: usage and opinions by students in the health domain", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218214", - "rel_abs": "BackgroundMany countries around the world have developed mobile phone apps capable of supporting instantaneous contact tracing to control the Covid-19 pandemic. In France, a few people have downloaded and are using the StopCovid contact tracing app. Reasons for this low uptake are unexplored. Students in the health domain are especially concerned and their usage and opinions about the app can inform improvements and diffusion of StopCovid among young people.\n\nObjectiveTo investigate health-related students knowledge, attitudes, beliefs and practices about the StopCovid app.\n\nMethodsA field survey was conducted among 318 students at the health sciences campus of the University of Bordeaux, France, between September 25th and October 16th, 2020. Quota sampling method was used and descriptive statistics were performed.\n\nResultsA total of 77.3% (246/318) students had heard about the app, but only 11.3% (36/318) had downloaded it and 4.7% (15/318) were still using it at the time of the survey. Main reasons for not using the app were: belief that it was not effective given its limited diffusion (17.6%, 37/210), lack of interest (17.6%, 37/210) and distrust in data security and fear to be geo-located (15.7%, 33/210). Among those who had not heard about the app, after a brief description of its functioning and confidentiality policy, 52.7% (38/72) would use it. Participants reported that the main solution for increasing the use of the app would be a better communication (71.4%, 227/318).\n\nConclusionEven among health students, the contact tracing app was poorly used. Findings suggest that improved communication describing its advantages and simplicity of use, and clarifying false beliefs about the app could help improving significantly its uptake.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ilaria Montagni", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Nicolas Roussel", - "author_inst": "Inria Bordeaux - Sud-Ouest" - }, - { - "author_name": "Rodolphe Thiebaut", - "author_inst": "University of Bordeaux Inria CHU" - }, - { - "author_name": "Christophe Tzourio", - "author_inst": "University of Bordeaux Inserm" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.10.23.20218461", "rel_title": "Detection and Segmentation of Lesion Areas in Chest CT Scans For The Prediction of COVID-19", @@ -1092805,6 +1089701,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.25.20216937", + "rel_title": "Reducing Covid-19 risk in schools: a qualitative examination of staff and family views and concerns", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20216937", + "rel_abs": "BackgroundThe Covid-19 pandemic has necessitated schools implementing Covid-19 risk-reduction measures.\n\nMethodsWe investigated young people, parent and school staff attitudes towards secondary school Covid-19 mitigation measures. Recruitment used school communication, community organisations and snowball sampling. Audio recorded online/phone individual/group interviews lasted 45 minutes. Interviews focused on social distancing, hand-hygiene and testing. Team framework analysis used interview notes and transcripts.\n\nResultsParticipants were 13 school staff, 20 parents and 17 young people. Concerns about Covid-19 risk at school, especially to vulnerable individuals, were outweighed by perceived risks of not returning to school. Some teachers anticipated guilt around being a potential spreader. Participants saw school mitigation measures as an acceptable and pragmatic solution to the impossibility of social distancing, although anticipated challenges in changing habitual behaviour. Participants supported school Covid-19 testing but identified the need to consider data security and stigma. Staff were concerned about unintended consequences of risk-reduction strategies and widening inequalities.\n\nConclusionFamilies and staff supported Covid-19 mitigation measures in schools. Clear messaging and engendering collective responsibility are important for compliance and success. However, schools and policy makers should consider unintended consequences of measures, supporting vulnerable individuals and those with additional needs, and avoiding widening inequalities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ava Lorenc", + "author_inst": "University of Bristol" + }, + { + "author_name": "Joanna May Kesten", + "author_inst": "University of Bristol" + }, + { + "author_name": "Judith Kidger", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rebecca Langford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jeremy Horwood", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.25.20219170", "rel_title": "Factors driving availability of COVID-19 convalescent plasma: Insights from a demand, production and supply model", @@ -1093696,37 +1090627,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.23.20217570", - "rel_title": "Tracking changes in reporting of epidemiological data during the COVID-19 pandemic in Southeast Asia: an observational study during the first wave", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20217570", - "rel_abs": "BackgroundWhen a new pathogen emerges, consistent case reporting is critical for public health surveillance. Tracking cases geographically and over time is key for understanding the spread of an infectious disease and how to effectively design interventions to contain and mitigate an epidemic. In this paper we describe the reporting systems on COVID-19 in Southeast Asia during the first wave in 2020, and highlight the impact of specific reporting methods.\n\nMethodsWe reviewed key epidemiological variables from various sources including a regionally comprehensive dataset, national trackers, dashboards, and case bulletins for 11 countries during the first wave of the epidemic in Southeast Asia. We recorded timelines of shifts in epidemiological reporting systems. We further described the differences in how epidemiological data are reported across countries and timepoints, and the accessibility of epidemiological data.\n\nFindingsOur findings suggest that countries in Southeast Asia generally reported precise and detailed epidemiological data during the first wave of the COVID-19 pandemic. However, changes in reporting were frequent and varied across data and countries. Changes in reporting rarely occurred for demographic data such as age and sex, while reporting shifts for geographic and temporal data were frequent. We also found that most countries provided COVID-19 individual-level data daily using HTML and PDF, necessitating scraping and extraction before data could be used in analyses.\n\nInterpretationCountries have different reporting systems and different capacities for maintaining consistent reporting of epidemiological data. As the pandemic progresses, governments may also change their priorities in data sharing. Our study thus highlights the importance of more nuanced analyses of epidemiological data of COVID-19 within and across countries because of the frequent shifts in reporting. Further, most countries provide data on a daily basis but not always in a readily usable format. As governments continue to respond to the impacts of COVID-19 on health and the economy, data sharing also needs to be prioritised given its foundational role in policymaking, and the implementation and evaluation of interventions.\n\nFundingThe work was supported through an Engineering and Physical Sciences Research Council (EPSRC) (https://epsrc.ukri.org/) Systems Biology studentship award (EP/G03706X/1) to TR. This project was also supported in part by the Oxford Martin School.\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arianna Maever L Amit", - "author_inst": "University of the Philippines Manila" - }, - { - "author_name": "Veincent Christian F Pepito", - "author_inst": "School of Medicine and Public Health, Ateneo de Manila University, Pasig, Philippines" - }, - { - "author_name": "Bernardo Gutierrez", - "author_inst": "Department of Zoology, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Thomas Rawson", - "author_inst": "Department of Zoology, University of Oxford, Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.20.20216085", "rel_title": "COVIDTrach; a prospective cohort study of mechanically ventilated COVID-19 patients undergoing tracheostomy in the UK", @@ -1094451,6 +1091351,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.26.20219634", + "rel_title": "Who is (Not) Complying with the Social Distancing Directive and Why? Testing a General Framework of Compliance with Multiple Measures of Social Distancing", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219634", + "rel_abs": "A study involving over 2000 online participants tested a general framework regarding compliance with a directive in the context of the COVID-19 pandemic. The study featured not only a self-report measure of social distancing but also behavioral measures -- simulations that presented participants with graphical depictions mirroring multiple real-world scenarios and asked them to position themselves in relation to others in the scene. The conceptual framework highlights three essential components of a directive: (1) the source, some entity is advocating for a behavioral change; (2) the surrounding context, the directive is in response to some challenge; and (3) the target, the persons to whom the directive is addressed. Belief systems relevant to each of these three components are predicted, and were found, to relate to compliance with the social distancing directive. The implications of the findings for public service campaigns encouraging people to engage in social distancing are discussed.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Russell H. Fazio", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Benjamin C. Ruisch", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Courtney A. Moore", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Javier A. Granados Samayoa", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shelby T. Boggs", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Jesse T. Ladanyi", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.25.20219279", "rel_title": "Inconsistent with the intent of public health strategies on incidence and fatality in states with extra mandatory stay-at-home and face masks orders during COVID-19 pandemic in the US", @@ -1095294,69 +1092233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.25.20219253", - "rel_title": "Staging and typing of chest CT images: A quantitative analysis based on an ambispective observational cohort study of 125 patients with COVID-19 in Xiangyang, China", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20219253", - "rel_abs": "BackgroundThe stage of CT images was rarely studied and the relationship between the severity of Coronavirus Disease 2019 (COVID-19) and CT images has not been studied based on systematic quantitative analysis currently.\n\nPurposeTo investigate the staging duration and classification of CT images of patients with COVID-19 based on quantitative analysis.\n\nMaterials and MethodsThis is an ambispective observational cohort study based on 125 patients with COVID-19 from Jan 23 to Feb 28, 2020. The stage of CT and pulmonary lesion size were quantitatively analyzed. The categorical regression analysis based on optimal scale (CATREG) was performed to evaluate the association of CT score, age, and gender with the clinical type.\n\nResultsThe CT images of 125 patients with COVID-19 (50.13 {+/-} 16.91 years, 66 women) were analyzed in this study. Except for pre-early stage, the duration of early, progression-consolidation, and dissipation stage of CT images was 3.40 {+/-} 2.31, 10.07 {+/-} 4.91, and 20.60 {+/-} 7.64 days, respectively. The median CT score was 5.00 (2.00-8.50) during the first 30 days, which reached a peak on the 11th day. Significant differences were found between the median CT scores of different clinical types (P<0.05). Besides, the age was correlated with the clinical type (P<0.001), the CT scores of 0.00-11.50, 11.50-16.00, and 16.00-20.00 were separately correlated with the moderate, severe, and critical type with the output accuracy 69.60%.\n\nConclusionThe four-stage staging method based on quantitative analysis is consistent with the change rules of staging features and COVID-19. Quantitative study by scoring pulmonary lesion sizes accurately revealed the evolvement of pulmonary lesions and differences between different clinical types.\n\nSummaryQuantitative study of the stage duration and classification of chest CT images can objectively reveal the relationship between Coronavirus Disease 2019 (COVID-19) and chest CT images.\n\nKey Results1. A four-stage staging method was proposed. Except for pre-early stage, the duration of early, progression-consolidation, and dissipation stage of CT images was 3.40 {+/-} 2.31, 10.07 {+/-} 4.91, and 20.60 {+/-} 7.64 days, respectively.\n\n2. The severer the disease, the higher the median CT scores and their peak value.\n\n3. The CT scores of 0.00-11.50, 11.50-16.00, and 16.00-20.00 were separately correlated with the moderate, severe, and critical type.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Guoxin Huang", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Yong Wang", - "author_inst": "Department of Radiology, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Xiaxia Wu", - "author_inst": "Department of Radiology, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Gaojing Qu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Junwen Chen", - "author_inst": "Department of Respiratory and Critical Care Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Hui Yu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Meiling Zhang", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Lisha Wang", - "author_inst": "Department of Radiology, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Jinwei Ai", - "author_inst": "Department of Orthopedic, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Haoming Zhu", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Lei Chen", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - }, - { - "author_name": "Bin Pei", - "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.10.26.20219600", "rel_title": "Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab", @@ -1096397,6 +1093273,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.10.27.20220400", + "rel_title": "The Incidence and Severity of COVID-19 in Adult Professional Soccer Players", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220400", + "rel_abs": "IntroductionAt present, there are no data regarding the incidence and clinical course of COVID-19 among professional soccer players, and the studies examining putative complications of COVID-19 infections are probabilistic. Thus, examining the incidence of COVID-19 and various aspects of its clinical course in a group of adult professional soccer players would be of great practical interest.\n\nMethodsThe incidence, clinical course, and severity of COVID-19 infection, as well as the duration of treatment and return to play were studied by the questioning of the team physicians and medical records assessment in the group of adult professional soccer players representing the clubs of the Russian Premier-League (RPL) during the period of championship resumption from 01.04.2020 until 20.09.2020.\n\nResultsCOVID-19 infection was detected in 103 soccer players in the course of COVID-19 screening. This number comprises 14.5% of all soccer players which were on the rosters of RPL soccer teams and which were subject to regular COVID-19 testing.\n\nThe asymptomatic course was observed in 43.7% of cases (n=45). These players were isolated and their clinical condition was monitored closely. Clinical symptoms were observed in 56.3% of cases (n=58), the most common symptoms being fatigue, headache, fever, and anosmia.\n\nConclusionsCOVID-19 infection was commonly diagnosed among adult professional soccer players continuously residing in Russia. However, the majority of infections had a mild course and did not impair return to regular exercise.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Eduard Bezuglov", + "author_inst": "Sechenov First Moscow State Medical University (Sechenov University); Federal Research and Clinical Center of Sports Medicine and Rehabilitation of Federal Medi" + }, + { + "author_name": "Artemii Lazarev", + "author_inst": "Sechenov First Moscow State Medical University (Sechenov University); High Performance Sport Laboratory, Moscow Witte University" + }, + { + "author_name": "Evgeniy Achkasov", + "author_inst": "Sechenov First Moscow State Medical University (Sechenov University)" + }, + { + "author_name": "Vladimir Khaitin", + "author_inst": "FC Zenit, St. Petersburg" + }, + { + "author_name": "Larisa Romanova", + "author_inst": "Head center for hygiene and epidemiology of the Federal Medical Biological Agency; Academy of Postgraduate Education under the Federal State Budgetary Unit Fede" + }, + { + "author_name": "Mikhail Butovskiy", + "author_inst": "FC Rubin, Kazan" + }, + { + "author_name": "Vladimir Khokhlov", + "author_inst": "FC Rostov, Rostov-on-Don" + }, + { + "author_name": "Maxim Tsyplenko", + "author_inst": "FC Tambov, Tambov" + }, + { + "author_name": "Alexander Linsky", + "author_inst": "FC Sochi, Sochi" + }, + { + "author_name": "Petr Chetverikov", + "author_inst": "FC Orenburh, Orenburg" + }, + { + "author_name": "Magomedtagir Sugaipov", + "author_inst": "FC Akhmat, Gronziy" + }, + { + "author_name": "Arseniy Petrov", + "author_inst": "University of Goettingen" + }, + { + "author_name": "Oleg Talibov", + "author_inst": "High Performance Sport Laboratory, Moscow Witte University; Moscow State University of Medicine and Dentistry" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2020.10.27.20220442", "rel_title": "Management of Acute Appendicitis in Children: Takeaway from Coronavirus Disease-2019, a Perspective of Pediatric Surgeons from South Asia", @@ -1097568,61 +1094511,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.10.22.20217638", - "rel_title": "Is increased mortality by multiple exposures to COVID-19 an overseen factor when aiming for herd immunity?", - "rel_date": "2020-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217638", - "rel_abs": "BackgroundGovernments across the globe responded with different strategies to the COVID-19 pandemic. While some countries adapted draconic measures, which have been perceived controversial others pursued a strategy aiming for herd immunity. The latter is even more controversial and has been called unethical by the WHO Director-General. Inevitably, without proper control measure, viral diversity increases and multiple infectious exposures become common, when the pandemic reaches its maximum. This harbors not only a potential threat overseen by simplified theoretical arguments in support of herd immunity, but also deserves attention when assessing response measures to increasing numbers of infection.\n\nMethods and findingsWe extend the simulation model underlying the pandemic preparedness web interface CovidSim 1.1 (http://covidsim.eu/) to study the hypothetical effect of increased morbidity and mortality due to multi infections, either acquired at by successive infective contacts during the course of one infection or by a single infective contact with a multi-infected individual.\n\nThe simulations are adjusted to reflect roughly the situation in the East Coast of the USA. We assume a phase of general contact reduction ( lockdown) at the beginning of the epidemic and additional case-isolation measures. We study the hypothetical effects of varying enhancements in morbidity and mortality, different likelihoods of multi-infected individuals to spread multi infections and different susceptibility to multi infectious in different disease phases. It is demonstrated that multi infections lead to a slight reduction in the number of infections, as these are more likely to get isolated due to their higher morbidity. However, the latter substantially increases the number of deaths. Furthermore, simulations indicate that a potential second lockdown can substantially decrease the epidemic peak, the number of multi-infections and deaths.\n\nConclusionsEnhanced morbidity and mortality due to multiple disease exposure is a potential threat in the COVID-19 pandemic that deserves more attention. Particularly it underlines another facet questioning disease management strategies aiming for herd immunity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kristina Barbara Helle", - "author_inst": "Hochschule Mittweida" - }, - { - "author_name": "Arlinda Sadiku", - "author_inst": "Hochschule Mittweida" - }, - { - "author_name": "Girma Mesfin Zelleke", - "author_inst": "AIMS Cameroon" - }, - { - "author_name": "Aliou Bouba", - "author_inst": "AIMS Cameroon" - }, - { - "author_name": "Toheeb Babantunde Ibrahim", - "author_inst": "Hochschule Mittweida" - }, - { - "author_name": "Henri Christian Junior Tsoungui Obama", - "author_inst": "Hochschule Mittweida" - }, - { - "author_name": "Vincent Appiah", - "author_inst": "University of Ghana" - }, - { - "author_name": "Gideon A. Ngwa", - "author_inst": "University of Buea" - }, - { - "author_name": "Miranda I. Teboh-Ewungkem", - "author_inst": "Lehigh University" - }, - { - "author_name": "Kristan Alexander Schneider", - "author_inst": "Hochschule Mittweida" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.22.20217554", "rel_title": "Extending the range of symptoms in a Bayesian Network for the Predictive Diagnosis of COVID-19", @@ -1098039,6 +1094927,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.22.20217752", + "rel_title": "Lockdown related travel behavior undermines thecontainment of SARS-CoV-2", + "rel_date": "2020-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217752", + "rel_abs": "In response to the SARS-CoV-2 pandemic, unprecedented policies of travel restrictions and stay-at-home orders were enacted around the world. Ultimately, the publics response to announcements of lockdowns - defined here as restrictions on both local movement or long distance travel - will determine how effective these kinds of interventions are. Here, we measure the impact of the announcement and implementation of lockdowns on human mobility patterns by analyzing aggregated mobility data from mobile phones. We find that following the announcement of lockdowns, both local and long distance movement increased. To examine how these behavioral responses to lockdown policies may contribute to epidemic spread, we developed a simple agent-based spatial model. We find that travel surges following announcements of lockdowns can increase seeding of the epidemic in rural areas, undermining the goal of the lockdown of preventing disease spread. Appropriate messaging surrounding the announcement of lockdowns and measures to decrease unnecessary travel are important for preventing these unintended consequences of lockdowns.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nishant Kishore", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rebecca Kahn", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Pamela P Martinez", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Pablo M De Salazar", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Ayesha S Mahmud", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Caroline Buckee", + "author_inst": "Harvard School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.22.20217851", "rel_title": "Clinical and laboratory characteristics in outpatient diagnosis of COVID-19 in healthcare professionals in Rio de Janeiro, Brazil", @@ -1098950,53 +1095877,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.21.20217034", - "rel_title": "Clinico-laboratory profile, intensive care needs, treatment details, and outcome of Pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS): A systematic review and Meta-analysis.", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217034", - "rel_abs": "ObjectivesTo synthesize the current data on clinico-laboratory features, intensive care needs, treatment, and outcome of Pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) or multisystem inflammatory syndrome in children (MIS-C).\n\nData SourcesArticles published in PubMed, Web of Science, Scopus, Google Scholar, and WHO COVID-19 research database, CDC database, and Cochrane COVID-19 study register between 1st December 2019 to 10th July 2020.\n\nStudy SelectionObservational studies involving patients [≤]21 years with PIMS-TS or MIS-C, that reported the clinico-laboratory features, intensive care needs, treatment, and outcome.\n\nData ExtractionThe search identified 422 citations and finally 18 studies with 833 participants were included and pooled estimate was calculated for parameters of interest utilising random effect model.\n\nData SynthesisThe median age was 9 (8-11) years. Fever, gastrointestinal symptoms, rash, conjunctival injection, and respiratory symptoms were common clinical features. Majority had positive SARS-CoV-2 antibody test and only 1/3rd had RT-PCR positive. The commonest laboratory abnormalities were elevated CRP, D-dimer, procalcitonin, BNP, fibrinogen, ferritin, troponin, and IL-6; and lymphopenia, hypoalbuminemia, and thrombocytopenia. The cardiovascular complications included shock (65%), myocardial dysfunction (61%), myocarditis (65%), and coronary artery abnormalities (39%). Three-fourth children required admission in PICU for mechanical ventilation (25%) and vasoactive drugs (61%). The common treatment provided was IVIG (82%), steroids (54%), antiplatelet drugs (64%), and anticoagulation (51%). The mortality was low (n=13).\n\nConclusionFever, gastrointestinal and mucocutaneous symptoms, cardiac dysfunction, shock, and hyperinflammation are common manifestations of PIMS-TS or MIS-C. The short-term outcome is good with supportive intensive care and immunomodulatory treatment.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vijai Williams", - "author_inst": "Gleneagles Global Health City, Perumbakkam, Chennai, India" - }, - { - "author_name": "Nabaneea Dash", - "author_inst": "Christian Medical College and Hospital, Vellore, Tamil Nadu, India." - }, - { - "author_name": "Renu Suthar", - "author_inst": "Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India" - }, - { - "author_name": "Vichithra Mohandoss", - "author_inst": "Practising Pediatrician, Chennai, India." - }, - { - "author_name": "Nishant Jaiswal", - "author_inst": "Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India" - }, - { - "author_name": "TK Kavitha", - "author_inst": "Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India" - }, - { - "author_name": "Karthi Nallasamy", - "author_inst": "Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India" - }, - { - "author_name": "Suresh Kumar Angurana", - "author_inst": "PGIMER, Chandigarh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.10.21.20216804", "rel_title": "Predictors of PTSD, depression and anxiety in UK frontline health and social care workers during COVID-19.", @@ -1099597,6 +1096477,41 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.10.20.20216440", + "rel_title": "Covid-19 in children: is there any correlation with renal function and severity of the disease?", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216440", + "rel_abs": "BackgroundKidney manifestations are life-threatening conditions, such as end-stage renal disease (ESRD), especially when attributed to viral infections. The severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), is an emerging health problem worldwide, potentially affecting all organs, including the kidney. Most reports on kidney manifestations were conducted mostly on the adult and elderly population, and limited on children. Therefore, this study aims to analyse the correlation between kidney manifestations with the renal function of pediatric patients suffering from COVID-19.\n\nMethodsAn observational analytic study was conducted in Hasan Sadikin General Hospital, Bandung, Indonesia, from March to August 2020. The demographic data, clinical signs, laboratory results, and notable kidney function were analysed, while the disease was classified as severe and nonsevere based on its clinical appearance. The Mann-Whitney test for nonparametric was used to analyze the collected data. Results. In this study, 16 COVID-19 children were selected as the research subjects, the median eGFR value in the severe group was lower (49.59 ml / minute / 1.73m2) compared to the nonsevere (113 ml / minute / 1.73m2), however, not statistically significant (p = 0.521). Significant high CRP and low thrombocyte levels were found in severe SARS-CoV-2 infection (p<0.05). Conclusion. A severe SARS-CoV-2 infection tends to affect the kidney, which is manifested as decreased glomerular filtration rate (GFR).", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dedi Rachmadi Sambas", + "author_inst": "Universitas Padjadjaran, Hasan Sadikin Hospital" + }, + { + "author_name": "Ahmedz AW Widiasta", + "author_inst": "Pediatric nephrology division, Hasan Sadikin Hospital" + }, + { + "author_name": "Dany Hilmanto", + "author_inst": "Pediatric nephrology division, RSHS, Bandung" + }, + { + "author_name": "Hadyana Sukandar", + "author_inst": "Epidemiology and biostatistic division, public heath department, faculty of medicine, Universitas Padjadjaran, Bandung" + }, + { + "author_name": "Nanan Sekarwana", + "author_inst": "Pediatric nephrology, child health, faculty of medicine, Hasan Sadikin Hospital, Bandung" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.10.20.20215616", "rel_title": "SARS-CoV-2 antibodies in the Southern Region of New Zealand, 2020", @@ -1100516,33 +1097431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20215251", - "rel_title": "Survey of Attitudes on Personal Protection Interventions Against COVID-19 Including MMR Vaccination and Future Anti-COVID Vaccines", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20215251", - "rel_abs": "An electronic survey was conducted in October, 2020 among individuals primarily age 60 and older regarding their degree of confidence of deriving personal protection from 8 different anti-COVID interventions - social isolation, lockdowns, avoiding restaurants, taking MMR vaccine, wearing masks when indoors with others, avoiding hotels, avoiding commercial air travel, and using the first future specific anti-COVID vaccine. Responses were received from 135 persons from many different U.S. regions and 5 foreign countries. Respondents were generally individuals with very high levels of education and personal achievement. Results demonstrated wide diversity of responses regarding each of these interventions. None were strongly supported by a majority of respondents, but those receiving the largest proportions of strong support were social isolation (41%), wearing masks indoors (41%), and using the first anti-COVID vaccine (41%). MMR (measles-mumps-rubella) vaccination was viewed much more positively than negatively but had the highest proportion of individuals who felt they had insufficient data to formulate an opinion. The largest number of strong negative assessments were toward lockdowns (37%). We speculate that the wide variation in perception of possible benefits from the surveyed interventions, most of which have been widely practiced by or imposed upon millions of individuals, in this highly accomplished older population at increased personal risk from COVID-19 reflects the current absence of rigorous scientific proof of the efficacy of any these interventions, and the continuation of the epidemic despite the widespread utilization of most of them.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Joseph D. Schulman", - "author_inst": "Genetics & IVF Institute, 3015 Williams Drive, Fairfax, VA 22031" - }, - { - "author_name": "James N. Cooper", - "author_inst": "Department of Medicine, Inova Fairfax Hospital, Falls Church, VA 22042" - }, - { - "author_name": "Gary W. Crooks", - "author_inst": "Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.21.20216820", "rel_title": "Seroprevalence of SARS-CoV-2 IgG antibodies in two regions of Estonia (KoroSero-EST-1)", @@ -1101107,6 +1097995,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.21.20216747", + "rel_title": "The wide spectrum of neuropsychiatric complications in Covid-19 patients within a multidisciplinary hospital context", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216747", + "rel_abs": "ObjectiveTo describe the spectrum of neurological and psychiatric complications in patients with Covid-19 seen in a multidisciplinary center over six months.\n\nMethodsWe conducted a retrospective, observational study on all patients showing neurological or psychiatric symptoms in the context of Covid-19 seen in the Department of Neurology and Psychiatry of the APHP-Sorbonne University. We collected demographic data, medical and treatment history, comorbidities, symptoms, date of onset, and severity of Covid-19 infection, neurological and psychiatric symptoms, neurological and psychiatric examination data and, when available, results from cerebrospinal fluid (CSF) analysis, brain magnetic resonance (MRI) imaging, 18-fluorodesoxyglucose-position emission computed tomography (FDG-PET/CT)), electroencephalography (EEG) and electroneuromyography (ENMG).\n\nResults245 patients were included in the analysis. One-hundred fourteen patients (47%) were admitted to the intensive care unit (ICU) and 10 (4%) died. The most frequently reported neuropsychiatric symptoms were motor deficit (41%), cognitive disturbance (35%), impaired consciousness (26%), psychiatric disturbance (24%), headache (20%) and behavioral disturbance (18%). The most frequent syndromes diagnosed were encephalopathy (43%), critical illness polyneuropathy and myopathy (26%), isolated psychiatric disturbance (18%), and cerebrovascular disorders (16%). No patients showed evidence of SARS-CoV-2 in their CSF. Encephalopathy was associated with greater age and higher risk of death. Critical illness neuromyopathy was associated with an extended stay in the ICU.\n\nConclusionsThe majority of the neuropsychiatric complications recorded could be imputed to critical illness, intensive care and systemic inflammation, which contrasts with the paucity of more direct SARS-CoV-2-related complications or post-infection disorders.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Cecile Delorme", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Marion Houot", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Charlotte Rosso", + "author_inst": "Urgences neurovasculaires - Pitie - Salpetriere" + }, + { + "author_name": "Stephanie Carvalho", + "author_inst": "Institut du Cerveau" + }, + { + "author_name": "Thomas Nedelec", + "author_inst": "Institut du Cerveau" + }, + { + "author_name": "Redwan Maatoug", + "author_inst": "Departement de Psychiatrie - Pitie Salpetriere" + }, + { + "author_name": "Victor Pitron", + "author_inst": "Departement de Psychiatrie - Pitie Salpetriere" + }, + { + "author_name": "Salimata Gassama", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Sara Sambin", + "author_inst": "Institut du Cerveau" + }, + { + "author_name": "Stephanie Bombois", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Bastien Herlin", + "author_inst": "Epileptology unit- Pitie Salpetriere" + }, + { + "author_name": "Gaelle Ouvrard", + "author_inst": "Neuro-orthopedie - Hopital Rothschild" + }, + { + "author_name": "Gaelle Bruneteau", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Adele Hesters", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Ana Zenovia Gales", + "author_inst": "Service des pathologies du sommeil - Pitie Salpetriere" + }, + { + "author_name": "Bruno Millet", + "author_inst": "Departement de Psychiatrie - Pitie Salpetriere" + }, + { + "author_name": "Foudil Lamari", + "author_inst": "Biochimie - Pitie Salpetriere" + }, + { + "author_name": "Stephane Lehericy", + "author_inst": "Neuroradiologie - Pitie Salpetriere" + }, + { + "author_name": "Vincent Navarro", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Benjamin Rohaut", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Sophie Demeret", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Thierry Maisonobe", + "author_inst": "Departement de Neurophysiologie - Pitie Salpetriere" + }, + { + "author_name": "Marion Yger", + "author_inst": "Neurologie - Saint Antoine" + }, + { + "author_name": "Bertrand Degos", + "author_inst": "Neurologie - Avicennes" + }, + { + "author_name": "Louise-Laure Mariani", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + }, + { + "author_name": "Christophe Bouche", + "author_inst": "Departement de Psychiatrie - Pitie Salpetriere" + }, + { + "author_name": "Nathalie Dzierzynski", + "author_inst": "Psychiatrie - Tenon" + }, + { + "author_name": "Bruno Oquendo", + "author_inst": "Geriatrie - Pitie Salpetriere Charles Foix" + }, + { + "author_name": "Flora Ketz", + "author_inst": "Geriatrie - Pitie Salpetriere Charles Foix" + }, + { + "author_name": "An-Hung Nguyen", + "author_inst": "Addictologie - Pitie Salpetriere" + }, + { + "author_name": "Aurelie Kas", + "author_inst": "Medecine Nucleaire - Pitie Salpetriere" + }, + { + "author_name": "Jean-Yves Delattre", + "author_inst": "Institut du Cerveau" + }, + { + "author_name": "Jean-Christophe Corvol", + "author_inst": "Departement de Neurologie - Pitie Salpetriere" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.10.23.351775", "rel_title": "mRNA based SARS-CoV-2 vaccine candidate CVnCoV induces high levels of virus neutralizing antibodies and mediates protection in rodents", @@ -1102002,33 +1099037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.20.20215541", - "rel_title": "Prevalence of COVID-19 in Adolescents and Youth Compared with Older Adults in States Experiencing Surges", - "rel_date": "2020-10-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215541", - "rel_abs": "PURPOSEThere has been considerable controversy regarding susceptibility of adolescents (10-19 years) and youth (15-24 years) to COVID-19. However, a number of studies have reported that adolescents are significantly less susceptible than older adults. Summer 2020 provided an opportunity to examine data on prevalence since after months of lockdowns, with the easing of restrictions, people were mingling, leading to surges in cases.\n\nMETHODSWe examined data from six U.S. states experiencing surges in the number of cases to determine prevalence of COVID-19, and two other measures, related to prevalence in adolescents and youth as compared to older adults. The two other measures were: (Percentage of cases observed in a given age group) / (percentage of cases expected based on population demographics); and percentage deviation, or [(% observed - % expected)/ % expected] x 100.\n\nRESULTSPrevalence of COVID-19 for adolescents and for youth was significantly greater than for older adults (p<.00001), as was percentage observed / percentage expected (p<.005). The percentage deviation was significantly greater in adolescents/youth than in older adults (p < 0.00001) when there was an excess of observed cases over what was expected, and significantly less when observed cases were fewer than expected (p< 0.00001).\n\nCONCLUSIONSOur results are contrary to previous findings that adolescents are less susceptible than older adults. The findings have implications for school re-openings. The age groups 10-19 and 15-24 are students in middle school, high school, college, and the first two years of professional/graduate school. The high prevalence in these age groups would argue against school re-openings in the near future.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Barbara T Rumain", - "author_inst": "New York Medical College" - }, - { - "author_name": "Moshe Schneiderman", - "author_inst": "SUNY Downstate College of Medicine" - }, - { - "author_name": "Allan Geliebter", - "author_inst": "Icahn School of Medicine at Mt. Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.10.22.328864", "rel_title": "Databiology Lab CORONAHACK: Collection of Public COVID-19 Data", @@ -1102673,6 +1099681,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.10.19.20215228", + "rel_title": "Use of dried blood spot samples for SARS-CoV-2 antibody detection using the Roche Elecsys high throughput immunoassay", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215228", + "rel_abs": "BackgroundDried blood spot samples (DBS) provide an alternative sample type to venous blood samples for antibody testing. DBS are used by NHS for diagnosing HCV and by PHE for large scale HIV and Hepatitis C serosurveillance; the applicability of DBS based approaches to SARS-CoV-2 antibody detection is uncertain.\n\nObjectiveTo compare antibody detection in dried blood spot eluates using the Roche Elecsys (R) immunoassay (index test) with antibody detection in paired plasma samples, using the same assay (reference test).\n\nSettingOne Police and one Fire & Rescue facility in England.\n\nParticipants195 participants within a larger sample COVID-19 serodiagnostics study of keyworkers, EDSAB-HOME.\n\nOutcome MeasuresSensitivity and specificity of DBS (the index test) relative to plasma (the reference test), at an experimental cut-off; quality of DBS sample collected; estimates of relative sensitivity of DBS vs. plasma immunoassay in a larger population.\n\nResults18/195 (9.2%) participants tested positive using plasma samples. DBS sample quality varied markedly by phlebotomist, and low sample volume significantly reduced immunoassay signals. Using a cut-off of ten median absolute deviations above the immunoassay result with negative samples, sensitivity and specificity of DBS were 89.0% (95% CI 67.2, 96.9%) and 100.0% (95% CI 97.9, 100%) respectively compared with using plasma. The limit of detection for DBS is about 30 times higher than for plasma.\n\nConclusionDBS use for SARS-CoV-2 serology, though feasible, is insensitive relative to immunoassays on plasma. Sample quality impacts on assay performance. Alternatives, including the collection of capillary blood samples, should be considered for screening programs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ranya Mulchandani", + "author_inst": "Public Health England" + }, + { + "author_name": "Benjamin Brown", + "author_inst": "Public Health England" + }, + { + "author_name": "Tim Brooks", + "author_inst": "Public Health England" + }, + { + "author_name": "Amanda Semper", + "author_inst": "Public Health England" + }, + { + "author_name": "Nicholas Machin", + "author_inst": "Public Health England" + }, + { + "author_name": "Ezra Linley", + "author_inst": "Public Health England" + }, + { + "author_name": "Ray Borrow", + "author_inst": "Public Health England" + }, + { + "author_name": "EDSAB-HOME Study Investigators", + "author_inst": "Public Health England, University of Bristol, University of Warwick" + }, + { + "author_name": "David Wyllie", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.19.20215202", "rel_title": "PERFORMANCE EVALUATION OF A SARS-COV-2 RAPID ANTIGENTEST: TEST PERFORMANCE IN THE COMMUNITY IN THE NETHERLANDS", @@ -1103595,49 +1100654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.10.19.20215558", - "rel_title": "Prevalence of SARS-CoV-2 IgG antibodies in a population from Veracruz (Southeastern Mexico).", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215558", - "rel_abs": "Introduction/AimRecent studies have shown that seroprevalence is quite variable depending on the country, the population and the time of the pandemic in which the serological tests are performed. Here, we investigated the prevalence of IgG antibodies against SARS-CoV-2 in a population living in Veracruz City, Mexico.\n\nMethodsFrom of June 1 to July 31, 2020, the consecutive adult patients (age [≥]18 years) that attended 2 ambulatory diagnostic private practice centers for testing were included. Samples were run on the Abbott Architect instrument using the commercial Abbott SARS-CoV-2 IgG assay. The main outcome was seroprevalence. Demographics, previous infection to SARS-CoV-2 (according to a previous positive polymerase-chain reaction nasopharyngeal swab), self-suspicious of virus of infection (according to have in the previous 4 weeks either fever, headache, respiratory symptoms but not a confirmatory PCR) or no having symptoms were also evaluated.\n\nResultsA total of 2174 subjects were tested, included 53.6% women (mean age 41.8{+/-}15.17 years, range 18-98 years). One thousand and forty-one (52.5%) subjects were asymptomatic, 722 (33.2%) had suspicious of infection and 311 (14.3%) had previous infection. Overall, 642 of 2174 (29.5% [95% CI 27.59%-31.47%]) of our population were seropositive. Seropositivity among groups was 21.3% in asymptomatic, 23.4% in self-suspicious patients and 73.9% in previous infection patients.\n\nConclusionsWe found one of the highest seroprevalences reported for SARS-CoV-2 worldwide in asymptomatic subjects (21.3%) as well in subjects with self-suspicious of COVID-19 (23.4%). The number of infected subjects in our population is not encouraging and it should be interpreted with caution.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jose Maria Remes-Troche", - "author_inst": "University of Veracruz" - }, - { - "author_name": "Antonio Ramos-de-la-Medina", - "author_inst": "Hospital Espanol de Veracruz" - }, - { - "author_name": "Marisol Manriquez-Reyes", - "author_inst": "Hospital Espanol de Veracruz" - }, - { - "author_name": "Laura Martinez-Perez Maldonado", - "author_inst": "Hospital Espanol de Veracruz" - }, - { - "author_name": "Maria Antonieta Solis-Gonzalez", - "author_inst": "Hospital Espanol de Veracruz" - }, - { - "author_name": "Karina Hernandez-Flores", - "author_inst": "Instituto de Investigaciones Medico Biologicas Universidad Veracruzana" - }, - { - "author_name": "Hector Vivanco-Cid", - "author_inst": "Instituto de Investigaciones Medico Biologicas, Universidad Veracruzana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20213116", "rel_title": "Prevalence of SARS-CoV-2 antibodies in France: results from nationwide serological surveillance", @@ -1104466,6 +1101482,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.10.19.20214528", + "rel_title": "SI epidemic model applied to COVID-19 data in mainland China", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20214528", + "rel_abs": "The article is devoted to the parameters identification in the SI model. We consider several methods, starting with an exponential fit of the early cumulative data of Sars-CoV2 in mainland China. The present methodology provides a way to compute the parameters at the early stage of the epidemic. Next, we establish an identifiability result. Then we use the Bernoulli-Verhulst model as a phenomenological model to fit the data and derive some results on the parameters identification. The last part of the paper is devoted to some numerical algorithms to fit a daily piecewise constant rate of transmission.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jacques Demongeot", + "author_inst": "University of Grenoble Alpes" + }, + { + "author_name": "Quentin Griette", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Pierre Magal", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.20.20215814", "rel_title": "Extending the range of COVID-19 risk factors ina Bayesian network model for personalised riskassessment", @@ -1105209,29 +1102252,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.10.15.20213363", - "rel_title": "Examining the decision to offer in-person college instruction during the COVID-19 era: A multilevel analysis of the factors that affected intentions to open", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213363", - "rel_abs": "At the end of Summer 2020 colleges and universities had to make difficult decisions about whether to return to in-person instruction. While opening campuses could pose a major health risk, keeping instruction online could dissuade students from enrolling. Taking an ecological approach that considers the influence of state, county, and college characteristics, this study uses mixed modeling techniques and data from 89% of two- and four-year public and four-year private US colleges to assess the factors that shaped their decision to provide mostly in-person instruction as of August 1, 2020. We consider the roles of the political and religious climate, COVID-19 infections, deaths, and mask mandates, college niche, finances, dormitory capacity, faculty resistance, online readiness, and enrollment pressures. Most notably, we find that decision-making was unrelated to cumulative COVID infection and related mortality rates. The strongest predictor of in-person instruction was the proportion of state residents who voted for Trump in the 2016 presidential election. We also find that dormitory capacity, percentage of revenue from tuition, institutional importance to the local economy, graduation rates, and per capita endowment were associated with providing in-person instruction.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jacob Felson", - "author_inst": "William Paterson University" - }, - { - "author_name": "Amy Adamczyk", - "author_inst": "City University of New York, John Jay College and The Graduate Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.10.15.20213371", "rel_title": "Impact of SARS-CoV-2 on Seasonal Respiratory Viruses: A Tale of Two Large Metropolitan Centers in the United States", @@ -1106180,6 +1103200,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.10.15.20213629", + "rel_title": "Correlation of COVID-19 Mortality with Clinical Parameters in an Urban and Suburban Nursing Home Population", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213629", + "rel_abs": "Importance and ObjectiveCOVID-19 has a high mortality rate amongst nursing home populations (26.4% nationally and 28.3% in New Jersey). Identification of factors influencing mortality in COVID-19 positive nursing home populations may help direct physicians towards appropriate glycemic, blood pressure, weight, kidney function, lipid, thyroid, and hematologic management to reduce COVID-19 mortality.\n\nDesign, Setting, and ParticipantsRetrospective cross-sectional study of patients in two nursing home facilities (one urban, one suburban) from 3/16/2020 to 7/13/2020 with positive COVID-19 PCR assays. Age, race, sex, lipids, hematologic parameters, body mass index, blood pressure, thyroid function, albumin, blood urea nitrogen, creatinine, and hemoglobin A1c were correlated with COVID-19 mortality by chi-squared analysis.\n\nMain Outcome and Results56 patients met the inclusion criteria for the study. Mortality was 14.3% while the New Jersey nursing home average mortality rate was 28.3% as of August 2020. Our patient cohort had a 49.5% reduction in mortality compared to the state average.\n\nIn our overall cohort, none of the clinical parameters correlated with COVID-19 mortality using chi-squared analysis. In the 56 patient cohort, average clinical and laboratory findings were 74.0 years, 62.5% female, 28.5% uncontrolled hypertension, BMI 25.6, hemoglobin A1c 6.4, TSH 2.4, vitamin B12 568.3, folate 12.4, iron 47.8, total iron binding capacity 271.8, hemoglobin 11.6, albumin 3.5, triglycerides 100.3, total cholesterol 133.5, HDL 40.9, and BUN to Creatinine ratio 22.2:1. Logistic multivariate regression analyses failed to demonstrate clinically significant correlation with COVID-19 mortality.\n\nIn the urban nursing home, BUN to creatinine ratio exceeding 20:1 was the only factor that showed statistical significance to COVID-19 mortality (p = 0.03). In the suburban nursing home, age over 80 was the only clinical factor demonstrating statistical significance to COVID-19 mortality (p = 0.003).\n\nConclusions and RelevanceIn our COVID-19 positive nursing home patients, no one parameter was clinically significant in the overall 56-patient cohort; however, mortality in our population was 14.3% compared to New Jerseys 28.3%, a 49.5% reduction in mortality. Rigorous control of the aforementioned clinical parameters may have contributed to this reduction in mortality. Further research requires analysis of more nursing home patients to determine whether rigorous control of clinical parameters decreases mortality from COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat clinical parameters lead to a lower mortality rate in nursing home patients with COVID-19?\n\nFindingsIn this cross-sectional analysis of 56 SARS-CoV-2 positive New Jersey nursing home residents from March to July 2020, controlling hemoglobin A1c, blood pressure, hematologic and lipid panels to recommended levels yielded a mortality rate of 14.3%, a 49.5% reduction from the 28.3% mortality rate of COVID-19 in New Jersey nursing homes.\n\nMeaningMaintaining rigorous control of clinical parameters in nursing home populations may account for a decreased mortality rate of COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Richard S Kirby", + "author_inst": "Sidney Kimmel Medical College" + }, + { + "author_name": "John A Kirby", + "author_inst": "Cooper University Healthcare" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.10.15.20213603", "rel_title": "Risks and Benefits of Antibiotics vs. COVID-19 Morbidity and Mortality", @@ -1106935,57 +1103978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.17.20214296", - "rel_title": "COVID-19 IN CHILDREN WITH RHEUMATIC DISEASES (RD) IN THE SPANISH NATIONAL COHORT EPICO-AEP.", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214296", - "rel_abs": "ObjectivesSARS-CoV-2 infection in adults with rheumatic diseases (RD) is a cause for concern. Data in the pediatric population are practically absent. We aimed to describe the prevalence of patients with RD and their complications among children admitted with COVID-19 in the Spanish national cohort EPICO-AEP; a multicenter prospective national study.\n\nMethodsChildren <18 years old with RD and COVID-19 enrolled in EPICO-AEP were included in this study.\n\nResultsBy June 30th 2020, 350 children were admitted in secondary and tertiary hospitals of Spain with SARS-CoV-2 infection. A total of 8 patients presented RD (2.2% of those hospitalized). All were female. The median age was 12.1 years (IQR 8.3-14.5). The diagnosis related with COVID-19 were febrile syndrome and/or upper respiratory infection (4 cases) and pneumonia (4 cases). One of the 8 (12.5%) patients with a severe juvenile dermatomyositis (JDM) with interstitial lung disease died. Juvenile idiopathic arthritis (JIA) was the most frequent diagnosis in 3/8 (37.5%) patients. In 5/8 (62.5%) cases, the RD was not fully controlled, and all patients except one received corticosteroid treatment.\n\nConclusionsChildren with RD have accounted for 2.2% of hospitalized patients with COVID-19 in our series. The evolution has been moderately favorable, with one deceased. In case of active disease and use of corticosteroids patients should be managed with caution.\n\nWhat is already known about this subject?O_LIStudies in adults with rheumatic disesases (RD) show that immune-mediated inflammatory disease and use of biologics are not associated with worse COVID-19.\nC_LIO_LIPoorly controlled active RD or some treatments such as corticosteroids, may have an increased risk of infection and serious disease in adults. No data in children.\nC_LI\n\nWhat does this study add?O_LIPediatric data from the national EPICO-AEP registry in Spain are presented, where children with RD and COVID-19 were 2.2% of those hospitalized.\nC_LIO_LIActive disease and the use of corticosteroids could be considered risk factors in the pediatric population as well as in adults.\nC_LI\n\nHow might this impact on clinical practice or future developments?O_LIThe rheumatologist pediatrician must be very careful in the management of children with COVID-19 infection, especially if they receive corticosteroid treatment or have active RD.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Cristina Calvo", - "author_inst": "Hospital Universtiario La Paz" - }, - { - "author_name": "Agustin Remesal", - "author_inst": "Hospital Universitario La Paz" - }, - { - "author_name": "Sara Murias", - "author_inst": "Hospital Universitario La Paz" - }, - { - "author_name": "Fatima Ara-Montojo", - "author_inst": "Hospital Unvierstario Quironsalud" - }, - { - "author_name": "Enrique Otheo", - "author_inst": "Hospital Univesitario Ramon y Cajal" - }, - { - "author_name": "Francisco J Sanz-Santaeufemia", - "author_inst": "Hospital Universitario Nino Jesus" - }, - { - "author_name": "Alvaro Villaroya", - "author_inst": "Hospital Universitari i Politecnic La Fe" - }, - { - "author_name": "Cinta Moraleda", - "author_inst": "Hospital Universitario 12 de Octubre" - }, - { - "author_name": "Alfredo Tagarro", - "author_inst": "Hospital Universitario 12 de Octubre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2020.10.18.20214221", "rel_title": "Structural and metabolic brain abnormalities in COVID-19 patients with sudden loss of smell", @@ -1107526,6 +1104518,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.18.20209189", + "rel_title": "Evaluation of Nowcasting for Real-Time COVID-19 Tracking - New York City, March-May 2020", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20209189", + "rel_abs": "To account for delays between specimen collection and report, the New York City Department of Health and Mental Hygiene used a time-correlated Bayesian nowcasting approach to support real-time COVID-19 situational awareness. We retrospectively evaluated nowcasting performance for case counts among residents diagnosed during March-May 2020, a period when the median reporting delay was 2 days. Nowcasts with a 2-week moving window and a negative binomial distribution had lower mean absolute error, lower relative root mean square error, and higher 95% prediction interval coverage than nowcasts conducted with a 3-week moving window or with a Poisson distribution. Nowcasts conducted toward the end of the week outperformed nowcasts performed earlier in the week, given fewer patients diagnosed on weekends and lack of day-of-week adjustments. When estimating case counts for weekdays only, metrics were similar across days the nowcasts were conducted, with Mondays having the lowest mean absolute error, of 183 cases in the context of an average daily weekday case count of 2,914. Nowcasting ensured that recent decreases in observed case counts were not overinterpreted as true declines and supported health department leadership in anticipating the magnitude and timing of hospitalizations and deaths and allocating resources geographically.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sharon K. Greene", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Sarah F. McGough", + "author_inst": "Harvard T.H. Chan School of Public Health; Genentech, Inc." + }, + { + "author_name": "Gretchen M. Culp", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Laura E. Graf", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Nicolas A. Menzies", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rebecca Kahn", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.16.20214189", "rel_title": "Real-life validation of the Panbio COVID-19 Antigen Rapid Test (Abbott) in community-dwelling subjects with symptoms of potential SARS-CoV-2 infection", @@ -1108665,57 +1105700,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.10.19.345702", - "rel_title": "Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.19.345702", - "rel_abs": "The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesized that the diversity of microbiome compositions and their genomic features are associated with different pathological conditions of these human respiratory tract diseases (COVID-19 and non-COVID; URTI and COPD). To test this hypothesis, we analyzed 21 whole metagenome sequences (WMS) including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the diversity of microbiomes, their genomic features and relevant metabolic functions. The WMS data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19>COPD>URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively, however, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID sequence data, respectively and of them 34.50% strains shared between the conditions. Functional annotation of metagenomics sequences of thevCOVID-19 and non-COVID groups identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, replication and repair, clustering-based subsystems, virulence, disease and defense, adhesion, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, a predominant higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes were detected in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful for developing the microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "M. Nazmul Hoque", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Agricultural University Gazipur-1706, Bangladesh" - }, - { - "author_name": "M. Shaminur Rahman", - "author_inst": "Dhaka University" - }, - { - "author_name": "Rasel Ahmed", - "author_inst": "Bangladesh Jute Research Institute" - }, - { - "author_name": "Md. Sabbir Hossain", - "author_inst": "Bangladesh Jute Research Institute" - }, - { - "author_name": "Md. Shahidul Islam", - "author_inst": "Bangladesh Jute Research Institute" - }, - { - "author_name": "Keith A Crandall", - "author_inst": "George Washington University" - }, - { - "author_name": "Tofazzal Islam", - "author_inst": "BSMRAU" - }, - { - "author_name": "Md. Anwar Hossain", - "author_inst": "University of Dhaka" - }, - { - "author_name": "AMAM Zonaed Siddiki", - "author_inst": "Chattogram Veterinary and Animal Sciences University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.10.18.344622", "rel_title": "An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants", @@ -1109388,6 +1106372,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.14.20212720", + "rel_title": "Predictors of severe symptomatic laboratory-confirmed SARS-COV-2 reinfection", + "rel_date": "2020-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212720", + "rel_abs": "BackgroundThere is a major concern regarding the prognosis of coronavirus disease 2019 (COVID-19) in patients who recovered to first-time illness.\n\nObjectiveTo evaluate factors predicting severe symptomatic laboratory-confirmed (reverse transcription-quantitative polymerase chain reaction, RT-qPCR) SARS-COV-2 (severe acute coronavirus-2) reinfection.\n\nMethodWe conducted a nationwide retrospective cohort study in Mexico and data from 258 reinfection cases (at least 28 days between both episodes onset) were analyzed. We used risk ratios (RR) and 95% confidence intervals (CI) to evaluate predictors of severe (dyspnea requiring hospital admission) secondary SARS-COV-2 infection.\n\nResultsThe risk of severe disease was 14.7% and the observed overall fatality rate was 4.3%. Patients with more serious primary disease were more likely to develop severe symptoms (39.5% vs. 5.5%, p < 0.001) during reinfection. In multiple analysis, factors associated with an increased risk of severe symptomatic SARS-COV-2 reinfection were increasing age (RR per year = 1.007, 95% CI 1.003-1.010), comorbidities (namely obesity [RR = 1.12, 95% CI 1.01-1.24], asthma [RR = 1.26, 95% CI 1.06-1.50], type 2 diabetes mellitus [RR = 1.22, 95% CI 1.07 - 1.38] and previous severe laboratory-confirmed COVID-19 (RR = 1.20, 95% CI 1.03-1.39).\n\nConclusionsTo the best of our knowledge this is the first study evaluating disease outcomes in a large set of laboratory-positive cases of symptomatic SARS-COV-2 reinfection and factors associated with illness severity was characterized. Our results may contribute to the current knowledge of SARS-COV-2 pathogenicity and to identify populations at increased risk of a poorer outcome after reinfection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Efren Murillo-Zamora", + "author_inst": "Mexican Institute of Social Security" + }, + { + "author_name": "Oliver Mendoza-Cano", + "author_inst": "Universidad de Colima" + }, + { + "author_name": "Ivan Delgado-Enciso", + "author_inst": "Universidad de Colima" + }, + { + "author_name": "CARLOS M HERNANDEZ-SUAREZ", + "author_inst": "UNIVERSIDAD DE COLIMA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.15.20213454", "rel_title": "Aging and COVID-19 mortality: A demographic perspective", @@ -1110278,33 +1107293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.14.20212563", - "rel_title": "On Modeling of COVID-19 for the Indian Subcontinent using Polynomial and Supervised Learning Regression", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212563", - "rel_abs": "COVID-19, a recently declared pandemic by WHO has taken the world by storm causing catastrophic damage to human life. The novel cornonavirus disease was first incepted in the Wuhan city of China on 31st December 2019. The symptoms include fever, cough, fatigue, shortness of breath or breathing difficulties, and loss of smell and taste. Since the devastating phenomenon is essentially a time-series representation, accurate modeling may benefit in identifying the root cause and accelerate the diagnosis. In the current analysis, COVID-19 modeling is done for the Indian subcontinent based on the data collected for the total cases confirmed, daily recovered, daily deaths, total recovered and total deaths. The data is treated with total confirmed cases as the target variable and rest as feature variables. It is observed that Support vector regressions yields accurate results followed by Polynomial regression. Random forest regression results in overfitting followed by poor Bayesian regression due to highly correlated feature variables. Further, in order to examine the effect of neighbouring countries, Pearson correlation matrix is computed to identify geographic cause and effect.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Dishita Neve", - "author_inst": "Adani Institute of Infrastructure Engineering, Ahmedabad, India" - }, - { - "author_name": "Honey Patel", - "author_inst": "Adani Institute of Infrastructure Engineering, Ahmedabad, India" - }, - { - "author_name": "Harsh S Dhiman", - "author_inst": "Adani Institute of Infrastructure Engineering, Ahmedabad, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.14.20212415", "rel_title": "CoViD-19, learning from the past: A wavelet and cross-correlation analysis of the epidemic dynamics looking to emergency calls and Twitter trends in Italian Lombardy region", @@ -1111045,6 +1108033,101 @@ "type": "contradictory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.16.342097", + "rel_title": "Duple extinguishment of COVID-19: single compound synergized inhibition of SARS-CoV-2 replication and direct suppression of inflammatory cytokines in vitro/vivo", + "rel_date": "2020-10-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.16.342097", + "rel_abs": "We firstly disclose single compound yields better therapeutic outcome than Remdesivir in COVID-19 hamster treatments as it is armed with direct inhibition viral replication and intrinsic suppression inflammatory cytokines expression. Crystal data reveals that Au (I), released from Au22Glutathione18 (GA), covalently binds thiolate of Cys145 of SARS-CoV-2 Mpro. GA directly decreases SARS-CoV-2 viral replication (EC50: ~0.24 M) and intrinsically down-regulates NF{kappa}B pathway therefore significantly inhibiting expression of inflammatory cytokines in cells. The lung viral load and inflammatory cytokines in GA-treated COVID-19 transgenic mice are found to be significantly lower than that of control mice. When COVID-19 golden hamsters are treated by GA, the lung inflammatory cytokines levels are significantly lower than that of Remdesivir while their lung viral load are decreased to same level. The pathological results show that GA treatment significantly reduce lung inflammatory injuries when compared to that of Remdesivir-treated COVID-19 golden hamsters.\n\nOne Sentence SummaryWe found that gold cluster molecule directly inhibits SARS-CoV-2 replication and intrinsically suppresses inflammatory cytokines expression in COVID-19 transgenic mouse and golden hamster model, gold cluster providing a better lung injury protection than Remdesivir in COVID-19 golden hamsters via intranasally dropping administration.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Xueyun Gao", + "author_inst": "Beijing University of Technology, Ping Le Yuan 100, Beijing, P. R. China." + }, + { + "author_name": "Yong Gong", + "author_inst": "Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China." + }, + { + "author_name": "Wenjie Tan", + "author_inst": "Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing1022" + }, + { + "author_name": "Huaidong Jiang", + "author_inst": "Shool of physical science and technology, ShanghaiTech University, Shanghai 201210, P. R. China." + }, + { + "author_name": "Jianxun Qi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China." + }, + { + "author_name": "Jincun Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affilia" + }, + { + "author_name": "Bo Sun", + "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences, No.239 Zhangheng Road, Shanghai, China, 201204." + }, + { + "author_name": "Xingfa Gao", + "author_inst": "College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China." + }, + { + "author_name": "Xuejiao Gao", + "author_inst": "College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China." + }, + { + "author_name": "Peng Cao", + "author_inst": "National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China." + }, + { + "author_name": "Bo He", + "author_inst": "Shool of physical science and technology, ShanghaiTech University, Shanghai 201210, P. R. China." + }, + { + "author_name": "Jiadong Fan", + "author_inst": "Shool of physical science and technology, ShanghaiTech University, Shanghai 201210, P. R. China." + }, + { + "author_name": "Yuhui Dong", + "author_inst": "Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China." + }, + { + "author_name": "Fuping Gao", + "author_inst": "Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China." + }, + { + "author_name": "Qing Yuan", + "author_inst": "Beijing University of Technology, Ping Le Yuan 100, Beijing, P. R. China." + }, + { + "author_name": "Wencong Zhao", + "author_inst": "Beijing University of Technology, Ping Le Yuan 100, Beijing, P. R. China." + }, + { + "author_name": "Chunyu Zhang", + "author_inst": "Beijing University of Technology, Ping Le Yuan 100, Beijing, P. R. China." + }, + { + "author_name": "Zhongying Du", + "author_inst": "Beijing University of Technology, Ping Le Yuan 100, Beijing, P. R. China." + }, + { + "author_name": "Fei Ye", + "author_inst": "Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing1022" + }, + { + "author_name": "Zhesheng He", + "author_inst": "Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P. R. China." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.15.341636", "rel_title": "Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers", @@ -1111948,57 +1109031,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.14.340034", - "rel_title": "A high throughput RNA displacement assay for screening SARS-CoV-2 nsp10-nsp16 complex towards developing therapeutics for COVID-19", - "rel_date": "2020-10-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.340034", - "rel_abs": "SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process including the nonstructural protein 16 (nsp16) which is an S-adenosyl-L-methionine (SAM)-dependent 2-O-methyltransferase. Nsp16 is significantly active when in complex with another nonstructural protein, nsp10, which plays a key role in its stability and activity. Here we report the development of a fluorescence polarization (FP)-based RNA displacement assay for nsp10-nsp16 complex in 384-well format with a Z'-Factor of 0.6, suitable for high throughput screening. In this process, we purified the nsp10-nsp16 complex to higher than 95% purity and confirmed its binding to the methyl donor SAM, product of the reaction, SAH, and a common methyltransferase inhibitor, sinefungin using Isothermal Titration Calorimetry (ITC). The assay was further validated by screening a library of 1124 drug-like compounds. This assay provides a cost-effective high throughput method for screening nsp10-nsp16 complex for RNA-competitive inhibitors towards developing COVID-19 therapeutics.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sumera Perveen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Aliakbar Khalili Yazdi", - "author_inst": "University of Toronto" - }, - { - "author_name": "Kanchan Devkota", - "author_inst": "University of Toronto" - }, - { - "author_name": "Fengling Li", - "author_inst": "University of Toronto" - }, - { - "author_name": "Pegah Ghiabi", - "author_inst": "University of Toronto" - }, - { - "author_name": "Taraneh Hajian", - "author_inst": "University of Toronto" - }, - { - "author_name": "Peter Loppnau", - "author_inst": "University of Toronto" - }, - { - "author_name": "Albina Bolotokova", - "author_inst": "University of Toronto" - }, - { - "author_name": "Masoud Vedadi", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.15.339838", "rel_title": "Inhibition of SARS-CoV-2 viral entry in vitro upon blocking N- and O-glycan elaboration", @@ -1112671,6 +1109703,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.11.20210922", + "rel_title": "Symptoms associated with SARS-CoV-2 infection in a community-based population: Results from an epidemiological study", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20210922", + "rel_abs": "BackgroundPrior studies examining symptoms of COVID-19 are primarily descriptive and measured among hospitalized individuals. Understanding symptoms of SARS-CoV-2 infection in pre-clinical, community-based populations may improve clinical screening, particularly during flu season. We sought to identify key symptoms and symptom combinations in a community-based population using robust methods.\n\nMethodsWe pooled community-based cohorts of individuals aged 12 and older screened for SARS-CoV-2 infection in April and June 2020 for a statewide seroprevalence study. Main outcome was SARS-CoV-2 positivity. We calculated sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for individual symptoms as well as symptom combinations. We further employed multivariable logistic regression and exploratory factor analysis (EFA) to examine symptoms and combinations associated with SARS-CoV-2 infection.\n\nResultsAmong 8214 individuals screened, 368 individuals (4.5%) were RT-PCR positive for SARS-CoV-2. Although two-thirds of symptoms were highly specific (>90.0%), most symptoms individually possessed a PPV <50.0%. The individual symptoms most greatly associated with SARS-CoV-2 positivity were fever (OR=5.34, p<0.001), anosmia (OR=4.08, p<0.001), ageusia (OR=2.38, p=0.006), and cough (OR=2.86, p<0.001). Results from EFA identified two primary symptom clusters most associated with SARS-CoV-2 infection: (1) ageusia, anosmia, and fever; and (2) shortness of breath, cough, and chest pain. Moreover, being non-white (13.6% vs. 2.3%, p<0.001), Hispanic (27.9% vs. 2.5%, p<0.001), or living in an Urban area (5.4% vs. 3.8%, p<0.001) was associated with infection.\n\nConclusionsSymptoms can help distinguish SARS-CoV-2 infection from other respiratory viruses, especially in community or urgent care settings where rapid testing may be limited. Symptoms should further be structured in clinical documentation to support identification of new cases and mitigation of disease spread by public health. These symptoms, derived from asymptomatic as well as mildly infected individuals, can also inform vaccine and therapeutic clinical trials.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSUsing multiple journal articles queried from MEDLINE as well as a Cochrane systematic review, we examined all studies that described symptoms known to be associated with COVID-19. We further examined the guidelines from WHO and CDC on the symptoms those public health authorities consider to be associated with COVID-19. Most of the evidence comes from China, Italy, and the United States. Collectively prior research and guidance suggests there are a dozen symptoms reported by individuals who tested positive for COVID-19 in multiple countries. Symptoms include fever, cough, fatigue, anosmia, ageusia, shortness of breath, chills, myalgias, headache, sore throat, chest pain, and gastrointestinal issues. The evidence is generally of low quality as it is descriptive in nature, and it is biased towards hospitalized patients. Most studies report the proportion of patients hospitalized or testing positive for infection who report one or more symptoms within 3-14 days prior to hospitalization or infection. There has been little validation of symptoms among hospitalized or non-hospitalized patients. Furthermore, according to a Cochrane review, no studies to date assess combinations of different signs and symptoms.\n\nAdded value of this studyThis study employs multiple, rigorous methods to examine the ability of specific symptoms as well as symptom combinations/groups to predict laboratory-confirmed (RT-PCR) infection of SARS-CoV-2. Furthermore, the study is unique in its large sample drawn exclusively from community-based populations rather than hospitalized patients.\n\nImplication of all the available evidenceCombining the evidence from this study with prior research suggests that anosmia and ageusia are key symptoms that differentiate COVID-19 from influenza-like symptoms. Clinical screening protocols for COVID-19 should look for these symptoms, which are not commonly asked of patients who present to urgent care or hospital with flu-like symptoms.\n\nKey pointsImportant symptoms specific to COVID-19 are fever, anosmia, ageusia, and cough. Two-thirds of symptoms were highly specific (>90.0%), yet most symptoms individually possessed a PPV <50.0%. This study confirms using robust methods the key symptoms associated with COVID-19 infection, and it also identifies combinations of symptoms strongly associated with positive infection", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brian E Dixon", + "author_inst": "Department of Epidemiology, IU Fairbanks School of Public Health" + }, + { + "author_name": "Kara Wools-Kaloustian", + "author_inst": "IU School of Medicine" + }, + { + "author_name": "William F Fadel", + "author_inst": "Department of Biostatistics, IU Fairbanks School of Public Health" + }, + { + "author_name": "Thomas J Duszynski", + "author_inst": "Department of Epidemiology, IU Fairbanks School of Public Health" + }, + { + "author_name": "Constantin Yiannoutsos", + "author_inst": "Department of Biostatistics, IU Fairbanks School of Public Health" + }, + { + "author_name": "Paul K Halverson", + "author_inst": "Department of Health Policy and Management, IU Fairbanks School of Public Health" + }, + { + "author_name": "Nir Menachemi", + "author_inst": "Department of Health Policy & Management, IU Fairbanks School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.11.20210724", "rel_title": "COVID-19 behavioural insights study: Preliminary findings from Finland, April-May, 2020", @@ -1113378,41 +1110453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.11.20210641", - "rel_title": "How Policies on Restaurants, Bars, Nightclubs, Masks, Schools, and Travel Influenced Swiss COVID-19 Reproduction Ratios", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20210641", - "rel_abs": "The role of complete lockdowns in reducing the reproduction ratios (Rt) of COVID-19 is now established. However, the persisting reality in many countries is no longer a complete lockdown, but restrictions of varying degrees using different choices of Non-pharmaceutical interaction (NPI) policies. A scientific basis for understanding the effectiveness of these graded NPI policies in reducing the Rt is urgently needed to address the concerns on personal liberties and economic activities. In this work, we develop a systematic relation between the degrees of NPIs implemented by the 26 cantons in Switzerland during March 9 - September 13 and their respective contributions to the Rt. Using a machine learning framework, we find that Rt which should ideally be lower than 1.0, has significant contributions in the post-lockdown scenario from the different activities - restaurants (0.0523 (CI. 0.0517-0.0528)), bars (0.030 (CI. 0.029-0.030)), and nightclubs (0.154 (CI. 0.154-0.156)). Activities which keep the land-borders open (0.177 (CI. 0.175-0.178)), and tourism related activities contributed comparably 0.177 (CI. 0.175-0.178). However, international flights with a quarantine did not add further to the Rt of the cantons. The requirement of masks in public transport and secondary schools contributed to an overall 0.025 (CI. 0.018-0.030) reduction in Rt, compared to the baseline usage even when there are no mandates. Although causal relations are not guaranteed by the model framework, it nevertheless provides a fine-grained justification for the relative merits of choice and the degree of the NPIs and a data-driven strategy for mitigating Rt.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "C. K. Sruthi", - "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" - }, - { - "author_name": "Malay Ranjan Biswal", - "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" - }, - { - "author_name": "Himanshu Joshi", - "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" - }, - { - "author_name": "Brijesh Saraswat", - "author_inst": "Jawaharlal Nehru Center for Advanced Scientific Research" - }, - { - "author_name": "Meher K Prakash", - "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.13.20211797", "rel_title": "Use of antivirals and antibiotics for COVID-19 in Mexico City: A Real-World Multicenter Cohort Study", @@ -1114217,6 +1111257,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.12.20211748", + "rel_title": "Prone positioning of non-intubated patients with COVID-19 - A Systematic Review and Meta-analysis", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211748", + "rel_abs": "PurposeSeveral studies have reported adopting prone positioning (PP) in non-intubated patients with COVID-19-related hypoxaemic respiratory failure. This systematic review and meta-analysis evaluated the impact of PP on oxygenation and clinical outcomes.\n\nMethodsWe searched PubMed, Embase and COVID-19 living systematic review from December1st 2019 to July23rd 2020. We included studies that reported using PP in hypoxaemic, non-intubated adult COVID-19 patients. Primary outcome measure was the weighted mean difference (MD) in oxygenation parameters (PaO2/FiO2, PaO2 or SpO2) pre and post-PP.\n\nResultsFifteen single arm observational studies reporting PP in 449 patients were included. Substantial heterogeneity was noted in terms of, location within hospital where PP was instituted, respiratory supports, frequency and duration of PP. Significant improvement in oxygenation was reported post-PP: PaO2/FiO2, (MD 37.6, 95%CI 18.8, 56.5); PaO2, (MD 30.4 mmHg, 95%CI 10.9, 49.9); and SpO2, (MD 5.8%, 95%CI 3.7, 7.9). Patients with a pre-PP PaO2/FiO2 [≤]150 experienced greater oxygenation improvements compared with those with a pre-PP PaO2/FiO2 >150 (MD 40.5, 95%CI -3.5, 84.6) vs. 37, 95%CI 17.1, 56.9). Respiratory rate decreased post-PP (MD -2.9, 95%CI -5.4, -0.4). Overall intubation and mortality rates were 21% (90/426) and 26% (101/390) respectively. No major adverse events were reported.\n\nConclusionsDespite significant variability in frequency and duration of PP and respiratory supports, PP was associated with improvements in oxygenation parameters without any reported serious adverse events. Major limitation being lack of control arm and adjustment for confounders. Clinical trials are required to determine the effect of awake PP on patient-centred outcomes.\n\nSystematic review registrationRegistration/protocol in PROSPERO (CRD42020194080).\n\nWhat is the key question?Is the novel approach of prone positioning in non-intubated patients associated with improvement in oxygenation?\n\nWhat is the bottom line?Prone position in non-intubated severe COIVD 19 suffers is associated with improvement of oxygenation while the short- and long-term patient centred out comes in this awake prone patient need more investigation.\n\nWhy read on?Our study is first of its kind (Systematic review and Meta-analysis) summarising the evidence surrounding the less invasive innovate technique of prone position in non-intubated COVID-19 patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mallikarjuna PONNAPA REDDY", + "author_inst": "Department of Intensive Care Medicine, Calvary Hospital, ACT, Australia ;\tDepartment of Intensive Care Medicine, Peninsula Health, Frankston, Vic, Australia" + }, + { + "author_name": "Ashwin SUBRAMANIAM", + "author_inst": "Department of Intensive Care Medicine, Peninsula Health, Frankston, Vic, Australia ;\tFaculty of Medicine, Nursing and Health Sciences, Monash University, Clayto" + }, + { + "author_name": "Zheng Jie LIM", + "author_inst": "Department of Intensive Care Medicine, Ballarat Health Services, Ballarat, Vic, Australia" + }, + { + "author_name": "Alexander ZUBAREV", + "author_inst": "Department of Intensive Care Medicine, Peninsula Health, Frankston, Vic, Australia" + }, + { + "author_name": "Afsana AFROZ", + "author_inst": "Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Vic, Australia" + }, + { + "author_name": "Baki BILLAH", + "author_inst": "Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Vic, Australia" + }, + { + "author_name": "Ravindranath TIRUVOIPATI", + "author_inst": "Department of Intensive Care Medicine, Peninsula Health, Frankston, Vic, Australia ;\tFaculty of Medicine, Nursing and Health Sciences, Monash University, Clayto" + }, + { + "author_name": "Kollengode RAMANATHAN", + "author_inst": "Yong Loo Lin School of Medicine, National University of Singapore, Singapore. ;\tNational University Hospital, Singapore ; Bond University, Gold Coast, Queenslan" + }, + { + "author_name": "Suei Nee WONG", + "author_inst": "Yong Loo Lin School of Medicine, National University of Singapore, Singapore." + }, + { + "author_name": "Daniel BRODIE", + "author_inst": "Bond University, Gold Coast, Queensland, Australia. ; Center for Acute Respiratory Failure, New York-Presbyterian Hospital, New York, USA." + }, + { + "author_name": "Eddy FAN", + "author_inst": "Interdepartmental Division of Critical Care Medicine and Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada" + }, + { + "author_name": "Kiran SHEKAR", + "author_inst": "Adult Intensive Care Services and Critical Care Research Group, the Prince Charles Hospital, Brisbane, Queensland, Australia ; Queensland University of Technolo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.10.13.20211763", "rel_title": "Healthcare workers with mild / asymptomatic SARS-CoV-2 infection show T cell responses and neutralising antibodies after the first wave", @@ -1115224,53 +1112327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.12.20211482", - "rel_title": "Frontline healthcare workers' experiences with personal protective equipment during the COVID-19 pandemic in the UK: a rapid qualitative appraisal", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211482", - "rel_abs": "ObjectivesTo report frontline healthcare workers (HCWs) experiences with personal protective equipment (PPE) during the COVID-19 pandemic in the UK. To understand HCWs fears and concerns surrounding PPE, their experiences following its guidance and how these affected their perceived ability to deliver care during the COVID-19 pandemic.\n\nMethodsA rapid qualitative appraisal study combining three sources of data: semi-structured in-depth telephone interviews with frontline HCWs (n=46), media reports (n=39 newspaper articles and 145,000 social media posts) and government PPE policies (n=25). HCWs interviewed were from secondary care, primary care and specialist community clinics. Media and policy data were from across the UK.\n\nResultsA major concern was running out of PPE, putting HCWs and patients at risk of infection. Following national-level guidance was often not feasible when there were shortages, leading to re-use and improvisation of PPE. Frequently changing guidelines generated confusion and distrust. PPE was reserved for high-risk secondary care settings and this translated into HCWs outside these settings feeling inadequately protected. Participants were concerned about inequitable access to PPE for community, lower seniority, female and ethnic minority HCWs. Participants continued delivering care despite the physical discomfort, practical problems and communication barriers associated with PPE use.\n\nConclusionThis study found that frontline HCWs persisted in caring for their patients despite multiple challenges including inappropriate provision of PPE, inadequate training and inconsistent guidance. In order to effectively care for patients during the COVID-19 pandemic, frontline HCWs need appropriate provision of PPE, training in its use, as well as comprehensive and consistent guidance. These needs must be addressed in order to protect the health and well-being of the most valuable healthcare resource in the COVID-19 pandemic: our HCWs.\n\nO_TEXTBOXWhat is already known?- PPE is an important component of infection prevention and control to protect HCWs delivering care on the frontline of an infectious disease outbreak.\n- Frontline HCWs have reported challenges delivering care in PPE during the COVID-19 pandemic.\n- Research understanding how HCWs responded to these challenges are lacking.\n\n\nWhat are the new findings?- HCWs faced multiple challenges delivering care including inadequate provision of PPE, inconsistent guidance and lack of training in its use.\n- HCWs persisted delivering care despite the negative physical effects, practical problems, lack of protected time for breaks and communication barriers associated with wearing PPE.\n- In the face of training, guidance and procurement gaps, HCWs improvised by developing their own informal communication channels to share information, they trained each other and bought their own PPE.\n- HCWs reported inequalities accessing PPE based on the healthcare sector, gender, level of seniority and ethnicity.\n\n\nWhat do the new findings imply?- To feel safe and confident caring for patients, frontline HCWs need to be provided with appropriate size, quality and level of PPE, as well as training in its use.\n- PPE guidance should be consistent, clearly communicated, and reflect the most up-to-date evidence-base for the safest level of PPE.\n- Regular breaks for staff working in full PPE should be prioritised even in contexts of understaffing and PPE shortages as these are key aspects of well-being.\n\n\nC_TEXTBOX", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Katarina Hoernke", - "author_inst": "University College London" - }, - { - "author_name": "Nehla Djellouli", - "author_inst": "University College London" - }, - { - "author_name": "Lily Jay Andrews", - "author_inst": "University College London" - }, - { - "author_name": "Sasha Lewis-Jackson", - "author_inst": "University College London" - }, - { - "author_name": "Louisa Manby", - "author_inst": "University College London" - }, - { - "author_name": "Sam Martin", - "author_inst": "Oxford Vaccine Group, University of Oxford" - }, - { - "author_name": "Samantha Vanderslott", - "author_inst": "Oxford Vaccine Group, University of Oxford" - }, - { - "author_name": "Cecilia Vindrola-Padros", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.13.20211839", "rel_title": "Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters", @@ -1115931,6 +1112987,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.10.12.336818", + "rel_title": "Structural stability of SARS-CoV-2 degrades with temperature", + "rel_date": "2020-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.12.336818", + "rel_abs": "SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter.\n\nStatement of Scientific SignificanceThe economic and public health impact of the COVID-19 pandemic are very significant. However scientific information needed to underpin policy decisions are limited partly due to novelty of the SARS-CoV-2 pathogen. There is therefore an urgent need for mechanistic studies of both COVID-19 disease and the SARS-CoV-2 virus. We show that individual virus particles suffer structural destabilization at relatively mild but elevated temperatures. Our nanoscale results are consistent with recent observations at larger scales. Our work strengthens the case for COVID-19 resurgence in winter.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Abhimanyu Sharma", + "author_inst": "University of Utah" + }, + { + "author_name": "Benjamin Preece", + "author_inst": "University of Utah" + }, + { + "author_name": "Heather Swann", + "author_inst": "University of Utah" + }, + { + "author_name": "Xiangyu Fan", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Richard J. McKenney", + "author_inst": "UC - Davis" + }, + { + "author_name": "Kassandra M Ori-McKenney", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Saveez Saffarian", + "author_inst": "University of Utah" + }, + { + "author_name": "Michael Vershinin", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.10.13.337907", "rel_title": "Obesity alters Ace2 and Tmprss2 expression in lung, trachea, and esophagus in a sex-dependent manner: Implications for COVID-19", @@ -1116773,45 +1113876,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.10.09.20210187", - "rel_title": "COVID-19 trends in Colombian regions with the highest disease burden", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210187", - "rel_abs": "IntroductionCOVID-19 pandemic is currently the most significant global public health challenge, with more than 31 million cases reported to date. Colombia first reported COVID-19 cases in the country by early March 2020, and six months later it has reached [~]750,471 clinical cases, with significant regional differences in morbidity, mortality, and hospitalization rates.\n\nAimsIdentify population characteristics and hospital capacity in the 13 municipalities with the highest disease notification and examine differences in cumulative reported cases, hospitalization, and mortality rates that may explain the regional differences.\n\nMaterials and methodsA multi-group ecological study was performed based on the information available from public databases. Notification of cases, hospitalization, and crude mortality and age-adjusted rates were calculated.\n\nResultsThe municipalities with the highest COVID-1 burden at different times during the study period displayed significant differences in population density and the proportion of elderly inhabitants, indigenous and afro descendants minorities; indices of unsatisfied basic needs and multidimensional poverty index, as well as the number of hospital beds. Likewise, essential variations in notification rates, hospitalization, and mortality were observed. The highest age-adjusted of reported cases (4,219 cases) and mortality (230.4 cases) rates were found in Leticia, the lowest general hospitalization rates in Buenaventura (37.5 cases) and the lowest ICU hospitalization rates (0) in Leticia and Tumaco due to a lack of these units in these municipalities.\n\nConclusionThe probability of getting sick, hospitalized, and dying from COVID-19 appeared closely related to socio-economic, ethnic, and cultural characteristics, and also to hospital bed capacity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Pablo Chaparro Sr.", - "author_inst": "INSTITUTO NACIONAL DE SALUD" - }, - { - "author_name": "Helmer Zapata Sr.", - "author_inst": "SECERETARIA DEPARTAMENTAL DE SALUD, CALI" - }, - { - "author_name": "ISABEL HURTADO", - "author_inst": "SECRETARIA DEPARTAMENTAL DE SALUD, CALI , COLOMBIA" - }, - { - "author_name": "ALBERTO ALZATE Sr.", - "author_inst": "UNIVERSIDAD LIBRE" - }, - { - "author_name": "MARIA CRISTINA LESMES", - "author_inst": "SECRETARIA DEPARTAMENTAL DE SALUD, CALI, COLOMBIA" - }, - { - "author_name": "SOCRATES HERRERA Sr.", - "author_inst": "CENTRO DE IVESTIGACION CINETIFICA CAUCASECO" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.09.20208876", "rel_title": "Using an Agent-Based Model to Assess K-12 School Re-openings Under Different COVID-19 Spread Scenarios - United States, School Year 2020/21", @@ -1118040,6 +1115104,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.13.337774", + "rel_title": "Degradation of SARS-CoV-2 receptor ACE2 by tobacco carcinogen-induced Skp2 in lung epithelial cells", + "rel_date": "2020-10-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.13.337774", + "rel_abs": "An unexpected observation among the COVID-19 pandemic is that smokers constituted only 1.4-18.5% of hospitalized adults, calling for an urgent investigation to determine the role of smoking in SARS-CoV-2 infection. Here, we show that cigarette smoke extract (CSE) and carcinogen benzo(a)pyrene (BaP) increase ACE2 mRNA but trigger ACE2 protein catabolism. BaP induces an aryl hydrocarbon receptor (AhR)-dependent upregulation of the ubiquitin E3 ligase Skp2 for ACE2 ubiquitination. ACE2 in lung tissues of non-smokers is higher than in smokers, consistent with the findings that tobacco carcinogens downregulate ACE2 in mice. Tobacco carcinogens inhibit SARS-CoV-2 Spike protein pseudovirions infection of the cells. Given that tobacco smoke accounts for 8 million deaths including 2.1 million cancer deaths annually and Skp2 is an oncoprotein, tobacco use should not be recommended and cessation plan should be prepared for smokers in COVID-19 pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Guang-Biao Zhou", + "author_inst": "Chinese Academy of Medical Sciences Cancer Institute and Hospital" + }, + { + "author_name": "Gui-Zhen Wang", + "author_inst": "Cancer Hospital, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Qun Zhao", + "author_inst": "Chinese Academy of Medical Sciences Cancer Institute and Hospital" + }, + { + "author_name": "Fan Liang", + "author_inst": "Institute of Zoology Chinese Academy of Sciences" + }, + { + "author_name": "Chen Zhang", + "author_inst": "Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Hui Zhang", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Jun Wang", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Zhen-Yin Chen", + "author_inst": "Chinese Academy of Medical Sciences Cancer Institute and Hospital" + }, + { + "author_name": "Ran Wu", + "author_inst": "Chinese Academy of Medical Sciences Cancer Institute and Hospital" + }, + { + "author_name": "Hong Yu", + "author_inst": "Beijing University of Chinese Medicine" + }, + { + "author_name": "Bei-Bei Sun", + "author_inst": "Chinese Academy of Medical Sciences Cancer Institute and Hospital" + }, + { + "author_name": "Ruie Feng", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Kai-Feng Xu", + "author_inst": "Peking Union Medical College Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.10.13.337980", "rel_title": "Structural impact on SARS-CoV-2 spike protein by D614G substitution", @@ -1118951,181 +1116082,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.09.20209957", - "rel_title": "Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209957", - "rel_abs": "Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Rishi K Gupta", - "author_inst": "University College London" - }, - { - "author_name": "Ewen M Harrison", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" - }, - { - "author_name": "Antonia Ho", - "author_inst": "Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Annemarie B Docherty", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Stephen R Knight", - "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh" - }, - { - "author_name": "Maarten van Smeden", - "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands" - }, - { - "author_name": "Ibrahim Abubakar", - "author_inst": "Institute for Global Health, University College London, Gower Street, London, WC1E 6BT" - }, - { - "author_name": "Marc Lipman", - "author_inst": "UCL Respiratory, Division of Medicine, University College London, London, UK" - }, - { - "author_name": "Matteo Quartagno", - "author_inst": "MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK" - }, - { - "author_name": "Riinu B Pius", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Iain Buchan", - "author_inst": "Institute of Population Health Sciences, University of Liverpool" - }, - { - "author_name": "Gail Carson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas M Drake", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" - }, - { - "author_name": "Jake Dunning", - "author_inst": "National Infection Service Public Health England" - }, - { - "author_name": "Cameron J Fairfield", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK" - }, - { - "author_name": "Carrol Gamble", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Christopher A Green", - "author_inst": "Institute of Microbiology & Infection, University of Birmingham" - }, - { - "author_name": "Sophie Halpin", - "author_inst": "Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Hayley Hardwick", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Karl Holden", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Peter Horby", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Clare Jackson", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Kenneth McLean", - "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh" - }, - { - "author_name": "Laura Merson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan S Nguyen-Van-Tam", - "author_inst": "Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK" - }, - { - "author_name": "Lisa Norman", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Piero L Olliaro", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark G Pritchard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Clark D Russell", - "author_inst": "Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "James Scott-Brown", - "author_inst": "School of Informatics, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Catherine A Shaw", - "author_inst": "Department of Clinical Surgery, University of Edinburgh" - }, - { - "author_name": "Aziz Sheikh", - "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh" - }, - { - "author_name": "Tom Solomon", - "author_inst": "NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life" - }, - { - "author_name": "Cathie LM Sudlow", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Olivia V Swann", - "author_inst": "Department of Child Life and Health, University of Edinburgh, UK" - }, - { - "author_name": "Lance Turtle", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Peter JM Openshaw", - "author_inst": "Imperial College London" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Malcolm Gracie Semple", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Mahdad Noursadeghi", - "author_inst": "Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.20208785", "rel_title": "Rapid and Low-cost Sampling for Detection of Airborne SARS-CoV-2 in Dehumidifier Condensate", @@ -1119693,6 +1116649,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.07.20207647", + "rel_title": "Rapid detection of SARS-CoV2 by Ambient Mass Spectrometry Techniques", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20207647", + "rel_abs": "Ambient Ionisation Mass Spectrometry techniques: Desorption Electrospray Ionisation (DESI) and Laser Desorption - Rapid Evaporative Ionisation Mass Spectrometry (LD-REIMS) were used to detect the SARS-CoV-2 in dry nasal swabs. 45 patients were studied from samples collected between April - June 2020 in a clinical feasibility study. Diagnostic accuracy was calculated as 86.7% and 84% for DESI and LD-REIMS respectively. Results can be acquired in seconds providing robust and quick analysis of COVID-19 status which could be carried out without the need for a centralised laboratory. This technology has the potential to provide an alternative to population testing and enable the track and trace objectives set by governments and curtail the effects of a second surge in COVID-19 positive cases. In contrast to current PCR testing, using this technique there is no requirement of specific reagents which can cause devastating delays upon breakdowns of supply chains, thus providing a promising alternative testing method.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Lauren Louise Ford", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniel Simon", + "author_inst": "Imperial College London" + }, + { + "author_name": "Julia Balog", + "author_inst": "Waters Research Centre" + }, + { + "author_name": "Natasha Jiwa", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Higginson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Emrys Jones", + "author_inst": "Waters Corporation" + }, + { + "author_name": "Eftychios Manoli", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sam Mason", + "author_inst": "Imperial College London" + }, + { + "author_name": "Vincen Wu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Stefania Stavrakaki", + "author_inst": "Imperial College London" + }, + { + "author_name": "James McKenzie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniel McGill", + "author_inst": "Rosalind Franklin Institute" + }, + { + "author_name": "Hanifa Koguna", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Kinross", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zoltan Takats", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.07.20208710", "rel_title": "Safely Reopening K-12 Schools During the COVID-19 Pandemic", @@ -1120512,41 +1117543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.11.20211011", - "rel_title": "Identifying Optimal COVID-19 Testing Strategies for Schools and Businesses: Balancing Testing Frequency, Individual Test Technology, and Cost", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20211011", - "rel_abs": "BackgroundCOVID-19 test sensitivity and specificity have been widely examined and discussed yet optimal use of these tests will depend on the goals of testing, the population or setting, and the anticipated underlying disease prevalence. We model various combinations of key variables to identify and compare a range of effective and practical surveillance strategies for schools and businesses.\n\nMethodsWe coupled a simulated data set incorporating actual community prevalence and test performance characteristics to a susceptible, infectious, removed (SIR) compartmental model, modeling the impact of base and tunable variables including test sensitivity, testing frequency, results lag, sample pooling, disease prevalence, externally-acquired infections, and test cost on outcomes case reduction.\n\nResultsIncreasing testing frequency was associated with a non-linear positive effect on cases averted over 100 days. While precise reductions in cumulative number of infections depended on community disease prevalence, testing every 3 days versus every 14 days (even with a lower sensitivity test) reduces the disease burden substantially. Pooling provided cost savings and made a high-frequency approach practical; one high-performing strategy, testing every 3 days, yielded per person per day costs as low as $1.32.\n\nConclusionsA range of practically viable testing strategies emerged for schools and businesses. Key characteristics of these strategies include high frequency testing with a moderate or high sensitivity test and minimal results delay. Sample pooling allowed for operational efficiency and cost savings with minimal loss of model performance.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gregory D. Lyng", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Natalie E. Sheils", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Caleb J. Kennedy", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Daniel Griffin", - "author_inst": "Columbia University & ProHealth Care,Optum" - }, - { - "author_name": "Ethan M. Berke", - "author_inst": "UnitedHealth Group" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.20209064", "rel_title": "Social Distancing with Movement Restrictions and the Effective Replication Number of COVID-19: Multi-Country Analysis Based on Phone Mobility Data", @@ -1121199,6 +1118195,121 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.10.12.335331", + "rel_title": "Integrated analysis of multimodal single-cell data", + "rel_date": "2020-10-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.12.335331", + "rel_abs": "The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce weighted-nearest neighbor analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 antibodies to construct a multimodal reference atlas of the circulating immune system. We demonstrate that integrative analysis substantially improves our ability to resolve cell states and validate the presence of previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets, and to interpret immune responses to vaccination and COVID-19. Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets, including paired measurements of RNA and chromatin state, and to look beyond the transcriptome towards a unified and multimodal definition of cellular identity.\n\nAvailabilityInstallation instructions, documentation, tutorials, and CITE-seq datasets are available at http://www.satijalab.org/seurat", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Yuhan Hao", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Stephanie Hao", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Erica Andersen-Nissen", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "William M. Mauck", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Shiwei Zheng", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Andrew Butler", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Maddie Jane Lee", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Aaron J. Wilk", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Charlotte Darby", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Michael Zagar", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Paul Hoffman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Marlon Stoeckius", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Efthymia Papalexi", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Eleni P. Mimitou", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Jaison Jain", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Avi Srivastava", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Tim Stuart", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Lamar B. Fleming", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Bertrand Yeung", + "author_inst": "BioLegend" + }, + { + "author_name": "Angela J. Rogers", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Juliana M. McElrath", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Catherine A. Blish", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Raphael Gottardo", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Peter Smibert", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Rahul Satija", + "author_inst": "New York Genome Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.10.07.20208553", "rel_title": "Diagnostic Accuracy of FDA Authorized Serology Tests to Detect SARS-CoV-2 Antibodies: A Systematic Review and Meta-analysis", @@ -1122234,105 +1119345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.09.20209775", - "rel_title": "Factors associated with progression to critical illness in 28 days among COVID-19 patients: results from a tertiary care hospital in Istanbul, Turkey", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209775", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) quickly spread worldwide to become a pandemic. This study aimed to define the predictors of critical illness development within 28 days postadmission.\n\nMethodsWe conducted a prospective cohort study including 477 PCR-positive COVID-19 patients admitted to a tertiary care hospital in Istanbul from March 12 to May 12, 2020. The development of critical illness, e.g., invasive mechanical ventilation and/or death, was followed for a period of 28 days postadmission. Demographic characteristics, number of comorbidities, illness severity at admission defined by the WHO scale, vital signs, laboratory findings and period of admission to the hospital were independent variables. Cox proportional hazards analysis was performed, and the C-index was calculated.\n\nResultsThe median (IQR) age of the cohort was 55.0 (44.0-67.0) years, and 50.1% were male. The most common presenting symptoms were cough, dyspnea and fatigue. Overall, 65.2% of the patients had at least one comorbidity. Hydroxychloroquine was given to 99.2% of the patients. Critical illness developed in 45 (9.4%; 95% CI: 7.0%-12.4%) patients. In the multivariable analysis, age (HR: 1.05, p<0.001), number of comorbidities (HR: 1.33, p=0.02), procalcitonin [≥]0.25 {micro}g/L (HR: 2.12, p=0.03) and LDH [≥]350 U/L (HR: 2.04, p=0.03) were independently associated with critical illness development. The WHO scale on admission was the strongest predictor of critical illness (HR: 4.15, p<0.001). Prognosis improved within the study period (p<0.05). The C-index of the model was 0.92.\n\nConclusionsAge, comorbidity number, WHO scale, LDH and procalcitonin were independently associated with critical illness development. Mortality from COVID-19 seems to be decreasing as the pandemic advances.\n\nsummaryWe analyzed 477 confirmed COVID-19 patients for the development of critical illness, e.g., invasive mechanical ventilation and/or death within 28 days postadmission. Age, comorbidity number, WHO scale, LDH and procalcitonin were independently associated with critical illness development.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Uluhan Sili", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Pinar Ay", - "author_inst": "Department of Public Health, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Ahmet Topuzoglu", - "author_inst": "Department of Public Health, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Huseyin Bilgin", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Elif Tukenmez Tigen", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Buket Erturk Sengel", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Dilek Yagci Caglayik", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Baran Balcan", - "author_inst": "Department of Pulmonary Medicine, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Derya Kocakaya", - "author_inst": "Department of Pulmonary Medicine, Marmara University School of Medicine, Istanbul, Turke" - }, - { - "author_name": "Sehnaz Olgun Yildizeli", - "author_inst": "Department of Pulmonary Medicine, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Fethi Gul", - "author_inst": "Department of Anesthesiology and Intensive Care, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Beliz Bilgili", - "author_inst": "Department of Anesthesiology and Intensive Care, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Rabia Can Sarinoglu", - "author_inst": "Department of Medical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Aysegul Karahasan Yagci", - "author_inst": "Department of Medical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Lutfiye Mulazimoglu Durmusoglu", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Emel Eryuksel", - "author_inst": "Department of Pulmonary Medicine, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Zekaver Odabasi", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Haner Direskeneli", - "author_inst": "Department of Internal Medicine, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Sait Karakurt", - "author_inst": "Department of Pulmonary Medicine, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Ismail Cinel", - "author_inst": "Department of Anesthesiology and Intensive Care, Marmara University School of Medicine, Istanbul, Turkey" - }, - { - "author_name": "Volkan Korten", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Turkey" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.07.20208645", "rel_title": "Low zinc levels at clinical admission associates with poor outcomes in COVID-19", @@ -1123009,6 +1120021,65 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.10.09.334136", + "rel_title": "Soluble Spike DNA vaccine provides long-term protective immunity against SAR-CoV-2 in mice and nonhuman primates", + "rel_date": "2020-10-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.09.334136", + "rel_abs": "The unprecedented and rapid spread of SARS-CoV-2 has motivated the need for a rapidly producible and scalable vaccine. Here, we developed a synthetic soluble SARS-CoV-2 spike (S) DNA-based vaccine candidate, GX-19. In mice, immunization with GX-19 elicited not only S-specific systemic and pulmonary antibody responses but also Th1-biased T cell responses in a dose-dependent manner. GX-19 vaccinated nonhuman primate seroconverted rapidly and exhibited detectable neutralizing antibody response as well as multifunctional CD4+ and CD8+ T cell responses. Notably, when the immunized nonhuman primates were challenged at 10 weeks after the last vaccination with GX-19, they did not develop fever and reduced viral loads in contrast to non-vaccinated primates as a control. These findings indicate that GX-19 vaccination provides durable protective immune response and also support further development of GX-19 as a vaccine candidate for SARS-CoV-2 in human clinical trials.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yong Bok Seo", + "author_inst": "SL VaxiGen Inc." + }, + { + "author_name": "You Suk Suh", + "author_inst": "Genexine Inc." + }, + { + "author_name": "Ji In Ryu", + "author_inst": "SL VaxiGen Inc." + }, + { + "author_name": "Hwanhee Jang", + "author_inst": "SL VaxiGen Inc." + }, + { + "author_name": "Hanseul Oh", + "author_inst": "Korea Research Institute of Bioscience and Biotechnology" + }, + { + "author_name": "Bon-Sang Koo", + "author_inst": "Korea Research Institute of Bioscience and Biotechnology" + }, + { + "author_name": "Sang-Hwan Seo", + "author_inst": "International Vaccine Institute" + }, + { + "author_name": "Jung Joo Hong", + "author_inst": "Korea Research Institute of Bioscience and Biotechnology" + }, + { + "author_name": "Manki Song", + "author_inst": "International Vaccine Institute" + }, + { + "author_name": "Sung-Joo Kim", + "author_inst": "GenNBio Inc." + }, + { + "author_name": "Young Chul Sung", + "author_inst": "Genexine Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.08.331645", "rel_title": "SARS-CoV-2 Elicits Robust Adaptive Immune Responses Regardless of Disease Severity", @@ -1123956,65 +1121027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.08.20202606", - "rel_title": "EFFECT OF CONVALESCENT PLASMA ON MORTALITY IN PATIENTS WITH COVID-19 PNEUMONIA", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20202606", - "rel_abs": "BackgroundConvalescent plasma, widely utilized in viral infections that induce neutralizing antibodies, has been proposed for COVID-19, and preliminary evidence shows that it might have beneficial effect. Our objective was to compare epidemiological characteristics and outcomes between patients who received convalescent plasma for COVID-19 and those who did not, admitted to hospitals in Buenos Aires Province, Argentina, throughout the pandemic.\n\nMethodsThis is a multicenter, retrospective cohort study of 2-month duration beginning on June 1, 2020, including unselected, consecutive adult patients with diagnosed COVID-19, admitted to 215 hospitals with pneumonia. Epidemiological and clinical variables were registered in the Provincial Hospital Bed Management System. Convalescent plasma was supplied as part of a centralized, expanded access program.\n\nResultsWe analyzed 3,529 patients with pneumonia, predominantly male, aged 62{+/-}17, with arterial hypertension and diabetes as main comorbidities; 51.4% were admitted to the ward, 27.1% to the Intensive Care Unit (ICU), and 21.7% to the ICU with mechanical ventilation requirement (ICU-MV). 28-day mortality was 34.9%; and was 26.3%, 30.1% and 61.4% for ward, ICU and ICU-MV patients. Convalescent plasma was administered to 868 patients (24.6%); their 28-day mortality was significantly lower (25.5% vs. 38.0%, p<0.001). No major adverse effects occurred.\n\nLogistic regression analysis identified age, ICU admission with and without MV requirement, diabetes and preexistent cardiovascular disease as independent predictors of 28-day mortality, whereas convalescent plasma administration acted as a protective factor.\n\nConclusionsOur study suggests that the administration of convalescent plasma in COVID-19 pneumonia admitted to the hospital might be associated with decreased mortality.\n\nKey PointsO_LIPreliminary evidence showed that convalescent plasma might be beneficial in COVID-19.\nC_LIO_LIIn a cohort of 3,529 patients with pneumonia due to COVID-19, convalescent plasma was administered to 868 patients, without major adverse effects.\nC_LIO_LIConvalescent plasma was independently associated with decreased mortality.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Martin R Salazar", - "author_inst": "Teaching and Research Service, San Martin Hospital, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Soledad E Gonzalez", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Lorena Regairaz", - "author_inst": "Immunology Unit. Children s Hospital Sor Maria Ludovica, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Noelia S Ferrando", - "author_inst": "Hemotherapy Institute of Buenos Aires Province \"Dra Nora Etchenique\", La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Veronica Gonzalez", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Patricia M Carrera", - "author_inst": "Pediatric Research Institute Prof. Fernando E. Vitieri, Children s Hospital Sor Maria Ludovica, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Laura Mu\u00f1oz", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Santiago A Pesci", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Juan M Vidal", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Nicolas Kreplak", - "author_inst": "Ministry of Health of the Province of Buenos Aires, La Plata, Buenos Aires, Argentina" - }, - { - "author_name": "Elisa Estenssoro", - "author_inst": "Intensive Care Unit. San Martin Hospital, La Plata, Buenos Aires, Argentina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.07.20207282", "rel_title": "COVID-19, Type-2 Diabetes, and Associated Health Outcomes in China: Results from a Nationwide Survey of 10,545 Adults", @@ -1124682,6 +1121694,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.10.06.20204487", + "rel_title": "System Dynamics Model of Possible Covid-19 Trajectories Under Various Non-Pharmaceutical Intervention Options in Low Resource Setting.", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20204487", + "rel_abs": "We present a population-based System Dynamics Model (SDM) of possible Covid-19 trajectories under various intervention options in the uniqueness of Kenya. We developed a stock and flow based SDM. We parametrized the SDM using published data and where data was not available, expert opinion was sought. Following validation test, the model was simulated to determined possible outcomes of non-pharmaceutical interventions in management of Covid-19. We simulate the possible impact of; social distancing, quarantining, curfew and cross-county travel restriction, lockdown of selected cities in Kenya and quarantining. We varied interventions in terms of start dates, duration of implementation and effectiveness of the interventions. We estimated the outcomes in terms of number of possible infections, recoveries and deaths. With the current state of interventions, we estimated a peak of Covid-19 in September 2020 with an estimated 13.5 Million Covid-19 cases and 33.8 thousand deaths in Kenya. The largest possible reduction in infections and mortality was achievable through increase in the effectiveness of the interventions. The suggested interventions would delay the epidemic peak of Covid-19 to between late Nov 2020 and early December 2020 with an estimated13M cases a 500 thousand reduction in Covid-19 cases and 32.4 deaths (a reduction in 1400 deaths). We conclude that SDM enables understanding of the complexity and impact of different interventions scenarios of Covid-19 in Kenya.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lucy W Kivuti-Bitok", + "author_inst": "University of Nairobi" + }, + { + "author_name": "Abiodun S Momodu", + "author_inst": "Centre for Energy Research and Development, Obafemi Awolowo University, Nigeria" + }, + { + "author_name": "Joyce C Jebet", + "author_inst": "School of Nursing Sciences, University of Nairobi" + }, + { + "author_name": "Fredrick Kimemia", + "author_inst": "HESMA" + }, + { + "author_name": "Isaac Gichuki", + "author_inst": "HESMA" + }, + { + "author_name": "Irene Ngune", + "author_inst": "Curtin University, Australia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.10.06.20206060", "rel_title": "Clinical and immunoserological status 12 weeks after infection with COVID-19: prospective observational study", @@ -1125545,29 +1122596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.06.20207761", - "rel_title": "Contact tracing and isolation reduces Covid-19 incidence in a structured agent-based model", - "rel_date": "2020-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207761", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSThe World Health Organization has identified contact tracing and isolation (CTI) as a key strategy to slow transmission of SARS-CoV-2. Structured agent-based models (ABMs) provide a means to investigate the efficacy of such strategies in heterogeneous populations and to explore the impact of factors such as changes in test turnaround times (TaT).\n\nMethodsWe developed a structured ABM to simulate key SARS-CoV-2 transmission and Covid-19 disease progression dynamics in populations of 10, 000 agents. We ran 10, 000 simulations of each of three scenarios: (1) No CTI with a TaT of two days, (2) CTI with a TaT of two days, and (3) CTI with a TaT of eight days. We conducted a secondary analysis in which TaT values were varied from two to 11. The primary outcome for all analyses was mean total infections.\n\nResultsCTI reduced the mean number of infections from 5, 577 to 4, 157 (a relative reduction of 25.5%) when TaT was held steady at two days. CTI with a TaT of eight days resulted in a mean of 5, 163 infections (a relative reduction of 7.4% compared to no CTI and a TaT of two days). In the secondary analysis, every additional day added to the TaT increased the total number of infections - with the greatest increase in infections between four and five days, and the smallest increase between ten and 11 days.\n\nConclusionsIn a structured ABM that simulates key dynamics of Covid-19 transmission and disease progression, CTI results in a substantial reduction in the mean number of total infections. The benefit is greater with shorter TaT times, but remained substantial even with TaTs of eight days. The results suggest that CTI may play a critical role in reducing the size of outbreaks and that TaTs should be kept as short as possible in order to maximise this benefit.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Marcus O Low", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Nathan Geffen", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.05.20206730", "rel_title": "Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya", @@ -1126264,6 +1123292,129 @@ "type": "new results", "category": "plant biology" }, + { + "rel_doi": "10.1101/2020.10.07.328302", + "rel_title": "Extremely potent human monoclonal antibodies from convalescent Covid-19 patients", + "rel_date": "2020-10-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.07.328302", + "rel_abs": "Human monoclonal antibodies are safe, preventive and therapeutic tools, that can be rapidly developed to help restore the massive health and economic disruption caused by the Covid-19 pandemic. By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. Up to 65,9% of monoclonals neutralized the wild type virus at a concentration of >500 ng/mL, 23,6% neutralized the virus in the range of 100 - 500 ng/mL and 9,1% had a neutralization potency in the range of 10 - 100 ng/mL. Only 1,4% neutralized the authentic virus with a potency of 1-10 ng/mL. We found that the most potent neutralizing antibodies are extremely rare and recognize the RBD, followed in potency by antibodies that recognize the S1 domain, the S-protein trimeric structure and the S2 subunit. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2.\n\nOne Sentence SummaryExtremely potent neutralizing human monoclonal antibodies isolated from Covid-19 convalescent patients for prophylactic and therapeutic interventions.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Emanuele Andreano", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Emanuele Nicastri", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Ida Paciello", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Piero Pileri", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Noemi Manganaro", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Giulia Piccini", + "author_inst": "VisMederi S.r.l, Siena, Italy" + }, + { + "author_name": "Alessandro Manenti", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Elisa Pantano", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Anna Kabanova", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences; Tumour Immunology Unit, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Marco Troisi", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Ita" + }, + { + "author_name": "Fabiola Vacca", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Ita" + }, + { + "author_name": "Dario Cardamone", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences; University of Turin, Turin, Italy" + }, + { + "author_name": "Concetta De Santi", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Linda Benincasa", + "author_inst": "VisMederi Research S.r.l., Siena, Italy" + }, + { + "author_name": "Chiara Agrati", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Maria Rosaria Capobianchi", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Concetta Castilletti", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Arianna Emiliozzi", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hosp" + }, + { + "author_name": "Massimiliano Fabbiani", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena, Siena, Italy" + }, + { + "author_name": "Francesca Montagnani", + "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hosp" + }, + { + "author_name": "Lorenzo Depau", + "author_inst": "MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena" + }, + { + "author_name": "Jlenia Brunetti", + "author_inst": "MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena" + }, + { + "author_name": "Luisa Bracci", + "author_inst": "12MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena" + }, + { + "author_name": "Emanuele Montomoli", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy" + }, + { + "author_name": "Claudia Sala", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences" + }, + { + "author_name": "Giuseppe Ippolito", + "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Rino Rappuoli", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab - Fondazione Toscana Life Sciences; Faculty of Medicine, Imperial College, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.07.329771", "rel_title": "SARS-CoV-2 has observably higher propensity to accept uracil as nucleotide substitution: Prevalence of amino acid substitutions and their predicted functional implications in circulating SARS-CoV-2 in India up to July, 2020", @@ -1127235,25 +1124386,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.10.03.20203232", - "rel_title": "Sars-Cov-2 in Argentina: Lockdown, Mobility, and Contagion", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20203232", - "rel_abs": "There is a debate in Argentina about the effectiveness of mandatory lockdown measures in containing COVID-19 that lasts five months making it one of the longest in the World. The population effort to comply the lockdown has been decreasing over time given the economic and social costs that it entails. We contributes by analyzing the Argentinian case through information of mobility and contagion given answers to recurrent questions on these topics. This paper aims to fill the gap in the literature by assessing the effects of lockdown measures and the regional relaxation on the numbers of rate of new infections. We also respond to issues of internal political discussion on regional contagion and the effect of marches and unexpected crowd events. We use pool, fixed and random effects panel data modeling and Granger causality tests identifying relations between mobility and contagion. Our results show that lockdown in Argentina has been effective in reducing the mobility but not in way that reduces the rate of contagion. Strict lockdown seems to be effective in short periods of time and by extend it without complementary measures loss effectiveness. Contagion rate seems to be discretely displaced in time and resurging amidst slowly increasing in mobility.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Juan M.C. Larrosa", - "author_inst": "Universidad Nacional del Sur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.04.20206680", "rel_title": "Serological testing in addition to PCR screening for the re-opening of American colleges and universities: potential for cost-savings without compromising pandemic mitigation", @@ -1127710,6 +1124842,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20206243", + "rel_title": "Diagnostic performance of the combined nasal and throat swab in patients admitted to hospital with suspected COVID-19", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206243", + "rel_abs": "BackgroundAccurate diagnosis in patients with suspected coronavirus disease 2019 (COVID-19) is essential to guide treatment and limit spread of the virus. The combined nasal and throat swab is used widely, but its diagnostic performance is uncertain.\n\nMethodsIn a prospective, multi-centre, cohort study conducted in secondary and tertiary care hospitals in Scotland, we evaluated the combined nasal and throat swab with reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in consecutive patients admitted to hospital with suspected COVID-19. Diagnostic performance of the index and serial tests was evaluated for a primary outcome of confirmed or probable COVID-19, and a secondary outcome of confirmed COVID-19 on serial testing. The diagnosis was adjudicated by a panel, who recorded clinical, laboratory and radiological features blinded to the test results.\n\nResultsWe enrolled 1,369 consecutive patients (68 [53-80] years, 47% women) who underwent a total of 3,822 tests (median 2 [1-3] tests per patient). The primary outcome occurred in 36% (496/1,369), of whom 65% (323/496) and 35% (173/496) had confirmed and probable COVID-19, respectively. The index test was positive in 255/496 (51%) patients with the primary outcome, giving a sensitivity and specificity of 51.4% (95% confidence interval [CI] 48.8 to 54.1%) and 99.5% (95% CI 99.0 to 99.8%). Sensitivity increased in those undergoing 2, 3 or 4 tests to 60.1% (95% CI 56.7 to 63.4%), 68.3% (95% CI 64.0 to 72.3%) and 77.6% (95% CI 72.7 to 81.9%), respectively. The sensitivity of the index test was 78.9% (95% CI 74.4 to 83.2%) for the secondary outcome of confirmed COVID-19 on serial testing.\n\nConclusionsIn patients admitted to hospital, a single combined nasal and throat swab with RT-PCR for SARS-CoV-2 has excellent specificity, but limited diagnostic sensitivity for COVID-19. Diagnostic performance is significantly improved by repeated testing.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kuan Ken Lee", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Dimitrios Doudesis", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Daniella Ross", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Anda Bularga", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Claire MacKintosh", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Oliver Koch", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Ingolfur Johannessen", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Kate Templeton", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Sara Jenks", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Andrew Chapman", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Anoop Shah", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Atul Anand", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Meghan Perry", + "author_inst": "NHS Lothian" + }, + { + "author_name": "Nicholas L Mills", + "author_inst": "The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.04.20205401", "rel_title": "Monitoring for COVID-19 by universal testing in a homeless shelter in Germany: a prospective feasibility cohort study", @@ -1128529,25 +1125732,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2020.10.04.20206383", - "rel_title": "Incidence and Case-Fatality Ratio of COVID-19 infection in relation to Tobacco Smoking, Population Density and Age Demographics in the USA : could Particulate Matter derived from Tobacco Smoking act as a Vector for COVID-19 transmission?", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206383", - "rel_abs": "BACKGROUNDTobacco smoking is known to increase the risk for bacterial and viral respiratory infections and this also applies to second-hand smoking. Smoking has been shown to increase the severity of COVID-19 infection and the consequent risk for intra-tracheal ventilation in smokers. Tobacco smoking exposes the user and nearby individuals to very high concentrations of particulate matter in a short period of time. Genes appertaining to COVID-19 have been found adherent to particulate matter. Particulate matter has been shown to travel beyond the social distance of 2 metres up to 10 metres. COVID-19 related mortality has been linked to elevated atmospheric levels of the particulate matter, PM2.5. The aim of the study was to observe the incidence of infection rate and case fatality ratios in the USA, comparing States with partial bans on tobacco smoking, to States with more restrictive smoking regulation, exploring a possible link between smoke-related particulate matter and COVID-19 transmission.\n\nMETHODOLOGYTwo groups of USA States, differentiated by the degree of smoking legislative restrictions, had a number of variables compared. The incidence of COVID-19 infection, case-fatality ratio and testing frequency were obtained from the John Hopkins Coronavirus Resource Centre. The degree of smoking bans in the USA States was obtained from the websites of the Nonsmokers Rights Foundation. The percentage of the State population which smokes was collected from the Centres of Disease Control database. Population density, Body Mass Index and population percentages of individuals 65+/75+years were obtained from databases concerning USA demographics.\n\nRESULTSWith the available data there was no significant difference in COVID-19 testing prevalence between the partial smoking ban group and the more restrictive regulated group. The incidence of COVID-19 infection in the States with limited bans on tobacco smoking was 2046/100,000 (sd+/-827) while the infection incidence in States with more restrictive rulings on tobacco smoking was 1660/100,000 (sd+/-686) (p<0.038). The population percentage of smokers in States with minor limitations to smoking was 18.3% (sd+/-3.28), while States with greater smoking restrictions had a smoking population percentage of 15.2% (sd+/-2.68) (p<0.0006).\n\nThe two populations of both groups did not differ numerically (p<0.24) and numbered 157,820,000 in the partial smoking ban group and 161,439,356 in the more restrictive group. Population density correlated significantly with the case-fatality ratio (R=0.66 p<0.0001), as did the 75+year age group (R=0.29 p<0.04). Reflecting the possibility of trans-border transmission, the smoking status of adjacent partial smoking ban States may influence the COVID-19 incidence of bordering States (e.g. Utah) even if the smoking regulations of the latter were stricter than the former.\n\nOther factors that could impact the COVID-19 pandemic in the USA such as the State case-fatality ratio, population density, population percentage with elevated body mass index and the percentage of the state population aged 65years or above did not show any significant difference between both groups of States.\n\nCONCLUSIONStates in the USA with high levels of tobacco smoking and limited regulation had significantly higher rates of COVID-19 infection incidences than States with greater smoking restrictions. Population density and the age group of 75+years, showed a positive significant correlation with the case-fatality ratio. Besides the adverse effects of tobacco smoking on pulmonary defences, it would be interesting to explore the possibility of infection transmission via coronavirus-laden particulate matter from exhaled fumes derived from tobacco smoking.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yves Muscat Baron", - "author_inst": "Mater Dei Hospital, University of Malta Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.03.20206128", "rel_title": "Characteristics and outcomes of hospitalized adults with COVID-19 in Nepal: a multicenter, prospective cohort study", @@ -1129360,6 +1126544,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.06.328138", + "rel_title": "The strength of a NES motif in the nucleocapsid protein of human coronaviruses is related to genus, but not to pathogenic capacity", + "rel_date": "2020-10-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.06.328138", + "rel_abs": "Seven members of the Coronaviridae family infect humans, but only three (SARS-CoV, SARS-CoV-2 and MERS-CoV) cause severe disease with a high case fatality rate. Using in silico analyses (machine learning techniques and comparative genomics), several features associated to coronavirus pathogenicity have been recently proposed, including a potential increase in the strength of a predicted novel nuclear export signal (NES) motif in the nucleocapsid protein.\n\nHere, we have used a well-established nuclear export assay to experimentally establish whether the recently proposed nucleocapsid NESs are capable of mediating nuclear export, and to evaluate if their activity correlates with coronavirus pathogenicity.\n\nThe six NES motifs tested were functional in our assay, but displayed wide differences in export activity. Importantly, these differences in NES strength were not related to strain pathogenicity. Rather, we found that the NESs of the strains belonging to the genus Alphacoronavirus were markedly stronger than the NESs of the strains belonging to the genus Betacoronavirus.\n\nWe conclude that, while some of the genomic features recently identified in silico could be crucial contributors to coronavirus pathogenicity, this does not appear to be the case of nucleocapsid NES activity, as it is more closely related to coronavirus genus than to pathogenic capacity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Maria Sendino", + "author_inst": "Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain" + }, + { + "author_name": "Miren Josu Omaetxebarria", + "author_inst": "Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain" + }, + { + "author_name": "Jose A Rodriguez", + "author_inst": "Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.10.06.328336", "rel_title": "Structural basis for repurposing a 100-years-old drug suramin for treating COVID-19", @@ -1130063,49 +1127274,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.10.02.20205930", - "rel_title": "A national study of self-reported COVID symptoms during the first viral wave in Canada", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205930", - "rel_abs": "ImportanceAccurate understanding of COVID pandemic during the first viral wave in Canada could help prepare for future epidemic waves.\n\nObjectiveTo track the early course of the pandemic by examining self-reported COVID symptoms over time before testing became widely available.\n\nDesignAdults from the nationally representative Angus Reid Forum were randomly invited to complete an online survey in May/June 2020. The study is a part of the Action to Beat Coronavirus antibody testing study.\n\nSettingA 20-item internet survey.\n\nParticipants14,408 adults age 18 years of age.\n\nExposuresThe months that respondents and any household members first experienced various respiratory, neurological, sleep, skin or gastric symptoms.\n\nMain Outcomes and Measure\"COVID symptom-positive,\" defined as fever (or fever with hallucinations) plus at least one of difficulty breathing, a dry severe cough, loss of smell or \"COVID toe.\"\n\nResultsIn total, 14,408 panel members (48% male and 52% female) completed the survey. Despite overrepresentation of higher levels of education, the prevalence of obesity, smoking, diabetes and hypertension were similar to national census and health surveys. A total of 811 (5.6%) were COVID symptom-positive; highest rates were at ages 18-44 years (8.3% among), declining at older ages. Females had higher odds of reporting COVID symptoms (OR = 1.32, 95%CI 1.11 - 1.56) as did visible minorities (OR = 1.74, 1.29 - 2.35). COVID symptom positivity for respondents and their household members peaked in March (OR = 1.93, 95% CI = 1.59 - 2.34 compared to earlier months).\n\nConclusions and RelevanceThis study enhances our current understanding of the progression of the COVID epidemic in Canada, with few laboratory-confirmed cases in January and February, peaking in April. The results suggest substantial viral transmission in March, before widespread testing began, and a gradual decline in cases since May.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Xuyang Tang", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Hellen Gelband", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Teresa Lam", - "author_inst": "Angus Reid Forum" - }, - { - "author_name": "Nico Nagelkerke", - "author_inst": "Centre for Global Health Research" - }, - { - "author_name": "Angus Reid", - "author_inst": "Angus Reid Forum" - }, - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - }, - { - "author_name": "- Action to beat Coronavirus (Ab-C) Study Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.04.325266", "rel_title": "Reference ontology and database annotation of the COVID-19 Open Research Dataset (CORD-19)", @@ -1130942,6 +1128110,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.10.02.20205914", + "rel_title": "Willingness of Nigerian residents to disclose COVID-19 symptoms and take COVID-19 test", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205914", + "rel_abs": "BackgroundAn understanding of willingness of people to disclose coronavirus disease 2019 (COVID-19) symptoms and take the COVID-19 test will help provide important insight for motivators towards the self-surveillance and testing strategies recommended by the World Health Organization to curtail and halt the transmission of COVID-19.\n\nObjectivesThis study assessed willingness to disclose symptoms suggestive of COVID-19 and willingness to take COVID-19 test as well as their predictors.\n\nMethodsA cross-sectional online survey of 524 Nigerian adults, aged [≥] 18 years, residing in Nigeria and who had not taken the COVID-19 test was conducted. Information on willingness to disclose COVID-19 symptoms, take COVID-19 test and possible predictors were collected. Data were analysed using descriptive and inferential statistics evaluated at 5% significance level.\n\nResultsMean age of respondents was 35.8 {+/-} 10.7 years and 57.0% were males. Majority (85.8% and 86.2% respectively) were willing to disclose COVID-19 symptoms and take COVID-19 test. Self-risk perception of contracting COVID-19 predicted both willingness to disclose COVID-19 symptoms (aOR=3.236; 95%CI=1.836-5.704) and take COVID-19 test (aOR=3.174; 95%CI=1.570-6.419). Willingness to disclose COVID-19 symptoms (aOR=13.060; 95%CI= 6.253-27.276), knowledge of someone who had taken the test (aOR= 4.106; 95%CI= 1.179-14.299) and thought that it was important for people to know their COVID-19 status (aOR=3.123; 95%CI= 1.516-6.434) also predicted willingness to take COVID-19 test.\n\nConclusionNigerians are willing to disclose symptoms suggestive of COVID-19 and take the COVID-19 test. Investment in interventions developed based on the predicting factors will help speed up the finding and testing of suspected COVID-19 cases.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Victoria Oluwabunmi Oladoyin", + "author_inst": "University of Medical Sciences, Ondo, Nigeria" + }, + { + "author_name": "Oluyemi Adewole Okunlola", + "author_inst": "University of Medical Sciences, Ondo, Nigeria" + }, + { + "author_name": "Oluwaseyi Kikelomo Israel", + "author_inst": "Bowen University, Iwo, Nigeria" + }, + { + "author_name": "Demilade Olusola Ibirongbe", + "author_inst": "University of Medical Sciences, Ondo, Nigeria" + }, + { + "author_name": "Joy Atonirehonmon Osifo", + "author_inst": "University of Medical Sciences, Ondo, Nigeria" + }, + { + "author_name": "Taiwo Akinyode Obembe", + "author_inst": "University of Ibadan, Ibadan, Nigeria" + }, + { + "author_name": "Paulinus Kunle Omode", + "author_inst": "Ondo State Primary Health Care Development Agency, Akure, Nigeria" + }, + { + "author_name": "Olugbenga Olusegun Osunmakinwa", + "author_inst": "University of Medical Sciences, Ondo, Nigeria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.02.20204859", "rel_title": "Pooled Saliva Specimens for SARS-CoV-2 Testing", @@ -1131825,201 +1129040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.01.20202820", - "rel_title": "Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium", - "rel_date": "2020-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20202820", - "rel_abs": "Introductory paragraphParticular host and environmental factors influence susceptibility to severe COVID-19. We analyzed RNA-sequencing data from bronchial epithelial brushings - a relevant tissue for SARS-CoV-2 infection - obtained from three cohorts of uninfected individuals, and investigated how non-genetic and genetic factors affect the regulation of host genes implicated in COVID-19. We found that ACE2 expression was higher in relation to active smoking, obesity, and hypertension that are known risk factors of COVID-19 severity, while an association with interferon-related inflammation was driven by the truncated, non-binding ACE2 isoform. We discovered that expression patterns of a suppressed airway immune response to early SARS-CoV-2 infection, compared to other viruses, are similar to patterns associated with obesity, hypertension, and cardiovascular disease, which may thus contribute to a COVID-19-susceptible airway environment. eQTL mapping identified regulatory variants for genes implicated in COVID-19, some of which had pheWAS evidence for their potential role in respiratory infections. These data provide evidence that clinically relevant variation in the expression of COVID-19-related genes is associated with host factors, environmental exposures, and likely host genetic variation.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Silva Kasela", - "author_inst": "New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA" - }, - { - "author_name": "Victor E Ortega", - "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Molly Martorella", - "author_inst": "New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA" - }, - { - "author_name": "Suresh Garudadri", - "author_inst": "Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Jenna Nguyen", - "author_inst": "Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Elizabeth Ampleford", - "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Anu Pasanen", - "author_inst": "New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA" - }, - { - "author_name": "Srilaxmi Nerella", - "author_inst": "Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Kristina L Buschur", - "author_inst": "New York Genome Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA" - }, - { - "author_name": "Igor Z Barjaktarevic", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA" - }, - { - "author_name": "R Graham Barr", - "author_inst": "Department of Medicine, Columbia University Medical Center, New York, NY, USA" - }, - { - "author_name": "Eugene R Bleecker", - "author_inst": "Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Russell P Bowler", - "author_inst": "Division of Pulmonary Medicine, Department of Medicine, National Jewish Health, Denver, CO, USA" - }, - { - "author_name": "Alejandro P Comellas", - "author_inst": "Division of Pulmonary and Critical Care, University of Iowa, Iowa City, IA, USA" - }, - { - "author_name": "Christopher B Cooper", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA" - }, - { - "author_name": "David J Couper", - "author_inst": "Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA" - }, - { - "author_name": "Gerard J Criner", - "author_inst": "Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA" - }, - { - "author_name": "Jeffrey L Curtis", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan Health System, Ann Arbor, MI, USA; Medicine Service, VA Ann Arb" - }, - { - "author_name": "MeiLan K Han", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan Health System, Ann Arbor, MI, USA" - }, - { - "author_name": "Nadia N Hansel", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA" - }, - { - "author_name": "Eric A Hoffman", - "author_inst": "Division of Physiologic Imaging, Department of Radiology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA" - }, - { - "author_name": "Robert J Kaner", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Genetic Medicine, We" - }, - { - "author_name": "Jerry A Krishnan", - "author_inst": "Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, IL, USA" - }, - { - "author_name": "Fernando J Martinez", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Merry-Lynn N McDonald", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA" - }, - { - "author_name": "Deborah A Meyers", - "author_inst": "Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Robert Paine III", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA" - }, - { - "author_name": "Stephen P Peters", - "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Mario Castro", - "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, KS, USA" - }, - { - "author_name": "Loren C Denlinger", - "author_inst": "Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA" - }, - { - "author_name": "Serpil C Erzurum", - "author_inst": "Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA" - }, - { - "author_name": "John V Fahy", - "author_inst": "Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Elliot Israel", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA" - }, - { - "author_name": "Nizar N Jarjour", - "author_inst": "Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA" - }, - { - "author_name": "Bruce D Levy", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA" - }, - { - "author_name": "Xingnan Li", - "author_inst": "Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Wendy C Moore", - "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC, USA" - }, - { - "author_name": "Sally E Wenzel", - "author_inst": "Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA" - }, - { - "author_name": "Joe Zein", - "author_inst": "Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA" - }, - { - "author_name": "- NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS)", - "author_inst": "" - }, - { - "author_name": "- NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium", - "author_inst": "" - }, - { - "author_name": "Charles Langelier", - "author_inst": "Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Prescott G Woodruff", - "author_inst": "Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" - }, - { - "author_name": "Tuuli Lappalainen", - "author_inst": "New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA" - }, - { - "author_name": "Stephanie A Christenson", - "author_inst": "Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.01.20205310", "rel_title": "Prognostic accuracy of MALDI mass spectrometric analysis of plasma in COVID-19", @@ -1132632,6 +1129652,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.30.20204727", + "rel_title": "High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study", + "rel_date": "2020-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204727", + "rel_abs": "BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020.\n\nMethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model.\n\nResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants.\n\nConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Haowei Wang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christina J Atchison", + "author_inst": "Imperial College London" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "Lancaster University" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "Lancaster University" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Imperial College" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Helen Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.27.20202739", "rel_title": "COVID-19 era, Preventive effect of no going out against co-infection of the seasonal influenza virus and SARS-CoV-2", @@ -1133515,241 +1130610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.30.318972", - "rel_title": "LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection", - "rel_date": "2020-10-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.318972", - "rel_abs": "SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection.\n\nOne Sentence SummaryLY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates against SARS-CoV-2 infection.", - "rel_num_authors": 55, - "rel_authors": [ - { - "author_name": "Bryan E Jones", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Patricia L Brown-Augsburger", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Kizzmekia S Corbett", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Kathryn Westendorf", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Julian Davies", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Thomas P Cujec", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Christopher M Wiethoff", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Jamie L Blackbourne", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Beverly A Heinz", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Denisa Foster", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Richard E Higgs", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Deepa Balasubramaniam", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Roza Bidshahri", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Lucas Kraft", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Yuri Hwang", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Stefanie Zentelis", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Kevin R Jepson", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Rodrigo Goya", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Maia A Smith", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "David W Collins", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Samuel J Hinshaw", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Sean A Tycho", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Davide Pellacani", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Ping Xiang", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Krithika Muthuraman", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Solmaz Sobhanifar", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Marissa H Piper", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Franz J Triana", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Jorg Hendle", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Anna Pustilnik", - "author_inst": "Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, USA" - }, - { - "author_name": "Andrew C Adams", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Shawn J Berens", - "author_inst": "Eli Lilly and Company, Indianapolis, IN, USA" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC, USA" - }, - { - "author_name": "David R Martinez", - "author_inst": "University of North Carolina at Chapel Hill, Chapel Hill, NC, USA" - }, - { - "author_name": "Robert W Cross", - "author_inst": "Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX; Department of Microbiology and Immunology, University of Texas Medical Branch," - }, - { - "author_name": "Thomas W Geisbert", - "author_inst": "Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX; Department of Microbiology and Immunology, University of Texas Medical Branch," - }, - { - "author_name": "Viktoriya Borisevich", - "author_inst": "Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX; Department of Microbiology and Immunology, University of Texas Medical Branch," - }, - { - "author_name": "Olubukola Abiona", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Hayley M Belli", - "author_inst": "Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Maren de Vries", - "author_inst": "Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Adil Mohamed", - "author_inst": "Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Meike Dittmann", - "author_inst": "Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Marie Samanovic", - "author_inst": "NYU Langone Vaccine Center, Department of Medicine, Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, N" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU Langone Vaccine Center, Department of Medicine, Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, N" - }, - { - "author_name": "Jory A Goldsmith", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA" - }, - { - "author_name": "Ching-Lin Hsieh", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA" - }, - { - "author_name": "Nicole V Johnson", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA" - }, - { - "author_name": "Jason S McLellan", - "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA" - }, - { - "author_name": "Bryan C Barnhart", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Barney S Graham", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "John R Mascola", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Carl L Hansen", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - }, - { - "author_name": "Ester Falconer", - "author_inst": "AbCellera Biologics Inc., Vancouver, BC, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.30.317818", "rel_title": "SARS-CoV-2 Spike protein promotes hyper-inflammatory response that can be ameliorated by Spike-antagonistic peptide and FDA-approved ER stress and MAP kinase inhibitors in vitro", @@ -1134462,6 +1131322,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.30.20203315", + "rel_title": "Widening the gap: greater racial and ethnic disparities in COVID-19 burden after accounting for missing race/ethnicity data", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20203315", + "rel_abs": "Black, Hispanic, and Indigenous persons in the United States have an increased risk of SARS-CoV-2 infection and death from COVID-19, due to persistent social inequities. The magnitude of the disparity is unclear, however, because race/ethnicity information is often missing in surveillance data. In this study, we quantified the burden of SARS-CoV-2 infection, hospitalization, and case fatality rates in an urban county by racial/ethnic group using combined race/ethnicity imputation and quantitative bias-adjustment for misclassification. After bias-adjustment, the magnitude of the absolute racial/ethnic disparity, measured as the difference in infection rates between classified Black and Hispanic persons compared to classified White persons, increased 1.3-fold and 1.6-fold respectively. These results highlight that complete case analyses may underestimate absolute disparities in infection rates. Collecting race/ethnicity information at time of testing is optimal. However, when data are missing, combined imputation and bias-adjustment improves estimates of the racial/ethnic disparities in the COVID-19 burden.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Katie Labgold", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Sarah Hamid", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Sarita Shah", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Neel R Gandhi", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Allison Chamberlain", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Fazle Khan", + "author_inst": "Fulton County Board of Health" + }, + { + "author_name": "Shamimul Khan", + "author_inst": "Fulton County Board of Health" + }, + { + "author_name": "Sasha Smith", + "author_inst": "Fulton County Board of Health" + }, + { + "author_name": "Steve Williams", + "author_inst": "Fulton County Board of Health" + }, + { + "author_name": "Timothy Lee Lash", + "author_inst": "Emory University, Department of Epidemiology" + }, + { + "author_name": "Lindsay J Collin", + "author_inst": "Huntsman Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.29.20201632", "rel_title": "Artificial intelligence to predict the risk of mortality from COVID-19: Insights from a Canadian Application", @@ -1135289,133 +1132208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.28.20201947", - "rel_title": "Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20201947", - "rel_abs": "The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre-symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved [~]100 copies/L sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Parinaz Fozouni", - "author_inst": "UCSF/Gladstone Institutes" - }, - { - "author_name": "Sungmin Son", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Mar\u00eda D\u00edaz de Le\u00f3n Derby", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Gavin J Knott", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Carley N Gray", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Michael V D'Ambrosio", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Chunyu Zhao", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Neil A Switz", - "author_inst": "UC Berkeley" - }, - { - "author_name": "G. Renuka Kumar", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Stephanie I Stephens", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Daniela Boehm", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Chia-Lin Tsou", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Jeffrey Shu", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Abdul Bhuiya", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Max Armstrong", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Andrew Harris", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Jeannette M Osterloh", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Anke Meyer-Franke", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Charles Langelier", - "author_inst": "UCSF" - }, - { - "author_name": "Katherine S Pollard", - "author_inst": "Gladstone Institutes" - }, - { - "author_name": "Emily D Crawford", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Andreas S Puschnik", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Maira Phelps", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Amy Kistler", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Joseph L DeRisi", - "author_inst": "UCSF/Chan Zuckerberg Biohub" - }, - { - "author_name": "Jennifer A Doudna", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Daniel A Fletcher", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institutes" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20194290", "rel_title": "Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test", @@ -1135992,6 +1132784,101 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.09.29.319061", + "rel_title": "BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response", + "rel_date": "2020-09-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.319061", + "rel_abs": "Effective vaccine against SARS-CoV-2 is the utmost importance in the current world. More than 1 million deaths are accounted for relevant pandemic disease COVID-19. Recent data showed that D614G genotype of the virus is highly infectious and responsible for almost all infection for 2nd wave. Despite of multiple vaccine development initiatives, there are currently no report that has addressed this critical variant D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine considering the D614G variant and characterization of the vaccine in preclinical trial. The surface plasmon resonance (SPR) data with spike protein as probe and competitive neutralization with RBD and S2 domain revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, immunization protected mice lungs from pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+ cells with a Th1 bias. The IgG2a to IgG1 and (IgG2a+IgG2b) to (IgG1+IgG3) ratios were found 1{+/-}0.2 and 1.24{+/-}0.1, respectively. These values are comparatively higher than relevant values for other published SARS-CoV-2 vaccine in development,1, 2 and suggesting higher viral clearance capacity for our vaccine. The data suggested great promise for immediate translation of the technology to the clinic.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Juwel Chandra Baray", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Maksudur Rahman Khan", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Asif Mahmud", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Jikrul Islam", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Sanat Myti", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Rostum Ali", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md Enamul Haq Sarker", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Samir Kumar", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Mobarak Hossain Chowdhury", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Rony Roy", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Faqrul Islam", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Uttam Barman", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Habiba Khan", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Sourav Chakraborty", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Manik Hossain", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Md. Mashfiqur Rahman Chowdhury", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Polash Ghosh", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Mohammad Mohiuddin", + "author_inst": "https://www.globe-biotech.com/" + }, + { + "author_name": "Naznin Sultana", + "author_inst": "Globe Biotech Limited" + }, + { + "author_name": "Kakon Nag", + "author_inst": "Globe Biotech Limited" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.30.318311", "rel_title": "The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells.", @@ -1137403,53 +1134290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.09.28.20203109", - "rel_title": "DeepCOVID: An Operational Deep Learning-driven Framework for Explainable Real-time COVID-19 Forecasting", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203109", - "rel_abs": "How do we forecast an emerging pandemic in real time in a purely data-driven manner? How to leverage rich heterogeneous data based on various signals such as mobility, testing, and/or disease exposure for forecasting? How to handle noisy data and generate uncertainties in the forecast? In this paper, we present DO_SCPLOWEEPC_SCPLOWCO_SCPLOWOVIDC_SCPLOW, an operational deep learning frame-work designed for real-time COVID-19 forecasting. DO_SCPLOWEEPC_SCPLOW-CO_SCPLOWOVIDC_SCPLOW works well with sparse data and can handle noisy heterogeneous data signals by propagating the uncertainty from the data in a principled manner resulting in meaningful uncertainties in the forecast. The deployed framework also consists of modules for both real-time and retrospective exploratory analysis to enable interpretation of the forecasts. Results from real-time predictions (featured on the CDC website and FiveThirtyEight.com) since April 2020 indicates that our approach is competitive among the methods in the COVID-19 Forecast Hub, especially for short-term predictions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alexander Rodr\u00edguez", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Anika Tabassum", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Jiaming Cui", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Jiajia Xie", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Javen Ho", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Pulak Agarwal", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Bijaya Adhikari", - "author_inst": "University of Iowa" - }, - { - "author_name": "B. Aditya Prakash", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.28.20203190", "rel_title": "Predictors of symptomatic laboratory-confirmed SARS-COV-2 reinfection", @@ -1137870,6 +1134710,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.09.29.20203737", + "rel_title": "Seroprevalence of SARS CoV-2 antibodies in healthcare workers and administration employees: a prospective surveillance study at a 1,400-bed university hospital in Germany", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20203737", + "rel_abs": "Background: Healthcare workers (HCWs) are at particular risk to acquire SARS-CoV-2 infections. Aim: The objectives of this study were to compare SARS-CoV-2 IgG seroprevalence and compliance to wear personal protective equipment (PPE) between HCWs working within (high-risk) or outside (intermediate-risk) units treating suspected or confirmed COVID-19 patients. In addition, administration staff (low-risk) was included. Materials: Co-HCW is a prospective cohort study among employees at the Jena University Hospital, Germany. Since 16th March 2020, 50 SARS-CoV-2 inpatients and 73 outpatients were treated in our hospital. Mandatory masking was implemented on 20th March 2020. We here evaluated seroprevalence using two IgG detecting immunoassays, assessed COVID-19 exposure, clinical symptoms and compliance to wear PPE. Findings: Between 19th May and 19th June 2020 we analysed 660 employees [out of 3,228; 20.4%]. Eighteen participants (2.7%) had SARS-CoV-2 antibodies in at least one immunoassay. Among them, 13 (72.2%) were not aware of direct COVID-19 exposure and 9 (50.0%) did not report any clinical symptoms. We observed no evidence for an association between seroprevalence and risk area (high-risk: 2 of 137 HCWs (1.5%), intermediate-risk: 10 of 343 HCWs (2.9%), low-risk: 6 of 180 administration employees (3.3%); p=0.574). Reported compliance to wear PPE differed (p<0.001) between working in high-risk (98.3%) and in intermediate-risk areas (69.8%). Conclusion: No evidence for higher seroprevalence against SARS-CoV-2 in HCWs working in high-risk COVID-19 areas could be observed, probably due to high compliance to wear PPE. Compared to administration employees, we observed no additional risk to acquire SARS-CoV-2 infections by patient care.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Christina Bahrs", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Aurelia Kimmig", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Sebastian Weis", + "author_inst": "Jena University Hospital" + }, + { + "author_name": "Juliane Ankert", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Stefan Hagel", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Jens Maschmann", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Andreas Stallmach", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Andrea Steiner", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Michael Bauer", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Wilhelm Behrigner", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Michael Baier", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Miriam Kesselmeier", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Cora Richert", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Florian Zepf", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Martin Walter", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Andre Scherag", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Michael Kiehntopf", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Bettina Loeffler", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + }, + { + "author_name": "Mathias W Pletz", + "author_inst": "Jena University Hospital, Friedrich-Schiller-University, Jena, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.29.20203695", "rel_title": "Coding Complete Genome Sequences of Twenty-three SARS-CoV-2 Strains Isolated in the Philippines", @@ -1138753,33 +1135684,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.25.20201996", - "rel_title": "The quantitative landscape of the neutralizing antibody response to SARS-CoV-2", - "rel_date": "2020-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201996", - "rel_abs": "Neutralizing antibodies (NAbs) appear promising interventions against SARS-CoV-2 infection. Over 100 NAbs have been identified so far and several are in clinical trials. Yet, which NAbs would be the most potent remains unclear. Here, we analysed reported in vitro dose-response curves (DRCs) of >70 NAbs and estimated corresponding 50% inhibitory concentrations, slope parameters, and instantaneous inhibitory potentials (IIPs), presenting a comprehensive quantitative landscape of NAb responses to SARS-CoV-2. NAbs with high IIPs are likely to be potent. To assess the applicability of the landscape in vivo, we analysed available DRCs of NAbs from individual patients and found that the responses closely resembled the landscape. Further, we created virtual patient plasma samples by randomly sampling NAbs from the landscape and found that they recapitulated plasma dilution assays from convalescent patients. The landscape thus offers a facile tool for benchmarking NAbs and would aid the development of NAb-based therapies for SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pranesh Padmanabhan", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Rajat Desikan", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Narendra M Dixit", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.25.20201921", "rel_title": "Improved Sensitivity, Safety, and Rapidity of COVID-19 Tests by Replacing Viral Storage Solution with Lysis Buffer", @@ -1139608,6 +1136512,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.26.20189522", + "rel_title": "Clinical Course And Risk Factors For In-hospital Death In Critical COVID-19 In Wuhan, China", + "rel_date": "2020-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20189522", + "rel_abs": "BACKGROUND The risk factors for mortality of COVID-19 classified as critical type have not been well described. OBJECTIVES This study aimed to described the clinical outcomes and further explored risk factors of in-hospital death for COVID-19 classified as critical type. METHODS This was a single-center retrospective cohort study. From February 5, 2020 to March 4, 2020, 98 consecutive patients classified as critical COVID-19 were included in Huo Shen Shan Hospital. The final date of follow-up was March 29, 2020. The primary outcome was all-cause mortality during hospitalization. Multivariable Cox regression model was used to explore the risk factors associated with in-hospital death. RESULTS Of the 98 patients, 43 (43.9%) died in hospital, 37(37.8%) discharged, and 18(18.4%) remained in hospital. The mean age was 68.5 (63, 75) years, and 57 (58.2%) were female. The most common comorbidity was hypertension (68.4%), followed by diabetes (17.3%), angina pectoris (13.3%). Except the sex (Female: 68.8% vs 49.1%, P=0.039) and angina pectoris (20.9% vs 7.3%, P = 0.048), there was no difference in other demographics and comorbidities between non-survivor and survivor groups. The proportion of elevated alanine aminotransferase, creatinine, D-dimer and cardiac injury marker were 59.4%, 35.7%, 87.5% and 42.9%, respectively, and all showed the significant difference between two groups. The acute cardiac injury, acute kidney injury (AKI), and acute respiratory distress syndrome (ARDS) were observed in 42.9%, 27.8% and 26.5% of the patients. Compared with survivor group, non-survivor group had more acute cardiac injury (79.1% vs 14.5%, P<0.0001), AKI (50.0% vs 10.9%, P<0.0001), and ARDS (37.2% vs 18.2%, P=0.034). Multivariable Cox regression showed increasing hazard ratio of in-hospital death associated with acute cardiac injury (HR, 6.57 [95% CI, 1.89-22.79]) and AKI (HR, 2.60 [95% CI, 1.15-5.86]). CONCLUSIONS COVID-19 classified as critical type had a high prevalence of acute cardiac and kidney injury, which were associated with a higher risk of in-hospital mortality.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Fei Li", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Yue Cai", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Chao Gao", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Lei Zhou", + "author_inst": "Clinical Laboratory, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Renjuan Chen", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Kan Zhang", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Weiqin Li", + "author_inst": "Department of Critical Care Medicine, Jinling Hospital, Nanjing, China" + }, + { + "author_name": "Ruining Zhang", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Xijing Zhang", + "author_inst": "Surgical ICU, Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Duolao Wang", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Yi Liu", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + }, + { + "author_name": "Ling Tao", + "author_inst": "Department of Cardiology, Xijing Hospital, Fourth Military Medical University, China" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.28.20202945", "rel_title": "A Systematic Review and Meta-analysis of Pregnancy and COVID-19: Signs and Symptoms, Laboratory Tests and Perinatal Outcomes", @@ -1140419,45 +1137386,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.25.20201533", - "rel_title": "Equity in Paediatric Emergency Departments during COVID-19", - "rel_date": "2020-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201533", - "rel_abs": "Childrens attendances in paediatric emergency departments have fallen precipitously in North East England and elsewhere in recent months. We analysed data from 3 hospitals to understand which children were not being brought during the COVID-19 lockdown. In our population there is no evidence of a disproportionate impact on children belonging to vulnerable sociodemographic groups and no obvious change in illness acuity among those children still attending. However we noted a marked reduction in infectious disease presentations which might reflect one positive impact of enhanced social distancing on child health. More granular data describing the collateral damage of the COVID-19 pandemic to childrens clinical services are needed to plan for the mitigation of its continuing effects.\n\nWhat is known on this topicO_LIPresentations to paediatric emergency departments in Europe and the United States have reduced dramatically during the COVID-19 pandemic lockdown.\nC_LI\n\nWhat this paper adds boxO_LIThis is the first paper to show that reduced attendance was proportionate across different deprivation and ethnicity groups.\nC_LIO_LIWe show that presentations of children with infectious diseases reduced more than those with other conditions or trauma.\nC_LIO_LIThere was no change in admission rates, taken as a broad indicator of illness acuity at presentation among the population still attending paediatric emergency departments.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sophie Thorne", - "author_inst": "Newcastle University" - }, - { - "author_name": "Sunil Bhopal", - "author_inst": "Population Health Sciences Institute, Newcastle University" - }, - { - "author_name": "Christian Harkensee", - "author_inst": "Gateshead Health NHS Foundation Trust" - }, - { - "author_name": "Alexandra Battersby", - "author_inst": "Newcastle Hospitals NHS Foundation Trust" - }, - { - "author_name": "Anna Brough", - "author_inst": "Newcastle Hospitals NHS Foundation Trust" - }, - { - "author_name": "Stephen Owens", - "author_inst": "Newcastle Hospitals NHS Foundation Trust & Population Health Sciences Institute, Newcastle University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.09.25.20194431", "rel_title": "The Use of Psychoactive Substances in the Context of the Covid-19 Pandemic in Brazil", @@ -1141058,6 +1137986,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.25.20201582", + "rel_title": "Airway emergency management in a pediatric hospital before and during the COVID-19 pandemic", + "rel_date": "2020-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201582", + "rel_abs": "ObjectiveChildrens hospitals frequently care for infants with various life-threatening airway anomalies. Management of these infants can be challenging given unique airway anatomy and potential malformations. Airway emergency management must be immediate and precise, often demanding specialized equipment and/or expertise. We developed a Neonatal-Infant Airway Safety Program to improve medical responses, communication, equipment usage and outcomes for infants requiring emergent airway interventions.\n\nPatients and MethodsAll patients admitted to our quaternary neonatal and infant intensive care unit (NICU) from 2008-2019 were included in this study. Our program consisted of a multidisciplinary airway response team, pager system, and emergency equipment cart. Respiratory therapists present at each emergency event recorded specialist response times, equipment utilization, and outcomes. A multidisciplinary oversite committee reviewed each incident.\n\nResultsSince 2008, there were 159 airway emergency events in our NICU ([~]12 per year). Mean specialist response times decreased from 5.9{+/-}4.9 min (2008-2012, mean{+/-}SD) to 4.3{+/-}2.2 min (2016-2019, p=0.12), and the number of incidents with response times >5 min decreased from 28.8{+/-}17.8% (2008-2012) to 9.3{+/-}11.4% (2016-2019, p=0.04 by linear regression). As our program became more standardized, we noted better equipment availability and subspecialist communication. Few emergency situations (n=9, 6%) required operating room management. There were 3 patient deaths (2%).\n\nConclusionsOur airway safety program, including readily available specialists and equipment, facilitated effective resolution of airway emergencies in our NICU and multidisciplinary involvement enabled rapid and effective changes in response to COVID-19 regulations. A similar program could be implemented in other centers.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christopher Thom", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Hitesh Deshmukh", + "author_inst": "Cincinnati Children's Hospital Medical Center" + }, + { + "author_name": "Leane Soorikian", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Ian Jacobs", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "John Fiadjoe", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Janet Lioy", + "author_inst": "Children's Hospital of Philadelphia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.09.25.20201731", "rel_title": "Antihypertensive Medications and COVID-19 Diagnosis and Mortality: Population-based Case-Control Analysis in the United Kingdom", @@ -1141909,129 +1138876,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.20199604", - "rel_title": "Safety and immunogenicity of the Ad26.COV2.S COVID-19 vaccine candidate: interim results of a phase 1/2a, double-blind, randomized, placebo-controlled trial", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20199604", - "rel_abs": "BACKGROUND The ongoing coronavirus disease (COVID)-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might be controlled by an efficacious vaccine. Multiple vaccines are in development, but no efficacious vaccine is currently available. METHODS We designed a multi-center phase 1/2a randomized, double-blinded, placebo-controlled clinical study to assesses the safety, reactogenicity and immunogenicity of Ad26.COV2.S, a non-replicating adenovirus 26 based vector expressing the stabilized pre-fusion spike (S) protein of SARS-CoV-2. Ad26.COV2.S was administered at a dose level of 5x1010 or 1x1011 viral particles (vp) per vaccination, either as a single dose or as a two-dose schedule spaced by 56 days in healthy adults (18-55 years old; cohort 1a & 1b; n= 402 and healthy elderly >65 years old; cohort 3; n=394). Vaccine elicited S specific antibody levels were measured by ELISA and neutralizing titers were measured in a wild-type virus neutralization assay (wtVNA). CD4+ T-helper (Th)1 and Th2, and CD8+ immune responses were assessed by intracellular cytokine staining (ICS). RESULTS We here report interim analyses after the first dose of blinded safety data from cohorts 1a, 1b and 3 and group unblinded immunogenicity data from cohort 1a and 3. In cohorts 1 and 3 solicited local adverse events were observed in 58% and 27% of participants, respectively. Solicited systemic adverse events were reported in 64% and 36% of participants, respectively. Fevers occurred in both cohorts 1 and 3 in 19% (5% grade 3) and 4% (0% grade 3), respectively, were mostly mild or moderate, and resolved within 1 to 2 days after vaccination. The most frequent local adverse event (AE) was injection site pain and the most frequent solicited AEs were fatigue, headache and myalgia. After only a single dose, seroconversion rate in wtVNA (50% inhibitory concentration - IC50) at day 29 after immunization in cohort 1a already reached 92% with GMTs of 214 (95% CI: 177; 259) and 92% with GMTs of 243 (95% CI: 200; 295) for the 5x1010 and 1x1011vp dose levels, respectively. A similar immunogenicity profile was observed in the first 15 participants in cohort 3, where 100% seroconversion (6/6) (GMTs of 196 [95%CI: 69; 560]) and 83% seroconversion (5/6) (GMTs of 127 [95% CI: <58; 327]) were observed for the 5x1010 or 1x1011 vp dose level, respectively. Seroconversion for S antibodies as measured by ELISA (ELISA Units/mL) was observed in 99% of cohort 1a participants (GMTs of 528 [95% CI: 442; 630) and 695 (95% CI: 596; 810]), for the 5x1010 or 1x1011 vp dose level, respectively, and in 100% (6/6 for both dose levels) of cohort 3 with GMTs of 507 (95% CI: 181; 1418) and 248 (95% CI: 122; 506), respectively. On day 14 post immunization, Th1 cytokine producing S-specific CD4+ T cell responses were measured in 80% and 83% of a subset of participants in cohort 1a and 3, respectively, with no or very low Th2 responses, indicative of a Th1-skewed phenotype in both cohorts. CD8+ T cell responses were also robust in both cohort 1a and 3, for both dose levels. CONCLUSIONS The safety profile and immunogenicity after only a single dose are supportive for further clinical development of Ad26.COV2.S at a dose level of 5x1010 vp, as a potentially protective vaccine against COVID-19. Trial registration number: NCT04436276", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Jerry Sadoff", - "author_inst": "Janssen" - }, - { - "author_name": "Mathieu Le Gars", - "author_inst": "Janssen Vaccines and Prevention" - }, - { - "author_name": "Georgi Shukarev", - "author_inst": "Janssen" - }, - { - "author_name": "Dirk Heerwegh", - "author_inst": "Janssen" - }, - { - "author_name": "Carla Truyers", - "author_inst": "Janssen" - }, - { - "author_name": "Anna Marit de Groot", - "author_inst": "Janssen" - }, - { - "author_name": "Jeroen Stoop", - "author_inst": "Janssen" - }, - { - "author_name": "Sarah Tete", - "author_inst": "Janssen" - }, - { - "author_name": "Wim Van Damme", - "author_inst": "Janssen" - }, - { - "author_name": "Isabel Leroux-Roels", - "author_inst": "CEVAC - University of Gent" - }, - { - "author_name": "Pieter-Jan Berghmans", - "author_inst": "SGS Life Sciences" - }, - { - "author_name": "Murray Kimmel", - "author_inst": "Optimal Research LLC" - }, - { - "author_name": "Pierre Van Damme", - "author_inst": "CEV University of Antwerp" - }, - { - "author_name": "Jan De Hoon", - "author_inst": "CCP LUVAC UZ Leuven" - }, - { - "author_name": "William Smith", - "author_inst": "VRG and NOCCR" - }, - { - "author_name": "Kathryn Stephenson", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Dan Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Stephen De Rosa", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Kristen Cohen", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Juliana McElrath", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Emmanuel Cormier", - "author_inst": "Janssen" - }, - { - "author_name": "Gert Scheper", - "author_inst": "Janssen" - }, - { - "author_name": "Jenny Hendriks", - "author_inst": "Janssen" - }, - { - "author_name": "Frank Struyf", - "author_inst": "Janssen" - }, - { - "author_name": "Macaya Douoguih", - "author_inst": "Janssen" - }, - { - "author_name": "Johan Van Hoof", - "author_inst": "Janssen" - }, - { - "author_name": "Hanneke Schuitemaker", - "author_inst": "Janssen" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.23.20200410", "rel_title": "Review of clinical characteristics and laboratory findings of COVID-19 in children-Systematic review and Meta-analysis", @@ -1142856,6 +1139700,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.24.20200782", + "rel_title": "Risk assessment of COVID-19 airborne infection during hybrid learning", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200782", + "rel_abs": "Converging lines of evidence seem to indicate that SARS-CoV-2, the novel coronavirus responsible for the COVID-19 pandemic, can be transmitted from person-to-person via aerosols that waft through the air and accumulate over time. The airborne nature of the virus could be a threat in indoor spaces in general and in particular for in-class education. We provide an assessment of the risk of SARS-CoV-2 infection during a 7-hour school day in elementary schools. We show that existing data are insufficient to establish a low (below 1\\%) probability of infection with high accuracy. The use of facemasks and social distancing could significantly decrease this risk.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luis Alfredo Anchordoqui", + "author_inst": "City University of New York" + }, + { + "author_name": "Eugene M. Chudnovsky", + "author_inst": "City University of New York" + }, + { + "author_name": "Thomas C Paul", + "author_inst": "City University of New York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.24.20200865", "rel_title": "What have we learned about positive changes experienced during COVID-19 lockdown? Evidence of the social patterning of change", @@ -1143679,69 +1140550,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.09.24.20201236", - "rel_title": "Behavioural barriers to COVID-19 testing in Australia", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20201236", - "rel_abs": "BackgroundThe current suppression strategy for COVID-19 in Australia is dependent on people getting tested and self-isolating while they have COVID-19 symptoms. However, there is very little research on the behaviours and behavioural barriers involved in getting tested, both in Australia and worldwide, despite there being some evidence that these barriers do exist.\n\nMethodsThe Sydney Health Literacy Lab (SHeLL) has been conducting a national longitudinal survey in Australia since April 2020. A list of testing barriers was included in Wave 3 in June 2020 (n=1369), along with intentions to test and self-isolate if symptomatic. Open responses were also collected. The test barriers identified were categorised using the COM-B framework.\n\nResultsOnly 49% of people strongly agreed they would get tested if they had COVID-19 symptoms, but most people agreed to some extent that they would get tested (96%). The most common barriers selected from the list provided were that testing is painful (11%), not knowing how to get tested (7%), and worry about getting infected at the testing centre (5%). Many participants (10%) indicated other reasons, and open responses included many additional barriers to testing than those provided in the initial list. These covered all components of the COM-B model.\n\nConclusionWe identified a wide range of barriers using both quantitative and qualitative methods, which need to be addressed in order to increase COVID-19 testing behaviour.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Carissa Bonner", - "author_inst": "University of Sydney" - }, - { - "author_name": "Carys Batcup", - "author_inst": "University of Sydney" - }, - { - "author_name": "Julie Ayre", - "author_inst": "University of Sydney" - }, - { - "author_name": "Kristen Pickles", - "author_inst": "University of Sydney" - }, - { - "author_name": "Rachael Dodd", - "author_inst": "University of Sydney" - }, - { - "author_name": "Tessa Copp", - "author_inst": "University of Sydney" - }, - { - "author_name": "Samuel Cornell", - "author_inst": "University of Sydney" - }, - { - "author_name": "Erin Cvejic", - "author_inst": "University of Sydney" - }, - { - "author_name": "Thomas Dakin", - "author_inst": "University of Sydney" - }, - { - "author_name": "Jennifer Isautier", - "author_inst": "University of Sydney" - }, - { - "author_name": "Brooke Nickel", - "author_inst": "University of Sydney" - }, - { - "author_name": "Kirsten J McCaffery", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.24.20201301", "rel_title": "Psychological preparedness for pandemic (COVID-19) management: Perceptions of nurses and nursing students in India", @@ -1144618,6 +1141426,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.25.313148", + "rel_title": "Rapid behavioral response of urban birds to covid-19 lockdown", + "rel_date": "2020-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.25.313148", + "rel_abs": "Biodiversity is threatened by the growth of urban areas. However, it is still poorly understood how animals can cope with and adapt to these rapid and dramatic transformations of natural environments. The COVID-19 pandemic provides us with a unique opportunity to unveil the mechanisms involved in this process. Lockdown measures imposed in most countries are causing an unprecedented reduction of human activities giving us an experimental setting to assess the effects of our lifestyle on biodiversity. We studied the birds response to the population lockdown by using more than 126,000 bird records collected by a citizen science project in north eastern Spain. We compared the occurrence and detectability of birds during the spring 2020 lockdown with baseline data from previous years in the same urban areas and dates. We found that birds did not increase their probability of occurrence in urban areas during the lockdown, refuting the hypothesis that nature has recovered its space in human emptied urban areas. However, we found an increase in bird detectability, especially during early morning, suggesting a rapid change in the birds daily routines in response to quieter and less crowded cities. In conclusion, urban birds showed high behavioural plasticity to rapidly adjust to novel environmental conditions, as those imposed by the COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Oscar Gordo", + "author_inst": "Catalan Ornithological Institute" + }, + { + "author_name": "Lluis Brotons", + "author_inst": "CTFC-CSIC" + }, + { + "author_name": "Sergi Herrando", + "author_inst": "Catalan Ornithological Institute" + }, + { + "author_name": "Gabriel Gargallo", + "author_inst": "Catalan Ornithological Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2020.09.22.20196204", "rel_title": "Risk factors for mortality among hospitalized patients with COVID-19", @@ -1145509,49 +1142348,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.22.308783", - "rel_title": "In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein", - "rel_date": "2020-09-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308783", - "rel_abs": "Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 spike protein interferes with pain signaling. Here, we report hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physico-chemical properties. Using an ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that almost all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Samantha Perez-Miller", - "author_inst": "University of Arizona" - }, - { - "author_name": "Marcel Patek", - "author_inst": "Brightrockpath LLC" - }, - { - "author_name": "Aubin Moutal", - "author_inst": "University of Arizona" - }, - { - "author_name": "Carly R Cabel", - "author_inst": "University of Arizona" - }, - { - "author_name": "Curtis A. Thorne", - "author_inst": "University of Arizona" - }, - { - "author_name": "Samuel K Campos", - "author_inst": "University of Arizona" - }, - { - "author_name": "Rajesh Khanna", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.09.22.308965", "rel_title": "Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection", @@ -1146408,6 +1143204,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.22.20199497", + "rel_title": "An analysis of clinical and geographical metadata of over 75,000 records in the GISAID COVID-19 database", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199497", + "rel_abs": "During the SARS-CoV-2 outbreak that caused the coronavirus pandemic it is important now more than ever that scientists and public health officials work side-by-side and use their available resources to track patient information from those that have been affected by the novel coronavirus. The ability to track the disease helps identify possible trends and patterns that can be used by public health officials to make more informed decisions. Tracking data like this may be the key to helping states and countries safely re-open. However, when analyzing large collections of data there is the occurrence of confounding factors such as biases in patient sampling. In this project, a massive collection of COVID-19 data was analyzed, and explored potential biases in patient sampling were explored.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anjelina Velazquez", + "author_inst": "California State University San Marcos" + }, + { + "author_name": "Mhealyssah Bustria", + "author_inst": "California State University San Marcos" + }, + { + "author_name": "Youwen Ouyang", + "author_inst": "California State University San Marcos" + }, + { + "author_name": "Niema Moshiri", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.22.20198820", "rel_title": "Heat Stress and PPE during COVID-19: Impact on health care workers' performance, safety and well-being in NHS settings.", @@ -1147339,41 +1144166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.22.20199810", - "rel_title": "Empirical transmission advantage of the D614G mutant strain of SARS-CoV-2", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199810", - "rel_abs": "The SARS-CoV-2 lineage carrying the amino acid change D614G has become the dominant variant in the global COVID-19 pandemic. The rapid spread of the G614 mutant suggests that it may have a transmission advantage over the D614 wildtype. Using our previous epidemiological framework to analyze COVID-19 surveillance and sequence data, we estimated that the G614 mutant is 31% (28-34%) more transmissible than the D614 wildtype. As such, interventions that were previously effective in containing or mitigating the D614 wildtype (e.g. in China, Vietnam, Thailand, etc.) might be less effective against the G614 mutant. Our framework can be readily integrated into current COVID-19 surveillance to monitor the emergence and fitness of mutant strains, such that pandemic surveillance, disease control and development of treatment and vaccines can be adjusted dynamically.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Kathy Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yao Pei", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gabriel M Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Tommy T. Y. Lam", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joseph T. Wu", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.20.20198283", "rel_title": "Exponential distribution of large excess death rates in Europe during the COVID-19 outbreak in the spring of 2020", @@ -1148230,6 +1145022,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.11.20193029", + "rel_title": "Covid-19 Cases in India: A Visual Exploratory Data Analysis Model", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20193029", + "rel_abs": "Covid-19 outbreak was first reported in Wuhan, China. The deadly virus spread not just the disease, but fear around the globe. On January 2020, WHO declared COVID-19 as a Public Health Emergency of International Concern (PHEIC). First case of Covid-19 in India was reported on January 30, 2020. By the time, India was prepared in fighting against the virus. India has taken various measures to tackle the situation. In this paper, an exploratory data analysis of Covid-19 cases in India is carried out. Data namely number of cases, testing done, Case Fatality ratio, Number of deaths, change in visits stringency index and measures taken by the government is used for modelling and visual exploratory data analysis.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jayesh S Jr.", + "author_inst": "School of Engineering,Cochin University of Science and Technology" + }, + { + "author_name": "Shilpa Sreedharan Jr.", + "author_inst": "Wellness Solutions" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.09.21.20196220", "rel_title": "Privacy-Protecting, Reliable Response Data Discovery Using COVID-19 Patient Observations", @@ -1149285,81 +1146100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.21.20193953", - "rel_title": "D-dimer dynamics in hospitalized COVID-19 patients: potential utility for diagnosis of pulmonary embolism.", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20193953", - "rel_abs": "Background: A higher incidence of thrombotic events, mainly pulmonary embolism (PE), has been reported in hospitalized patients with COVID-19. Objectives: To assess clinical and weekly laboratory differences in hospitalized COVID-19 patients according to occurrence of PE. Methods: This retrospective study included all consecutive patients hospitalized with COVID-19 who underwent a computed tomography (CT) angiography for PE clinical suspicion. Clinical data and median blood test results distributed into weekly periods from COVID-19 symptoms onset were compared between PE and non-PE patients. Results: Ninety-two patients were included, 29 (32%) had PE. PE patients were younger (63.9 (SD13.7) vs 69.9 (SD12.5) years). Clinical symptoms and COVID-19 CT features were similar in both groups. PE was diagnosed after a mean of 20.0 (SD8.6) days from the onset of COVID-19 symptoms. Corticosteroid boluses were more frequently used in PE patients (62% vs. 43%). Median values [IQR] of D-dimer in PE vs non-PE patients were: week 2 (2010.7 [770.1-11208.9] vs 626.0 [374.0-2382.2]; p=0.04); 3 (3893.1 [1388.2-6694.0] vs 1184.4 [461.8-2447.8]; p=0.03); and 4 (2736.3 [1202.1-8514.1] vs 1129.1 [542.5-2834.6]; p=0.01). Median fold-increase of D-dimer between week 1 and 2 differed between groups (6.64 [3.02-23.05] vs 1.57 [0.64-2.71], p=0.003); ROC curve AUC was 0.879 (p=0.003) with a sensitivity and specificity for PE of 86% and 80%, respectively. Conclusions: Among hospitalized COVID-19 patients, D-dimer levels are higher at weeks 2, 3 and 4 after COVID-19 symptom onset in patients who develop PE. This difference is more pronounced when the fold increase between weeks 1 and 2 is compared.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pau Cerda", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Jesus Ribas", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Adriana Iriarte", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Jose Maria Mora-Lujan", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Raque Torres", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Belen del Rio", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Hector Ignacio Jofre", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Yolanda Ruiz", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Marta Huguet", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Maria Paz Fuset", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Sergio Martinez-Yelamos", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Salud Santos", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Nuria Llecha", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Xavier Corbella", - "author_inst": "Hospital Universitari de Bellvitge" - }, - { - "author_name": "Antoni Riera-Mestre", - "author_inst": "Hospital Universitari de Bellvitge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.23.308239", "rel_title": "The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization", @@ -1149944,6 +1146684,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.19.20198051", + "rel_title": "COVID-19: Risks of Re-emergence, Re-infection, and Control Measures -- A Long Term Modelling Study", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.19.20198051", + "rel_abs": "In this work we define a modified SEIR model that accounts for the spread of infection during the latent period, infections from asymptomatic or pauci-symptomatic infected individuals, potential loss of acquired immunity, people's increasing awareness of social distancing and the use of vaccination as well as non-pharmaceutical interventions like social confinement. We estimate model parameters in three different scenarios - in Italy, where there is a growing number of cases and re-emergence of the epidemic, in India, where there are significant number of cases post confinement period and in Victoria, Australia where a re-emergence has been controlled with severe social confinement program. Our result shows the benefit of long-term confinement of 50% or above population and extensive testing. With respect to loss of acquired immunity, our model suggests higher impact for Italy. We also show that a reasonably effective vaccine with mass vaccination program can be successful in significantly controlling the size of infected population. We show that for India, a reduction in contact rate by 50% compared to a reduction of 10% in the current stage can reduce death from 0.0268% to 0.0141% of population. Similarly, for Italy we show that reducing contact rate by half can reduce a potential peak infection of 15% population to less than 1.5% of population, and potential deaths from 0.48% to 0.04%. With respect to vaccination, we show that even a 75% efficient vaccine administered to 50% population can reduce the peak number of infected populations by nearly 50% in Italy. Similarly, for India, a 0.056% of population would die without vaccination, while 93.75% efficient vaccine given to 30% population would bring this down to 0.036% of population, and 93.75% efficient vaccine given to 70% population would bring this down to 0.034%.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Subhas Kumar Ghosh", + "author_inst": "CBA" + }, + { + "author_name": "Sachchit Ghosh", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.18.20197376", "rel_title": "Age groups that sustain resurging COVID-19 epidemics in the United States", @@ -1150951,109 +1147714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.21.305698", - "rel_title": "AI-guided discovery of the invariant host response to viral pandemics", - "rel_date": "2020-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.21.305698", - "rel_abs": "We sought to define the host immune response, a.k.a, the \"cytokine storm\" that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a seed gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. Surprisingly, this 166-gene signature was conserved in all viral pandemics, including COVID-19, and a subset of 20-genes classified disease severity, inspiring the nomenclatures ViP and severe-ViP signatures, respectively. The ViP signatures pinpointed a paradoxical phenomenon wherein lung epithelial and myeloid cells mount an IL15 cytokine storm, and epithelial and NK cell senescence and apoptosis determines severity/fatality. Precise therapeutic goals were formulated and subsequently validated in high-dose SARS-CoV-2-challenged hamsters using neutralizing antibodies that abrogate SARS-CoV-2*ACE2 engagement or a directly acting antiviral agent, EIDD-2801. IL15/IL15RA were elevated in the lungs of patients with fatal disease, and plasma levels of the cytokine tracked with disease severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.\n\nOne Sentence SummaryThe host immune response in COVID-19.\n\nPANEL: RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe SARS-CoV-2 pandemic has inspired many groups to find innovative methodologies that can help us understand the host immune response to the virus; unchecked proportions of such immune response have been implicated in fatality. We searched GEO and ArrayExpress that provided many publicly available gene expression data that objectively measure the host immune response in diverse conditions. However, challenges remain in identifying a set of host response events that are common to every condition. There are no studies that provide a reproducible assessment of prognosticators of disease severity, the host response, and therapeutic goals. Consequently, therapeutic trials for COVID-19 have seen many more misses than hits. This work used multiple (> 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them.\n\nAdded value of this studyThis work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the cytokine storm mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs.\n\nImplications of all the available evidenceThe ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Debashis Sahoo", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Gajanan D. Katkar", - "author_inst": "UCSD" - }, - { - "author_name": "Soni Khandelwal", - "author_inst": "UCSD" - }, - { - "author_name": "Mahdi Behroozikhah", - "author_inst": "UCSD" - }, - { - "author_name": "Amanraj Claire", - "author_inst": "UCSD" - }, - { - "author_name": "Vanessa Castillo", - "author_inst": "UCSD" - }, - { - "author_name": "Courtney Tindle", - "author_inst": "UCSD" - }, - { - "author_name": "MacKenzie Fuller", - "author_inst": "UCSD" - }, - { - "author_name": "Sahar Taheri", - "author_inst": "UCSD" - }, - { - "author_name": "Thomas F. Rogers", - "author_inst": "UCSD" - }, - { - "author_name": "Nathan Beutler", - "author_inst": "Scripps Institute La Jolla" - }, - { - "author_name": "Sydney Ramirez", - "author_inst": "JLI" - }, - { - "author_name": "Stephen A. Rawlings", - "author_inst": "UCSD" - }, - { - "author_name": "Victor Pretorius", - "author_inst": "UCSD" - }, - { - "author_name": "Davey Smith", - "author_inst": "UCSD" - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "UCSD" - }, - { - "author_name": "Laura Crotty Alexander", - "author_inst": "UCSD" - }, - { - "author_name": "Jason M. Duran", - "author_inst": "UCSD" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute For Immunology (LJI)" - }, - { - "author_name": "Jennifer M Dan", - "author_inst": "La Jolla Institute for Allergy and Immunology" - }, - { - "author_name": "Soumita Das", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Pradipta Ghosh", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.22.308098", "rel_title": "Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation", @@ -1151609,6 +1148269,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.19.20197749", + "rel_title": "How super-spreader cities, highways, hospital bed availability, and dengue fever influenced the COVID-19 epidemic in Brazil", + "rel_date": "2020-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.19.20197749", + "rel_abs": "Although its international airports served as the country's main entry points for SARS-CoV-2, the factors driving the uneven geographic spread of COVID-19 cases and deaths in Brazil remain largely unknown. Here we show that four major factors likely accounted for the entire dynamics of COVID-19 in Brazil. Mathematical modeling revealed that, initially, the \"super-spreading\" city of Sao Paulo accounted for roughly 80% of the case spread in the entire country. During the first 3 months of the epidemic, by adding only 16 other spreading cities, we accounted for 98-99% of the cases reported in Brazil at the time. Moreover, 26 of the major Brazilian federal highways accounted for about 30% of SARS-CoV-2's case spread. As cases accumulated rapidly in the Brazilian countryside, the distribution of COVID-19 deaths began to correlate with a third parameter: the geographic distribution of the country's hospital intensive care unit (ICU) beds, which is highly skewed towards state capitals where the epidemic began. That meant that severely ill patients living in the countryside had to be transported to state capitals to access ICU beds where they often died, creating a \"boomerang effect\" that contributed to the skew of the geographic distribution of COVID-19 deaths. Finally, we discovered that the geographic distribution of dengue fever, amounting to more than 3.5 million cases from January 2019 to July 2020, was highly complementary to that of COVID-19. This was confirmed by the identification of significant negative correlations between COVID-19's incidence, infection growth rate, and mortality to the percentage of people with antibody (IgM) levels for dengue fever in each of the country's states. No such correlations were observed when IgM data for chikungunya virus, which is transmitted by the same mosquito vector as dengue, was used. Thus, states in which a large fraction of the population had contracted dengue fever in 2019-2020 reported lower COVID-19 cases and deaths, and took longer to reach exponential community transmission, due to slower SARS-CoV-2 infection growth rates. This inverse correlation between COVID-19 and dengue fever was further observed in a sample of countries around Asia and Latin America, as well as in islands in the Pacific and Indian Oceans. This striking finding raises the intriguing possibility of an immunological cross-reactivity between DENV serotypes and SARS-CoV-2. If proven correct, this hypothesis could mean that dengue infection or immunization with an efficacious and safe dengue vaccine could produce some level of immunological protection for SARS-CoV-2, before a vaccine for SARS-CoV-2 becomes available.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Miguel A. L. Nicolelis", + "author_inst": "Duke University" + }, + { + "author_name": "Rafael L. G. Raimundo", + "author_inst": "Federal University of Paraiba" + }, + { + "author_name": "Pedro S. Peixoto", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Cecilia Siliansky de Andreazzi", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.16.20194787", "rel_title": "COVID-19 herd immunity in the Brazilian Amazon", @@ -1152604,41 +1149295,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.19.20197830", - "rel_title": "Rapid transition to distance learning due to COVID-19: Perceptions of postgraduate dental learners and instructors", - "rel_date": "2020-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.19.20197830", - "rel_abs": "The outbreak of COVID-19 necessitated abrupt transition from on campus, face-to- face sessions to online, distance learning in higher education institutions. The purpose of this study was to investigate the perceptions of postgraduate dental learners and instructors about the transition to distance learning, including the changes to the learning and teaching and its efficaciousness.\n\nA mixed-methods approach to research was utilized. All the instructors and postgraduate learners were invited to participate in the online survey. Quantitative data was analyzed using descriptive and inferential analyses on SPSS for Windows version 25.0, and for the responses to the open-ended questions, multi-staged Thematic Analysis was utilized.\n\nBoth groups of stakeholders: learners and instructors, were quite satisfied with the rapid transition to distance learning due to COVID-19. Instructors were significantly more satisfied than the learners. The stakeholders adapted well to the change. The perception of the stakeholders regarding the case-based scenarios significantly influenced their level of satisfaction. As perceived by the stakeholders, the transition to distance learning entailed advantages and challenges. Going through the experience equipped the stakeholders with lessons learned and enabled them to develop informed opinions of how best to sustain learning and teaching irrespective of how matters unfold in relation to the pandemic.\n\nIn conclusion, the worldwide dental education community faced unprecedented challenges due to the onset of COVID-19. Yet, in the grand scheme of things, it is important for decision-makers not to miss-out on the worthwhile opportunities, inherent in the experience, to reinforce curriculums, and maximize the learning and teaching.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Fatemeh Amir Rad", - "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences" - }, - { - "author_name": "Farah Otaki", - "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences" - }, - { - "author_name": "Zaid baqain", - "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences" - }, - { - "author_name": "Nabil Zary", - "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences" - }, - { - "author_name": "Manal Al-Halabi", - "author_inst": "Mohammed Bin Rashed University of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.09.18.302901", "rel_title": "SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism", @@ -1153147,6 +1149803,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.15.20159749", + "rel_title": "Limited specificity of commercially available SARS-CoV-2 IgG ELISAs in serum samples of African origin", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20159749", + "rel_abs": "Specific serological tests are mandatory for reliable SARS-CoV-2 seroprevalence studies but assay specificity may vary considerably between populations due to interference of immune responses to other pathogens. Here, we assess the false positive rates obtained with four commercially available IgG ELISAs in serum panels originating from three different African countries.\n\nArticle summary lineSeveral commercially available SARS-CoV-2 ELISAs show limited specificity when applied to serum panels of African origin", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Petra Emmerich", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, University of Rostock" + }, + { + "author_name": "Carolin Murawski", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Christa Ehmen", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Ronald von Possel", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Neele Pekarek", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Meike Pahlmann", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Lisa Oestereich", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Sophie Duraffour", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Nicole S Struck", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Daniel Eibach", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Ralf Krumkamp", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "John Amuasi", + "author_inst": "Kumasi Centre for Collaborative Research in Tropical Medicine" + }, + { + "author_name": "Oumou Maiga-Ascofare", + "author_inst": "Kumasi Centre for Collaborative Research in Tropical Medicine, German Center for Infection Research (DZIF)" + }, + { + "author_name": "Raphael Rakotozandrindrainy", + "author_inst": "University of Antananarivo" + }, + { + "author_name": "Danny Asogun", + "author_inst": "Irrua Specialist Teaching Hospital" + }, + { + "author_name": "Yemisi Ighodalo", + "author_inst": "Irrua Specialist Teaching Hospital" + }, + { + "author_name": "Simone Kann", + "author_inst": "Medical Mission Institute" + }, + { + "author_name": "Juergen May", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Egbert Tannich", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Pathogens" + }, + { + "author_name": "Christina Deschermeier", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.14.20194381", "rel_title": "Pentoxifylline and Covid-19: A Systematic Review", @@ -1153998,81 +1150749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.15.20194829", - "rel_title": "Longitudinal Mediators of Early Pandemic Distress", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194829", - "rel_abs": "We leverage powerful time-series data from a national longitudinal sample measured before the COVID-19 pandemic and during the worlds eighth most stringent COVID-19 lockdown (New Zealand, March-April 2020, N = 940) and apply Bayesian multilevel mediation models to rigorously test five theories of pandemic distress. Findings: (1) during lockdown, rest diminished distress; without rest psychological distress would have been ~ 1.74 times greater; (2) an elevated sense of community reduced distress, a little, but elevated government satisfaction was inert. Thus, the psychological benefits of lockdown extended to political discontents; (3) most lockdown distress arose from dissatisfaction from personal relationships. Social captivity, more than isolation, proved challenging; (4-5) Health and business satisfaction were stable; were they challenged substantially more distress would have ensued. Thus, lockdown benefited psychological health by affording safety, yet only because income remained secure. These national longitudinal findings clarify the mental health effects of stringent infectious disease containment.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Joseph A Bulbulia", - "author_inst": "Victoria University of Wellington" - }, - { - "author_name": "Sofia D Piven", - "author_inst": "University of Auckland" - }, - { - "author_name": "Fiona Kate Barlow", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Don E. Davis", - "author_inst": "Georgia State University" - }, - { - "author_name": "Lara M Greaves", - "author_inst": "University of Auckland" - }, - { - "author_name": "Benjamin Highland", - "author_inst": "University of Auckland" - }, - { - "author_name": "Carla A Houkamau", - "author_inst": "University of Auckland" - }, - { - "author_name": "Taciano L Milfont", - "author_inst": "University of Waikato" - }, - { - "author_name": "Danny Osborne", - "author_inst": "University of Auckland" - }, - { - "author_name": "Nickola C Overall", - "author_inst": "University of Auckland" - }, - { - "author_name": "John H Shaver", - "author_inst": "University of Otago" - }, - { - "author_name": "Geoffrey Troughton", - "author_inst": "Victoria University of Wellington" - }, - { - "author_name": "Marc Wilson", - "author_inst": "Victoria University of Wellington" - }, - { - "author_name": "Kumar Yogeeswaran", - "author_inst": "University of Canterbury" - }, - { - "author_name": "Chris G Sibley", - "author_inst": "University of Auckland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.15.20194944", "rel_title": "COVID-19 pandemic increased the magnitude of mortality risks associated with cold temperature in Italy: A nationwide time-stratified case-crossover study", @@ -1154965,6 +1151641,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.16.20182915", + "rel_title": "COVID-19 epidemic modelling and the effect of publichealth interventions in India- SEIQHRF model", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20182915", + "rel_abs": "A dynamic epidemic modeling, based on real time data, of COVID19 has been attempted for India and few selected Indian states . Various scenarios of intervention strategies to contain the spread of the disease are explored.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Pooja Sengupta", + "author_inst": "International Management Institute, Kolkata" + }, + { + "author_name": "Bhaswati Ganguli", + "author_inst": "University of Calcutta, Department of Statistics" + }, + { + "author_name": "Aditya Chatterjee", + "author_inst": "University of Calcutta, Department of Statistics" + }, + { + "author_name": "Sugata SenRoy", + "author_inst": "University of Calcutta, Department of Statistics" + }, + { + "author_name": "Moumita Chatterjee", + "author_inst": "Aliah University, Department of Mathematics and Statistics" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.15.20195545", "rel_title": "Heterogeneity and temporal variation in the management of COVID-19: a multinational drug utilization study including 71,921 hospitalized patients from China, South Korea, Spain, and the United States of America", @@ -1155964,109 +1152675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.16.20196154", - "rel_title": "SARS-CoV-2 antibody signatures robustly predict diverse antiviral functions relevant for convalescent plasma therapy", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196154", - "rel_abs": "Convalescent plasma has emerged as a promising COVID-19 treatment. However, the humoral factors that contribute to efficacy are poorly understood. This study functionally and phenotypically profiled plasma from eligible convalescent donors. In addition to viral neutralization, convalescent plasma contained antibodies capable of mediating such Fc-dependent functions as complement activation, phagocytosis and antibody-dependent cellular cytotoxicity against SARS-CoV-2. These activities expand the antiviral functions associated with convalescent plasma and together with neutralization efficacy, could be accurately and robustly from antibody phenotypes. These results suggest that high-throughput profiling could be used to screen donors and plasma may provide benefits beyond neutralization.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Harini Natarajan", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Andrew R Crowley", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Savannah E Butler", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Shiwei Xu", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Joshua A Weiner", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Evan M Bloch", - "author_inst": "Johns Hopkins Medicine" - }, - { - "author_name": "Kirsten Littlefield", - "author_inst": "Johns Hopkins Bloomberg School of Public Health," - }, - { - "author_name": "Wendy Wieland-Alter", - "author_inst": "Dartmouth Hitchcock Medical Center" - }, - { - "author_name": "Ruth I Connor", - "author_inst": "Dartmouth Hitchcock Medical Center" - }, - { - "author_name": "Peter F Wright", - "author_inst": "Dartmouth Hitchcock Medical Center" - }, - { - "author_name": "Sarah E Benner", - "author_inst": "Johns Hopkins Medical Institutions" - }, - { - "author_name": "Tania S Bonny", - "author_inst": "Johns Hopkins Medical Institutions" - }, - { - "author_name": "Oliver Laeyendecker", - "author_inst": "NIAID & JHMI" - }, - { - "author_name": "David J Sullivan", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Shmuel Shoham", - "author_inst": "The Johns Hopkins Hospital, , MD" - }, - { - "author_name": "Thomas Quinn", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "H Benjamin Larman", - "author_inst": "Johns Hopkins Medical Institutions" - }, - { - "author_name": "Arturo Casadevall", - "author_inst": "Johns Hopkins School of Public Health" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Andrew Redd", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Aaron AR Tobian", - "author_inst": "Johns Hopkins Hospital" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.16.20196071", "rel_title": "COVID-19 and human milk: SARS-CoV-2, antibodies, and neutralizing capacity", @@ -1156683,6 +1153291,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.17.20196501", + "rel_title": "Epidemiology of SARS-CoV-2 infection in Karnataka State, South India: Transmission dynamics of symptomatic vs. asymptomatic infections", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196501", + "rel_abs": "Background: In this report, we describe the epidemiology of SARS-CoV-2 infection, specifically examining how the symptomatic persons drove the transmission in the state of Karnataka, India, during the lockdown phase. Methods: The study included all the cases reported from March 8 to May 31, 2020 in the state. Any person with history of international or domestic travel from high burden states, those presenting with Influenza-like or Severe Acute Respiratory Illness and high-risk contacts of COVID19 cases, who were SARS-CoV-2 RT-PCR positive were included. Detailed analysis based on contact tracing data available from line-list of the state surveillance unit was performed using cluster analysis software package. Findings: Amongst the 3404 COVID-19 positive cases, 3096 (91%) were asymptomatic while 308 (9%) were symptomatic. Majority of the asymptomatic cases were in the age range of 16-50 years while symptomatic cases were between 31-65 years. Most of those affected were males. Cluster analysis of 822 cases indicated that the secondary attack rate, size of the cluster (dispersion) and occurrence of overt clinical illness is significantly higher when the index case in a cluster was symptomatic compared to an asymptomatic. Interpretation: Our findings indicate that both asymptomatic and symptomatic SARS-CoV-2 cases transmit the infection; however, the main driving force behind the spread of infection within the state was significantly higher from symptomatic cases. This has major implications for policies related to testing. Active search for symptomatic cases, subjecting them to testing and treatment should be prioritized for containing the spread of COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Narendra Kumar", + "author_inst": "National Institute of Mental Health and Neurosciences" + }, + { + "author_name": "Shafeeq K S Hameed", + "author_inst": "National Institute of Mental Health and Neurosciences" + }, + { + "author_name": "Giridhara R Babu", + "author_inst": "Indian Institute of Public Health, Bengaluru, Public Health Foundation of India" + }, + { + "author_name": "Manjunatha M Venkataswamy", + "author_inst": "National Institute of Mental Health and Neurosciences" + }, + { + "author_name": "Prameela Dinesh", + "author_inst": "State Surveillance Unit, Directorate of Health and Family Welfare, Government of Karnataka" + }, + { + "author_name": "Prakash B G Kumar", + "author_inst": "State Surveillance Unit, Directorate of Health and Family Welfare, Government of Karnataka" + }, + { + "author_name": "Daisy A John", + "author_inst": "Indian Institute of Public Health, Bengaluru, Public Health Foundation of India" + }, + { + "author_name": "Anita Desai", + "author_inst": "National Institute of Mental Health and Neurosciences" + }, + { + "author_name": "Ravi Vasanthapuram", + "author_inst": "National Institute of Mental Health and Neurosciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.18.20197095", "rel_title": "The COVID-19 Spread in the State of Assam, India", @@ -1157690,49 +1154349,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.17.20196949", - "rel_title": "Investigating the implications of COVID-19 for the rural and remote population of Northern Ontario using a mathematical model", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196949", - "rel_abs": "BackgroundCOVID-19 has the potential to disproportionately affect the rural, remote, and Indigenous populations who typically have a worse health status and live in substandard housing, often with overcrowding. Our aim is to investigate the potential effect of COVID-19 on intensive care unit (ICU) resources and mortality in northwestern Ontario.\n\nMethodsThis study was conducted in northwestern Ontario which has a population of 230,000. A set of differential equations were used to represent a modified Susceptible-Infectious-Recovered (SIR) model with urban and rural hospital resources (i.e., ICU and hospital beds). Rural patients requiring ICU care flowed into the urban ICU. Sensitivity analyses were used to investigate the effect of poorer health status (i.e., increased hospital admission, ICU admission, and mortality) and overcrowding (i.e., increased contact rate) in the rural population as compared to the urban population. Physical distancing within the urban population was modelled as a decreased contact rate.\n\nResultsAt the highest contact rate, the peak in daily active cases, ICU bed requirements and mortality was higher and occurred earlier than lower contact rates. The urban population with a lower contact rate and baseline health status had a lower predicted prevalence of active cases and lower mortality than the rural population.\n\nInterpretationAn increased contact rate and worse health status in the rural population will likely increase the required ICU resources and mortality as compared to the urban population. Rural populations will likely be affected disproportionately more than urban populations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David Savage", - "author_inst": "Northern Ontario School of Medicine" - }, - { - "author_name": "Andrew Fisher", - "author_inst": "Lakehead University" - }, - { - "author_name": "Salimur Choudhury", - "author_inst": "Lakehead University" - }, - { - "author_name": "Robert Ohle", - "author_inst": "Northern Ontario School of Medicine" - }, - { - "author_name": "Roger Strasser", - "author_inst": "Northern Ontario School of Medicine" - }, - { - "author_name": "Aaron Orkin", - "author_inst": "University of Toronto" - }, - { - "author_name": "Vijay Mago", - "author_inst": "Lakehead University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.09.17.20194860", "rel_title": "High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in healthcare workers: results of the CoV-CONTACT prospective cohort", @@ -1158625,6 +1155241,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.09.16.20195552", + "rel_title": "How the clinical research community responded to the COVID-19 pandemic: An analysis of the COVID-19 clinical studies in ClinicalTrials.gov", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195552", + "rel_abs": "ObjectiveThe novel coronavirus disease (COVID-19), broke out in December 2019, is a global pandemic. Rapidly in the past few months, a large number of clinical studies have been initiated worldwide to find effective therapeutics, vaccines, and preventive strategies. In this study, we aim to understand the landscape of COVID-19 clinical research and identify the gaps and issues that may cause difficulty in recruitment and the lack of population representativeness.\n\nMaterials and MethodsWe analyzed 2,034 COVID-19 studies registered in the largest public registry - ClinicalTrials.gov. Leveraging natural language processing, descriptive analysis, association analysis, and clustering analysis, we characterized COVID-19 clinical studies by phase and design features. Particularly, we analyzed their eligibility criteria to understand: (1) whether they considered the reported underlying health conditions that may lead to severe illnesses, and (2) if these studies excluded older adults, either explicitly or implicitly, which may reduce the generalizability of these studies in older adults.\n\nResultsThe 5 most frequently tested drugs are Hydroxychloroquine (N=148), Azithromycin (N=46), Tocilizumab (N=29), Lopinavir (N=20), and Ritonavir (N=20). Most trials did not have an upper age limit and did not exclude patients with common chronic conditions such as hypertension and diabetes that are prevalent in older adults. However, known risk factors that may lead to severe illnesses have not been adequately considered by existing studies.\n\nConclusionsA careful examination of the registered COVID-19 clinical studies can identify the research gaps and inform future COVID-19 trial design towards balanced internal validity and generalizability.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Zhe He", + "author_inst": "Florida State University" + }, + { + "author_name": "Arslan Erdengasileng", + "author_inst": "Florida State University" + }, + { + "author_name": "Xiao Luo", + "author_inst": "Indiana University Purdue University Indianapolis" + }, + { + "author_name": "Aiwen Xing", + "author_inst": "Florida State University" + }, + { + "author_name": "Neil Charness", + "author_inst": "Florida State University" + }, + { + "author_name": "Jiang Bian", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.09.16.20115972", "rel_title": "CLINICALLY DISTINCT COVID-19 CASES SHARE STRIKINGLY SIMILAR IMMUNE RESPONSE PROGRESSION: A FOLLOW-UP ANALYSIS", @@ -1159868,33 +1156523,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.09.17.301614", - "rel_title": "Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome", - "rel_date": "2020-09-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.17.301614", - "rel_abs": "We are in the midst of the third severe coronavirus outbreak caused by SARS-CoV-2 with unprecedented health and socio-economic consequences due to the COVID-19. Globally, the major thrust of scientific efforts has shifted to the design of potent vaccine and anti-viral candidates. Earlier genome analyses have shown global dominance of some mutations purportedly indicative of similar infectivity and transmissibility of SARS-CoV-2 worldwide. Using high-quality large dataset of 25k whole-genome sequences, we show emergence of new cluster of mutations as result of geographic evolution of SARS-CoV-2 in local population ([≥]10%) of different nations. Using statistical analysis, we observe that these mutations have either significantly co-occurred in globally dominant strains or have shown mutual exclusivity in other cases. These mutations potentially modulate structural stability of proteins, some of which forms part of SARS-CoV-2-human interactome. The high confidence druggable host proteins are also up-regulated during SARS-CoV-2 infection. Mutations occurring in potential hot-spot regions within likely T-cell and B-cell epitopes or in proteins as part of host-viral interactome, could hamper vaccine or drug efficacy in local population. Overall, our study provides comprehensive view of emerging geo-clonal mutations which would aid researchers to understand and develop effective countermeasures in the current crisis.\n\nSignificanceOur comparative analysis of globally dominant mutations and region-specific mutations in 25k SARS-CoV-2 genomes elucidates its geo-clonal evolution. We observe locally dominant mutations (co-occurring or mutually exclusive) in nations with contrasting COVID-19 mortalities per million of population) besides globally dominant ones namely, P314L (ORF1b) and D164G (S) type. We also see exclusive dominant mutations such as in Brazil (I33T in ORF6 and I292T in N protein), England (G251V in ORF3a), India (T2016K and L3606F in ORF1a) and in Spain (L84S in ORF8). The emergence of these local mutations in ORFs within SARS-CoV-2 genome could have interventional implications and also points towards their potential in modulating infectivity of SARS-CoV-2 in regional population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Syed Asad Rahman", - "author_inst": "BioInception Pvt. Ltd" - }, - { - "author_name": "Jasdeep Singh", - "author_inst": "Institute of Molecular Medicine Jamia Hamdard, India" - }, - { - "author_name": "Hina Singh", - "author_inst": "Institute of Molecular Medicine, Jamia Hamdard, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.16.300459", "rel_title": "The flexibility of ACE2 in the context of SARS-CoV-2 infection", @@ -1160615,6 +1157243,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.09.12.20193235", + "rel_title": "The impact of COVID-19 in diabetic kidney disease and chronic kidney disease: A population-based study", + "rel_date": "2020-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193235", + "rel_abs": "BackgroundThe spectrum of pre-existing renal disease is known as a risk factor for severe COVID-19 outcomes. However, little is known about the impact of COVID-19 on patients with diabetic nephropathy in comparison to patients with chronic kidney disease.\n\nMethodsWe used the Mexican Open Registry of COVID-19 patients 11 to analyze anonymized records of those who had symptoms related to COVID-19 to analyze the rates of SARS-CoV-2 infection, development of COVID-19 pneumonia, admission, intubation, Intensive Care Unit admission and mortality. Robust Poisson regression was used to relate sex and age to each of the six outcomes and find adjusted prevalences and adjusted prevalence ratios. Also, binomial regression models were performed for those outcomes that had significant results to generate probability plots to perform a fine analysis of the results obtained along age as a continuous variable.\n\nResultsThe adjusted prevalence analysis revealed that that there was a a 87.9% excess probability of developing COVID-19 pneumonia in patients with diabetic nephropathy, a 5% excess probability of being admitted, a 101.7% excess probability of intubation and a 20.8% excess probability of a fatal outcome due to COVID-19 pneumonia in comparison to CKD patients (p< 0.01).\n\nConclusionsPatients with diabetic nephropathy had nearly a twofold rate of COVID-19 pneumonia, a higher probability of admission, a twofold probability of intubation and a higher chance of death once admitted compared to patients with chronic kidney disease alone. Also, both diseases had higher COVID-19 pneumonia rates, intubation rates and case-fatality rates compared to the overall population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Juan Alonso Leon-Abarca", + "author_inst": "Universidad Peruana Cayetano Heredia, Instituto de Investigaciones de la Altura" + }, + { + "author_name": "Roha Saeed Memon", + "author_inst": "Dow Medical College" + }, + { + "author_name": "Bahar Rehan", + "author_inst": "Dow Medical College" + }, + { + "author_name": "Maimoona Iftikhar", + "author_inst": "Akhtar Saeed Medical & Dental College" + }, + { + "author_name": "Antara Chatterjee", + "author_inst": "Breach Candy Hospital Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.09.15.20194209", "rel_title": "Nowcasting CoVID-19 Deaths in England by Age and Region", @@ -1161506,121 +1158169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.14.20193995", - "rel_title": "Predicting clinical outcome with phenotypic clusters in COVID-19 pneumonia: 2 an analysis of 12,066 hospitalized patients from the Spanish registry SEMI-3 COVID-19.", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20193995", - "rel_abs": "(1) Background: This study aims to identify different clinical phenotypes in COVID-19 88 pneumonia using cluster analysis and to assess the prognostic impact among identified clusters in 89 such patients. (2) Methods: Cluster analysis including 11 phenotypic variables was performed in a 90 large cohort of 12,066 COVID-19 patients, collected and followed-up from March 1, to July 31, 2020, 91 from the nationwide Spanish SEMI-COVID-19 Registry. (3) Results: Of the total of 12,066 patients 92 included in the study, most were males (7,052, 58.5%) and Caucasian (10,635, 89.5%), with a mean 93 age at diagnosis of 67 years (SD 16). The main pre-admission comorbidities were arterial 94 hypertension (6,030, 50%), hyperlipidemia (4,741, 39.4%) and diabetes mellitus (2,309, 19.2%). The 95 average number of days from COVID-19 symptom onset to hospital admission was 6.7 days (SD 7). 96 The triad of fever, cough, and dyspnea was present almost uniformly in all 4 clinical phenotypes 97 identified by clustering. Cluster C1 (8,737 patients, 72.4%) was the largest, and comprised patients 98 with the triad alone. Cluster C2 (1,196 patients, 9.9%) also presented with ageusia and anosmia; 99 cluster C3 (880 patients, 7.3%) also had arthromyalgia, headache, and sore throat; and cluster C4 100 (1,253 patients, 10.4%) also manifested with diarrhea, vomiting, and abdominal pain. Compared to 101 each other, cluster C1 presented the highest in-hospital mortality (24.1% vs. 4.3% vs. 14.7% vs. 102 18.6%; p<0.001). The multivariate study identified phenotypic clusters as an independent factor for 103 in-hospital death. (4) Conclusion: The present study identified 4 phenotypic clusters in patients with 104 COVID-19 pneumonia, which predicted the in-hospital prognosis of clinical outcomes.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Manuel Rubio-Rivas", - "author_inst": "Bellvitge University Hospital" - }, - { - "author_name": "Xavier Corbella", - "author_inst": "Department of Internal Medicine, Bellvitge University Hospital, Bellvitge. Biomedical Research Institute-IDIBELL, University of Barcelona, Barcelona, Spain." - }, - { - "author_name": "Jose Maria Mora-Lujan", - "author_inst": "Department of Internal Medicine, Bellvitge University Hospital, Bellvitge. Biomedical Research Institute-IDIBELL, University of Barcelona, Barcelona, Spain" - }, - { - "author_name": "Jose Loureiro Amigo", - "author_inst": "Internal Medicine Department, Moises Broggi Hospital, Sant Joan Despi, Barcelona, Spain" - }, - { - "author_name": "Almudena Lopez Sampalo", - "author_inst": "Internal Medicine Department, Regional University Hospital of Malaga, Malaga, Spain" - }, - { - "author_name": "Carmen Yera Bergua", - "author_inst": "Internal Medicine Department, Virgen de la Salud Hospital, Toledo, Spain" - }, - { - "author_name": "Pedro Jesus Esteve Atienzar", - "author_inst": "Internal Medicine Department, San Juan de Alicante University Hospital, San Juan de Alicante (Alicante), Spain" - }, - { - "author_name": "Luis Felipe Diez Garcia", - "author_inst": "Internal Medicine Department, Torrecardenas Hospital, Almeria, Spain" - }, - { - "author_name": "Ruth Gonzalez Ferrer", - "author_inst": "Internal Medicine Department, Tajo Hospital, Aranjuez (Madrid), Spain" - }, - { - "author_name": "Susana Plaza Canteli", - "author_inst": "Internal Medicine Department, Severo Ochoa University Hospital, Leganes (Madrid), Spain" - }, - { - "author_name": "Antia Perez Pineiro", - "author_inst": "Internal Medicine Department, Valle del Nalon Hospital, Riano (Langreo, Asturias), Spain" - }, - { - "author_name": "Begona Cortes Rodriguez", - "author_inst": "Internal Medicine Department, Alto Guadalquivir Hospital, Andujar (Jaen), Spain" - }, - { - "author_name": "Leyre Jorquer Vidal", - "author_inst": "Internal Medicine Department, Francesc de Borja Hospital, Gandia (Valencia), Spain" - }, - { - "author_name": "Ignacio Perez Catalan", - "author_inst": "Internal Medicine Department, Castellon General University Hospital, Castellon de la Plana, Spain" - }, - { - "author_name": "Marta Leon Tellez", - "author_inst": "Internal Medicine Department, Santa Barbara Hospital, Soria, Spain" - }, - { - "author_name": "Jose Angel Martin Oterino", - "author_inst": "Internal Medicine Department, Salamanca University Hospital Complex, Salamanca, Spain" - }, - { - "author_name": "Maria Candelaria Martin Gonzalez", - "author_inst": "Internal Medicine Department, Canarias University Hospital, Santa Cruz de Tenerife, Spain" - }, - { - "author_name": "Jose Luis Serrano Carrillo de Albornoz", - "author_inst": "Internal Medicine Department, Poniente Hospital, Almeria, Spain" - }, - { - "author_name": "Eva Garcia Sardon", - "author_inst": "Internal Medicine Department, San Pedro de Alcantara Hospital, Caceres, Spain" - }, - { - "author_name": "Jose Nicolas Alcala Pedrajas", - "author_inst": "Internal Medicine Department, Pozoblanco Hospital, Pozoblanco (Cordoba), Spain" - }, - { - "author_name": "Anabel Martin Urda Diez Canseco", - "author_inst": "Internal Medicine Department, Palamos Hospital, Palamos (Girona), Spain" - }, - { - "author_name": "Maria Jose Esteban Giner", - "author_inst": "Internal Medicine Department, Virgen de los Lirios Hospital, Alcoy (Alicante), Spain" - }, - { - "author_name": "Pablo Telleria Gomez", - "author_inst": "Internal Medicine Department, Valladolid Clinical University Hospital, Valladolid, Spain" - }, - { - "author_name": "Ricardo Gomez Huelgas", - "author_inst": "Internal Medicine Department, Regional University Hospital of Malaga. Instituto de 61 Investigacion Biomedica de Malaga (IBIMA), Malaga, Spain" - }, - { - "author_name": "Jose Manuel Ramos Rincon", - "author_inst": "Department of Clinical Medicine, Miguel Hernandez University of Elche (Alicante), Spain" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.14.20194472", "rel_title": "SARS-CoV-2 in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed", @@ -1162473,6 +1159021,73 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.09.14.296889", + "rel_title": "CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations", + "rel_date": "2020-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.14.296889", + "rel_abs": "Systemic analysis of available large-scale biological and biomedical data is critical for developing novel and effective treatment approaches against both complex and infectious diseases. Owing to the fact that different sections of the biomedical data is produced by different organizations/institutions using various types of technologies, the data are scattered across individual computational resources, without any explicit relations/connections to each other, which greatly hinders the comprehensive multi-omics-based analysis of data. We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. As a use-case study, we constructed CROssBAR COVID-19 KGs (available at: https://crossbar.kansil.org/covid_main.php) that incorporate relevant virus and host genes/proteins, interactions, pathways, phenotypes and other diseases, as well as known and completely new predicted drugs/compounds. Our COVID-19 graphs can be utilized for a systems-level evaluation of relevant virus-host protein interactions, mechanisms, phenotypic implications and potential interventions.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tunca Dogan", + "author_inst": "Hacettepe University" + }, + { + "author_name": "Heval Atas", + "author_inst": "METU" + }, + { + "author_name": "Vishal Joshi", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Ahmet Atakan", + "author_inst": "METU" + }, + { + "author_name": "Ahmet Sureyya Rifaioglu", + "author_inst": "METU" + }, + { + "author_name": "Esra Nalbat", + "author_inst": "METU" + }, + { + "author_name": "Andrew Nightingale", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Rabie Saidi", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Vladimir Volynkin", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Hermann Zellner", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Rengul Cetin-Atalay", + "author_inst": "University of Chicago" + }, + { + "author_name": "Maria Martin", + "author_inst": "EMBL-EBI" + }, + { + "author_name": "Volkan Atalay", + "author_inst": "METU" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.12.20193219", "rel_title": "Sero-surveillance (IgG) of SARS-CoV-2 among Asymptomatic General population of Paschim Medinipur District, West Bengal, India(Conducted during last week of July and 1st week of August 2020) - A Joint Venture of VRDL Lab (ICMR), Midnapore Medical College & Hospital & Department of Health and Family Welfare,Govt. of West Bengal, Paschim Medinipur", @@ -1163172,77 +1159787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.13.20193615", - "rel_title": "Alternative or Complementary Role of Serological Rapid Antibody Test in the Management of Possible COVID-19 Cases", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193615", - "rel_abs": "BackgroundAlthough the gold diagnostic method for COVID-19 is accepted as the detection of viral particles by reverse transcription polymerase chain reaction (RT-PCR), serology testing for SARS-CoV-2 is at increased demand. A primary aim for utilization of serological tests are to better quantify the number of COVID-19 cases including those RT-PCR samples were negative but showing clinical and radiological signs of COVID-19. In this study, we aimed to report the features of the patients that were diagnosed and treated as possible COVID-19 cases whose multiple nasopharyngeal swab samples were negative by RTPCR but serological IgM/IgG antibody against SARS-CoV-2 were detected by rapid antibody test.\n\nMethodWe retrospectively analyzed eighty suspected COVID-19 cases that have at least two negative consecutive COVID-19 PCR test and were subjected to serological rapid antibody test.\n\nResultThe specific antibodies against SARS-CoV-2 were detected as positive in twenty-two patients. The mean age of patient group was 63.2 {+/-} 13.1 years old with male /female ratio 11/11. Cough was the most common symptom with 90.9%. Most common presenting chest CT findings were bilateral ground glass opacities (77.2%) and alveolar consolidations (50.09%). The mean duration from symptom initiation to hospital admission, to hospitalization, to treatment initiation and to detection of antibody positivity were 8.6 {+/-} 7.2, 11.2 {+/-} 5.4, 7.9 {+/-} 3.2 and 24 {+/-} 17 days, respectively.\n\nConclusionOur study demonstrated the feasibility of COVID-19 diagnosis based on rapid antibody test in the cases of patients whose RT-PCR samples were negative. We suggest that the detection of antibodies against SARS-CoV-2 with rapid antibody test should be included in the diagnostic algorithm in suspected COVID-19 patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Fatma Yildirim", - "author_inst": "Department of Pulmonary&Critical Care Medicine, Diskapi Yildirim Beyazit Research and Education Hospital, University of Health Sciences, Ankara, Turkey." - }, - { - "author_name": "Pinar Yildiz Gulhan", - "author_inst": "Department of Pulmonary Medicine, Duzce University, Faculty of Medicine, Duzce, Turkey." - }, - { - "author_name": "Ozlem Ercen Diken", - "author_inst": "Department of Pulmonary Medicine, Adana Research and Education Hospital, University of Health Sciences, Adana, Turkey." - }, - { - "author_name": "Aylin Capraz", - "author_inst": "Department of Pulmonary Medicine, Sabuncuoglu Serefeddin Research and Education Hospital, Amasya University, Amasya, Turkey." - }, - { - "author_name": "Meltem Simsek", - "author_inst": "Diskapi Yildirim Beyazit Research and Education Hospital, University of Health Sciences, Ankara, Turkey" - }, - { - "author_name": "Berna Botan Yildirim", - "author_inst": "Department of Pulmonary Medicine, Research and Education Hospital of Baskent University, Konya, Turkey." - }, - { - "author_name": "Muhammet Ridvan Taysi", - "author_inst": "Diskapi Yildirim Beyazit Research and Education Hospital, University of Health Sciences, Ankara, Turkey" - }, - { - "author_name": "Sakine Yilmaz Ozturk", - "author_inst": "Department of Pulmonary Medicine, Vezirkopru State Hospital, Samsun, Turkey." - }, - { - "author_name": "Nurcan Demirtas", - "author_inst": "Department of Pulmonary Medicine, Kumluca State Hospital, Antalya, Turkey. Julide Ergil, MD, Assoc Prof., Department of Anaesthesiology and Reanimation, Diskapi" - }, - { - "author_name": "Julide Ergil", - "author_inst": "Department of Anaesthesiology and Reanimation, Diskapi Yildirim Beyazit Research and Education Hospital, University of Health Sciences, Ankara, Turkey." - }, - { - "author_name": "Adem Dirican", - "author_inst": "Samsun Medicalpark Hospital, Department of Pulmonary Medicine, Samsun, Turkey." - }, - { - "author_name": "Tugce Uzar", - "author_inst": "Bahcesehir University Faculty of Medicine, Istanbul,Turkey." - }, - { - "author_name": "Irem Karaman", - "author_inst": "Bahcesehir University Faculty of Medicine, Istanbul,Turkey." - }, - { - "author_name": "Sevket OZKAYA", - "author_inst": "Bahcesehir University, faculty of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.09.13.20193581", "rel_title": "Rapid, accurate, nucleobase detection using FnCas9", @@ -1163943,6 +1160487,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.09.13.295691", + "rel_title": "Ambroxol Hydrochloride Inhibits the Interaction between Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein's Receptor Binding Domain and Recombinant Human ACE2.", + "rel_date": "2020-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.13.295691", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), enters the host cells through two main pathways, both involving key interactions between viral envelope-anchored spike glycoprotein of the novel coronavirus and the host receptor, angiotensin-converting enzyme 2 (ACE2). To date, SARS-CoV-2 has infected up to 26 million people worldwide; yet, there is no clinically approved drug or vaccine available. Therefore, a rapid and coordinated effort to re-purpose clinically approved drugs that prevent or disrupt these critical entry pathways of SARS-CoV-2 spike glycoprotein interaction with human ACE2, could potentially accelerate the identification and clinical advancement of prophylactic and/or treatment options against COVID-19, thus providing possible countermeasures against viral entry, pathogenesis and survival. Herein, we discovered that Ambroxol hydrochloride (AMB), and its progenitor, Bromhexine hydrochloride (BHH), both clinically approved drugs are potent effective modulators of the key interaction between the receptor binding domain (RBD) of SARS-CoV-2 spike protein and human ACE2. We also found that both compounds inhibited SARS-CoV-2 infection-induced cytopathic effect at micromolar concentrations. Therefore, in addition to the known TMPRSS2 activity of BHH; we report for the first time that the BHH and AMB pharmacophore has the capacity to target and modulate yet another key protein-protein interaction essential for the two known SARS-CoV-2 entry pathways into host cells. Altogether, the potent efficacy, excellent safety and pharmacologic profile of both drugs along with their affordability and availability, makes them promising candidates for drug repurposing as possible prophylactic and/or treatment options against SARS-CoV-2 infection.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Omonike A Olaleye", + "author_inst": "Texas Southern University" + }, + { + "author_name": "Manvir Kaur", + "author_inst": "Texas Southern University" + }, + { + "author_name": "Collins Chidi Onyenaka", + "author_inst": "Texas Southern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.09.11.293951", "rel_title": "Non-permissive SARS-CoV-2 infection of neural cells in the developing human brain and neurospheres", @@ -1164754,37 +1161325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.12.20193078", - "rel_title": "Effect of Lockdown Implementation, Environmental & Behavioural factors, Diet and Virus Mutations on COVID-19 Outcomes: A Study on Critical Containment Zones of Indian state of Maharashtra", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193078", - "rel_abs": "This work details the study of critical containment zones in Maharashtra within a time (April 9 2020 - July 31 2020) in the context of COVID-19. The effects of lockdown implementation, community isolation, environmental factors, demographic aspects, behavioural factors, diet etc. have been investigated. The effect of the aforementioned factors on the infected cases, cumulative infected cases, recoveries, cumulative recoveries, active cases, deaths and cumulative deaths are analyzed. The integrated effects of the aforementioned factors on COVID-19 outcomes are further amplified due to adequate and inadequate health facilities. The study will be helpful to scientists, researchers, pharmacists and biotechnologists in new vaccine design & to accommodate above factors for the betterment of susceptible & infected people of Maharashtra and similar demographies across the globe. Further, it pinpoints the need for more awareness and control strategies among the people to reduce the havoc, stress, fear, anxiety, pathogenicity and thereby reducing mortality.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "ONKAR TANAJI MOHITE", - "author_inst": "Saraswati College of Engineering, Kharghar, Navi-Mumbai, India" - }, - { - "author_name": "Arvind Subhash Avhad", - "author_inst": "Terna Engineering College, Navi Mumbai , University of Mumbai" - }, - { - "author_name": "Prasad Sutar", - "author_inst": "Saraswati College Of Engineering, Kharghar, Navi-Mumbai, India" - }, - { - "author_name": "Vaibhav S Pawar", - "author_inst": "Annasaheb Dange College of Engg& Technology Ashta, Sangli, Maharashtra, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20193052", "rel_title": "Adapting Lot Quality Assurance Sampling to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti", @@ -1165545,6 +1162085,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.09.20191353", + "rel_title": "Covid-19 epidemic curve in Brazil: A sum of multiple epidemics, whose income inequality and population density in the states are correlated with growth rate and daily acceleration", + "rel_date": "2020-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191353", + "rel_abs": "Introduction: Recently, we demonstrated that the polynomial interpolation method can be used to accurately calculate the daily acceleration of cases and deaths by Covid-19. The acceleration of new cases is important for the characterization and comparison of epidemic curves. The objective of this work is to measure the diversity of epidemic curves and understand the importance of socioeconomic variables in the acceleration, peak cases and deaths by Covid-19 in Brazilian states. Methods: This is an ecological study with time series analysis of new cases and deaths by Covid-19 in Brazil and its 27 federation units. Using the polynomial interpolation method, we calculated the daily cases and deaths with the measurement of the respective acceleration. We calculated the correlation coefficient between the epidemic curve data and socioeconomic data. Results: The combination of daily data and acceleration determined that the states of Brazil are in different stages of the epidemic. Maximum acceleration of peak cases, peak of cases, maximum acceleration of deaths and peak of deaths are associated with the Gini index and population density, but did not correlate with HDI and per capita income. Conclusion: Brazilian states showed heterogeneous data curves. Densitypopulation and socioeconomic inequality are associated with worse control of the epidemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Airandes S Pinto", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Carlos A Rodrigues", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Carlito L Sobrinho", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Edval G Santos Jr.", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Livia A Cruz", + "author_inst": "Grupo Baiano de Oncologia" + }, + { + "author_name": "Paulo C Nunes", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Matheus G Costa", + "author_inst": "Universidade Estadual de Feira de Santana" + }, + { + "author_name": "Manoel O Rocha", + "author_inst": "Universidade Federal de Minas Gerais" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.11.294231", "rel_title": "Type I Interferon Limits Viral Dissemination-Driven Clinical Heterogeneity in a Native Murine Betacoronavirus Model of COVID-19", @@ -1166456,97 +1163043,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.11.20192484", - "rel_title": "A novel sample pooling strategy and its application for mass screening of SARS-CoV-2 in an outbreak of COVID-19 in Vietnam", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192484", - "rel_abs": "We present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Our approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. 22/32 asymptomatic cases would have been missed without mass screening.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ton That Thanh", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Nguyen Thi Thanh Nhan", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Huynh Kim Mai", - "author_inst": "IP, Nha Trang, Vietnam" - }, - { - "author_name": "Nguyen Bao Trieu", - "author_inst": "IP, Nha Trang, Vietnam" - }, - { - "author_name": "Le Xuan Huy", - "author_inst": "IP, Nha Trang, Vietnam" - }, - { - "author_name": "Ho Thi Thanh Thuy", - "author_inst": "Viet A, Vietnam" - }, - { - "author_name": "Le Thanh Chung", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Nguyen Ngoc Anh", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Nguyen Thi Thu Hong", - "author_inst": "OUCRU, Vietnam" - }, - { - "author_name": "Bui Duc Thang", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Nguyen Thi Hoai Thu", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Le Thi Kim Chi", - "author_inst": "Da Nang CDC, Vietnam" - }, - { - "author_name": "Nguyen Thi Hanh", - "author_inst": "Da Nang University of Medical Technology and Pharmacy, Da Nang city, Vietnam" - }, - { - "author_name": "Nguyen Huy Hoang", - "author_inst": "Da Nang University of Medical Technology and Pharmacy, Da Nang city, Vietnam" - }, - { - "author_name": "Chau Nguyen", - "author_inst": "Hospital for Tropical Diseases" - }, - { - "author_name": "Guy Thwaites", - "author_inst": "OUCRU, Vietnam" - }, - { - "author_name": "Do Thai Hung", - "author_inst": "IP, Nha Trang, Vietnam" - }, - { - "author_name": "Le Van Tan", - "author_inst": "OUCRU-VN" - }, - { - "author_name": "Ngo Thi Kim Yen", - "author_inst": "DoH, Da Nang, Vietnam" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.10.20192120", "rel_title": "Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020", @@ -1167083,6 +1163579,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.20192492", + "rel_title": "Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192492", + "rel_abs": "Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Haowei Wang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christina J Atchison", + "author_inst": "Imperial College London" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "Lancaster University" + }, + { + "author_name": "Peter J Diggle", + "author_inst": "Lancaster University" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Imperial College" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Helen Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.10.20191882", "rel_title": "Bacterial pulmonary superinfections are associated with unfavourable outcomes in critically ill COVID-19 patients", @@ -1168122,25 +1164693,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2020.09.10.20192203", - "rel_title": "Relationship between nursing home COVID-19 outbreaks and staff neighborhood characteristics", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192203", - "rel_abs": "The COVID-19 pandemic has taken a significant toll on nursing homes in the US, with upwards of a third of deaths occurring in nursing homes, and more in long-term care facilities. By combining data on facility-level COVID-19 deaths with facility-level data on the neighborhoods where nursing home staff reside for a sample of eighteen states, this paper finds that staff neighborhood characteristics are a large and significant predictor of COVID-19 outbreaks. One standard deviation increases in average staff tract population density, public transportation use, and non-white share were associated with 1.3 (SE .33), 1.4 (SE .35), and 0.9 (SE .24) additional deaths per 100 beds, respectively. These effects are larger than all facility management or quality variables, and larger than the effect of the nursing homes own neighborhood characteristics. These results suggest that staff communities are likely to be an important source of infection, and that disparities in nursing home outbreaks may be related to differences in the types of neighborhoods nursing home staff live in.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Karen Shen", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.09.11.20192591", "rel_title": "Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2", @@ -1168913,6 +1165465,25 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.09.09.20191684", + "rel_title": "Malaria Endemicity Influence on COVID -19 Mortality: New Evidence Added to BCG and TB Prevalence", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191684", + "rel_abs": "BackgroundRegarding SARS-CoV-2 it is well known that a substantial percentage of adult population cannot get infected if exposed to this novel coronavirus. Several studies give primary indication about the possible role of preexisting immunity whether cross immunity or not. Possible role of latent TB, BCG and malaria have been already suggested to create innate cross heterogeneous immunity. We look for influence of these factors on Covid-19 mortality in malarious countries.\n\nMaterial and methods80 malarious countries were enrolled in this study. Hierarchical multiple regression type of analysis was used for data analyses. TB prevalence/ 100,000 population standardized to BCG coverage rates was taken as direct factor in the test. Malaria incidence /1000 population was considered as intermediate factor and the outcome was COVID-19 mortality/ 1 million (M) population.\n\nResultsHierarchical multiple regression analysis showed significant associations between standardized TB prevalence to BCG coverage and reduced COVID-19 mortality. This analysis also showed that malaria have an additional effect in reducing COVID-19 mortality with high significant association too.\n\nConclusionsMalaria and standardized TB prevalence are statistical significant factors predicting COVID-19 mortality in negative associations.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tareef Fadhil Raham", + "author_inst": "MOH Iraq" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.11.292730", "rel_title": "In silico prediction of COVID-19 test efficiency with DinoKnot", @@ -1169692,29 +1166263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.04.20188417", - "rel_title": "Rapid Scoping Review of Evidence of Outdoor Transmission of COVID-19", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188417", - "rel_abs": "The COVID-19 pandemic is both a global health crisis, and a civic emergency for national governments, including the UK. As countries across the world loosen their lockdown restrictions, the assumption is generally made that the risk of COVID-19 transmission is lower outdoors, and this assumption has shaped decisions about what activities can recommence, the circumstances in which they should re-commence, and the conditions under which they should re-commence. This is important for events and activities that generate outdoor gatherings of people, including both participatory and spectator sport events, protests, concerts, carnivals, festivals, and other celebrations.\n\nThe review, which was designed to be undertaken rapidly in 15 days, returned 14 sources of evidence of outdoor transmission of COVID-19, and a further 21 sources that were used to set the context and understand the caveats that should be considered in interpreting the review findings.\n\nThe review found very few examples of outdoor transmission of COVID-19 in everyday life among c. 25,000 cases considered, suggesting a very low risk. However risk of outdoor transmission increases when the natural social distancing of everyday life is breached, and gathering density, circulation and size increases, particularly for an extended duration. There was also evidence that weather had a behavioural effect on transmission, with temperatures that encourage outdoor activity associated with lower COVID-19 transmission. Due to lack of surveillance and tracing systems, and confounding factors and variables, there was no evidence that robustly tested transmission at outdoor mass gatherings (circa 10,000+ people), which are as likely to generate transmission from the activities they prompt (e.g. communal travel and congregation in bars) as from outdoor transmission at the gathering itself.\n\nThe goal of hosts and organisers of events and activities that generate outdoor gatherings of people is to prevent the escalation of risk from sporadic transmission to the risk of transmission through a cluster outbreak. Considerations for such hosts and organisers include: (1) does the gathering prompt other behaviours that might increase transmission risk?; (2) for each part of the event or activity, how dense is the gathering, how much do people circulate, how large is the gathering, and how long are people there?; (3) is rapid contact tracing possible in the event of an outbreak? These considerations should take place relevant to the size of the underlying risk, which includes the rate of infection in the community and the likely attendance of vulnerable groups. Risk must be balanced and mitigated across the risk factors of density, circulation, size and duration. No one risk factor presents an inherently larger risk than any other, but neither is any one risk factor a magic bullet to eliminate risk.\n\nFinally, it is clear that the largest risks from gatherings come from spontaneous or informal unregulated and unmitigated events or activities which do not consider any of the issues, risks and risk factors outlined in this paper", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mike Weed", - "author_inst": "Canterbury Christ Church University" - }, - { - "author_name": "Abby Foad", - "author_inst": "Canterbury Christ Church University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.08.20189555", "rel_title": "The Impact of COVID-19 Pandemic on The Preventive Services in Qatar", @@ -1170307,6 +1166855,105 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.09.10.286948", + "rel_title": "Real-time conformational dynamics of SARS-CoV-2 spikes on virus particles", + "rel_date": "2020-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.10.286948", + "rel_abs": "SARS-CoV-2 spike (S) mediates entry into cells and is critical for vaccine development against COVID-19. Structural studies have revealed distinct conformations of S, but real-time information that connects these structures, is lacking. Here we apply single-molecule Forster Resonance Energy Transfer (smFRET) imaging to observe conformational dynamics of S on virus particles. Virus-associated S dynamically samples at least four distinct conformational states. In response to hACE2, S opens sequentially into the hACE2-bound S conformation through at least one on-path intermediate. Conformational preferences of convalescent plasma and antibodies suggest mechanisms of neutralization involving either competition with hACE2 for binding to RBD or allosteric interference with conformational changes required for entry. Our findings inform on mechanisms of S recognition and conformations for immunogen design.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Maolin Lu", + "author_inst": "Yale University" + }, + { + "author_name": "Pradeep D. Uchil", + "author_inst": "Yale University" + }, + { + "author_name": "Wenwei Li", + "author_inst": "Yale University" + }, + { + "author_name": "Desheng Zheng", + "author_inst": "Yale University" + }, + { + "author_name": "Jason Gorman", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Wei Shi", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda" + }, + { + "author_name": "Baoshan Zhang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda" + }, + { + "author_name": "Shilei Ding", + "author_inst": "McGill University" + }, + { + "author_name": "Romain Gasser", + "author_inst": "University of Montreal" + }, + { + "author_name": "Jeremie Prevost", + "author_inst": "University of Montreal" + }, + { + "author_name": "Guillaume Beaudoin-Bussieres", + "author_inst": "University of Montreal" + }, + { + "author_name": "Sai Priya Anand", + "author_inst": "McGill University" + }, + { + "author_name": "Annemarie Laumaea", + "author_inst": "University of Montreal" + }, + { + "author_name": "Jonathan R. Grover", + "author_inst": "Yale University" + }, + { + "author_name": "Liu Lihong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "John Mascola", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Andres Finzi", + "author_inst": "University of Montreal" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda" + }, + { + "author_name": "Walther Mothes", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.09.196220", "rel_title": "COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases.", @@ -1171318,153 +1167965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.04.20187781", - "rel_title": "Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187781", - "rel_abs": "BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality.\n\nMethodsWe pre-specified and conducted an observational, population-based cohort study using national primary care data and linked death registrations in the OpenSAFELY platform, representing 40% of the general population in England. We used Cox regression to estimate the association between ongoing routine hydroxychloroquine use prior to the COVID-19 outbreak in England and risk of COVID-19 mortality among people with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Model adjustment was informed by a directed acyclic graph.\n\nResultsOf 194,637 patients with RA or SLE, 30,569 (15.7%) received [≥] 2 prescriptions of hydroxychloroquine in the six months prior to 1 March 2020. Between 1 March 2020 and 13 July 2020, there were 547 COVID-19 deaths, 70 among hydroxychloroquine users. Estimated standardised cumulative COVID-19 mortality was 0.23% (95% CI 0.18-0.29) among users and 0.22% (95% CI 0.20-0.25) among non-users; an absolute difference of 0.008% (95% CI -0.051-0.066). After accounting for age, sex, ethnicity, use of other immunuosuppressives, and geographic region, no association with COVID-19 mortality was observed (HR 1.03, 95% CI 0.80-1.33). We found no evidence of interactions with age or other immunosuppressives. Quantitative bias analyses indicated observed associations were robust to missing information regarding additional biologic treatments for rheumatological disease. We observed similar associations with the negative control outcome of non-COVID-19 mortality.\n\nConclusionWe found no evidence of a difference in COVID-19 mortality among patients who received hydroxychloroquine for treatment of rheumatological disease prior to the COVID-19 outbreak in England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials and observational studies to date have shown no evidence of benefit of hydroxychloroquine as a treatment for hospitalised patients who already have COVID-19. A separate question remains: whether routine ongoing use of hydroxychloroquine in people without COVID-19 protects against new infections or severe outcomes. We searched MEDLINE/PubMed for pharmacoepidemiological studies evaluating hydroxychloroquine for prevention of severe COVID-19 outcomes. The keywords \"hydroxychloroquine AND (COVID OR coronavirus OR SARS-CoV-2) AND (prophyl* OR prevent*) AND (rate OR hazard OR odds OR risk)\" were used and results were filtered to articles from the last year with abstracts available. 109 papers were identified for screening; none investigated pre-exposure prophylactic use of hydroxychloroquine for prevention of severe COVID-19 outcomes. Clinical trials of prophylactic use of hydroxychloroquine are ongoing; however, the largest trial does not expect to meet recruitment targets due to \"...unjustified extrapolation and exaggerated safety concerns together with intense politicisation and negative publicity.\" In the absence of reported clinical trials, evidence can be generated from real-world data to support the need for randomised clinical trials.\n\nAdded value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data.\n\nImplications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nicholas J DeVito", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Jeremy P Brown", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "William J Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Chris Bates", - "author_inst": "The Phoenix Partnership" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Henry Drysdale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Medicine and Tropical Medicine" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "The Phoenix Partnership" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "John Parry", - "author_inst": "The Phoenix Partnership" - }, - { - "author_name": "Frank Hester", - "author_inst": "The Phoenix Partnership" - }, - { - "author_name": "Sam Harper", - "author_inst": "The Phoenix Partnership" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "William G Dixon", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.07.20189860", "rel_title": "Ongoing natural selection drives the evolution of SARS-CoV-2 genomes", @@ -1172041,6 +1168541,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.09.20190389", + "rel_title": "Passive, open access data measures movement and predicts COVID-19 cases", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20190389", + "rel_abs": "Following the emergence of SARS-CoV-2, early outbreak response relied on behavioral interventions. In the United States, local governments implemented restrictions aimed at reducing movements and contacts to limit viral transmission. In Pennsylvania, restrictions closed schools and businesses in the spring of 2020 and interventions eased later through the summer. In a rural Pennsylvania county, we use passive monitoring of vehicular traffic volume and mobile device derived visits to points of interest as proxies for movements and contacts. Rural areas have limited health care resources, which magnifies the importance of disease prevention. These data show the lowest levels of movement occurred during the strictest phase of restrictions, indicating high levels of compliance with behavioral intervention. We find that increases in movement correlated with increases in SARS-CoV-2 cases 9-18 days later. The methodology used in this study can be adapted to inform outbreak management strategies for other locations and future outbreaks that use behavioral interventions to reduce pathogen transmission.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christina L. Faust", + "author_inst": "Penn State University" + }, + { + "author_name": "Brian Lambert", + "author_inst": "Penn State University" + }, + { + "author_name": "Cale Kochenour", + "author_inst": "Penn State University" + }, + { + "author_name": "Anthony C. Robinson", + "author_inst": "Penn State University" + }, + { + "author_name": "Nita Bharti", + "author_inst": "Penn State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.07.20190108", "rel_title": "Covid-19 Belgium: Extended SEIR-QD model with nursery homes and long-term scenarios-based forecasts from school opening", @@ -1172796,109 +1169331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.08.20189092", - "rel_title": "Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20189092", - "rel_abs": "With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Andre F Rendeiro", - "author_inst": "Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Joseph Casano", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Charles Kyriakos Vorkas", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Harjot Singh", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Ayana Morales", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Robert A DeSimone", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Grant B Ellsworth", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Rosemary Soave", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Shashi N Kapadia", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Kohta Saito", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Christopher D Brown", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "JingMei Hsu", - "author_inst": "Division of Hematology/Oncology, Department of Medicine Weill Cornell Medicine, New York, NY, 10065, USA" - }, - { - "author_name": "Christopher Kyriakides", - "author_inst": "Department of Rehabilitation Medicine at NYU Grossman School of Medicine New York, NY, USA" - }, - { - "author_name": "Steven Chui", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Luca Cappelli", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Maria Teresa Cacciapuoti", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Wayne Tam", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Lorenzo Galluzzi", - "author_inst": "Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Paul D Simonson", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Olivier Elemento", - "author_inst": "Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Mirella Salvatore", - "author_inst": "Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Giorgio Inghirami", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.08.20190496", "rel_title": "Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution", @@ -1173919,6 +1170351,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.08.286732", + "rel_title": "Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells", + "rel_date": "2020-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.08.286732", + "rel_abs": "Recombinant forms of the spike protein of SARS-CoV-2 and related viruses have proven difficult to produce with good yields in mammalian cells. Given the panoply of potential COVID-19 diagnostic tools and therapeutic candidates that require purified spike protein and its importance for ongoing SARS-CoV-2 research, we have explored new approaches for spike production and purification. Three transient gene expression methods based on PEI-mediated transfection of CHO or HEK293 cells in suspension culture in chemically-defined media were compared for rapid production of full-length SARS-CoV-2 ectodomain. A high-cell-density protocol using DXB11-derived CHOBRI/rcTA cells gave substantially better yields than the other methods. Different forms of the spike were expressed, including the wild-type SARS-CoV-2 sequence and a mutated/stabilized form (to favor expression of the full-length spike in prefusion conformation), with and without fusion to putative trimerization domains. An efficient two-step affinity purification method was also developed. Ultimately, we have been able to produce highly homogenous preparations of full-length spike, both monomeric and trimeric, with yields of 100-150 mg/L. The speed and productivity of this method support further development of CHO-based approaches for recombinant spike protein manufacturing.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Matthew Stuible", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Christian Gervais", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Simon Lord-Dufour", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Sylvie Perret", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Joseph Schrag", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Gilles St-Laurent", + "author_inst": "National Research Council Canada" + }, + { + "author_name": "Yves Durocher", + "author_inst": "National Research Council Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.09.09.289355", "rel_title": "Tracking SARS-CoV-2 T cells with epitope T-cell receptor recognition models", @@ -1174770,81 +1171245,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.05.20188920", - "rel_title": "Covid 19 and orthopaedic surgery in a large trauma centre in India", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188920", - "rel_abs": "BackgroundWe are in the midst of a pandemic caused by the novel SARS-Cov-2 virus. A large percentage of the patients are asymptomatic and hospitals around the world are struggling to restart routine services. We report the results of a universal testing protocol of all patients who underwent orthopaedic surgery in the month of July 2020 in a large orthopaedic speciality hospital in Bangalore, India.\n\nMethodsA retrospective study of all patients who underwent orthopaedic surgery in the month of July 2020 at a tertiary care orthopaedic speciality hospital in Bangalore, India. All patients underwent nasopharyngeal swab test before surgery. A questionnaire was used to assess the patient before the RT-PCR nasopharyngeal swab test. Data regarding imaging, investigations and follow up was recorded.\n\nResultsIn the month of July 2020, 168 patients underwent routine nasopharyngeal RT-PCR swab test for COVID-19 prior to planned orthopaedic surgical procedure (Both trauma and elective cases). 16 of the RT-PCR tests were positive. However vascular cases and absolute emergencies were done without a RT - PCR test with PPE and all universal precautions. 11 patients underwent emergency surgery without a RT-PCR test. All 16 cases who were positive were asymptomatic. The asymptomatic positive rate was 9.52%. Of the 11 patients who underwent emergency surgery without a RT-PCR test, only one patient had a positive test post-operatively.\n\nConclusionsRoutine nasopharyngeal RT-PCR testing revealed a high rate of asymptomatic cases. If the RT-PCR test is positive, it is best to defer the case till the test returns negative. All precautions must be taken while performing emergency surgeries. Our algorithm in managing patients has proven to be effective and can be replicated with ease to continue operating and taking care of orthopaedic patients during this pandemic.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Kannan Karuppiah Kumar", - "author_inst": "Hosmat hospital" - }, - { - "author_name": "Thomas Chandy", - "author_inst": "Hosmat hospital" - }, - { - "author_name": "M N Kumar", - "author_inst": "Hosmat hospital" - }, - { - "author_name": "Muniramaiah Ravishankar", - "author_inst": "Hosmat hospital" - }, - { - "author_name": "Krishan Prasad", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Chetan Rai", - "author_inst": "Hosmat hospital" - }, - { - "author_name": "Chetan A", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Girish Vijayakumar", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Noel nalin kumar", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Harshavardhan v", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Harish Puranik", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Krishna Kumar", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Praveen S Battepatti", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Deepu N K", - "author_inst": "Hosmat Hospital" - }, - { - "author_name": "Mayur Shetty", - "author_inst": "Hosmat Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "orthopedics" - }, { "rel_doi": "10.1101/2020.09.06.20189258", "rel_title": "Superspreaders and High Variance Infectious Diseases", @@ -1176717,6 +1173117,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.07.286567", + "rel_title": "Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins", + "rel_date": "2020-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.07.286567", + "rel_abs": "A novel severe acute respiratory (SARS)-like coronavirus (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The viral entry of SARS-CoV-2 depends on an interaction between the receptor binding domain of its trimeric Spike glycoprotein and the human angiotensin converting enzyme 2 (ACE2) receptor. A better understanding of the Spike/ACE2 interaction is still required to design anti-SARS-CoV-2 therapeutics. Here, we investigated the degree of cooperativity of ACE2 within both the SARS-CoV-2 and the closely related SARS-CoV-1 membrane-bound S glycoproteins. We show that there exist differential inter-protomer conformational transitions between both Spike trimers. Interestingly, the SARS-CoV-2 spike exhibits a positive cooperativity for monomeric soluble ACE2 binding when compared to the SARS-CoV-1 spike, which might have more structural restrains. Our findings can be of importance in the development of therapeutics that block the Spike/ACE2 interaction.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sai Priya Anand", + "author_inst": "CRCHUM / McGill University" + }, + { + "author_name": "Yaozong Chen", + "author_inst": "USUHS" + }, + { + "author_name": "Jeremie Prevost", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Romain Gasser", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Guillaume Beaudoin-Bussieres", + "author_inst": "CRCHUM / Universite de Montreal" + }, + { + "author_name": "Cameron F Abrams", + "author_inst": "Drexel University" + }, + { + "author_name": "Marzena Pazgier", + "author_inst": "USUHS" + }, + { + "author_name": "Andres Finzi", + "author_inst": "CRCHUM / Universite de Montreal" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.04.20188268", "rel_title": "The link between vitamin D deficiency and Covid-19 in a large population", @@ -1177756,33 +1174203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.04.20188532", - "rel_title": "Modeling COVID-19 dynamics in the sixteen West African countries", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188532", - "rel_abs": "The current COVID-19 pandemic has caused several damages to the world, especially in public health sector. This study considered a simple deterministic SIR (Susceptible-Infectious-Recovered) model to characterize and predict future course of the pandemic in the West African countries. We estimated specific characteristics of the diseases dynamics such as its initial conditions, reproduction numbers, true peak, reported peak with their corresponding times, final epidemic size and time-varying attack ratio. Our findings revealed a relatively low proportion of susceptible individuals in the region and in the different countries (1.2% across West Africa). The detection rate of the disease was also relatively low (0.9% for West Africa as a whole) and < 2% for most countries, except for Cape-Verde (9.5%), Mauritania (5.9%) and Ghana (4.4%). The reproduction number varied between 1.15 (Burkina-Faso) and 4.45 (Niger) and the peak time of the pandemic was between June and July for most countries. Most generally, the reported peak time came a week (7-8 days) after the true peak time. The model predicted 222,100 actual active cases in the region at peak time while the final epidemic size accounted for 0.6% of the West African population (2,526,700 individuals). Results obtained showed that the COVID-19 pandemic has not severely affected West Africa as noticed in other regions of the world, but current control measures and standard operating procedures should be maintained over time to ensure trends observed and even accelerate the declining trend of the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sewanou H. Honfo", - "author_inst": "Laboratoire de Biomath\u00e9matiques et d'Estimations Foresti\u00e8res, Universit\u00e9 d'Abomey-Calavi" - }, - { - "author_name": "Beaugard H. Taboe", - "author_inst": "Laboratoire de Biomath\u00e9matiques et d'Estimations Foresti\u00e8s, Universit\u00e9 d'Abomey-Calavi" - }, - { - "author_name": "Romain Glele Kakai", - "author_inst": "Laboratoire de Biomath\u00e9matiques et d'Estimations Foresti\u00e8res, Universit\u00e9 d'Abomey-Calavi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20188326", "rel_title": "Variations in state-level SARS-COV-2 testing recommendations in the United States, March-July 2020", @@ -1178455,6 +1174875,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.04.283853", + "rel_title": "Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection", + "rel_date": "2020-09-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.04.283853", + "rel_abs": "There is an urgent need to develop efficacious vaccines against SARS-CoV-2 that also address the issues of deployment, equitable access, and vaccine acceptance. Ideally, the vaccine would prevent virus infection and transmission as well as preventing COVID-19 disease. We previously developed an oral adenovirus-based vaccine technology that induces both mucosal and systemic immunity in humans. Here we investigate the immunogenicity of a range of candidate adenovirusbased vaccines, expressing full or partial sequences of the spike and nucleocapsid proteins, in mice. We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Antigen-specific CD4+ and CD8+ T cells were induced by this leading vaccine candidate at low and high doses. This fulllength spike antigen plus nucleocapsid adenovirus construct has been prioritized for further clinical development.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Anne C Moore", + "author_inst": "School of Biochemistry and Cell Biology; University College Cork; Cork, Ireland" + }, + { + "author_name": "Emery G Dora", + "author_inst": "Vaxart, Inc." + }, + { + "author_name": "Nadine Peinovich", + "author_inst": "Vaxart, Inc." + }, + { + "author_name": "Kiersten P Tucker", + "author_inst": "Vaxart, Inc." + }, + { + "author_name": "Karen Lin", + "author_inst": "Vaxart, Inc." + }, + { + "author_name": "Mario Cortese", + "author_inst": "Vaxart, Inc." + }, + { + "author_name": "Sean Tucker", + "author_inst": "Vaxart" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.06.285023", "rel_title": "New insights into nCOVID-19 binding domain and its cellular receptors", @@ -1179310,41 +1175773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20186957", - "rel_title": "Adjusted Dynamics of COVID-19 Pandemic due to Herd Immunity in Bangladesh", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20186957", - "rel_abs": "Amid growing debate between scientists and policymakers on the trade-off between public safety and reviving economy during the COVID-19 pandemic, the government of Bangladesh decided to relax the countrywide lockdown restrictions from the beginning of June 2020. Instead, the Ministry of Public Affairs officials have declared some parts of the capital city and a few other districts as red zones or high-risk areas based on the number of people infected in the late June 2020. Nonetheless, the COVID-19 infection rate had been increasing in almost every other part of the country. Ironically, rather than ensuring rapid tests and isolation of COVID-19 patients, from the beginning of July 2020, the Directorate General of Health Services restrained the maximum number of tests per laboratory. Thus, the health experts have raised the question of whether the government is heading toward achieving herd immunity instead of containing the COVID-19 pandemic. In this article, the dynamics of the pandemic due to SARS-CoV-2 in Bangladesh are analyzed with the SIRD model. We demonstrate that the herd immunity threshold can be reduced to 31% than that of 60% by considering age group cluster analysis resulting in a total of 53.0 million susceptible populations. With the data of Covid-19 cases till July 22, 2020, the time-varying reproduction numbers are used to explain the nature of the pandemic. Based on the estimations of active, severe, and critical cases, we discuss a set of policy recommendations to improve the current pandemic control methods in Bangladesh.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Enamul Hoque", - "author_inst": "Shahjalal University of Science and Technology" - }, - { - "author_name": "Md. Shariful Islam", - "author_inst": "North South University, Dhaka, Bangladesh" - }, - { - "author_name": "Mohammad Ruhul Amin", - "author_inst": "Fordham Data Science Research Initiative, Computer and Information Science, Fordham University, New York, USA" - }, - { - "author_name": "Susanta Kumar Das", - "author_inst": "Shahjalal University of Science and Technology, Sylhet, Bangladesh." - }, - { - "author_name": "Dipak Kumar Mitra", - "author_inst": "North South University, Dhaka, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.03.20187377", "rel_title": "Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study", @@ -1179909,6 +1176337,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.03.20187393", + "rel_title": "Effect of Renin-Angiotensin-Aldosterone System inhibitors on outcomes of COVID-19 patients with hypertension: Systematic review and Meta-analysis", + "rel_date": "2020-09-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187393", + "rel_abs": "ObjectiveThis research aimed to systematically review and summarize the influence of Renin-Angiotensin-Aldosterone System (RAAS) inhibitors on the outcome of COVID_19 patients with hypertension.\n\nMethodsElectronic databases; PubMed/Medline, CINAHL, the Cochrane Central Register of Controlled Trials, clinical trial.gov, and Google Scholar were searched from 2019 to June 1, 2020. Additionally, the references of identified articles were also searched.\n\nResultsA total of 9 articles comprising 3,823 patients were incorporated; 1416 patients on RAAS inhibitors and 3469 on non-RAAS inhibitors. The study demonstrated that the taking of RAAS inhibitors in COVID_19 patients with hypertension significantly reduced mortality where patients on RAAS inhibitors had a 27% decrease of mortality (RR = 0.73 [95% CI: 0.63- 0.85, p< 0.0001, I2 = 0%, random-effects model]) compared to those not taking ACEI/ARB. No significant association were observed in disease severity (RR = 0.92 (95% CI: 0.74- 1.14) and hospitalization (WMD = -2.33[95% CI: -5.60, 0.75]), random-effects model.\n\nConclusionThis study supports RAAS inhibitors safe use among COVID_19 patients with hypertension.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Tamirat Bekele Beressa", + "author_inst": "Ambo University" + }, + { + "author_name": "Tamiru Sahilu", + "author_inst": "Assosa University" + }, + { + "author_name": "Serawit Deyno", + "author_inst": "Hawassa University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.09.04.282616", "rel_title": "Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients", @@ -1180904,57 +1177359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.01.20186387", - "rel_title": "Systematic evaluation of SARS-CoV-2 spike protein derived peptides for diagnosis of COVID-19 patients", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186387", - "rel_abs": "Serological test plays an essential role in monitoring and combating COVID-19 pandemic. Recombinant spike protein (S protein), especially S1 protein is one of the major reagents for serological tests. However, the high cost in production of S protein, and the possible cross-reactivity with other human coronaviruses poses unneglectable challenges. Taking advantage of a peptide microarray of full spike protein coverage, we analyzed 2,434 sera from 858 COVID-19 patients, sera from 63 asymptomatic patients and 610 controls collected from multiple clinical centers. Based on the results of the peptide microarray, we identified several S protein derived 12-mer peptides that have high diagnosis performance. Particularly, for monitoring IgG response, one peptide (aa 1148-1159 or S2-78) has a comparable sensitivity (95.5%, 95% CI 93.7-96.9%) and specificity (96.7%, 95% CI 94.8-98.0%) to that of S1 protein for detection of both COVID-19 patients and asymptomatic infections. Furthermore, the performance of S2-78 IgG for diagnosis was successfully validated by ELISA with an independent sample cohort. By combining S2-78/ S1 with other peptides, a two-step strategy was proposed to ensure both the sensitivity and specificity of S protein based serological assay. The peptide/s identified in this study could be applied independently or in combination with S1 protein for accurate, affordable, and accessible COVID-19 diagnosis.\n\nOne Sentence SummaryEight S protein-derived peptides, particularly S2-78 (aa 1148-1159), are of high performance for diagnosis of COVID-19 as well as discrimination of other coronaviruses.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yang Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Danyun Lai", - "author_inst": "Shanghai JiaoTong University" - }, - { - "author_name": "Qing Lei", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Zhaowei Xu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Hongyan Hou", - "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Hong Shan", - "author_inst": "The Fifth Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Feng Wang", - "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xionglin Fan", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Sheng-ce Tao", - "author_inst": "Shanghai Jiao Tong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20186395", "rel_title": "Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada", @@ -1181543,6 +1177947,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.02.20183830", + "rel_title": "Pooling saliva to increase SARS-CoV-2 testing capacity", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20183830", + "rel_abs": "Expanding testing capabilities is integral to managing the further spread of SARS-CoV-2 and developing reopening strategies, particularly in regards to identifying and isolating asymptomatic and pre-symptomatic individuals. Central to meeting testing demands are specimens that can be easily and reliably collected and laboratory capacity to rapidly ramp up to scale. We and others have demonstrated that high and consistent levels of SARS-CoV-2 RNA can be detected in saliva from COVID-19 inpatients, outpatients, and asymptomatic individuals. As saliva collection is non-invasive, extending this strategy to test pooled saliva samples from multiple individuals could thus provide a simple method to expand testing capacity.\n\nHowever, hesitation towards pooled sample testing arises due to the dilution of positive samples, potentially shifting weakly positive samples below the detection limit for SARS-CoV-2 and thereby decreasing the sensitivity. Here, we investigated the potential of pooling saliva samples by 5, 10, and 20 samples prior to RNA extraction and RT-qPCR detection of SARS-CoV-2. Based on samples tested, we conservatively estimated a reduction of 7.41%, 11.11%, and 14.81% sensitivity, for each of the pool sizes, respectively. Using these estimates we modeled anticipated changes in RT-qPCR cycle threshold to show the practical impact of pooling on results of SARS-CoV-2 testing. In tested populations with greater than 3% prevalence, testing samples in pools of 5 requires the least overall number of tests. Below 1% however, pools of 10 or 20 are more beneficial and likely more supportive of ongoing surveillance strategies.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Anne E Watkins", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Eli P. Fenichel", + "author_inst": "Yale School of the Environment, Yale University, New Haven, CT 06510, USA" + }, + { + "author_name": "Daniel M. Weinberger", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Doug E. Brackney", + "author_inst": "Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 065" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "John Fournier", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Santos Bermejo", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Rupak Datta", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "- the Yale IMPACT Research Team", + "author_inst": "" + }, + { + "author_name": "Charles S. Dela Cruz", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Shelli F. Farhadian", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Medicine, Section of Infectious Diseases" + }, + { + "author_name": "Nathan D. Grubaugh", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Anne L. Wyllie", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20187070", "rel_title": "Multiplexed Detection and Quantification of Human Antibody Response to COVID-19 Infection Using a Plasmon Enhanced Biosensor Platform", @@ -1182434,61 +1178921,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.09.02.20186486", - "rel_title": "SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186486", - "rel_abs": "BackgroundSARS-CoV-2 infection has caused 64,469 deaths in India, with 7, 81, 975 active cases till 30th August 2020, lifting it to 3rd rank globally. To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. Various studies have been conducted worldwide to assess the antibody stability. However, there is very limited data available from India. Healthcare workers (HCW) are the frontline workforce and more exposed to the COVID-19 infection (SARS-CoV-2) compared to the community. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW.\n\nMethodsStaff of a tertiary care hospital in Delhi and individuals visiting that hospital were recruited between April to August 2020. Venous blood sample, demographic, clinical, COVID-19 symptoms, and RT-PCR data was collected from all participants. Serological testing was performed using the electro-chemiluminescence based assay developed by Roche Diagnostics, in Cobas Elecsys 411. Seropositive participants were followed- upto 83 days to check for the presence of antibodies.\n\nResultsA total of 780 participants were included in this study, which comprised 448 HCW and 332 individuals from the general population. Among the HCW, seroprevalence rates increased from 2.3% in April to 50.6% in July. The cumulative prevalence was 16.5% in HCW and 23.5% (78/332) in the general population with a large number of asymptomatic individuals. Out of 74 seropositive HCWs, 51 were followed-up for the duration of this study. We observed that in all seropositive cases the antibodies were sustained even up to 83 days.\n\nConclusionThe cumulative prevalence of seropositivity was lower in HCWs than the general population. There were a large number of asymptomatic cases and the antibodies developed persisted through the duration of the study. More such longitudinal serology studies are needed to better understand the antibody response kinetics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Samreen Siddiqui", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism Max Healthcare, Max Super Speciality Hospital, Saket, New Delhi, India" - }, - { - "author_name": "Salwa Naushin", - "author_inst": "2 CSIR-Institute of Genomics and Integrative Biology,New Delhi-110025, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India" - }, - { - "author_name": "Shalini Pradhan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology,New Delhi-110025, India" - }, - { - "author_name": "Archa Misra", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism, Max Healthcare, Max Super Speciality Hospital, Saket,New Delhi, India" - }, - { - "author_name": "Akansha Tyagi", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism, Max Healthcare, Max Super Speciality Hospital, Saket,New Delhi, India" - }, - { - "author_name": "Menka Loomba", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism, Max Healthcare, Max Super Speciality Hospital, Saket,New Delhi, India" - }, - { - "author_name": "Swati Waghdhare", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism, Max Healthcare, Max Super Speciality Hospital, Saket,New Delhi, India" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology,New Delhi-110025, India" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology,New Delhi-110025, India" - }, - { - "author_name": "Sujeet Jha", - "author_inst": "Institute of Endocrinology, Diabetes, and Metabolism, Max Healthcare, Max Super Speciality Hospital, Saket,New Delhi, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.02.20186676", "rel_title": "Estimating the number of COVID-19 cases being introduced into British Higher Education Institutions during Autumn 2020", @@ -1183065,6 +1179497,141 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.03.280446", + "rel_title": "A Single Dose of Self-Transcribing and Replicating RNA Based SARS-CoV-2 Vaccine Produces Protective Adaptive Immunity In Mice", + "rel_date": "2020-09-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.03.280446", + "rel_abs": "A self-transcribing and replicating RNA (STARR) based vaccine (LUNAR(R)-COV19) has been developed to prevent SARS-CoV-2 infection. The vaccine encodes an alphavirus-based replicon and the SARS-CoV-2 full length spike glycoprotein. Translation of the replicon produces a replicase complex that amplifies and prolong SARS-CoV-2 spike glycoprotein expression. A single prime vaccination in mice led to robust antibody responses, with neutralizing antibody titers increasing up to day 60. Activation of cell mediated immunity produced a strong viral antigen specific CD8+ T lymphocyte response. Assaying for intracellular cytokine staining for IFN-{gamma} and IL-4 positive CD4+ T helper lymphocytes as well as anti-spike glycoprotein IgG2a/IgG1 ratios supported a strong Th1 dominant immune response. Finally, single LUNAR-COV19 vaccination at both 2 g and 10 g doses completely protected human ACE2 transgenic mice from both mortality and even measurable infection following wild-type SARS-CoV-2 challenge. Our findings collectively suggest the potential of Lunar-COV19 as a single dose vaccine.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Ruklanthi M de Alwis", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Esther S Gan", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Shiwei Chen", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Yan Shan Leong", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Hwee Cheng Tan", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Summer L. Zhang", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Clement Yau", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Daiki Matsuda", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Elizabeth Allen", + "author_inst": "Arcturus, Therapeutics, Inc." + }, + { + "author_name": "Paula Hartman", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Jenny Park", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Maher Alayyoubi", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Hari Bhaskaran", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Adrian Dukanovic", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Belle Bao", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Brenda Clemente", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Jerel Vega", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Scott Roberts", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Jose A. Gonzalez", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Marciano Sablad", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Rodrigo Yelin", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Wendy Taylor", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Kiyoshi Tachikawa", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Suezanne Parker", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Priya Karmali", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Jared Davis", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Sean M Sullivan", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Steve G. Hughes", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Pad Chivukula", + "author_inst": "Arcturus Therapeutics, Inc." + }, + { + "author_name": "Eng Eong Ooi", + "author_inst": "Duke-NUS Medical School, Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.03.281774", "rel_title": "Phylo-geo-network and haplogroup analysis of 611 novel Coronavirus (nCov-2019) genomes from India", @@ -1183848,41 +1180415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.28.20184077", - "rel_title": "The methodological quality of COVID-19 systematic reviews is low, except for Cochrane reviews: a meta-epidemiological study", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20184077", - "rel_abs": "ObjectivesThe objective of this study was to investigate the methodological quality of COVID-19 systematic reviews (SRs) indexed in medRxiv and PubMed, compared with Cochrane COVID Reviews.\n\nStudy Design and SettingThis is a cross-sectional meta-epidemiological study. We searched medRxiv, PubMed, and Cochrane Database of Systematic Reviews for SRs of COVID-19. We evaluated the methodological quality using A MeaSurement Tool to Assess systematic Reviews (AMSTAR) checklists. The maximum AMSTAR score is 11, and minimum is 0. Higher score means better quality.\n\nResultsWe included 9 Cochrane reviews as well as randomly selected 100 non-Cochrane reviews in medRxiv and PubMed. Compared with Cochrane reviews (mean 9.33, standard deviation 1.32), the mean AMSTAR scores of the articles in medRxiv were lower (mean difference -2.85, 95%confidence intervals (CI): -0.96 to -4.74) and those in PubMed was also lower (mean difference -3.28, 95% CI: -1.40 to -5.15), with no difference between the latter two.\n\nConclusionsIt should be noted that AMSTAR is not a perfect tool of assessing quality SRs other than intervention. Readers should pay attention to the potentially low methodological quality of COVID-19 SRs in both PubMed and medRxiv but less so in Cochrane COVID reviews.\n\nPROTOCOL AND REGISTRATIONWe developed the protocol before conducting this study (Kataoka Y, Oide S, Ariie T, Tsujimoto Y, Furukawa TA. Quality of COVID-19 research in preprints: a meta-epidemiological study protocol. Protocols.io 2020. https://doi.org/10.17504/protocols.io.bhm8j49w.).\n\nWhat is new?O_LSTKey findingsC_LST- The methodological quality of COVID-19 systematic reviews (SRs) in medRxiv and PubMed were lower than Cochrane COVID reviews.\n- The methodological quality of reviews in medRxiv and PubMed did not differ.\n\n\nO_LSTWhat this study adds to what was knownC_LST- Expert opinions and a preliminary review suggested the low quality of COVID-19 SRs but this hypothesis has not been examined empirically.\n- We evaluated the methodological quality of COVID-19 SRs using comprehensive search and confirmed that the quality was low except for Cochrane reviews.\n\n\nWhat is the implication and what should change now?Readers should pay attention to the potentially low methodological quality of COVID-19 SRs in both PubMed and medRxiv but less so in Cochrane COVID reviews.\n\nThe methodological quality of COVID-19 SRs except for Cochrane COVID reviews needed to be improved.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yuki KATAOKA", - "author_inst": "Hyogo Prefectural Amagasaki General Medical Center" - }, - { - "author_name": "Shiho Oide", - "author_inst": "Department of Gynecology, Womens center, Yotsuya Medical Cube" - }, - { - "author_name": "Takashi Ariie", - "author_inst": "Department of Physical Therapy, School of Health Sciences at Fukuoka, International University of Health and Welfare" - }, - { - "author_name": "Yasushi Tsujimoto", - "author_inst": "Department of Nephrology and Dialysis, Kyoritsu Hospital" - }, - { - "author_name": "Toshi A. Furukawa", - "author_inst": "Department of Health Promotion and Human Behavior, Kyoto University Graduate School of Medicine / School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.30.20184705", "rel_title": "Analyzing inherent biases in SARS-CoV-2 PCR and serological epidemiologic metrics", @@ -1184487,6 +1181019,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.29.20184093", + "rel_title": "Quantifying the Risk of Indoor Drainage System in Multi-unit Apartment Building as a Transmission Route of SARS-CoV-2", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184093", + "rel_abs": "The COVID-19 pandemic has had a profound impact on human society. The isolation of SARS-CoV-2 from patients feces on human cell line raised concerns of possible transmission through human feces including exposure to aerosols generated by toilet flushing and through the indoor drainage system. Currently, routes of transmission, other than the close contact droplet transmission, are still not well understood. A quantitative microbial risk assessment was conducted to estimate the health risks associated with two aerosol exposure scenarios: 1) toilet flushing, and 2) faulty connection of a floor drain with the buildings main sewer pipe. SARS-CoV-2 data were collected from the emerging literature. The infectivity of the virus in feces was estimated based on a range of assumption between viral genome equivalence and infectious unit. The human exposure dose was calculated using Monte Carlo simulation of viral concentrations in aerosols under each scenario and human breathing rates. The probability of COVID-19 illness was generated using the dose-response model for SARS-CoV-1, a close relative of SARS-CoV-2, that was responsible for the SARS outbreak in 2003. The results indicate the median risks of developing COVID-19 for a single day exposure is 1.11 x 10-10 and 3.52 x 10-11 for toilet flushing and faulty drain scenario, respectively. The worst case scenario predicted the high end of COVID-19 risk for the toilet flushing scenario was 5.78 x 10-4 (at 95th percentile). The infectious viral loads in human feces are the most sensitive input parameter and contribute significantly to model uncertainty.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kuang-wei Shi", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yen-Hsiang Huang", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Hunter Quon", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Zi-Lu Ou-Yang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Chengwen Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Sunny Jiang", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.29.20184358", "rel_title": "Plasma tissue plasminogen activator and plasminogen activator inhibitor-1 in hospitalized COVID-19 patients", @@ -1185638,141 +1182209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.01.20183897", - "rel_title": "A neutrophil activation signature predicts critical illness and mortality in COVID-19", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20183897", - "rel_abs": "Pathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of over 3,300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, HGF, IL-8, and G-CSF, as the strongest predictors of critical illness. Neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, we define an essential role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular neutrophil markers that distinguish patients at risk of future clinical decompensation.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Matthew L. Meizlish", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Alexander B. Pine", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jason D. Bishai", - "author_inst": "Yale University" - }, - { - "author_name": "George Goshua", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Emily R. Nadelmann", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Michael Simonov", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "C-Hong Chang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Hanming Zhang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Marcus Shallow", - "author_inst": "Yale University" - }, - { - "author_name": "Parveen Bahel", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Kent Owusu", - "author_inst": "Yale-New Haven Hospital" - }, - { - "author_name": "Yu Yamamoto", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Tanima Arora", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Deepak S. Atri", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Amisha Patel", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Rana Gbyli", - "author_inst": "Yale University" - }, - { - "author_name": "Jennifer Kwan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Christine H. Won", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Charles Dela Cruz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Christina Price", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jonathan Koff", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Brett A. King", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Henry M. Rinder", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "F. Perry Wilson", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "John Hwa", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Stephanie Halene", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "William Damsky", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "David van Dijk", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Alfred Ian Lee", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Hyung Chun", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20185017", "rel_title": "First snap-shot meta-analysis to estimate the prevalence of serum antibodies to SARS-CoV-2 in humans", @@ -1186541,6 +1182977,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.09.01.20182642", + "rel_title": "Covid-19 SEIDRD Modelling for Pakistan with implementation of seasonality, healthcare capacity and behavioral risk reduction", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20182642", + "rel_abs": "INTRODUCTIONO_ST_ABSIntroductionC_ST_ABSDecember 2019 saw the origins of a new Pandemic which would soon spread to the farthest places of the planet. Several efforts of modelling of the geo-temporal transmissibility of the virus have been undertaken, but none describes the incorporation of effect of seasonality, contact density, primary care and ICU bed capacity and behavioral risk reduction measures such as lockdowns into the simulation modeling for Pakistan. We use above variables to create a close to real data curve function for the active cases of covid-19 in Pakistan.\n\nObjectiveThe objective of this study was to create a new computational epidemiological model for Pakistan by implementing symptomatology, healthcare capacity and behavioral risk reduction mathematically to predict of Covid-19 case trends and effects of changes in community characteristics and policy measures.\n\nMethodsWe used a modified version of SEIR model called SEIDRD (Susceptible - Exposed Latent - Diagnosed as Mild or severe - Recovered - Deaths). This was developed using Vensim PLE software version 8.0. This model also incorporated the seasonal and capacity variables for Pakistan and was adjusted for behavioral risk reduction measures such as lockdowns.\n\nResultsThe SEIDRD model was able to closely replicate the active covid-19 cases curve function for Pakistan until now. It was able to show that given current trends, though the number of active cases are dropping, if the smart lockdown measures were to end, the cases are expected to show a rise from 28th August 2020 onwards reaching a second peak around 28th September 2020. It was also seen that increasing the ICU bed capacity in Pakistan from 4000 to 40000 will not make a significant difference in active case number. Another simulation for a vaccination schedule of 100000 vaccines per day was created which showed a decrease in covid cases in a slow manner over a period of months rather than days.\n\nConclusionThis study attempts to successfully model the active covid-19 cases curve function of Pakistan and mathematically models the effect of seasonality, contact density, ICU bed availability and Lockdown measures. We were able to show the effectiveness of smart lockdowns and were also to predict that in case of no smart lockdowns, Pakistan can see a rise in active case number starting from 28th of August 2020.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shoab Saadat", + "author_inst": "East and North Hertfordshire NHS Trust" + }, + { + "author_name": "Salman Mansoor", + "author_inst": "Sligo University Hospital Ireland" + }, + { + "author_name": "Ammad Fahim", + "author_inst": "NUST Pakistan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.01.20185868", "rel_title": "Social multipliers and the Covid-19 epidemic: Analysis through constrained maximum entropy modeling", @@ -1187476,69 +1183939,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.01.278630", - "rel_title": "Prime-boost protein subunit vaccines against SARS-CoV-2 are highly immunogenic in mice and macaques", - "rel_date": "2020-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.01.278630", - "rel_abs": "SARS-CoV-2 vaccines are advancing into human clinical trials, with emphasis on eliciting high titres of neutralising antibodies against the viral spike (S). However, the merits of broadly targeting S versus focusing antibody onto the smaller receptor binding domain (RBD) are unclear. Here we assessed prototypic S and RBD subunit vaccines in homologous or heterologous prime-boost regimens in mice and non-human primates. We find S is highly immunogenic in mice, while the comparatively poor immunogenicity of RBD was associated with limiting germinal centre and T follicular helper cell activity. Boosting S-primed mice with either S or RBD significantly augmented neutralising titres, with RBD-focussing driving moderate improvement in serum neutralisation. In contrast, both S and RBD vaccines were comparably immunogenic in macaques, eliciting serological neutralising activity that generally exceed levels in convalescent humans. These studies confirm recombinant S proteins as promising vaccine candidates and highlight multiple pathways to achieving potent serological neutralisation.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Hyon-Xhi Tan", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Wen Shi Lee", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Isaac Barber-Axthelm", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Hannah G Kelly", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Kathleen M Wragg", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Robyn Esterbauer", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Thakshila Amarasena", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Francesca L Mordant", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Kanta Subbarao", - "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Adam K Wheatley", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.01.278689", "rel_title": "Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility", @@ -1188287,6 +1184687,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.26.20180968", + "rel_title": "Racial and workplace disparities in seroprevalence of SARS-CoV-2 in Baton Rouge, Louisiana, July 15-31, 2020", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20180968", + "rel_abs": "Using paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence and seroprevalence in a municipality in Louisiana, USA during the second phase of reopening. Infections were highly variable by race, work environment, and ZIP code. Census-weighted seroprevalence and point prevalence were 3.6% and 3.0%, respectively.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amy K Feehan", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA; University of Queensland, Ochsner Clinical School, New Orleans, LA, USA" + }, + { + "author_name": "Cruz Velasco", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA" + }, + { + "author_name": "Daniel Fort", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA" + }, + { + "author_name": "Jeffrey H Burton", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA" + }, + { + "author_name": "Eboni Price-Haywood", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA; University of Queensland, Ochsner Clinical School, New Orleans, LA, USA" + }, + { + "author_name": "Peter T Katzmarzyk", + "author_inst": "Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA" + }, + { + "author_name": "Julia Garcia-Diaz", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA; University of Queensland, Ochsner Clinical School, New Orleans, LA, USA" + }, + { + "author_name": "Leonardo Seoane", + "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA; University of Queensland, Ochsner Clinical School, New Orleans, LA, USA ;Louisiana State University Health Scie" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20182816", "rel_title": "SalivaAll: Clinical validation of a sensitive test for saliva collected in healthcare and community settings with pooling utility for SARS-CoV-2 mass surveillance.", @@ -1189470,49 +1185917,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.26.20182543", - "rel_title": "Ethnic disparities in COVID-19 mortality in Mexico: a cross-sectional study based on national data", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182543", - "rel_abs": "ObjectiveTo analyze the mortality associated with ethnicity, particularly of Indigenous peoples, in a large sample of patients with COVID-19 in Mexico.\n\nDesignNational, cross-sectional study.\n\nSettingMexico.\n\nParticipants416546 adult patients; 4178 Indigenous peoples with COVID-19 were the primary population under study.\n\nMain outcome measuresThe primary outcome was mortality from COVID-19 up to August 3rd, 2020. Logistic regression was used to calculate odds ratios while adjusting for confounders.\n\nResultsAmong all patients with COVID-19, whether hospitalized or not, a higher proportion of Indigenous peoples died compared to non-Indigenous people (16.5% vs 11.1%, respectively). Among hospitalized patients, a higher proportion of Indigenous peoples died (37.1%) compared to non-Indigenous peoples (36.3%). Deaths outside the hospital were also higher among Indigenous peoples (3.7% vs 1.7%). A higher proportion of Indigenous peoples died in both the private and public health care sectors. The adjusted odds ratio for COVID-19 mortality among Indigenous peoples with COVID-19 was 1.13 (95% confidence interval 1.03 to 1.24). The adjusted odds ratio for COVID-19 mortality among Indigenous peoples with COVID-19 was higher among those who received only ambulatory care (1.55, 95% confidence interval 1.24 to 1.92).\n\nConclusionsIn the large sample of patients with COVID-19, the findings suggest that Indigenous peoples in Mexico have a higher risk of death from COVID-19, especially outside the hospital. These findings suggest Indigenous peoples lack access to care more so than non-Indigenous people during the COVID-19 pandemic in Mexico. More research is needed regarding the impact of the COVID-19 among racial and ethnic minorities in Mexico.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ismael Ibarra-Nava", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Kathia G. Flores-Rodriguez", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Violeta Ruiz-Herrera", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Hilda C. Ochoa-Bayona", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Alfonso Salinas-Zertuche", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Magaly Padilla-Orozco", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Raul G. Salazar-Montalvo", - "author_inst": "Universidad Autonoma de Nuevo Leon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.26.20182303", "rel_title": "Risk factors for SARS-CoV-2 infection, hospitalisation, and death in Catalonia, Spain: a population-based cross-sectional study", @@ -1190113,6 +1186517,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20182832", + "rel_title": "Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182832", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30%-60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. The LoD (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI): 363.23-1145.69) for ORF1ab and 528.1 (95% CI: 347.7-1248.7) for N, 401.8 (95% CI: 284.8-938.3) for ORF1ab and 336.8 (95% CI: 244.6-792.5) for N, and 194.74 (95% CI: 139.7-430.9) for ORF1ab and 189.1 (95% CI: 130.9-433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yang Zhang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + }, + { + "author_name": "Chunyang Dai", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + }, + { + "author_name": "Huiyan Wang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + }, + { + "author_name": "Yong Gao", + "author_inst": "Fuyang Second People's Hospital, Fuyang Infectious Disease Clinical College, Anhui Medical University" + }, + { + "author_name": "Tuantuan Li", + "author_inst": "Fuyang Second People's Hospital, Fuyang Infectious Disease Clinical College, Anhui Medical University" + }, + { + "author_name": "Yan Fang", + "author_inst": "Fuyang Second People's Hospital, Fuyang Infectious Disease Clinical College, Anhui Medical University" + }, + { + "author_name": "Zuojun Shen", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + }, + { + "author_name": "Lichang Chen", + "author_inst": "Fuyang Second People's Hospital, Fuyang Infectious Disease Clinical College, Anhui Medical University" + }, + { + "author_name": "Zhaowu Chen", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + }, + { + "author_name": "Xuejun Ma", + "author_inst": "National Institute for Viral Disease Control and prevention" + }, + { + "author_name": "Ming Li", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183228", "rel_title": "Disease burden and clinical severity of the first pandemic wave of COVID-19 in Wuhan, China", @@ -1190796,57 +1187259,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.08.28.20167379", - "rel_title": "Acute kidney injury in patients with severe COVID-19 in Mexico", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20167379", - "rel_abs": "IntroductionSome patients with COVID-19 pneumonia present systemic disease involving multiple systems. There is limited information about the clinical characteristics and events leading to acute kidney injury (AKI). We described the factors associated with the development of AKI and explored the relation of AKI and mortality in Mexican population with severe COVID-19.\n\nMethodsWe retrospectively reviewed the medical records of individuals with severe pneumonia caused by SARS-CoV-2 hospitalized at the largest third-level reference institution for COVID-19 care in Mexico between March and April 2020. Demographic information, comorbidities, clinical and laboratory data, dates of mechanical ventilation and hospitalization, mechanical-ventilator settings and use of vasoactive drugs were recorded.\n\nResultsOf 99 patients studied, 58 developed AKI (58.6%). The group with AKI had higher body mass index (p=0.0003) and frequency of obesity (p=0.001); a higher requirement of invasive mechanical ventilation (p=0.008) and vasoactive drugs (p=0.004); greater levels of serum creatinine (p<0.001) and D-dimer on admission (p<0.001); and lower lymphocyte counts (p=0.001) than the non-AKI group. The multivariate analysis indicated that risk factors for AKI were obesity (adjusted hazard ratio (HR)=2.71, 95% confidence interval (CI)=1.33-5.51, p=0.005); higher serum creatinine (HR=1.44, CI=1.02- 2.02, p=0.035) and D-dimer levels on admission (HR=1.14, CI=1.06-1.23, p<0.001). Inhospital mortality was higher in the AKI group than in the non-AKI group (65.5% vs. 14.6%; p=0.001).\n\nConclusionsAKI was common in our cohort of patients with severe COVID-19 and it was associated with mortality. The risk factors for AKI were obesity, elevated creatinine levels and higher D-dimer levels on admission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "GUSTAVO CASAS", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "MARIA-ISABEL LEON", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "MAURICIO GONZALEZ-NAVARRO", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "CLAUDIA ALVARADO DE LA BARRERA", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Santiago Avila-Rios", - "author_inst": "National Institute of Respiratory Diseases" - }, - { - "author_name": "amy peralta-prado", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "YARA LUNA-VILLALOBOS", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "ALEJANDRO VELASCO-MORALES", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - }, - { - "author_name": "NATALIA CALDERON", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2020.08.28.20181883", "rel_title": "Clinical, cerebrospinal fluid and neuroimaging findings in COVID-19 encephalopathy: a case series", @@ -1191695,6 +1188107,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.30.20177543", + "rel_title": "Bronchoscopy on Intubated COVID-19 Patients is Associated with Low Infectious Risk to Operators at a High-Volume Center Using an Aerosol-minimizing Protocol", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20177543", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic raised concern for exposure to healthcare providers through aerosol generating procedures, such as bronchoalveolar lavage (BAL). Current society guidelines recommended limiting use of BAL to reduce operators risk for infection, yet data on the infection rate for providers after BAL is sparse. Since March 2020, our institution used a modified protocol to perform over 450 BALs on intubated COVID-19 patients. We therefore sought to describe the subsequent infectious risks to providers associated with BAL.\n\nMethodsFifty-two pulmonary and critical care providers (faculty and fellows) at our tertiary-care, urban medical center were surveyed. Survey participants were asked to provide the number of BALs on COVID-19 patients they performed, the number of weeks they cared for intensive care unit (ICU) patients with COVID-19, and the results of any SARS-CoV-2 testing that they received. Participants were asked to assess the difficulty of BAL on intubated COVID-19 patients as compared to routine ICU BAL using a numeric perceived difficulty score ranging from 1 (easier) to 10 (harder).\n\nResultsWe received forty-seven responses from fifty-two surveyed (90% response rate), with 2 declining to participate. Many respondents (19/45, 42%) spent >5 weeks on an ICU service with COVID-19 patients. The number of BALs performed by providers ranged from 0 to >60. Sixteen of the 35 providers (46%) who performed BALs underwent at least one nasopharyngeal (NP) swab to test for SARS-CoV-2, but none were positive. Twenty-seven of the 35 providers (77%) who performed BALs underwent SARS- CoV-2 serology testing, and only one (3.7%) was positive. Respondents indicated occasionally not being able to follow aerosol-minimizing steps but overall felt BALs in COVID-19 patients was only slightly more difficult than routine bronchoscopy.\n\nDiscussionAt a high-volume center having performed >450 BALs on intubated COVID-19 patients with aerosol-limiting precautions, our survey of bronchoscopists found no positive NP SARS-CoV-2 tests and only one positive antibody test result. While the optimal role for COVID-19 BAL remains to be determined, these data suggest that BAL can be safely performed in intubated COVID-19 patients if experienced providers take precautions to limit aerosol generation and wear personal protective equipment.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Catherine A. Gao", + "author_inst": "Northwestern" + }, + { + "author_name": "Joseph Isaac Bailey", + "author_inst": "Northwestern" + }, + { + "author_name": "James M. Walter", + "author_inst": "Northwestern" + }, + { + "author_name": "John M. Coleman III", + "author_inst": "Northwestern" + }, + { + "author_name": "Elizabeth S. Malsin", + "author_inst": "Northwestern" + }, + { + "author_name": "A. Christine Argento", + "author_inst": "Northwestern" + }, + { + "author_name": "Michelle H. Prickett", + "author_inst": "Northwestern" + }, + { + "author_name": "- NU COVID Investigators", + "author_inst": "" + }, + { + "author_name": "Richard G. Wunderink", + "author_inst": "Northwestern" + }, + { + "author_name": "Sean B. Smith", + "author_inst": "Northwestern" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.08.28.20184028", "rel_title": "Epidemiology of Venous Thromboembolism in SARS- CoV-2 Infected Patients: A Systematic Review and Meta-Analysis", @@ -1192766,133 +1189233,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.31.274639", - "rel_title": "Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro", - "rel_date": "2020-09-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.31.274639", - "rel_abs": "There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Nir Drayman", - "author_inst": "University of Chicago" - }, - { - "author_name": "Krysten A Jones", - "author_inst": "University of Chicago" - }, - { - "author_name": "Sarra-Anne Azizi", - "author_inst": "University of Chicago" - }, - { - "author_name": "Heather M Froggatt", - "author_inst": "Duke" - }, - { - "author_name": "Kemin Tan", - "author_inst": "University of Chicago" - }, - { - "author_name": "Natalia Ivanova Maltseva", - "author_inst": "University of Chicago" - }, - { - "author_name": "Siquan Chen", - "author_inst": "University of Chicago" - }, - { - "author_name": "Vlad Nicolaescu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Steve Dvorkin", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kevin Furlong", - "author_inst": "University of Chicago" - }, - { - "author_name": "Rahul S Kathayat", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mason R Firpo", - "author_inst": "Loyola University" - }, - { - "author_name": "Vincent Mastrodomenico", - "author_inst": "Loyoloa University" - }, - { - "author_name": "Emily A Bruce", - "author_inst": "University of Vermont" - }, - { - "author_name": "Madaline M Schmidt", - "author_inst": "University of Vermont" - }, - { - "author_name": "Robert Jedrzejczak", - "author_inst": "University of Chicago" - }, - { - "author_name": "Miguel A Munoz-Alia", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Brooke Schuster", - "author_inst": "University of Chicago" - }, - { - "author_name": "Vishnu Nair", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jason W Botten", - "author_inst": "University of Vermont" - }, - { - "author_name": "Christopher B Brooke", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Susan C Baker", - "author_inst": "Loyola University" - }, - { - "author_name": "Bryan C Mounce", - "author_inst": "Loyola University" - }, - { - "author_name": "Nicholas S Heaton", - "author_inst": "Duke" - }, - { - "author_name": "Bryan C Dickinson", - "author_inst": "University of Chicago" - }, - { - "author_name": "Andrzej Jaochimiak", - "author_inst": "University of Chicago" - }, - { - "author_name": "Glenn Randall", - "author_inst": "University of Chicago" - }, - { - "author_name": "Sava\u015f Tay", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.30.274506", "rel_title": "From Face-to-Face to Online Modality: Implications for Undergraduate Learning While the World is Temporarily Closed in the Age of COVID-19", @@ -1193349,6 +1189689,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.08.24.20180877", + "rel_title": "Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180877", + "rel_abs": "The SARS-CoV-2 pandemic is continuing to impact the global population. This study was designed to assess the interplay of antibodies with the systemic cytokine response in SARS-CoV-2 patients. We demonstrate that significant anti-SARS-CoV-2 antibody production to Receptor Binding Domain (RBD), Nucleocapsid (N), and Spike S1 subunit (S1) of SARS-CoV-2 develops over the first 10 to 20 days of infection. The majority of patients produced antibodies against all three antigens (219/255 SARS-CoV-2 positive patient specimens, 86%) suggesting a broad response to viral proteins. Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations. To better understand the systemic immune response, we analyzed the production of 20 cytokines by SARS-CoV-2 patients over the course of infection. Cytokine analysis of SARS-CoV-2 positive patients exhibited increases in proinflammatory markers (IL-6, IL-8, IL-18) and chemotactic markers (IP-10, SDF-1, MIP-1{beta}, MCP-1, and eotaxin) relative to healthy individuals. Patients who succumbed to infection produced decreased IL-2, IL-4, IL-12, IL-13, RANTES, TNF-, GRO-, and MIP-1 relative to patients who survived infection. We also observed that the chemokine CXCL13 was particularly elevated in patients that succumbed to infection. CXCL13 is involved in B cell activation, germinal center development, and antibody maturation, and we observed that CXCL13 levels in blood trended with anti-SARS-CoV-2 antibody production. Furthermore, patients that succumbed to infection produced high CXCL13 and also tended to have high ratio of nucleocapsid to RBD antibodies. This study provides insights into SARS-CoV-2 immunity implicating the magnitude and specificity of response in relation to patient outcomes.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alexander M. Horspool", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Theodore Kieffer", + "author_inst": "Department of Pathology, Anatomy and Laboratory Medicine, West Virginia University School of Medicine" + }, + { + "author_name": "Brynnan P. Russ", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Megan A. DeJong", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "M. Allison Wolf", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Jacqueline M. Karakiozis", + "author_inst": "Department of Pathology, Anatomy and Laboratory Medicine, West Virginia University School of Medicine, Morgantown, West Virginia, USA" + }, + { + "author_name": "Brice J. Hickey", + "author_inst": "Department of Pathology, Anatomy and Laboratory Medicine, West Virginia University School of Medicine, Morgantown, West Virginia, USA" + }, + { + "author_name": "Paolo Fagone", + "author_inst": "Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Danyel H. Tacker", + "author_inst": "Department of Pathology, Anatomy and Laboratory Medicine, West Virginia University School of Medicine, Morgantown, West Virginia, USA" + }, + { + "author_name": "Justin R. Bevere", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Ivan Martinez", + "author_inst": "West Virginia University Cancer Institute, Morgantown, West Virginia, USA" + }, + { + "author_name": "Mariette Barbier", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + }, + { + "author_name": "Peter L. Perrotta", + "author_inst": "Department of Pathology, Anatomy and Laboratory Medicine, West Virginia University School of Medicine, Morgantown, West Virginia, USA" + }, + { + "author_name": "F. Heath Damron", + "author_inst": "Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.25.20181396", "rel_title": "PRELIMINARY ASSESSMENT OF STRUCTURE AND COLLECTIVE DOSE FROM CT EXAMINATIONS RELATED TO COVID-19 DIAGNOSTICS IN THE RUSSIAN FEDERATION IN MARCH -JUNE 2020", @@ -1194700,37 +1191111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.25.20180265", - "rel_title": "Analysis and prediction of Covid-19 spreading through Bayesian modelling with a case study of Uttar Pradesh, India", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20180265", - "rel_abs": "The pandemic of coronavirus disease 2019 (COVID-19) started in Wuhan, China, and spread worldwide. In India, COVID-19 cases increased rapidly throughout India. Various measures like awareness program, social distancing, and contact tracing have been implemented to control the COVID-19 outbreak. In the absence of any vaccine, the prediction of the confirmed, deceased, and recovered cases is required to enhance the health care systems capacity and control the transmission. In this study, the cumulative and daily confirmed, deceased, and recovered cases in Uttar Pradesh, India, were analyzed. We used the logistic and Gompertz non-linear regression model using a Bayesian paradigm. We build the prior distribution of the model using information obtained from some other states of India, which are already reached at the advanced stage of COVID-19. Results from the analysis indicated that the predicted maximum number of confirmed, deceased, and recovered cases will be around 1157335, 5843, and 1145829 respectively. The daily number of confirmed, deceased, and recovered cases will be maximum at 104th day, 73rd day, and 124th day from 16 June 2020. Further from this analysis we can conclude that the COVID-19 will be over probably by early-June, 2021. The analysis did not consider any changes in government control measures. We hope this study can provide some relevant information to the government and health officials.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Deepmala", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Nishant Kumar Srivastava", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Vineet Kumar", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Sanjay Kumar Singh", - "author_inst": "Banaras Hindu University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.25.20181198", "rel_title": "The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya", @@ -1195631,6 +1192011,141 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.30.273235", + "rel_title": "The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR", + "rel_date": "2020-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.30.273235", + "rel_abs": "On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by our in-house automated pipeline. Of particular note, 2019nCoVR performs systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. It also generates visualization of the spatiotemporal change for each variant and yields historical viral haplotype network maps for the course of the outbreak from all complete and high-quality genomes. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on COVID-19 (Coronavirus Disease 2019), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB-NGDC, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with National Center for Biotechnology Information. Collectively, all SARS-CoV-2 genome sequences, variants, haplotypes and literature are updated daily to provide timely information, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Shuhui Song", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Lina Ma", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Dong Zou", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Dongmei Tian", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Cuiping Li", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Junwei Zhu", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Meili Chen", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Anke Wang", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yingke Ma", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Mengwei Li", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Xufei Teng", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Ying Cui", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Guangya Duan", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Mochen Zhang", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Tong Jin", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Chengmin Shi", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhenglin Du", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yadong Zhang", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Chuandong Liu", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Rujiao Li", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Jingyao Zeng", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Lili Hao", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Shuai Jiang", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Hua Chen", + "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" + }, + { + "author_name": "Dali Han", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Jingfa Xiao", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhang Zhang", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Wenming Zhao", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yongbiao Xue", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + }, + { + "author_name": "Yiming Bao", + "author_inst": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.08.30.273920", "rel_title": "Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies", @@ -1196210,7 +1192725,7 @@ "rel_date": "2020-08-29", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.273425", - "rel_abs": "The human placenta is increasingly a focus of research related to early child development and the impact of maternal hyperimmune states. Primary human trophoblast stem cells (hTSC) and human pluripotent stem cells (hPSC) differentiated to hTSC can potentially model placental processes in vitro. Yet, it remains controversial how the differentiation of human pluripotent stem cells to trophectoderm relates to in vivo development and the factors required for this differentiation. Here, we demonstrate that the primed pluripotent state retains potency to generate trophoblast stem cells by activating EGF and WNT and inhibiting TGFb, HDAC and ROCK signaling without exogenous BMP4 (named TS). We map this specification by temporal single cell RNAseq compared to activating BMP4 or activating BMP4 and inhibiting WNT. TS conditions generate a stable proliferating cell type that is highly similar to six-week placental cytotrophoblasts with activation of endogenous retroviral genes and without amnion expression. Multiple primed iPSC and ES lines differentiate to iPS-derived-TSCs that can be passaged for at least 30 passages and differentiate to pure populations of multinucleated syncytiotrophoblasts and extravillous trophoblast cells. Our findings establish that primed iPS cell specification to hTSC with TS conditions involves induction of TMSB4X, BMP5/7, GATA3 and TFAP2A without transitioning through a naive state. Collectively, our results suggest that the primed state is on a continuum of potency and can differentiate to trophoblast stem cells via multiple paths.", + "rel_abs": "The human placenta is increasingly a focus of research related to early child development and the impact of maternal hyperimmune states. Primary human trophoblast stem cells (hTSC) and human pluripotent stem cells (hPSC) differentiated to hTSC can potentially model placental processes in vitro. Yet, it remains controversial how the differentiation of human pluripotent stem cells to trophectoderm relates to in vivo development and the factors required for this differentiation. Here, we demonstrate that the primed pluripotent state retains potency to generate trophoblast stem cells by activating EGF and WNT and inhibiting TGFb, HDAC and ROCK signaling without exogenous BMP4 (named TS). We map this specification by temporal single cell RNAseq compared to activating BMP4 or activating BMP4 and inhibiting WNT. TS conditions generate a stable proliferating cell type that is highly similar to six-week placental cytotrophoblasts with activation of endogenous retroviral genes and without amnion expression. Multiple primed iPSC and ES lines differentiate to iPS-derived-TSCs that can be passaged for at least 30 passages and differentiate to pure populations of multinucleated syncytiotrophoblasts and extravillous trophoblast cells. Our findings establish that primed iPS cell specification to hTSC with TS conditions involves induction of TMSB4X, BMP5/7, GATA3 and TFAP2A without transitioning through a naive state. Collectively, our results suggest that the primed state is on a continuum of potency and can differentiate to trophoblast stem cells via multiple paths.\n\nSignificance StatementIn the present study, we map the specification of primed induced pluripotent stem cells to trophoblast stem cells (TSC). Primed iPS-derived-TSC share transcriptional, morphological and functional characteristics with human ex vivo cytotrophoblasts including capacity of self-renewal and the ability to differentiate to pure extravillous and syncytiotrophoblasts. iPS-derived TSC display a uniquely active transcriptional network of human endogenous retroviruses similar to in vivo trophoblast. In addition, the fast conversion of primed iPSC to TSC allows for modeling placental diseases from large pluripotent stem cell cohorts which are traditionally banked at the primed state. Collectively, our results suggest that the primed state is on a continuum of potency which can differentiate to trophoblast stem cells via multiple paths.", "rel_num_authors": 22, "rel_authors": [ { @@ -1196718,61 +1193233,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.28.269175", - "rel_title": "A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research", - "rel_date": "2020-08-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.269175", - "rel_abs": "Key steps of viral replication take place at host cell membranes, but the detection of membrane-associated protein-protein interactions using standard affinity-based approaches (e.g. immunoprecipitation coupled with mass spectrometry, IP-MS) is challenging. To learn more about SARS-CoV-2 - host protein interactions that take place at membranes, we utilized a complementary technique, proximity-dependent biotin labeling (BioID). This approach uncovered a virus-host topology network comprising 3566 proximity interactions amongst 1010 host proteins, highlighting extensive virus protein crosstalk with: (i) host protein folding and modification machinery; (ii) membrane-bound vesicles and organelles, and; (iii) lipid trafficking pathways and ER-organelle membrane contact sites. The design and implementation of sensitive mass spectrometric approaches for the analysis of complex biological samples is also important for both clinical and basic research proteomics focused on the study of COVID-19. To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. Together, these datasets comprise a valuable resource for MS-based SARS-CoV-2 research, and identify novel virus-host protein interactions that could be targeted in COVID-19 therapeutics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jonathan R St-Germain", - "author_inst": "Princess Margaret Cancer Centre" - }, - { - "author_name": "Audrey Astori", - "author_inst": "Princess Margaret Cancer Centre" - }, - { - "author_name": "Payman Samavarchi-Tehrani", - "author_inst": "Lunenfeld-Tanenbaum Research Institute" - }, - { - "author_name": "Hala Abdouni", - "author_inst": "Lunenfeld-Tanenbaum Research Institute" - }, - { - "author_name": "Vinitha Macwan", - "author_inst": "Princess Margaret Cancer Centre" - }, - { - "author_name": "Dae-Kyun Kim", - "author_inst": "Lunenfeld-Tanenbaum Research Institute" - }, - { - "author_name": "Jennifer J Knapp", - "author_inst": "Lunenfeld-Tanenbaum Research Institute" - }, - { - "author_name": "Frederick P. Roth", - "author_inst": "University of Toronto" - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "Lunenfeld-Tanenbaum Research Institute" - }, - { - "author_name": "Brian Raught", - "author_inst": "Princess Margaret Cancer Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.08.27.270819", "rel_title": "Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics", @@ -1197361,6 +1193821,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.28.271957", + "rel_title": "Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2", + "rel_date": "2020-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.271957", + "rel_abs": "A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 42 drugs emerged as top candidates, and after visual analyses of the predicted structures of their complexes with Mpro, 17 were chosen for evaluation in a kinetic assay for Mpro inhibition. Remarkably 14 of the compounds at 100-M concentration were found to reduce the enzymatic activity and 5 provided IC50 values below 40 M: manidipine (4.8 M), boceprevir (5.4 M), lercanidipine (16.2 M), bedaquiline (18.7 M), and efonidipine (38.5 M). Structural analyses reveal a common cloverleaf pattern for the binding of the active compounds to the P1, P1, and P2 pockets of Mpro. Further study of the most active compounds in the context of COVID-19 therapy is warranted, while all of the active compounds may provide a foundation for lead optimization to deliver valuable chemotherapeutics to combat the pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohammad M. Ghahremanpour", + "author_inst": "Yale University" + }, + { + "author_name": "Julian Tirado-Rives", + "author_inst": "Yale University" + }, + { + "author_name": "Maya Deshmukh", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Chun-Hui Zhang", + "author_inst": "Yale University" + }, + { + "author_name": "Israel Cabeza de Vaca", + "author_inst": "Yale University" + }, + { + "author_name": "Maria-Elena Liosi", + "author_inst": "Yale University" + }, + { + "author_name": "Karen S. Anderson", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "William L. Jorgensen", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.08.28.271601", "rel_title": "Sequence analysis of Indian SARS-CoV-2 isolates shows a stronger interaction of mutated receptor binding domain with ACE2 receptor", @@ -1198195,49 +1194702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.22.20179911", - "rel_title": "Clinical Outcomes of Hospitalized Patients with COVID-19 on Therapeutic Anticoagulants", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20179911", - "rel_abs": "BackgroundCOVID-19 is associated with hypercoagulability and an increased incidence of thrombosis. We evaluated the clinical outcomes of adults hospitalized with COVID-19 who either continued therapeutic anticoagulants previously prescribed or who were newly started on anticoagulants during hospitalization.\n\nMethodsWe performed an observational study of adult inpatients with COVID-19 at 10 hospitals affiliated with Northwestern Medicine in the Chicagoland area from March 9 to June 26, 2020. We evaluated clinical outcomes of subjects with COVID-19 who were continued on their outpatient therapeutic anticoagulation during hospitalization and those who were newly started on these medications compared to those who were on prophylactic doses of these medications based on the World Health Organization (WHO) Ordinal Scale for Clinical Improvement. The primary outcome was overall death while secondary outcomes were critical illness (WHO score [≥]5), need for mechanical ventilation, and death among those subjects who first had critical illness adjusted for age, sex, race, body mass index (BMI), Charlson score, glucose on admission, and use of antiplatelet agents.\n\nResults1,716 subjects with COVID-19 were included in the analysis. 171 subjects (10.0%) were continued on their outpatient therapeutic anticoagulation and 201(11.7%) were started on new therapeutic anticoagulation during hospitalization. In subjects continued on home therapeutic anticoagulation, there were no differences in overall death, critical illness, mechanical ventilation, or death among subjects with critical illness compared to subjects on prophylactic anticoagulation. Subjects receiving new therapeutic anticoagulation for COVID-19 were more likely to die (OR 5.93; 95% CI 3.71-9.47), have critical illness (OR 14.51; 95% CI 7.43-28.31), need mechanical ventilation (OR 11.22; 95% CI 6.67-18.86), and die after first having critical illness. (OR 5.51; 95% CI 2.80 -10.87).\n\nConclusionsContinuation of outpatient prescribed anticoagulant was not associated with improved clinical outcomes. Therapeutic anticoagulation for COVID-19 in absence of other indications was associated with worse clinical outcomes.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Niti G Patel", - "author_inst": "Northwestern University Feinberg School of medicine" - }, - { - "author_name": "Ajay Bhasin", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Joseph M Feinglass", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Steven M Belknap", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Michael P Angarone", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Elaine R Cohen", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Jeffrey H Barsuk", - "author_inst": "Northwestern University Feinberg School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.08.19.20178376", "rel_title": "Preventing disease after exposure to COVID-19 using hydroxychloroquine: A summary of a protocol for exploratory re-analysis of age and time-nuanced effects.", @@ -1198846,6 +1195310,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.24.20155713", + "rel_title": "In-house assembled protective devices in laboratory safety against SARS-nCoV-2 in clinical biochemistry laboratory of a COVID dedicated hospital", + "rel_date": "2020-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20155713", + "rel_abs": "Health Care Workers (HCWs) of diagnostic laboratory handling COVID positive samples are at risk and need to take protective measures. Many protective materials were not available when the pandemic reached India forcing laboratory managers to take innovative measures to protect the laboratory staffs. We made face shields from OHP sheets and substitute of biosafety cabinets from cardboard boxes fitted with hypochlorite spraying devices. Here we present if these two in-house developed safety devices when incorporated in standard operating procedure (SOP) of laboratory safety were effective in clinical biochemistry laboratory of dedicated COVID hospitals. We assessed contamination of laboratory surfaces (n=6) and rate of SARS-nCov-2 positivity from their nasal and throat swab by RT-PCR among laboratory personnel (n=18) after 14 days of their use along with other routine safety devices like use of gloves, surgical masks, OT gowns etc. These HCWs were checked regularly for signs and symptoms of COVID-19 and none had any signs and symptoms during these 14days. The SARS-nCov-2 test report was negative for the staff members and no surface contamination was detected. We conclude that innovative and cost effective protective devices can be built in-house with locally available resources and are effective in preventing the spread of COVID 19 among the staff working in clinical biochemistry laboratories. Laboratory managers in resource scarce areas need to be innovative to face such sudden safety challenges like COVID-19 pandemic.\n\nThe highlight of the manuscript areO_LIStrengthening the Basics Approaches to protect the lab personnel in dedicated COVID hospital of Low-Resource Settings.\nC_LIO_LIDesigned and developed in-house standard operating procedure (SOP) to fill the gap and evaluate the effect in dedicated COVID-19 hospitals.\nC_LIO_LIInnovative protective devices made from OHP sheets and cardboard boxes fitted with hypochlorite spraying devices as alternatives to biosafety cabinets on contamination of laboratory surfaces.\nC_LIO_LIPerformance of the devices were clinically validated and it can be used as alternative in low resources settings.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Abhishek Dubey", + "author_inst": "Department of Biochemistry, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + }, + { + "author_name": "Aastha Bansal", + "author_inst": "Department of Biochemistry, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + }, + { + "author_name": "Subash Chandra Sonkar", + "author_inst": "Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India-110002" + }, + { + "author_name": "Binita Goswami", + "author_inst": "Department of Biochemistry, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + }, + { + "author_name": "Naina Makwane", + "author_inst": "Department of Biochemistry, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + }, + { + "author_name": "Vikas Manchanda", + "author_inst": "Department of Microbiology, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + }, + { + "author_name": "Bidhan Chandra Koner", + "author_inst": "Department of Biochemistry, Maulana Azad Medical College & Associated Hospitals New Delhi- 110002" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.24.20180695", "rel_title": "Parameter Estimation of COVID-19 Pandemic Model with Self Protection Behavior Changes", @@ -1200073,61 +1196580,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.24.20168955", - "rel_title": "Risk factors for outbreaks of COVID-19 in care homes following hospital discharge: a national cohort analysis", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20168955", - "rel_abs": "BackgroundAdult residential and nursing care homes are settings in which older and often vulnerable people live in close proximity. This population experiences a higher proportion of respiratory and gastrointestinal illnesses than the general population and has been shown to have a high morbidity and mortality in relation to COVID-19.\n\nMethodsWe examined 3,115 hospital discharges to 1,068 Welsh adult care homes and the subsequent outbreaks of COVID-19 occurring over an 18 week period between 22 February and 27 June 2020. A Cox proportional hazards regression model was used to assess the impact of time-dependent exposure to hospital discharge on the incidence of the first known outbreak, over a window of 7-21 days after discharge, and adjusted for care home characteristics, including size, type of provision and health board.\n\nResultsA total of 330 homes experienced an outbreak of COVID-19, and 544 homes received a discharge from hospital over the study period. The exposure to discharge from hospital was not associated with a significant increase in the risk of a new outbreak (hazard ratio 1{middle dot}15, 95% CI 0{middle dot}89, 1{middle dot}47, p = 0{middle dot}29) after adjusting for care home characteristics. Care home size was by far the most significant predictor. Hazard ratios (95% CI) in comparison to homes of <10 residents were: 3{middle dot}40 (1{middle dot}99, 5{middle dot}80) for 10-24 residents; 8{middle dot}25 (4{middle dot}93, 13{middle dot}81) for 25-49 residents; and 17{middle dot}35 (9{middle dot}65, 31{middle dot}19) for homes of 50+ residents. When stratified for care home size, the outbreak rates were similar for periods when homes were exposed to a hospital discharge, in comparison to periods when homes were unexposed.\n\nConclusionOur analyses showed that large homes were at considerably greater risk of outbreaks throughout the epidemic, and after adjusting for care home size, a discharge from hospital was not associated with a significant increase in risk.\n\nResearch in contextO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LICare home populations experience more respiratory outbreaks than the general population1 and older people have been more severely affected by COVID-19, with a case fatality proportion of 2{middle dot}3% overall but 8% in those aged 70-79 and 14{middle dot}8% in those aged over 802\nC_LIO_LIEvidence and modelling suggested that up to half of all COVID-19 fatalities could come from the care home population3 and that testing prior to hospital discharge was not always available or undertaken9\nC_LIO_LIType and use of PPE6 and the number of staff employed can have an impact on care home outbreaks of COVID-196,7\nC_LI\n\nWhat this study addsO_LIOur analysis found no effect of hospital discharges on care home outbreaks once care home size had been adjusted for. In line with previous studies, larger care homes were much more likely to experience an outbreak\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Chris Emmerson", - "author_inst": "Public Health Wales" - }, - { - "author_name": "James P Adamson", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Drew Turner", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Mike B Gravenor", - "author_inst": "Swansea University" - }, - { - "author_name": "Jane Salmon", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Simon Cottrell", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Victoria Middleton", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Buffy Thomas", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Brendan Mason", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Chris J Williams", - "author_inst": "Public Health Wales" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.26.267831", "rel_title": "SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution", @@ -1201016,6 +1197468,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.22.20179929", + "rel_title": "SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20179929", + "rel_abs": "BackgroundDevelopment of strategies for mitigating the severity of COVID-19 is now a top global public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions such as social distancing, self-isolation, tracing and quarantine, wearing facial masks/ personal protective equipment.\n\nMethodsWe developed an individual-based model for COVID-19 transmission among healthcare workers in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan in a Bayesian framework. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss.\n\nResultsWe estimated that work-related stress increases susceptibility to COVID-19 infection among healthcare workers by 52% (90% Credible Interval (CrI): 16.4% - 93.0%). The use of high efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% CrI: 73.1% - 85.7%) and 87% (CrI: 80.0% - 92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. A strict quarantine policy with the isolation of symptomatic cases and a high fraction of pre-symptomatic/ asymptomatic cases (via contact tracing or high test rate), could only prolong outbreak duration with minimal impact on the outbreak size. Our results indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation.\n\nConclusionsOur analysis shows that a COVID-19 outbreak in a hospitals non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qimin Huang", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Anirban Mondal", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Xiaobing Jiang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Mary Ann Horn", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Fei Fan", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Peng Fu", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Xuan Wang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Hongyang Zhao", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Martial Ndeffo-Mbah", + "author_inst": "Texas A&M University" + }, + { + "author_name": "David Gurarie", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.21.20179358", "rel_title": "The analysis of the long-term impact of SARS-CoV-2 on the cellular immune system in individuals recovering from COVID-19 reveals a profound NKT cell impairment", @@ -1201715,45 +1198222,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.24.20180638", - "rel_title": "Evaluation of the current therapeutic approaches for COVID-19: a meta-analysis", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180638", - "rel_abs": "Background and rationaleLimited data on the efficacy and safety of currently applied COVID-19 therapeutics and their impact on COVID-19 outcomes have raised additional concern.\n\nAim and MethodsWe estimated the impact of the current treatments on the efficacy and safety of COVID-19 by a meta-analysis. The comprehensive search included studies reporting clinical features and treatment strategies published from January 21, 2020, to May 15, 2020.\n\nResultsWe included 52 studies that involved 13,966 COVID-19 patients. We found that the most prevalent treatments were antivirals (proportion: 0.74, 95% CI1: [0.65, 0.83]) and antibiotics (proportion: 0.73, 95% CI: [0.62, 0.83]). The COVID-19 severity increased among patients taking glucocorticoids (risk ratio (RR)2 = 1.71, 95% CI: [1.06, 2.76]) or immunoglobulins (RR = 3.83, 95% CI: [1.27, 11.53]), and renal replacement therapy (RRT) and glucocorticoids increased the length of ICU stay (RRT3: RR = 11.89, 95% CI: [3.26, 43.39]; glucocorticoids: RR = 3.10, 95% CI: [1.52, 6.29]). The COVID-19 severity and mortality increased among patients taking tocilizumab (severity: F = 25.53, P = 0.02; mortality: F4 = 19.37, P = 0.02). The most effective treatment was the combination of arbidol with lopinavir/ritonavir compared with placebo (mean difference = 0.5, 95% CI [-0.60, 1.66]), and the safest combination was remdesivir and lopinavir/ritonavir (RR = 0.78, 95% CI [0.32, 1.91]).\n\nConclusionglucocorticoids, immunoglobulins, RRT, and tocilizumab might worsen COVID-19 outcomes, and themost effective and safest treatment strategy for COVID-19 is the combination of different antivirals.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zeinab Abdelrahman", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Qian Liu", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Shanmei Jiang", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Mengyuan Li", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Yue Zhang", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Xiaosheng Wang", - "author_inst": "China Pharmaceutical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.22.20180042", "rel_title": "Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection", @@ -1202645,6 +1199113,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.24.265645", + "rel_title": "SARS-CoV-2 3CLpro Whole Human Proteome Cleavage Prediction and Enrichment/Depletion Analysis", + "rel_date": "2020-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.265645", + "rel_abs": "A novel coronavirus (SARS-CoV-2) has devastated the globe as a pandemic that has killed more than 1,600,000 people. Widespread vaccination is still uncertain, so many scientific efforts have been directed toward discovering antiviral treatments. Many drugs are being investigated to inhibit the coronavirus main protease, 3CLpro, from cleaving its viral polyprotein, but few publications have addressed this proteases interactions with the host proteome or their probable contribution to virulence. Too few host protein cleavages have been experimentally verified to fully understand 3CLpros global effects on relevant cellular pathways and tissues. Here, I set out to determine this proteases targets and corresponding potential drug targets. Using a neural network trained on cleavages from 388 coronavirus proteomes with a Matthews correlation coefficient of 0.983, I predict that a large proportion of the human proteome is vulnerable to 3CLpro, with 4,460 out of approximately 20,000 human proteins containing at least one putative cleavage site. These cleavages are nonrandomly distributed and are enriched in the epithelium along the respiratory tract, brain, testis, plasma, and immune tissues and depleted in olfactory and gustatory receptors despite the prevalence of anosmia and ageusia in COVID-19 patients. Affected cellular pathways include cytoskeleton/motor/cell adhesion proteins, nuclear condensation and other epigenetics, host transcription and RNAi, ribosomal stoichiometry and nascent-chain detection and degradation, coagulation, pattern recognition receptors, growth factors, lipoproteins, redox, ubiquitination, and apoptosis. This whole proteome cleavage prediction demonstrates the importance of 3CLpro in expected and nontrivial pathways affecting virulence, lead me to propose more than a dozen potential therapeutic targets against coronaviruses, and should therefore be applied to all viral proteases and subsequently experimentally verified.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Lucas Prescott", + "author_inst": "N/A" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.08.24.265827", "rel_title": "Unique mutational changes in SARS-CoV2 genome of different state of India", @@ -1203624,157 +1200111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.21.20177246", - "rel_title": "Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20177246", - "rel_abs": "Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19, and this GWAS benefits from the larger sample size to provide new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, we recommend repeatedly collecting data of disease-related symptoms.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Irene V van Blokland", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica" - }, - { - "author_name": "Pauline Lanting", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - }, - { - "author_name": "Anil PS Ori", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and University of Groningen, University Medica" - }, - { - "author_name": "Judith M Vonk", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands" - }, - { - "author_name": "Robert CA Warmerdam", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - }, - { - "author_name": "Johanna C Herkert", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - }, - { - "author_name": "Floranne Boulogne", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - }, - { - "author_name": "Annique Claringbould", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Structural Computational Biology unit, EMB" - }, - { - "author_name": "Esteban A Lopera-Maya", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - }, - { - "author_name": "Meike Bartels", - "author_inst": "Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC" - }, - { - "author_name": "Jouke-Jan Hottenga", - "author_inst": "Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands" - }, - { - "author_name": "Andrea Ganna", - "author_inst": "Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland" - }, - { - "author_name": "Juha Karjalainen", - "author_inst": "Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA and Analytic and Tra" - }, - { - "author_name": "- Lifelines COVID-19 cohort study", - "author_inst": "" - }, - { - "author_name": "- The COVID-19 Host Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Caroline Hayward", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Chloe Fawns-Ritchie", - "author_inst": "Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ" - }, - { - "author_name": "Archie Campbell", - "author_inst": "Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "David Porteous", - "author_inst": "Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Elizabeth T Cirulli", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Kelly M Schiabor Barrett", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Stephen Riffle", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Alexandre Bolze", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Simon White", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Francisco Tanudjaja", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Xueqing Wang", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Jimmy M Ramirez III", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Yan Wei Lim", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "James T Lu", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Nicole L Washington", - "author_inst": "Helix, 101 S Ellsworth Ave Suite 350, San Mateo, California 94401, USA" - }, - { - "author_name": "Eco JC de Geus", - "author_inst": "Department of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands and Amsterdam Public Health research institute, Amsterdam UMC" - }, - { - "author_name": "Patrick Deelen", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands and Department of Genetics, University Medical" - }, - { - "author_name": "H Marike Boezen", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands" - }, - { - "author_name": "Lude H Franke", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.08.21.20166355", "rel_title": "Platelet-to-lymphocyte ratio (PLR), a novel biomarker to predict the severity of COVID-19 patients: a systematic review and meta-analysis", @@ -1204439,6 +1200775,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.21.20179499", + "rel_title": "The effect of BMI and physical activity levels on the duration of symptomatic days with Covid-19 infection", + "rel_date": "2020-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20179499", + "rel_abs": "Regular exercise is known to boost immunity, increase immune response to fight infection, as well as speeding up recovery times and healing processes. This study seeks to assess if exercising regularly pre-SARS-CoV-2 (COVID-19) and/or BMI status has an effect on recovery time.\n\nA total of 215 people infected with COVD-19 from the Kingdom of Saudi Arabia took part in this study (age 36{+/-}16 years, mass 72{+/-}15 kg, stature 166{+/-}11 cm). Only 10 patients were physically active and fulfil WHO physical activity requirement (Age 30{+/-}7 years, Mass 77{+/-}9 kg, Stature 176{+/-}1 cm).\n\nThere was a significant difference in recovery time between active and inactive patients (P = 0.00) with active patients recovery 2.7 times faster than inactive patients. Active patients showed a lower BMI level (p = 0.043).\n\nAnthropometric measurement characteristics and the fitness level could be used in decision making scenarios for the estimation of the risk of complications in patients with COVID-19.\n\nNoveltyO_LICovid-19 physical active patients shows faster recovery time.\nC_LIO_LIActive patients recorded a BMI of over 25kg/m2, recovered faster than those inactive patients with similar BMIs.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Boukhemis Boukelia", + "author_inst": "Hull university" + }, + { + "author_name": "Abdulazeem S S Alataibi", + "author_inst": "Al Qasseem University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.21.20179283", "rel_title": "Correlation of National and Healthcare Workers COVID-19 Infection Data; Implications for Large-scale Viral Testing Programs", @@ -1205206,49 +1201565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.20.20178798", - "rel_title": "Dynamic causal modeling of the COVID-19 pandemic in northern Italy predicts possible scenarios for the second wave", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178798", - "rel_abs": "The COVID-19 pandemic has sparked an intense debate about the factors underlying the dynamics of the outbreak. Mitigating virus spread could benefit from reliable predictive models that inform effective social and healthcare strategies. Crucially, the predictive validity of these models depends upon incorporating behavioral and social responses to infection that underwrite ongoing social and healthcare strategies. Formally, the problem at hand is not unlike the one faced in neuroscience when modelling brain dynamics in terms of the activity of a neural network: the recent COVID-19 pandemic develops in epicenters (e.g. cities or regions) and diffuses through transmission channels (e.g., population fluxes). Indeed, the analytic framework known as \"Dynamic Causal Modeling\" (DCM) has recently been applied to the COVID-19 pandemic, shedding new light on the mechanisms and latent factors driving its evolution. The DCM approach rests on a time-series generative model that provides -- through Bayesian model inversion and inference -- estimates of the factors underlying the progression of the pandemic. We have applied DCM to data from northern Italian regions, which were the first areas in Europe to contend with the COVID-19 outbreak. We used official data on the number of daily confirmed cases, recovered cases, deaths and performed tests. The model -- parameterized using data from the first months of the pandemic phase -- was able to accurately predict its subsequent evolution (including social mobility, as assessed through GPS monitoring, and seroprevalence, as assessed through serologic testing) and revealed the potential factors underlying regional heterogeneity. Importantly, the model predicts that a second wave could arise due to a loss of effective immunity after about 7 months. This second wave was predicted to be substantially worse if outbreaks are not promptly isolated and contained. In short, dynamic causal modelling appears to be a reliable tool to shape and predict the spread of the COVID-19, and to identify the containment and control strategies that could efficiently counteract its second wave, until effective vaccines become available.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniela Gandolfi", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Giuseppe Pagnoni", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Tommaso Filippini", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Alessia Goffi", - "author_inst": "TerraAria" - }, - { - "author_name": "Marco Vinceti", - "author_inst": "University of Modena and Reggio Emilia" - }, - { - "author_name": "Egidio Ugo D'Angelo", - "author_inst": "University of Pavia" - }, - { - "author_name": "Jonathan Mapelli", - "author_inst": "University of Modena and Reggio Emilia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.20.20178822", "rel_title": "COVID-19 Risk Perception Among U.S. Adults: Changes from February to May 2020", @@ -1206045,6 +1202361,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.18.20177691", + "rel_title": "Genetically-predicted vitamin D status, ambient UVB during the pandemic and COVID-19 risk in UK Biobank: Mendelian Randomisation study", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177691", + "rel_abs": "A growing body of evidence shows that poor vitamin D status has been associated with an increased susceptibility to viral and bacterial respiratory infections. In this study, we aimed to examine the association between vitamin D and COVID-19 risk and outcomes, and to explore potential causal effects. We used logistic regression to identify associations between different vitamin D variables (25-hydroxyvitamin D concentration (25-OHD), ambient UVB and genetically-predicted 25-OHD concentrations) and COVID-19 (risk of infection, hospitalisation and death) in 495,780 participants from UK Biobank. We subsequently performed a Mendelian Randomisation (MR) study to test if there was any causal effect. In total, 1,746 COVID-19 cases and 399 COVID-19 deaths occurred between March and June 2020. We found significant inverse associations between COVID-19 infection and 25-OHD in univariable models, but these associations were non-significant after adjustment for confounders. Ambient UVB was strongly and inversely associated with hospitalization and death. Although the main MR analysis showed that genetically-predicted vitamin D levels were not causally associated with COVID-19 risk, MR sensitivity analysis using weighted mode method indicated a potential causal effect (OR=0.72, 95% CI:0.53-0.98; P=0.041). In conclusion, our study found suggestive evidence of association between vitamin D and the risk or severity of COVID-19 but further studies are needed.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Xue Li", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University" + }, + { + "author_name": "Jos van Geffen", + "author_inst": "Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands" + }, + { + "author_name": "Michiel van Weele", + "author_inst": "Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands" + }, + { + "author_name": "Xiangrui Meng", + "author_inst": "Vanke School of public Health,Tsinghua University" + }, + { + "author_name": "XIAOMENG ZHANG", + "author_inst": "Usher Institute" + }, + { + "author_name": "Yazhou He", + "author_inst": "Centre for Global Health, Usher Institute, University of Edinburgh" + }, + { + "author_name": "Maria Timofeeva", + "author_inst": "DIAS, Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark" + }, + { + "author_name": "Harry Campbell", + "author_inst": "Centre for Global Health, Usher Institute, University of Edinburgh" + }, + { + "author_name": "Malcolm G Dunlop", + "author_inst": "Institute of Genetics and Molecular Medicine" + }, + { + "author_name": "Lina Zgaga", + "author_inst": "Department of Public Health and Primary Care, Institute of Population Health, Trinity College Dublin" + }, + { + "author_name": "Evropi Theodoratou", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.18.20174540", "rel_title": "3D Printed Snorkel Mask Adapter for Failed N95 Fit Tests and PPE Shortages", @@ -1206804,33 +1203179,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.19.20178343", - "rel_title": "The Effects of Coronavirus Victimization Distress and Coronavirus Racial Bias on Mental Health Among Black, Indigenous and Latinx Young Adults in the United States", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178343", - "rel_abs": "RationaleU.S. Racial/ethnic minorities have been disproportionately impacted by the COVID-19 pandemic in rates of infection and morbidity. Pre-pandemic racial discrimination has been associated with depression and general anxiety. However, the effect of Coronavirus specific forms of discrimination on mental health have not been examined. This study assessed the effect of previously identified social determinants of mental health and COVID-19 specific victimization and racial bias beliefs on depression and anxiety among young adults of color in the U.S.\n\nMethodsA national online survey of 399 AIAN, Asian, Black, and Latinx adults (18 - 25 years) included demographic variables, COVID-19 health risks, and standardized measures of depression, anxiety, Coronavirus related victimization distress and perceptions of Coronavirus-related racial bias across a range of contexts.\n\nResultsEmployment, financial and prescription insecurity, COVID-19 health risks, Coronavirus victimization distress and Coronavirus racial bias beliefs were positively correlated with depression and anxiety. Scores on the Coronavirus racial bias scale were significantly higher among Asian and Black respondents. Structural equation modeling controlling for race/ethnicity and demographic variables indicated perceived Coronavirus racial bias mediated the effect of Coronavirus victimization distress on both mental health indices.\n\nConclusionResults suggest the COVID-19 pandemic has created new pathways to mental health disparities among young adults of color by reversing formerly protective factors such as employment, and by exacerbating structural and societal inequities linked to race. Findings highlight the necessity of creating mental health services tailored to the specific needs of racial/ethnic minorities during the current and future health crises.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Celia B. Fisher", - "author_inst": "Fordham University" - }, - { - "author_name": "Xiangyu Tao", - "author_inst": "Fordham University" - }, - { - "author_name": "Tiffany Yip", - "author_inst": "Fordham University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.08.19.20177980", "rel_title": "Prevalence and correlation of symptoms and comorbidities in COVID-19 patients: A systematic review and meta-analysis", @@ -1207447,6 +1203795,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.19.20178368", + "rel_title": "Inhaled corticosteroids downregulate SARS-CoV-2-related gene expression in COPD: results from a RCT", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178368", + "rel_abs": "RationaleChronic obstructive pulmonary disease (COPD) is a risk factor for severe COVID-19. Inhaled corticosteroids (ICS) are commonly prescribed for the prevention of acute exacerbations in people with COPD, but their use is associated with increased risk of respiratory infections. The effects of ICS on SARS-CoV-2 susceptibility or COVID-19 severity are currently unknown.\n\nObjectivesTo determine the effects of ICS treatment on the bronchial epithelial cell expression of key SARS-CoV-2-related genes in volunteers with COPD.\n\nMethodsWe performed a randomized, open-label, parallel treatment trial of 12 weeks treatment with ICS in combination with long-acting beta-agonist (formoterol/budesonide 12/400 {micro}g twice daily or salmeterol/fluticasone propionate 25/250 {micro}g twice daily), or treatment with LABA only (formoterol 12 {micro}g twice daily), in volunteers with mild to very severe COPD. We obtained bronchial epithelial cell samples via bronchoscopy before and after treatment, and determined transcriptome-wide gene expression by RNA sequencing.\n\nMain Results63 volunteers were randomized to receive treatment. Compared to formoterol alone, formoterol/budesonide treatment decreased the expression of the SARS-CoV-2 receptor gene ACE2 and the host cell protease gene ADAM17. These genes were highly co-expressed with innate immune response genes, particularly those of the type I interferon and anti-viral response pathways, which also tended to decrease following ICS treatment.\n\nConclusionsThis is the first randomized controlled trial to show that ICS affect the expression of key SARS-CoV-2-related genes in COPD. Their relation to important anti-viral response genes may have critical implications for SARS-CoV-2 susceptibility or COVID-19 severity in this vulnerable population.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Stephen Milne", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation and Division of Respiratory Medicine" + }, + { + "author_name": "Xuan Li", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation" + }, + { + "author_name": "Chen Xi Yang", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation" + }, + { + "author_name": "Ana I Hernandez Cordero", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation" + }, + { + "author_name": "Fernando Sergio Leitao Filho", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation" + }, + { + "author_name": "Cheng Wei Tony Yang", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation and Providence Health Care - Providence Airway Centre" + }, + { + "author_name": "Tawimas Shaipanich", + "author_inst": "University of British Columbia Division of Respiratory Medicine" + }, + { + "author_name": "Stephan F van Eeden", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation and Division of Respiratory Medicine" + }, + { + "author_name": "Janice M Leung", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation and Division of Respiratory Medicine" + }, + { + "author_name": "Stephen Lam", + "author_inst": "BC Cancer Research Centre Department of Integrative Oncology and University of British Columbia Division of Respiratory Medicine" + }, + { + "author_name": "Don D Sin", + "author_inst": "University of British Columbia Centre for Heart Lung Innovation and Division of Respiratory Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.08.20.20178525", "rel_title": "Clinical Characteristics and Outcomes of Diabetic COVID-19 patients in Kuwait", @@ -1208438,57 +1204845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.18.20177071", - "rel_title": "Use, reuse or discard: quantitatively defined variance in N95 respirator integrity following vaporized hydrogen peroxide decontamination during the COVID-19 pandemic", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177071", - "rel_abs": "BackgroundCOVID-19 has stretched the ability of many institutions to supply needed personal protective equipment, especially N95 respirators. N95 decontamination and reuse programs provide one potential solution to this problem. Unfortunately, a comprehensive evaluation of the effects of decontamination on the integrity of various N95 models using a quantitative fit test (QTFT) approach is lacking.\n\nAims1) To investigate the effects of up to eight rounds of vaporized H2O2 (VHP) decontamination on the integrity of N95 respirators currently in use in a hospital setting. 2) To examine if N95 respirators worn by one user can adapt to the face shape of a second user with no compromise of integrity following VHP decontamination.\n\nMethodsThe PortaCount Pro+ Respirator Fit Tester Model 8038 was used to quantitatively define the integrity, measured by fit, of N95 respirators following decontamination with VHP.\n\nFindingsThere was an observable downward trend in the integrity of Halyard Fluidshield 46727 N95 respirators throughout eight cycles of decontamination with VHP. The integrity of 3M 1870 N95 respirators was significantly reduced after the respirator was worn, decontaminated with VHP, and then quantitatively fit tested on a second user. Furthermore, we uncovered inconsistencies between qualitative fit test and QTFT results that may have strong implications on the fit testing method used by institutions.\n\nConclusionsOur data revealed variability in the integrity of different N95 models after VHP decontamination and exposed potential limitations of N95 decontamination and reuse programs.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Carly Levine", - "author_inst": "Rutgers University" - }, - { - "author_name": "Courtney Grady", - "author_inst": "Rutgers University" - }, - { - "author_name": "Thomas Block", - "author_inst": "Rutgers University" - }, - { - "author_name": "Harry Hurley", - "author_inst": "Rutgers University" - }, - { - "author_name": "Riccardo Russo", - "author_inst": "Rutgers University" - }, - { - "author_name": "Blas Peixoto", - "author_inst": "Rutgers University" - }, - { - "author_name": "Alexis Frees", - "author_inst": "Rutgers University" - }, - { - "author_name": "Alejandro Ruiz", - "author_inst": "Rutgers University" - }, - { - "author_name": "David Alland", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20176743", "rel_title": "Breastmilk; a source of SARS-CoV-2 specific IgA antibodies", @@ -1209293,6 +1205649,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.20.259242", + "rel_title": "In Silico Modeling of Virus Particle Propagation and Infectivity along the Respiratory Tract: A Case Study for SARS-COV-2", + "rel_date": "2020-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.259242", + "rel_abs": "Respiratory viruses including Respiratory syncytial virus (RSV), influenza virus and cornaviruses such as Middle Eastern respiratory virus (MERS) and SARS-CoV-2 infect and cause serious and sometimes fatal disease in thousands of people annually. It is critical to understand virus propagation dynamics within the respiratory system because new insights will increase our understanding of virus pathogenesis and enable infection patterns to be more predictable in vivo, which will enhance targeting of vaccines and drug delivery. This study presents a computational model of virus propagation within the respiratory tract network. The model includes the generation network branch structure of the respiratory tract, biophysical and infectivity properties of the virus, as well as air flow models that aid the circulation of the virus particles. The model can also consider the impact of the immune response aim to inhibit virus replication and spread. The model was applied to the SARS-CoV-2 virus by integrating data on its life-cycle, as well as density of Angiotensin Converting Enzyme (ACE2) expressing cells along the respiratory tract network. Using physiological data associated with the respiratory rate and virus load that is inhaled, the model can improve our understanding of the concentration and spatiotemporal dynamics of virus.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Dixon Vimalajeewa", + "author_inst": "Waterford Institute ofTechnology" + }, + { + "author_name": "Sasitharan Balasubramaniam", + "author_inst": "Waterford Institute of technology" + }, + { + "author_name": "Donagh P Berry", + "author_inst": "Teagasc, Animal & Grassland Research and Innovation" + }, + { + "author_name": "Gerald Barry", + "author_inst": "University Collage Dublin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.08.20.259937", "rel_title": "SARS-CoV-2 infects brain choroid plexus and disrupts the blood-CSF-barrier", @@ -1210112,61 +1206499,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20176982", - "rel_title": "Look before diving into pooling of SARS-CoV-2 samples on high throughput analyzers", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176982", - "rel_abs": "Given the unprecedented demand for SARS-CoV-2 testing during the COVID-19 pandemic, the benefits of specimen pooling have recently been explored. As previous studies were limited to mathematical modeling or testing on low throughput PCR instruments, this study aimed to assess pooling on high throughput analyzers. To assess the impact of pooling, SARS-CoV-2 dilutions were performed at varying pool depths (i.e. 1:2, 1:4, and 1:8) into test-negative nasopharyngeal or oropharynx/anterior nares swabs matrix. Testing was evaluated on the automated Roche Cobas 6800 system, or the Roche MagNApure LC 2.0 or MagNAPure 96 instruments paired with a laboratory-developed test using a 96-well PCR format. The frequency of detection in specimens with low viral loads was evaluated using archived specimens collected throughout the first pandemic wave. The proportion of detectable results per pool depths was used to estimate the potential impact. In addition, workflow at the analytical stage, and pre-and post-stages of testing were also considered. The current study estimated that pool depths of 1:2, 1:4, and 1:8 would have allowed the detection of 98.3%, 96.0%, and 92.6% of positive SARS-CoV-2 results identified in the first wave of the pandemic in Nova Scotia. Overall, this study demonstrated that pooling on high throughput instrumentation can dramatically increase the overall testing capacity to meet increased demands, with little compromising to sensitivity at low pool depths. However, the human resources required at the pre-analytical stage of testing is a particular challenging to achieve.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jason J LeBlanc", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada." - }, - { - "author_name": "Glenn Patriquin", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Janice Pettipas", - "author_inst": "Nova Scotia Provincial Public Health Laboratory Network (PPHLN), Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Michelle Warhuus", - "author_inst": "Canadian Center for Vaccinology (CCfV), Dalhousie University, IWK Health Centre, and Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Darren Sarty", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Colleen Jackson", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Charles Heinstein", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "James MacDonald", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "David Haldane", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Todd F Hatchette", - "author_inst": "Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20168807", "rel_title": "Laboratory biomarkers associated with COVID-19 severity and management.", @@ -1210919,6 +1207251,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.18.20177444", + "rel_title": "Environmental risk factors of airborne viral transmission: Humidity, Influenza and SARS-CoV-2 in the Netherlands", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177444", + "rel_abs": "ObjectiveThe relationship between specific humidity and influenza/SARS-CoV-2 in the Netherlands is evaluated over time and at regional level.\n\nDesignParametric and non-parametric correlation coefficients are calculated to quantify the relationship between humidity and influenza, using five years of weekly data. Bayesian spatio-temporal models--with a Poisson and a Gaussian likelihood--are estimated to find the relationship between regional humidity and the daily cases of SARS-CoV-2 in the municipalities and provinces of the Netherlands.\n\nResultsAn inverse (negative) relationship is observed between specific humidity and the incidence of influenza between 2015 and 2019. The space-time analysis indicates that an increase of specific humidity of one gram of water vapor per kilogram of air (1 g/kg) is related to a reduction of approximately 5% in the risk of COVID-19 infections.\n\nConclusionsThe increase in humidity during the outbreak of the SARS-CoV-2 in the Netherlands helped to reduce the risk of regional COVID-19 infections. Public policies that promote higher levels of specific humidification--above 6 g/Kg--can lead to significant reductions in the spread of respiratory viruses, such as influenza and SARS-CoV-2.\n\nSummary BoxO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LIEnvironmental conditions have been related to the airborne transmission of respiratory viruses.\nC_LIO_LIPrevious observational studies have found an inverse correlation between humidity and the spread of SARS-CoV-2.\nC_LI\n\nWhat does this study add?O_LIWe analyzed the relation between specific humidity and airborne virus transmission using data with a higher temporal and spatial resolution.\nC_LIO_LISpatio-temporal risk estimates of SARS-CoV-2 are obtained after controlling for humidity levels at sub-national level in the Netherlands.\nC_LIO_LIOur results indicate that the increase of specific humidity during the outbreak of the SARS-CoV-2 helped to reduce the risk of regional COVID-19 cases in the Netherlands. Specifically, an increase of specific humidity of one gram of water vapor per kilogram of air (1 g/kg) is related to a reduction of approximately 5% in the risk of COVID-19 cases.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Edsard Ravelli", + "author_inst": "Ravelli Management" + }, + { + "author_name": "Rolando Gonzales Martinez", + "author_inst": "Universitetet i Agder" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.18.20177147", "rel_title": "OxCOVID19 Database: a multimodal data repository for better understanding the global impact of COVID-19", @@ -1211890,169 +1208245,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.08.19.253369", - "rel_title": "A rapid and efficient screening system for neutralizing antibodies and its application for the discovery of potent neutralizing antibodies to SARS-CoV-2 S-RBD", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.253369", - "rel_abs": "Neutralizing antibodies (Abs) have been considered as promising therapeutics for the prevention and treatment of pathogens. After the outbreak of COVID-19, potent neutralizing Abs to SARS-CoV-2 were promptly developed, and a few of those neutralizing Abs are being tested in clinical studies. However, there were few methodologies detailly reported on how to rapidly and efficiently generate neutralizing Abs of interest. Here, we present a strategically optimized method for precisive screening of neutralizing monoclonal antibodies (mAbs), which enabled us to identify SARS-CoV-2 receptor-binding domain (RBD) specific Abs within 4 days, followed by another 2 days for neutralization activity evaluation. By applying the screening system, we obtained 198 Abs against the RBD of SARS-CoV-2. Excitingly, we found that approximately 50% (96/198) of them were candidate neutralizing Abs in a preliminary screening of SARS-CoV-2 pseudovirus and 20 of these 96 neutralizing Abs were confirmed with high potency. Furthermore, 2 mAbs with the highest neutralizing potency were identified to block authentic SARS-CoV-2 with the half-maximal inhibitory concentration (IC50) at concentrations of 9.88 ng/ml and 11.13 ng/ml. In this report, we demonstrated that the optimized neutralizing Abs screening system is useful for the rapid and efficient discovery of potent neutralizing Abs against SARS-CoV-2. Our study provides a methodology for the generation of preventive and therapeutic antibody drugs for emerging infectious diseases.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "XiaoJian Han", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yingming Wang", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Shenglong Li", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chao Hu", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Tingting Li", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chenjian Gu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, Fudan University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Meiying Shen", - "author_inst": "Department of Breast Surgery, Harbin Medical University Cancer Hospital" - }, - { - "author_name": "Jianwei Wang", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Jie Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ruixin Wu", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Song Mu", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Fang Gong", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University (CQMU) (YCH)" - }, - { - "author_name": "Qian Chen", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Fengxia Gao", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Jingjing Huang", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yingyi Long", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Feiyang Luo", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Shuyi Song", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Shunhua Long", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yanan Hao", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Luo Li", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yang Wu", - "author_inst": "Fudan University" - }, - { - "author_name": "Wei Xu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, Fudan University" - }, - { - "author_name": "Xia Cai", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, Fudan University" - }, - { - "author_name": "Qingzhu Gao", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Guiji Zhang", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Changlong He", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Kun Deng", - "author_inst": "The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Li Du", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yaru Nai", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Wang Wang", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Youhua Xie", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and" - }, - { - "author_name": "Di Qu", - "author_inst": "Fudan University" - }, - { - "author_name": "Ailong Huang", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ni Tang", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Aishun Jin", - "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.19.256800", "rel_title": "Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection", @@ -1212909,6 +1209101,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.18.256776", + "rel_title": "SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells", + "rel_date": "2020-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.256776", + "rel_abs": "Disrupted antiviral immune responses are associated with severe COVID-19, the disease caused by SAR-CoV-2. Here, we show that the 73-amino-acid protein encoded by ORF9c of the viral genome contains a putative transmembrane domain, interacts with membrane proteins in multiple cellular compartments, and impairs antiviral processes in a lung epithelial cell line. Proteomic, interactome, and transcriptomic analyses, combined with bioinformatic analysis, revealed that expression of only this highly unstable small viral protein impaired interferon signaling, antigen presentation, and complement signaling, while inducing IL-6 signaling. Furthermore, we showed that interfering with ORF9c degradation by either proteasome inhibition or inhibition of the ATPase VCP blunted the effects of ORF9c. Our study indicated that ORF9c enables immune evasion and coordinates cellular changes essential for the SARS-CoV-2 life cycle.\n\nOne-sentence summarySARS-CoV-2 ORF9c is the first human coronavirus protein localized to membrane, suppressing antiviral response, resembling full viral infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ana Dominguez Andres", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Yongmei Feng", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Alexandre Rosa Campos", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Jun Yin", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Chih-Cheng Yang", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Brian James", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Rabi Murad", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Hyungsoo Kim", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Aniruddha J Deshpande", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "David E Gordon", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Nevan J Krogan", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Raffaella Pippa", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.08.18.256578", "rel_title": "NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge", @@ -1213772,113 +1210027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.16.20175505", - "rel_title": "Abnormal Upregulation of Cardiovascular Disease Biomarker PLA2G7 Induced by Proinflammatory Macrophages in COVID-19 patients", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175505", - "rel_abs": "BACKGROUNDCoronavirus disease 2019 (COVID-19) triggers distinct patterns of pneumonia progression with multiorgan disease, calling for cell- and/or tissue-type specific host injury markers.\n\nMETHODSAn integrated hypothesis-free single biomarker analysis framework was performed on nasal swabs (n = 484) from patients with COVID-19 in GSE152075. The origin of candidate biomarker was assessed in single-cell RNA data (GSE145926). The candidate biomarker was validated in a cross-sectional cohort (n = 564) at both nucleotide and protein levels.\n\nRESULTSPhospholipase A2 group VII (PLA2G7) was identified as a candidate biomarker in COVID-19. PLA2G7 was predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, PLA2G7 was found in patients with COVID-19 and pneumonia, especially in severe pneumonia, rather than patients suffered mild H1N1 influenza infection. Up to 100% positive rates of PLA2G7 were positively correlated with not only viral loads in patients with COVID-19 but also severity of pneumonia in non-COVID-19 patients. Although Ct values of PLA2G7 in severe pneumonia was significantly lower than that in moderate pneumonia (P = 7.2e-11), no differences were observed in moderate pneumonia with COVID-19 between severe pneumonia without COVID-19 (P = 0.81). Serum protein levels of PLA2G7, also known as lipoprotein-associated phospholipase A2 (Lp-PLA2), were further found to be elevated and beyond the upper limit of normal in patients with COVID-19, especially among the re-positive patients.\n\nCONCLUSIONSWe firstly identified and validated PLA2G7, a biomarker for cardiovascular diseases (CVDs), was abnormally enhanced in COVID-19 patients at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in COVID-19 patients. PLA2G7 could be a hallmark of COVID-19 for monitoring disease progress and therapeutic response.\n\nFUNDINGThis study was supported by grants from China Mega-Projects for Infectious Disease (2018ZX10711001), National Natural Science Foundation of China (82041023).", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Yang LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Yongzhong JIANG", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Yi ZHANG", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Naizhe LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Qiangling YIN", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Linlin LIU", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Xin LV", - "author_inst": "Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University & Jinan Children's Hospital, Jinan 250022, China" - }, - { - "author_name": "Yan LIU", - "author_inst": "Department of Microbiology, School of Basic Medical Science, Anhui Medical University, Hefei 230032, China" - }, - { - "author_name": "Aqian LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Bin FANG", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Jiajia LI", - "author_inst": "The Center for Scientific Research of the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China" - }, - { - "author_name": "Hengping YE", - "author_inst": "Xiantao Center for Disease Control and Prevention, Xiantao 433000, China" - }, - { - "author_name": "Gang YANG", - "author_inst": "Xiangyang Center for Disease Control and Prevention, Xiangyang 441000, China" - }, - { - "author_name": "Xiaoxian CUI", - "author_inst": "Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China" - }, - { - "author_name": "Yang LIU", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Yuanyuan QU", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Chuan LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Jiandong LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Dexin LI", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Shiwen WANG", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - }, - { - "author_name": "Zhongtao GAI", - "author_inst": "Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University & Jinan Children's Hospital, Jinan 250022, China" - }, - { - "author_name": "Faxian ZHAN", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention, Wuhan 430065, China" - }, - { - "author_name": "Mifang LIANG", - "author_inst": "NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and P" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.16.20035691", "rel_title": "COVID-19 ICU and mechanical ventilation patient characteristics and outcomes - A systematic review and meta-analysis", @@ -1214675,6 +1210823,137 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2020.08.18.255935", + "rel_title": "IFITM proteins promote SARS-CoV-2 infection in human lung cells", + "rel_date": "2020-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.255935", + "rel_abs": "Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) are thought to restrict numerous viral pathogens including severe acute respiratory syndrome coronaviruses (SARS-CoVs). However, most evidence comes from single-round pseudovirus infection studies of cells that overexpress IFITMs. Here, we verified that artificial overexpression of IFITMs blocks SARS-CoV-2 infection. Strikingly, however, endogenous IFITM expression was essential for efficient infection of genuine SARS-CoV-2 in human lung cells. Our results indicate that the SARS-CoV-2 Spike protein interacts with IFITMs and hijacks them for efficient viral entry. IFITM proteins were expressed and further induced by interferons in human lung, gut, heart and brain cells. Intriguingly, IFITM-derived peptides and targeting antibodies inhibited SARS-CoV-2 entry and replication in human lung cells, cardiomyocytes and gut organoids. Our results show that IFITM proteins are important cofactors for SARS-CoV-2 infection of human cell types representing in vivo targets for viral transmission, dissemination and pathogenesis and suitable targets for therapeutic approaches.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Caterina Prelli Bozzo", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Rayhane Nchioua", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Meta Volcic", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Jana Krueger", + "author_inst": "Department of Internal Medicine I, Ulm University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Sandra Heller", + "author_inst": "Department of Internal Medicine I, Ulm University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Christina Martina Stuerzel", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Carina Conzelmann", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Janis A Mueller", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Fabian Zech", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Desiree Schuetz", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Lennart Koepke", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Elisabeth Braun", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Ruediger Gross", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Lukas Wettstein", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Tatjana Weil", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Johanna Weiss", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Daniel Sauter", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Jan Muench", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Federica Diofano", + "author_inst": "Department of Internal Medicine II (Cardiology), Ulm University, 89081 Ulm, Germany" + }, + { + "author_name": "Christine Goffinet", + "author_inst": "Institute of Virology, Campus Charite Mitte, Charite - Universitaetsmedizin Berlin, 10117 Berlin, Germany" + }, + { + "author_name": "Alberto Catanese", + "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm Germany" + }, + { + "author_name": "Michael Schoen", + "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm Germany" + }, + { + "author_name": "Tobias Boeckers", + "author_inst": "Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm Germany" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Institute of Medical Microbiology and Hygiene, Ulm University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Kei Sato", + "author_inst": "Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan." + }, + { + "author_name": "Steffen Just", + "author_inst": "Department of Internal Medicine II (Cardiology), Ulm University, 89081 Ulm, Germany" + }, + { + "author_name": "Alexander Kleger", + "author_inst": "Department of Internal Medicine I, Ulm University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Konstantin Maria Johannes Sparrer", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + }, + { + "author_name": "Frank Kirchhoff", + "author_inst": "Institute for Molecular Virology Ulm, University Medical Centre, 89081 Ulm, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.17.254979", "rel_title": "The effect of whey protein on viral infection and replication of SARS-CoV-2 and pangolin coronavirus in vitro", @@ -1215586,37 +1211865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.16.20175976", - "rel_title": "GIS-based spatial modeling to identify factors affecting COVID-19 incidence rates in Bangladesh", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175976", - "rel_abs": "The outbreak of the COVID-19 pandemic is an unprecedented shock throughout the world which leads to generate a massive social, human, and economic crisis. However, there is a lack of research on geographic modeling of COVID-19 as well as identification of contributory factors affecting the COVID-19 in the context of developing countries. To fulfill the gap, this study aimed to identify the potential factors affecting the COVID-19 incidence rates at the district-level in Bangladesh using spatial regression model (SRM). Therefore, data related to 32 demographic, economic, weather, built environment, health, and facilities related factors were collected and analyzed to explain the spatial variability of this disease incidence. Three global (Ordinary least squares (OLS), spatial lag model (SLM) and spatial error model (SEM)) and one local (geographically weighted regression (GWR)) SRMs were developed in this study. The results of the models showed that four factors significantly affected the COVID-19 incidence rates in Bangladesh. Those four factors are urban population percentage, monthly consumption, number of health workers, and distance from the capital. Among the four developed models, the GWR model performed the best in explaining the variation of COVID-19 incidence rates across Bangladesh with a R2 value of 78.6%. Findings from this research offer a better insight into the COVID-19 situation and would help to develop policies aimed to prevent the future epidemic crisis.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Md. Hamidu Rahman", - "author_inst": "GIS Assistant, Asian Disaster Preparedness Center (ADPC), Dhaka-1206, Bangladesh" - }, - { - "author_name": "Niaz Mahmud Zafri", - "author_inst": "Lecturer, Department of Urban and Regional Planning, Bangladesh University of Engineering and Technology (BUET), Dhaka-1000, Bangladesh" - }, - { - "author_name": "Fajle Rabbi Ashik", - "author_inst": "Research Assistant, BUET-JIDPUS, Bangladesh University of Engineering and Technology (BUET), Bangladesh Dhaka-1000, Bangladesh" - }, - { - "author_name": "Md Waliullah", - "author_inst": "Undergraduate Student, Department of Urban and Regional Planning, Bangladesh University of Engineering and Technology (BUET), Dhaka-1000, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.15.20175562", "rel_title": "Impact of COVID-19 on Primary Care Mental Health Services: A Descriptive, Cross-Sectional Timeseries of Electronic Healthcare Records", @@ -1216269,6 +1212517,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.14.20174961", + "rel_title": "Rates of COVID-19-related Outcomes in Cancer compared to non-Cancer Patients", + "rel_date": "2020-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20174961", + "rel_abs": "Cancer patients are a vulnerable population postulated to be at higher risk for severe COVID-19 infection. Increased COVID-19 morbidity and mortality in cancer patients may be attributable to age, comorbidities, smoking, healthcare exposure, and cancer treatments, and partially to the cancer itself. Most studies to date have focused on hospitalized patients with severe COVID-19, thereby limiting the generalizability and interpretability of the association between cancer and COVID-19 severity. We compared outcomes of SARS-CoV-2 infection in 323 patients enrolled prior to the pandemic in a large academic biobank (n=67 cancer patients and n=256 non-cancer patients). After adjusting for demographics, smoking status, and comorbidities, a diagnosis of cancer was independently associated with higher odds of hospitalization (OR 2.16, 95% CI 1.12-4.18) and 30-day mortality (OR 5.67, CI 1.49-21.59). These associations were primarily driven by patients with active cancer. These results emphasize the critical importance of preventing SARS-CoV-2 exposure and mitigating infection in cancer patients.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lova Sun", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Surya Sanjna", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Anh Le", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Heena Desai", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Abigail Doucette", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Peter Gabriel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Marylyn Ritchie", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Daniel Rader", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ivan Maillard", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Erin Bange", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alexander Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Robert H Vonderheide", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Angela DeMichele", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Anurag Verma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronac Mamtani", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kara N Maxwell", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.08.14.20174805", "rel_title": "The basic reproduction number can be accurately estimated within 14 days after societal lockdown: The early stage of the COVID-19 epidemic in Denmark", @@ -1217216,33 +1213543,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.08.15.250647", - "rel_title": "Sampling SARS-CoV-2 proteomes for predicted CD8 T-cell epitopes as a tool for understanding immunogenic breadth and rationale vaccine design", - "rel_date": "2020-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.15.250647", - "rel_abs": "Predictive models for vaccine design have become a powerful and necessary resource for the expeditiousness design of vaccines to combat the ongoing SARS-CoV-2 global pandemic. Here we use the power of these predicted models to assess the sequence diversity of circulating SARS-CoV-2 proteomes in the context of an individuals CD8 T-cell immune repertoire to identify potential. defined regions of immunogenicity. Using this approach of expedited and rational CD8 T-cell vaccine design, it may be possible to develop a therapeutic vaccine candidate with the potential for both global and local coverage.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jonathan Hare", - "author_inst": "IAVI" - }, - { - "author_name": "David Morrison", - "author_inst": "Bitefirst" - }, - { - "author_name": "Morten Nielsen", - "author_inst": "Technical University of Denmark" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.15.252320", "rel_title": "A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model", @@ -1218067,6 +1214367,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174136", + "rel_title": "Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region", + "rel_date": "2020-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174136", + "rel_abs": "BackgroundThe early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility.\n\nMethodsWe performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region.\n\nResultsWe analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades.\n\nConclusionsWe established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Peter M. Thielen", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Shirlee Wohl", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Thomas Mehoke", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Srividya Ramakrishnan", + "author_inst": "Johns Hopkins University Department of Computer Science" + }, + { + "author_name": "Melanie Kirsche", + "author_inst": "Johns Hopkins University Department of Computer Science" + }, + { + "author_name": "Oluwaseun Falade-Nwulia", + "author_inst": "Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease" + }, + { + "author_name": "Nidia S Trovao", + "author_inst": "National Institutes of Health, Fogarty International Center" + }, + { + "author_name": "Amanda Ernlund", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Craig Howser", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Norah Sadowski", + "author_inst": "Johns Hopkins University, Departments of Biomedical Engineering and Molecular Biology and Genetics" + }, + { + "author_name": "Paul Morris", + "author_inst": "Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology" + }, + { + "author_name": "Mark Hopkins", + "author_inst": "Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology" + }, + { + "author_name": "Matthew Schwartz", + "author_inst": "Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology" + }, + { + "author_name": "Yunfan Fan", + "author_inst": "Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics" + }, + { + "author_name": "Victoria Gniazdowski", + "author_inst": "Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lauren Sauer", + "author_inst": "Johns Hopkins University Department of Emergency Medicine" + }, + { + "author_name": "Michael C Schatz", + "author_inst": "Johns Hopkins University Department of Computer Science" + }, + { + "author_name": "Jared D Evans", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Stuart C Ray", + "author_inst": "Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease" + }, + { + "author_name": "Winston Timp", + "author_inst": "Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics" + }, + { + "author_name": "Heba H Mostafa", + "author_inst": "Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20157222", "rel_title": "Quantifying absolute neutralization titers against SARS-CoV-2 by a standardized virus neutralization assay allows for cross-cohort comparisons of COVID-19 sera", @@ -1219106,41 +1215509,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.14.20174433", - "rel_title": "Stethoscope and Non-Infrared Thermometer Disinfection among Physicians: A Cross-Sectional Study with Implications for the Control of COVID-19", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20174433", - "rel_abs": "BackgroundStethoscopes and non-infrared thermometers are the customary medical equipment used by the physicians on a daily basis, among various patients. With the rise of potential infections in the healthcare facilities and the transmission nature of the current volantly evolving COVID-19, consistent and correct disinfections of these devices after each use should not be pardoned. This study, therefore, describes the level of stethoscope and non-infrared thermometer disinfection practices among physicians and determines its associated factors during the COVID-19 pandemic.\n\nMethodsA nationwide cross-sectional online survey was circulated using an anonymous and self-reporting questionnaire via Google form with a consent form appended to it.\n\nResultsFour hundred twenty-two physicians participated (62.80% medical doctors, 33.65% seniors, and 3.55% residents). The proportion of stethoscope and non-Infrared thermometer disinfections after every use was 13.9% (95%CI: 10.9-17.6) and 20.4% (95%CI: 16.7-24.5), respectively. In adjusted analyses, taking COVID-19 training (Adjusted Odds Ratio [AOR]: 2.52; 95% [Confidence Interval (CI)]: 1.29-4.92) and the availability of stethoscope disinfection materials at the workplace (AOR: 3.03; 95% CI: 1.29-7.10) were significantly increased the odds of stethoscope disinfection after every use. The odds of stethoscope disinfection after every use was significantly decreased for those who reported the use of shared stethoscope (AOR: 0.34; 95% CI: 0.12-0.92). Among the physicians, disinfection after every use was significantly higher in resident physicians compared to those of general practitioners for both stethoscope (AOR: 4.61; 95%CI: 1.29-16.52) and non-Infrared thermometers (AOR: 7.10; 95%CI: 2.30-21.95).\n\nConclusionOnly a wee share of the respondents reported that they have disinfected their stethoscopes and non-infrared thermometers after every use - possibly jeopardizing both patients and clinicians safety, particularly during the COVID-19 pandemic - and these results must be sternly dealt with. Provisions of training and securing constant and available stethoscope disinfection supplies can significantly increase disinfection practices among the physicians after every use. These simple interventions could be replicated by other healthcare facilities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Biniyam Sahiledengle", - "author_inst": "Madda Walabu University Goba Referral hospital, Department of Public Health, Bale-Goba, Ethiopia" - }, - { - "author_name": "Yohannes Tekalegn", - "author_inst": "Madda Walabu University Goba Referral hospital, Department of Public Health, Bale-Goba," - }, - { - "author_name": "Kebebe Bekele", - "author_inst": "Madda Walabu University Goba Referral hospital, Department of Surgery, Bale-Goba, Ethiopia" - }, - { - "author_name": "Abdi Tesemma", - "author_inst": "Madda Walabu University Goba Referral hospital, Department of Surgery, Bale-Goba, Ethiopia" - }, - { - "author_name": "Bruce John Edward Quisido", - "author_inst": "Madda Walabu University Goba Referral hospital, Department of Nursing, Bale-Goba, Ethiopia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.08.13.20174755", "rel_title": "Dynamical balance between the transmission, intervention of COVID-19 and economic development", @@ -1219813,6 +1216181,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.11.20172775", + "rel_title": "Trends in Covid-19 risk-adjusted mortality rates in a single health system", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20172775", + "rel_abs": "Early reports showed high mortality from Covid-19; by contrast, the current outbreaks in the southern and western United States are associated with fewer deaths, raising hope that treatments have improved. However, in Texas for instance, 63% of diagnosed cases are currently under 50, compared to only 52% nationally in March-April. Current demographics in Arizona and Florida are similar. Therefore, whether decreasing Covid-19 mortality rates are a reflection of changing demographics or represent improvements in clinical care is unknown. We assessed outcomes over time in a single health system, accounting for changes in demographics and clinical factors.\n\nMethods\n\nWe analyzed biweekly mortality rates for admissions between March 1 and June 20, 2020 in a single health system in New York City. Outcomes were obtained as of July 14, 2020. We included all hospitalizations with laboratory-confirmed Covid-19 disease. Patients with multiple hospitalizations (N=157, 3.3%) were included repeatedly if they continued to have laboratory-confirmed disease. Mortality was defined as in-hospital death or discharge to hospice care. Based on prior literature, we constructed a multivariable logistic regression model to generate expected risk of death, adjusting for age; sex; self-reported race and ethnicity; body mass index; smoking history; presence of hypertension, heart failure, hyperlipidemia, coronary artery disease, diabetes, cancer, chronic kidney disease, or pulmonary disease individually as dummy variables; and admission oxygen saturation, D-dimer, C reactive protein, ferritin, and cycle threshold for RNA detection. All data were obtained from the electronic health record. We then calculated the sum of observed and expected deaths in each two-week period and multiplied each period's observed/expected (O/E) risk by the overall average crude mortality to generate biweekly adjusted rates. We calculated Poisson control limits and indicated points outside the control limits as significantly different, following statistical process control standards. The NYU institutional review board approved the study and granted a waiver of consent.\n\nResults\n\nWe included 4,689 hospitalizations, of which 4,661 (99.4%) had died or been discharged. The median age, and the proportion male or with any comorbidity decreased over time; median real-time PCR cycle threshold increased (indicating relatively less concentration of virus) (Table). For instance, median age decreased from 67 years in the first two weeks to 49 in the last two. Peak hospitalizations were during the fifth and sixth study weeks, which accounted for 40% of the hospitalizations. Median length of stay for patients who died or were discharged to hospice was 8 days (interquartile range, 4-16).\n\nUnadjusted mortality dropped each period, from 30.2% in the first two weeks to 3% in the last two weeks, with the last eight weeks being lower than the 95% control limits. Risk adjustment partially attenuated the mortality decline, but adjusted mortality rates in the second-to-last two weeks remained outside the control limits (Figure, Table). The O/E risk of mortality decreased from 1.07 (0.64-1.67) in the first two weeks to 0.39 (0.08-1.12) in the last two weeks.\n\nDiscussion\n\nIn this 16-week study of Covid-19 mortality at a single health system, we found that changes in demographics and severity of illness at presentation account for some, but not all, of the decrease in unadjusted mortality. Even after risk adjustment for a variety of clinical and demographic factors, mortality was significantly lower towards the end of the study period.\n\nIncremental improvements in outcomes are likely a combination of increasing clinical experience, decreasing hospital volume, growing use of new pharmacologic treatments (such as corticosteroids, remdesivir and anti-cytokine treatments), non-pharmacologic treatments (such as proning), earlier intervention, community awareness, and lower viral load exposure from increasing mask wearing and social distancing. It is also possible that earlier periods had a more virulent circulating strain.\n\nIn summary, data from one health system suggest that Covid-19 remains a serious disease for high risk patients, but that outcomes may be improving.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Leora Horwitz", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Simon A. Jones", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Robert J. Cerfolio", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Fritz Francois", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Joseph Greco", + "author_inst": "NYU Winthrop Hospital" + }, + { + "author_name": "Bret Rudy", + "author_inst": "NYU Langone Hospital - Brooklyn" + }, + { + "author_name": "Christopher M Petrilli", + "author_inst": "NYU Langone Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.11.20173112", "rel_title": "Development and Validation of a Simple Risk Score for Diagnosing COVID-19 in the Emergency Room", @@ -1220672,41 +1217083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.12.20173740", - "rel_title": "Strengthening Policy Coding Methodologies to Improve COVID-19 Disease Modeling and Policy Responses: A Proposed Coding Framework and Recommendations", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173740", - "rel_abs": "In recent months, multiple efforts have sought to characterize COVID-19 social distancing policy responses. These efforts have used various coding frameworks, but most have relied on binary coding that may not adequately describe the gradient in social distancing policies as states \"re-open.\" We developed a COVID-19 social distancing intensity framework that is sufficiently specific and sensitive to capture this gradient. Based on a review of policies from a 12-state sample, we developed a social distancing intensity framework consisting of 16 domains and intensity scales of 0-5 for each domain. We found that the states with the highest average daily intensity from our sample were Pennsylvania, Washington, Colorado, California, and New Jersey, with Georgia, Florida, Massachusetts, and Texas having the lowest. While some domains (such as restaurants and movie theaters) showed bimodal policy intensity distributions compatible with binary (yes/no) coding, others (such as childcare and religious gatherings) showed broader variability that would be missed without more granular coding. We also present a range of methodological recommendations to strengthen COVID-19 comparative policy coding efforts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jeff Lane", - "author_inst": "University of Washington" - }, - { - "author_name": "Michelle M Garrison", - "author_inst": "University of Washington" - }, - { - "author_name": "James Kelley", - "author_inst": "University of Washington" - }, - { - "author_name": "Priya Sarma", - "author_inst": "University of Washington" - }, - { - "author_name": "Aaron Katz", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.08.11.20167353", "rel_title": "Pharmacological inhibition of the kinin-kallikrein system in severe COVID-19 A proof-of-concept study", @@ -1221559,6 +1217935,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.12.20173831", + "rel_title": "Temporal Dynamics of Viral Load and False Negative Rate Influence the Levels of Testing Necessary to Combat COVID19 Spread", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173831", + "rel_abs": "Colleges and other organizations are considering testing plans to return to operation as the COVID19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~17% to ~48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Katherine F Jarvis", + "author_inst": "University of Maine" + }, + { + "author_name": "Joshua B Kelley", + "author_inst": "University of Maine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.12.20173674", "rel_title": "Double-zero-event studies matter: a re-evaluation of physical distancing, face masks, and eye protection for preventing person-to-person transmission of COVID-19 and its policy impact", @@ -1222354,33 +1218753,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.11.20173203", - "rel_title": "A simple numerical and analytical analysis of Covid-19 progression, infection inhibition and control in various countries", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173203", - "rel_abs": "Covid-19 disease outspread and its subsequent control and inhibition strategies in various countries have been different which led to quite drastic difference in the outcome of the disease progression. In this paper we present an analytical and numerical study of Covid-19 disease spread and control by applying the modified SIR model of epidemic outbreak to explain the Covid spread from February-July 2020 in various countries. Two approaches are evident from the disease progression; one focused on disease eradication and inhibition, and the other is less restrictive dynamic response. Both the approaches are analytically modeled to determine the parameters that characterize the effectiveness of dealing with the disease progression. The model successfully explains the Covid-19 evolution and control of various countries over a vast span of four-five months. The study is highly beneficial to simply analytically and numerically model this complex problem of epidemic proliferation. It assists to easily determine the mathematical parameters for the Covid-19 control measures, helps in predicting the end of the epidemic, and most importantly conceiving the judicious way of unlock process to restore communication between cities, states and countries.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Uday Chakravarty", - "author_inst": "Raja Ramanna Centre for Advanced Technology, Indore" - }, - { - "author_name": "Deepa Chaturvedi", - "author_inst": "Department Applied Science, Alard College of Engineering and Management, Marunji, Pune" - }, - { - "author_name": "Mukesh P Joshi", - "author_inst": "Raja Ramanna Centre for Advanced Technology, Indore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.10.20171819", "rel_title": "Investigation of pooling strategies using clinical COVID-19 samples for more efficient diagnostic testing", @@ -1222941,6 +1219313,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.11.20173179", + "rel_title": "Water, Sanitation, Hygiene and Covid-19 pandemic: a global socioeconomic analysis", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173179", + "rel_abs": "Socioeconomic achievement of WASH (access to safe water, sanitation and hygiene) services are being acknowledged as anticipatory actors, indispensable in safeguarding health during this Covid-19 pandemic. However, on a global scale, it is currently not clear whether deprivation or non-obtainability of which of the various WASH services are closely related to Covid-19 dynamics and up to which degree. We have analysed data (March - June 2020) related to five Covid-19 indicators for most of the countries in the world with indicators of safe water, sanitation and hygiene to understand this. We have found a strong positive correlation between lesser effects of Covid-19 and better access to safe water, sanitation as well as hygiene throughout this time for most of the indicators. However, some indicators show the opposite nature of the relationship, for which we have given probable explanation accordingly. The hypothesis of an inversely proportional association between Covid-19 and poor WASH facilities on a global scale is confirmed in this study. We propose that this study should be perceived as an expanded comprehensive view on the complexities of WaSH-Covid19 interrelationships, which could help to shape an agenda for research into some unanswered questions.\n\nHighlightsO_LIWASH indicators are highly correlated to cumulative indicators of Covid-19.\nC_LIO_LITrends of this correlation have been changing from March-June, 2020.\nC_LIO_LIIncome groups and geographic locations have no distinguishing effects on countries.\nC_LIO_LIBetter WASH performance does not always correlate against Covid-19.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ajishnu Roy", + "author_inst": "Integrative Biology Research Unit, Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata - 700073, India" + }, + { + "author_name": "Aman Basu", + "author_inst": "Department of Environmental Studies, Siksha Bhavana (Institute of Science), Visva-Bharati, West Bengal - 731235, India" + }, + { + "author_name": "Kousik Pramanick", + "author_inst": "Integrative Biology Research Unit, Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata - 700073, India" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.13.20147595", "rel_title": "The operational impact of deploying SARS-CoV-2 vaccines in countries of the WHO African Region", @@ -1223900,37 +1220299,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.08.13.249904", - "rel_title": "Pandemic danger to the deep: the risk of marine mammals contracting SARS-CoV-2 from wastewater", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.249904", - "rel_abs": "We are in unprecedented times with the ongoing COVID-19 pandemic. The pandemic has impacted public health, the economy and our society on a global scale. In addition, the impacts of COVID-19 permeate into our environment and wildlife as well. Here, we discuss the essential role of wastewater treatment and management during these times. A consequence of poor wastewater management is the discharge of untreated wastewater carrying infectious SARS-CoV-2 into natural water systems that are home to marine mammals. Here, we predict the susceptibility of marine mammal species using a modelling approach. We identified that many species of whale, dolphin and seal, as well as otters, are predicted to be highly susceptible to infection by the SARS-CoV-2 virus. In addition, geo-mapping highlights how current wastewater management in Alaska may lead to susceptible marine mammal populations being exposed to the virus. Localities such as Cold Bay, Naknek, Dillingham and Palmer may require additional treatment of their wastewater to prevent virus spillover through sewage. Since over half of these susceptibility species are already at risk worldwide, the release of the virus via untreated wastewater could have devastating consequences for their already declining populations. For these reasons, we discuss approaches that can be taken by the public, policymakers and wastewater treatment facilities to reduce the risk of virus spillover in our natural water systems. Thus, we indicate the potential for reverse zoonotic transmission of COVID-19 and its impact on marine wildlife; impacts that can be mitigated with appropriate action to prevent further damage to these vulnerable populations.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sabateeshan Mathavarajah", - "author_inst": "Department of Pathology, Dalhousie University" - }, - { - "author_name": "Amina K. Stoddart", - "author_inst": "Department of Civil and Resource Engineering, Dalhousie University" - }, - { - "author_name": "Graham A. Gagnon", - "author_inst": "Department of Civil and Resource Engineering, Dalhousie University" - }, - { - "author_name": "Graham Dellaire", - "author_inst": "Department of Pathology, Dalhousie University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2020.08.14.251538", "rel_title": "Differential methylation as a mediator of COVID-19 susceptibility", @@ -1224675,6 +1221043,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.08.11.20168773", + "rel_title": "Challenges and proposed solutions in making clinical research on COVID-19 ethical. A status quo analysis across German research ethics committees", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20168773", + "rel_abs": "BackgroundIn the course of the COVID-19 pandemic, the biomedical research communitys attempt to focus the attention on fighting COVID-19, led to several challenges within the field of research ethics. However, we know little about the practical relevance of these challenges for Research Ethics Committees (RECs).\n\nMethodsWe conducted a qualitative survey across all 52 German RECs on the challenges and potential solutions with reviewing proposals for COVID-19 studies. We de-identified the answers and applied thematic text analysis for the extraction and synthesis of challenges and potential solutions that we grouped under established principles for clinical research ethics.\n\nResultsWe received an overall response rate of 42%. The 22 responding RECs reported that they had assessed a total of 441 study proposals on COVID-19 until 21 April 2020. For the review of these proposals the RECs indicated a broad spectrum of challenges regarding i) social value (e.g. lack of coordination), ii) scientific validity (e.g. provisional study planning), iii) favourable risk-benefit ratio (e.g. difficult benefit assessment), iv) informed consent (e.g. strict isolation measures), v) independent review (e.g. lack of time), vi) fair selection of trial participants (e.g. inclusion of vulnerable groups), and vii) respect for study participants (e.g. data security). Mentioned solutions ranged from improved local/national coordination, over guidance on modified consent procedures, to priority setting across clinical studies.\n\nConclusionsRECs are facing a broad spectrum of pressing challenges in reviewing COVID-19 studies. Some challenges for consent procedures are well known from research in intensive care settings but are further aggravated by infection measures. Other challenges such as reviewing several clinical studies at the same time that potentially compete for the recruitment of in-house COVID-19 patients are unique to the current situation. For some of the challenges the proposed solutions in our survey could relatively easy be translated into practice. Others need further conceptual and empirical research. Our findings together with the increasing body of literature on COVID-19 research ethics, and further stakeholder engagement should inform the development of hands-on guidance for researchers, funders, RECs, and further oversight bodies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alice Faust", + "author_inst": "Charite Universitaetsmedizin Berlin / BIH Berlin Institute of Health" + }, + { + "author_name": "Anna Sierawska", + "author_inst": "Charite Universitaetsmedizin Berlin / BIH Berlin Institute of Health" + }, + { + "author_name": "Katharina Krueger", + "author_inst": "Association of Medical Ethics Committees in Germany (AKEK, Arbeitskreis der Medizinischen Ethik-Kommissionen in der Bundesrepublik Deutschland e.V.), Berlin" + }, + { + "author_name": "Anne Wisgalla", + "author_inst": "Association of Medical Ethics Committees in Germany (AKEK, Arbeitskreis der Medizinischen Ethik-Kommissionen in der Bundesrepublik Deutschland e.V.), Berlin" + }, + { + "author_name": "Joerg Hasford", + "author_inst": "Association of Medical Ethics Committees in Germany (AKEK, Arbeitskreis der Medizinischen Ethik-Kommissionen in der Bundesrepublik Deutschland e.V.), Berlin; In" + }, + { + "author_name": "Daniel Strech", + "author_inst": "Charite Universitaetsmedizin Berlin / BIH Berlin Institute of Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical ethics" + }, { "rel_doi": "10.1101/2020.08.07.20170373", "rel_title": "Protocol for a Rapid Scoping Review of Evidence of Outdoor Transmission of COVID-19", @@ -1225530,61 +1221937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.10.20150060", - "rel_title": "A highly specific assay for the detection of SARS-CoV-2-reactive CD4+ and CD8+ T cells in COVID-19 patients", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20150060", - "rel_abs": "Gaining detailed insights into the role of host immune responses in viral clearance is critical for understanding COVID-19 pathogenesis and future treatment strategies. While studies analyzing humoral immune responses against SARS-CoV-2 were available rather early during the pandemic, cellular immunity came into focus of investigations just recently.\n\nFor the present work, we have adapted a protocol, designed for the detection of rare neoantigen-specific Memory T cells in cancer patients for studying cellular immune responses against SARS-CoV-2. Both, CD4+ and CD8+ T cells were detected after 6 days of in vitro expansion using overlapping peptide libraries representing the whole viral protein. The assay readout was an Intracellular cytokine staining and flow cytometric analysis detecting four functional markers simultaneously (CD154, TNF, IL-2, IFN-{gamma}).\n\nWe were able to detect SARS-CoV-2-specific T cells in 9 of 9 COVID-19 patients with mild symptoms. All patients had reactive T cells against at least one of 12 analyzed viral antigens and all patients had Spike-specific T cells. While some antigens were detected by CD4+ and CD8+ T cells, Membrane protein was mainly recognized by CD4+ T cells. Strikingly, we were not able to detect SARS-CoV-2-specific T cells in 9 unexposed healthy individuals.\n\nWe are presenting a highly specific protocol for the detection of SARS-CoV-2-reactive T cells. Our data confirmed the important role of cellular immune responses in understanding SARS-CoV-2 clearance. We showed that Spike is the most immunogenic antigen. We have introduced Membrane protein as interesting target for studying humoral immune responses in convalescent COVID-19 patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Henning Zelba", - "author_inst": "CeGaT GmbH" - }, - { - "author_name": "David Worbs", - "author_inst": "CeGaT GmbH" - }, - { - "author_name": "Johannes Harter", - "author_inst": "CeGaT GmbH" - }, - { - "author_name": "Natalia Pieper", - "author_inst": "CeGaT GmbH" - }, - { - "author_name": "Christina Kyzirakos-Feger", - "author_inst": "Praxis fuer Humangenetik" - }, - { - "author_name": "Simone Kayser", - "author_inst": "Praxis fuer Humangenetik" - }, - { - "author_name": "Marcel Seibold", - "author_inst": "Praxis fuer Humangenetik" - }, - { - "author_name": "Oliver Bartsch", - "author_inst": "Praxis fuer Humangenetik" - }, - { - "author_name": "Jiri Koedding", - "author_inst": "CeGaT GmbH" - }, - { - "author_name": "Saskia Biskup", - "author_inst": "Praxis fuer Humangenetik" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20170894", "rel_title": "Deciphering the state of immune silence in fatal COVID-19 patients", @@ -1226177,6 +1222529,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20170506", + "rel_title": "A \"Tail\" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20170506", + "rel_abs": "I describe SIR modeling of the COVID-19 pandemic in two U.S. urban environments, New York City (NYC) and Cook County, IL, from onset through mid-June, 2020. Since testing was not widespread early in the pandemic in the U.S., I rely on public fatality data to estimate model parameters and use case data only as a lower bound. Fits to the first 20 days of data determine a degenerate combination of the basic reproduction number, R0, and the mean time to removal from the infectious population,{gamma} -1, with{gamma} (R0 - 1)= 0.25(0.21) inverse days for NYC (Cook County). Equivalently, the initial doubling time was td = 2.8(3.4) days for NYC (Cook). The early fatality data suggest that both locations had infections in early February. I model the mitigation measures implemented in mid-March in both locations (distancing, quarantine, isolation, etc) via a time-dependent reproduction number Rt that declines monotonically from R0 to a smaller asymptotic value, R0(1 - X), with a parameterized functional form. The timing (mid-March) and duration (several days) of the transitions in Rt appear well determined by the data. With flat priors on model parameters and the lower bound from reported cases, the NYC fatality data imply 95.45% credible intervals of R0 = 2.6 - 2.9, social contact reduction X = 69 - 76% and infection fatality rate f = 1 - 1.5%, with 19 - 27% of the population asymptotically infected. The case data relative to daily deaths suggest that the reported case rate as a fraction of true case rate grew monotonically, reaching a plateau around April 20 for both NYC and Cook County; the models also suggest that the late-time NYC reported case rate was comparable to the true rate, while for Cook County it remained an underestimate. For Cook County, the fatality evolution was qualitatively different from NYC: after mitigation measures were implemented, daily fatality counts reached a plateau for about a month before tailing off. This is consistent with an SIR model that exhibits \"critical slowing-down\", in which Rt plateaus at a value just above unity. For Cook County, the 95.45% credible intervals for the model parameters are not constrained by the case data and are much broader, R0 = 1.4 - 4.7, X = 26 - 54%, and f = 0.1 - 0.6% with 15 - 88% of the population asymptotically infected. Despite the apparently lower efficacy of its social contact reduction measures, Cook County has had significantly fewer fatalities per population than NYC, D{infty} /N = 100 vs. 270 per 100,000. In the model, this is attributed to the lower inferred IFR for Cook; an external prior pointing to similar values of the IFR for the two locations would instead chalk up the difference in D/N to differences in the relative growth rate of the disease. I derive a model-dependent threshold, [Formula], for safe re-opening, that is, for easing of contact reduction that would not trigger a second wave; for NYC, the models predict that increasing social contact by more than 20% from post-mitigation levels will lead to renewed spread, while for Cook County the threshold value is very uncertain, given the parameter degeneracies. The timing of 2nd-wave growth will depend on the amplitude of contact increase relative to [Formula] and on the asymptotic growth rate, and the impact in terms of fatalities will depend on the parameter f.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Joshua Frieman", + "author_inst": "Fermilab" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.10.20171561", "rel_title": "Low awareness of past SARS-CoV-2 infection in healthy adults", @@ -1227236,33 +1223607,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.09.243246", - "rel_title": "Discovery of COVID-19 Inhibitors Targeting the SARS-CoV2 Nsp13 Helicase", - "rel_date": "2020-08-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.09.243246", - "rel_abs": "The raging COVID-19 pandemic caused by SARS-CoV2 has infected millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV2 helicase (Nsp13), which is critical for viral replication and the most conserved non-structural protein within the coronavirus family. Using homology modeling and molecular dynamics approaches, we generated structural models of the SARS-CoV2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ~970,000 chemical compounds against the ATP binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mark A White", - "author_inst": "The University of Texas Medical Branch, Galveston, TX 77555, USA" - }, - { - "author_name": "Wei Lin", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Xiaodong Cheng", - "author_inst": "University of Texas Health Science Center at Houston" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.09.20149286", "rel_title": "The effect of public health policies in the transmission of COVID-19 for South American countries", @@ -1228059,6 +1224403,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.06.20169839", + "rel_title": "Expanding COVID-19 symptom screening to retail, restaurants, and schools by preserving privacy using relaxed digital signatures", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169839", + "rel_abs": "Symptom screening is a widely deployed strategy to mitigate the COVID-19 pandemic and many public health authorities are mandating its use by employers for all employees in the workplace. While symptom screening has the benefit of reducing the number of infected individuals in the workplace, it raises some inherently difficult privacy issues as a traditional approach requires the employer to collect symptom data from each employee which is essentially medical information. In this paper, we describe a system to implement Cryptographic Anonymous Symptom Screening (CASS) which allows for individuals to perform COVID symptom screening anonymously while avoiding the privacy issues of traditional approaches. In the system, individuals report their symptoms without any identifying information and are issued a completion certificate. This certificate contains a cryptographic code which certifies that the certificate was obtained from the screener after reporting no symptoms. The codes can be verified using a cryptographic algorithm which is publicly available. A standard cryptography approach to implement such a system would be to use digital signatures. Unfortunately, standard digital signatures have some limitations for this application in that the signatures are often hundreds of characters long and if the signature contains the name of the individual, then there is also a risk of compromising privacy. In our approach, we develop and utilize a relaxed digital signature scheme to provide 16 character long codes and handle names using equivalence classes which helps preserve privacy. Both of these extensions technically compromise the security but in a way that is negligible for this application. Our system can either serve the function of standard symptom screening system approaches for employees, but can also extend symptom screening to non-employees such as visitors or customers. In this case, the system can be utilized in retail, restaurants and schools to ensure that everyone in the physical space, including employees, customers, visitors and students have performed symptom screening.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Brandon Jew", + "author_inst": "UCLA" + }, + { + "author_name": "Alexis Korb", + "author_inst": "UCLA" + }, + { + "author_name": "Paul Lou", + "author_inst": "UCLA" + }, + { + "author_name": "Jeffrey N Chiang", + "author_inst": "UCLA" + }, + { + "author_name": "Ulzee An", + "author_inst": "UCLA" + }, + { + "author_name": "Amit Sahai", + "author_inst": "UCLA" + }, + { + "author_name": "Eran Halperin", + "author_inst": "UCLA" + }, + { + "author_name": "Eleazar Eskin", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.06.20162859", "rel_title": "Whole Care Home Testing for Covid-19 in a Local Authority Area in the United Kingdom", @@ -1229058,45 +1225449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.08.07.20170225", - "rel_title": "Population perspective comparing COVID-19 to all and common causes of death in seven European countries", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170225", - "rel_abs": "BackgroundMortality statistics on the COVID-19 pandemic have led to widespread concern and fear. To contextualise these data, we compared mortality related to COVID-19 with all and common causes of death, stratifying by age and sex. We also calculated deaths as a proportion of the population by age and sex.\n\nMethodsCOVID-19 related mortality and population statistics from seven European countries were extracted: England and Wales, Italy, Germany, Spain, France, Portugal and Netherlands. Available data spanned 14-16 weeks since the first recorded deaths in each country, except Spain, where only comparable stratified data over an 8-week time period was available. The Global Burden of Disease database provided data on all deaths and those from pneumonia, cardiovascular disease combining ischaemic heart disease and stroke, chronic obstructive pulmonary disease, cancer, road traffic accidents and dementia.\n\nFindingsDeaths related to COVID-19, while modest overall, varied considerably by age. Deaths as a percentage of all cause deaths during the time period under study ranged from <0.01% in children in Germany, Portugal and Netherlands, to as high as 41.65% for men aged over 80 years in England and Wales. The percentage of the population who died from COVID-19 was less than 0.2% in every age group under the age of 80. In each country, over the age of 80, these proportions were: England and Wales 1.27% males, 0.87% females; Italy 0.6% males, 0.38% females; Germany 0.13% males, 0.09% females; France 0.39% males, 0.2% females; Portugal 0.2% males, 0.15% females; and Netherlands 0.6% males, 0.4% females.\n\nInterpretationMortality rates from COVID-19 remains low including when compared to other common causes of death and will likely decline further while control measures are maintained. These data may help people contextualise their risk and policy makers in decision-making.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bayanne Olabi", - "author_inst": "Department of Dermatology, Lauriston Building, Lauriston Place, Edinburgh, EH3 9EN" - }, - { - "author_name": "Jayshree Bagaria", - "author_inst": "Independent Consultant in Global Public Health" - }, - { - "author_name": "Sunil Bhopal", - "author_inst": "Population Health Sciences Institute, Newcastle upon Tyne, NE1 7RU" - }, - { - "author_name": "Gwenetta Curry", - "author_inst": "The University of Edinburgh Usher Institute of Population Health Sciences and Informatics Edinburgh, Edinburgh, EH3 9AG" - }, - { - "author_name": "Nazmy Villarroel", - "author_inst": "University of Sheffield, S10 2TG" - }, - { - "author_name": "Raj Bhopal", - "author_inst": "The University of Edinburgh Usher Institute of Population Health Sciences and Informatics Edinburgh, Edinburgh, EH3 9AG" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.07.20167957", "rel_title": "Mask-associated de novo headache in healthcare workers during the Covid-19 pandemic.", @@ -1229817,6 +1226169,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.04.20167205", + "rel_title": "Telmisartan for treatment of Covid-19 patients: an open randomized clinical trial. Preliminary report.", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167205", + "rel_abs": "BackgroundCovid-19 is associated with respiratory-related morbidity and mortality. Angiotensin receptor blockers (ARB) have been postulated as tentative pharmacological agents to treat Covid-19-induced inflammation.\n\nMethodsThis is a randomized, two-arm, open, multicenter trial. Participants were 18 years or older and had been hospitalized with confirmed Covid-19 with 4 or fewer days since symptom onset. Exclusion criteria included intensive care unit admission prior to randomization and ARB or angiotensin converting enzyme inhibitors use. Treatment arm received telmisartan 80 mg bid during 14 days plus standard care; control arm received standard care. Primary outcome were differences in C-reactive protein levels at days 5 and 8. Secondary outcomes included time to discharge evaluated at 15 days and death at 30 days post randomization.\n\nResultsThis interim analysis included 40 patients in telmisartan and 38 in control groups. CRP levels in the control and telmisartan groups were 51.1{+/-}44.8 mg/L vs 24.2{+/-}31.4 mg/L at day 5 (mean {+/-} SD; n=28 and n=32, p<0.05), and 41.6{+/-}47.6 mg/L vs 9.0{+/-}10.0 mg/L at day 8 (mean {+/-} SD; n=16 and n=13; p<0.05), respectively. Telmisartan treated patients had statistically significant lower time to discharge (log-rank test p=0.0124, median time: 15 days in control group vs 9 days in telmisartan group). Mortality at day 30 was 11.76% in control group vs 5.26% in telmisartan group (p=0.41).\n\nConclusionsIn this study, ARB telmisartan, a well-known inexpensive safe antihypertensive drug, administered in high doses, was superior to standard care demonstrating anti-inflammatory effects and improved morbidity in hospitalized patients infected with SARS-CoV-2 (NCT04355936).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Mariano Duarte", + "author_inst": "Joint first authorship. Laboratorio de Hipertension, Division de Cardiologia, Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buen" + }, + { + "author_name": "Facundo G Pelorosso", + "author_inst": "Joint first authorship. Asociacion Argentina de Medicamentos, Ciudad de Buenos Aires, Argentina. Servicio de Anatomia Patologica, Hospital de Alta Complejidad E" + }, + { + "author_name": "Liliana Nicolosi", + "author_inst": "Division de Cardiologia, Hospital Espanol de Buenos Aires." + }, + { + "author_name": "M. Victoria Salgado", + "author_inst": "Centro de Estudios de Estado y Sociedad; Servicio de Medicina Familiar, Hospital de Alta Complejidad El Calafate SAMIC." + }, + { + "author_name": "Hector Vetulli", + "author_inst": "Sanatorio Otamendi y Miroli, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Analia Aquieri", + "author_inst": "Laboratorio de Hipertension, Division de Cardiologia, Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Francisco Azzato", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Mauro Basconcel", + "author_inst": "Hospital Espanol de Buenos Aires" + }, + { + "author_name": "Marcela Castro", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Javier Coyle", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Ignacio Davolos", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Eduardo Esparza", + "author_inst": "Hospital Espanol de Buenos Aires" + }, + { + "author_name": "Ignacio Fernandez Criado", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Rosana Gregori", + "author_inst": "Hospital Espanol de Buenos Aires" + }, + { + "author_name": "Pedro Mastrodonato", + "author_inst": "Hospital Espanol de Buenos Aires." + }, + { + "author_name": "Maria Rubio", + "author_inst": "Hospital Espanol de Buenos Aires" + }, + { + "author_name": "Sergio Sarquis", + "author_inst": "Hospital de Clinicas Jose de San Martin, Facultad de Medicina, Universidad de Buenos Aires" + }, + { + "author_name": "Fernando Wahlmann", + "author_inst": "Hospital Espanol de Buenos Aires" + }, + { + "author_name": "Rodolfo Pedro Rothlin", + "author_inst": "Sociedad Argentina de Farmacologia Clinica, Asociacion Medica Argentina; Asociacion Argentina de Medicamentos, Ciudad de Buenos Aires, Argentina" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2020.08.10.20171421", "rel_title": "Long-term exposure to air-pollution and COVID-19 mortality in England: a hierarchical spatial analysis", @@ -1230728,29 +1227171,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.08.10.245290", - "rel_title": "The selection of reference genome and the search for the origin of SARS-CoV-2", - "rel_date": "2020-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.10.245290", - "rel_abs": "AbstractsThe pandemic caused by SARS-CoV-2 has a great impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins were considered a potential intermediate host. To assemble the coronavirus found in pangolins, SARS-CoV-2 were used a reference genome in most of studies, assuming that pangolins CoV and SARS-CoV-2 are the closest neighbors in the evolution. However, this assumption may not be true. We investigated how the selection of reference genome affect the resulting CoV genome assembly. We explored various representative CoV as reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yuan Liu", - "author_inst": "North Dakota State University" - }, - { - "author_name": "Changhui Yan", - "author_inst": "North Dakota State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.10.20172106", "rel_title": "Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow", @@ -1231727,6 +1228147,65 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.08.10.243717", + "rel_title": "Comparative analyses of SARS-CoV-2 binding (IgG, IgM, IgA) and neutralizing antibodies from human serum samples", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.10.243717", + "rel_abs": "A newly identified coronavirus, named SARS-CoV-2, emerged in December 2019 in Hubei Province, China, and quickly spread throughout the world; so far, it has caused more than 18 million cases of disease and 700,000 deaths. The diagnosis of SARS-CoV-2 infection is currently based on the detection of viral RNA in nasopharyngeal swabs by means of molecular-based assays, such as real-time RT-PCR. Furthermore, serological assays aimed at detecting different classes of antibodies constitute the best surveillance strategy for gathering information on the humoral immune response to infection and the spread of the virus through the population, in order to evaluate the immunogenicity of novel future vaccines and medicines for the treatment and prevention of COVID-19 disease. The aim of this study was to determine SARS-CoV-2-specific antibodies in human serum samples by means of different commercial and in-house ELISA kits, in order to evaluate and compare their results first with one another and then with those yielded by functional assays using wild-type virus. It is important to know the level of SARS-CoV-2-specific IgM, IgG and IgA antibodies in order to predict population immunity and possible cross-reactivity with other coronaviruses and to identify potentially infectious subjects. In addition, in a small sub-group of samples, we performed a subtyping Immunoglobulin G ELISA. Our data showed an excellent statistical correlation between the neutralization titer and the IgG, IgM and IgA ELISA response against the receptor-binding domain of the spike protein, confirming that antibodies against this portion of the virus spike protein are highly neutralizing and that the ELISA Receptor-Binding Domain-based assay can be used as a valid surrogate for the neutralization assay in laboratories which do not have Biosecurity level-3 facilities.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Livia Mazzini", + "author_inst": "Vismederi S.r.l." + }, + { + "author_name": "Donata Martinuzzi", + "author_inst": "Vismederi Research S.r.l." + }, + { + "author_name": "Inesa Hyseni", + "author_inst": "Vismederi Research S.r.l." + }, + { + "author_name": "Giulia Lapini", + "author_inst": "Vismederi S.r.l." + }, + { + "author_name": "Linda Benincasa", + "author_inst": "Vismederi Research S.r.l." + }, + { + "author_name": "Pietro Piu", + "author_inst": "Vismederi S.r.l." + }, + { + "author_name": "Claudia Maria Trombetta", + "author_inst": "University of Siena" + }, + { + "author_name": "Serena Marchi", + "author_inst": "University of Siena" + }, + { + "author_name": "Ilaria Razzano", + "author_inst": "Vismederi Research S.r.l." + }, + { + "author_name": "Alessandro Manenti", + "author_inst": "VisMederi Research S.r.l." + }, + { + "author_name": "Emanuele Montomoli", + "author_inst": "Vismederi S.r.l." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.09.242917", "rel_title": "DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist", @@ -1232882,45 +1229361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.06.20160515", - "rel_title": "The association between lockdown due to COVID-19 epidemic and searches for toothache using Google Trends in Iran", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20160515", - "rel_abs": "ObjectiveTo assess the association between the lockdowns due to COVID-19 and online searches for toothache in Iran using Google Trends (GT).\n\nMethodsWe investigated GT online searches for the search term [Formula] within the past five years. The time frame for data gathering was considered as the initiation and end dates of lockdown in Iran. Relative search volumes (RSVs) for online Google Search queries in 2019 was considered as the control. We performed one-way ANOVA statistical test to identify whether there is a statistical difference for RSV scores between the year 2020 and 2016-2019 for the whole country. Then we investigated the possible association of RSVs in provinces with dentists density, prevalence of current daily smokers, Human Development Index (HDI), Internet access, and fluoride concentration in water with linear regression. A p-value<0.05 was considered as statistically significant.\n\nResultsWhen comparing 2020 with previous four years, there is a statistically significant difference between RSVs of 2020 with all previous years combined and each of these years (P<0.001 for all of them). In the linear model for the year 2020, HDI (B=-3.29, 95% CI: (-5.80, - 0.78), P=0.012), fluoride concentration (B=-0.13, 95% CI: (-0.24, -0.03), P=0.017), and prevalence of daily smokers (B=0.33, 95% CI: (0.13, 0.53), P=0.002) were significantly associated with RSVs. These covariates were not statistically significant for other years, except for Internet access in 2016 (B=-1.13, 95% CI: (-2.26, 0.00), P=0.050).\n\nConclusionThe RSVs for toothache in 2020 have significantly increased due to COVID-19-imposed lockdowns compared to the same period of the year in the past four years. Knowing that this period mostly overlaps with the national holidays of Nowruz in Iran, reinforces the impacts of lockdowns on peoples CSB about the toothache. In the subnational scale, the RSVs were significantly correlated with HDI, fluoride concentration, and prevalence of daily smokers which emphasises the role of socioeconomic factors in dental health and care-seeking behaviour.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ahmad Sofi-Mahmudi", - "author_inst": "Cochrane Iran Associate Centre, National Institute for Medical Research Development (NIMAD), Tehran, Iran." - }, - { - "author_name": "Erfan Shamsoddin", - "author_inst": "National Institute for Medical Research Development (NIMAD), Tehran, Iran." - }, - { - "author_name": "Peyman Ghasemi", - "author_inst": "Department of Health Economics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran." - }, - { - "author_name": "Ali Mehrabi Bahar", - "author_inst": "Department of Health Policy and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran." - }, - { - "author_name": "Mansour Shaban Azad", - "author_inst": "Department of Cardiovascular Surgery, Shahid Chamran Heart Educational, Medical and Research Center, Isfahan University of Medical Sciences, Isfahan, Iran." - }, - { - "author_name": "Ghasem Sadeghi", - "author_inst": "Bureau of Dentistry, Vice Chancellery for Treatment, Ministry of Health and Education, Tehran, Iran." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2020.08.06.20169896", "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Using a Two Parameter Transmission Model Incorporating Outdoor Temperature and School Re-Opening Effects", @@ -1233825,6 +1230265,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.06.20169326", + "rel_title": "Age disaggregation of crude excess deaths during the 2020 spring COVID-19 outbreak in Spain and Netherlands", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169326", + "rel_abs": "Spanish and Dutch official records of mortality and population during the 21st century are analyzed to determine the age specific crude death rate in the 2020 spring COVID-19 outbreak.\n\nExcess death rate increases exponentially with age showing a doubling time [5.0, 5.6]a (Spain) and [3.9, 6.7]a (Netherlands), roughing doubling every five years of increase in age.The effective infection fatality rate in Spain also shows this doubling time.\n\nStatistically significant mortality increase is noted above 45 a (Spain) and 60 a (Netherlands).\n\nA statistically significant increase of mortality is also noted in Spain for the youngest age group.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jose Maria Martin-Olalla", + "author_inst": "Universidad de Sevilla" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.03.20162883", "rel_title": "SARS-CoV-2 surveillance in decedents in a large, urban medical examiner's office", @@ -1234844,125 +1231303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.07.20163840", - "rel_title": "Prevalence of SARS-CoV-2 among high-risk populations in Lomé (Togo) in 2020", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20163840", - "rel_abs": "ObjectiveThis survey aims at estimating the prevalence of SARS-CoV-2 in high risk populations in Lome.\n\nMethodsFrom April 23rd to May 8th 2020, we recruited a random sample of participants from five sectors: healthcare, air transport, police, road transport and informal. We collected oropharyngeal swab for direct detection through real time reverse transcription polymerase chain reaction (rRT-PCR), and blood for antibodies detection by serological tests. The overall prevalence (current and past) of infection was defined by positivity for both tests.\n\nResultsA total of 955 participants with a median age of 36 (IQR 32-43) were included and 71.6% (n=684) were men. Around 22.1% (n=212) were from the air transport sector, 20.5% (n=196) in the police, and 38.7% (n=370) in the health sector. Seven participants (0.7%, 95% CI: 0.3-1.6%) had a positive rRT-PCR at the time of recruitment and nine (0.9%, 95% CI: 0.4-1.8%) were seropositive for IgM or IgG against SARS-CoV-2. We found an overall prevalence of 1.6% (n=15), 95% CI: 0.9-2.6%.\n\nConclusionThe prevalence of the SARS-CoV-2 infection among high-risk populations in Lome was relatively low and could be explained by the various measures taken by the Togolese government. Therefore, we recommend targeted screening.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Wemboo Afiwa Halatoko", - "author_inst": "Institut National d'Hygiene, Lome, Togo" - }, - { - "author_name": "Yao Rodion KONU", - "author_inst": "Universite de Lome, Departement de Sante Publique, Lome, Togo" - }, - { - "author_name": "Fifonsi Adjidossi Gbeasor-Komlanvi", - "author_inst": "Universite de Lome, Departement de Sante Publique, Lome, Togo" - }, - { - "author_name": "Arnold Junior Sadio", - "author_inst": "Centre Africain de Recherche en Epidemiologie et en Sante Publique, Lome, Togo" - }, - { - "author_name": "Martin Kouame Tchankoni", - "author_inst": "Centre Africain de Recherche en Epidemiologie et en Sante Publique (CARESP), Lome, Togo" - }, - { - "author_name": "Koffi Segbeaya Komlanvi", - "author_inst": "Centre Africain de Recherche en Epidemiologie et en Sante Publique (CARESP), Lome, Togo" - }, - { - "author_name": "Mounerou Salou", - "author_inst": "Universite de Lome, Laboratoire de Biologie Moleculaire et d'Immunologie (BIOLIM), Lome, Togo" - }, - { - "author_name": "Ameyo Monique Dorkenoo", - "author_inst": "Universite de Lome, Faculte des Sciences de la Sante, Lome, Togo" - }, - { - "author_name": "Issaka Maman", - "author_inst": "Institut National d'Hygiene (INH), Lome, Togo" - }, - { - "author_name": "Ametepe Agbobli", - "author_inst": "Universite de Lome, Faculte des Sciences de la Sante, Lome, Togo" - }, - { - "author_name": "Majeste Ihou Wateba", - "author_inst": "Universite de Lome, Faculte des Sciences de la Sante, Lome, Togo" - }, - { - "author_name": "Komi Seraphin Adjoh", - "author_inst": "Universite de Lome, Faculte des Sciences de la Sante, Lome, Togo" - }, - { - "author_name": "Edem Goeh Akue", - "author_inst": "Universite de Lome, Faculte des Sciences de la Sante, Lome, Togo" - }, - { - "author_name": "Yem-bla Kao", - "author_inst": "Conseil Scientifique pour la Riposte contre la pandemie de Covid-19, Lome, Togo" - }, - { - "author_name": "Innocent Kpeto", - "author_inst": "Conseil Scientifique pour la Riposte contre la pandemie de Covid-19, Lome, Togo" - }, - { - "author_name": "Paul Pana", - "author_inst": "Conseil Scientifique pour la Riposte contre la pandemie de Covid-19, Lome, Togo" - }, - { - "author_name": "Rebecca Kinde-Sossou", - "author_inst": "Ministere de la Sante et de l'Hygiene Publique, Lome, Togo" - }, - { - "author_name": "Agbeko Tamakloe", - "author_inst": "Ministere de la Sante et de l'Hygiene Publique, Lome, Togo" - }, - { - "author_name": "Josee Nayo-Apetsianyi", - "author_inst": "Ministere de la Sante et de l'Hygiene Publique, Lome, Togo" - }, - { - "author_name": "Simon-Pierre Hamadi Assane", - "author_inst": "Ministere de la Sante et de l'Hygiene Publique, Lome, Togo" - }, - { - "author_name": "Mireille Prince-David", - "author_inst": "Universite de Lome, Laboratoire de Biologie Moleculaire et d'Immunologie (BIOLIM), Lome, Togo" - }, - { - "author_name": "Sossinou Marcel Awoussi", - "author_inst": "Coordination Nationale de Gestion de la Riposte contre la Covid-19, Lome, Togo" - }, - { - "author_name": "Mohaman Djibril", - "author_inst": "Coordination Nationale de Gestion de la Riposte contre la Covid-19, Lome, Togo" - }, - { - "author_name": "Moustafa Mijiyawa", - "author_inst": "Ministere de la Sante et de l'Hygiene Publique, Lome, Togo" - }, - { - "author_name": "Anoumou Claver Dagnra", - "author_inst": "Universite de Lome, Laboratoire de Biologie Moleculaire et d'Immunologie (BIOLIM), Lome, Togo" - }, - { - "author_name": "Didier Koumavi Ekouevi", - "author_inst": "Universite de Lome, Departement de Sante Publique, Lome, Togo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20169656", "rel_title": "Obtaining prevalence estimates of COVID-19: A model to inform decision-making", @@ -1235615,6 +1231955,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.04.20168583", + "rel_title": "COVID-19: Beliefs in misinformation in the Australian community", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168583", + "rel_abs": "ObjectivesTo investigate prevalence of beliefs in COVID-19 misinformation and examine whether demographic, psychosocial and cognitive factors are associated with these beliefs, and how they change over time.\n\nStudy designProspective national longitudinal community online survey.\n\nSettingAustralian general public.\n\nParticipantsAdults aged over 18 years (n=4362 baseline/Wave 1; n=1882 Wave 2; n=1369 Wave 3).\n\nMain outcome measureCOVID-19 misinformation beliefs.\n\nResultsStronger agreement with misinformation beliefs was significantly associated with younger age, male gender, lower education, and primarily speaking a language other than English at home (all p<0.01). After controlling for these variables, misinformation beliefs were significantly associated (p<0.001) with lower digital health literacy, lower perceived threat of COVID-19, lower confidence in government, and lower trust in scientific institutions. The belief that the threat of COVID-19 is \"greatly exaggerated\" increased between Wave 1-2 (p=0.002), while belief that herd immunity benefits were being covered up decreased (p<0.001). Greatest support from a list of Australian Government identified myths was for those regarding hot temperatures killing the virus (22%) and Ibuprofen exacerbates COVID-19 (13%). Lower institutional trust and greater rejection of official government accounts were associated with greater support for COVID-19 myths after controlling for sociodemographic variables.\n\nConclusionThese findings highlight important gaps in communication effectiveness. Stronger endorsement of misinformation was associated with male gender, younger age, lower education and language other than English spoken at home. Misinformation can undermine public health efforts. Public health authorities must urgently target groups identified in this study when countering misinformation and seek ways to enhance public trust of experts, governments, and institutions.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Kristen Pickles", + "author_inst": "University of Sydney" + }, + { + "author_name": "Erin Cvejic", + "author_inst": "University of Sydney" + }, + { + "author_name": "Brooke Nickel", + "author_inst": "University of Sydney" + }, + { + "author_name": "Tessa Copp", + "author_inst": "University of Sydney" + }, + { + "author_name": "Carissa Bonner", + "author_inst": "University of Sydney" + }, + { + "author_name": "Julie Leask", + "author_inst": "University of Sydney" + }, + { + "author_name": "Julie Ayre", + "author_inst": "University of Sydney" + }, + { + "author_name": "Carys Batcup", + "author_inst": "University of Sydney" + }, + { + "author_name": "Samuel Cornell", + "author_inst": "University of Sydney" + }, + { + "author_name": "Thomas Dakin", + "author_inst": "University of Sydney" + }, + { + "author_name": "Rachael Dodd", + "author_inst": "University of Sydney" + }, + { + "author_name": "Jennifer MJ Isautier", + "author_inst": "University of Sydney" + }, + { + "author_name": "Kirsten J McCaffery", + "author_inst": "University of Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.04.20154203", "rel_title": "Safety of hot and cold site admissions within a high volume urology department in the United Kingdom at the peak of the COVID-19 pandemic", @@ -1236530,69 +1232937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168815", - "rel_title": "Serology assessment of antibody response to SARS-CoV-2 in patients with COVID-19 by rapid IgM/IgG antibody test", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168815", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has created a global health- and economic crisis. Lifting confinement restriction and resuming to normality depends greatly on COVID-19 immunity screening. Detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which causes COVID-19 by serological methods is important to diagnose a current or resolved infection. In this study, we applied a rapid COVID-19 IgM/IgG antibody test and performed serology assessment of antibody response to SARS-CoV-2. In PCR-confirmed COVID-19 patients (n=45), the total antibody detection rate is 92% in hospitalized patients and 79% in non-hospitalized patients. We also studied antibody response in relation to time after symptom onset and disease severity, and observed an increase in antibody reactivity and distinct distribution patterns of IgM and IgG following disease progression. The total IgM and IgG detection is 63% in patients with < 2 weeks from disease onset; 85% in non-hospitalized patients with > 2 weeks disease duration; and 91% in hospitalized patients with > 2 weeks disease duration. We also compared different blood sample types and suggest a potentially higher sensitivity by serum/plasma comparing with whole blood measurement. To study the specificity of the test, we used 69 sera/plasma samples collected between 2016-2018 prior to the COVID-19 pandemic, and obtained a test specificity of 97%. In summary, our study provides a comprehensive validation of the rapid COVID-19 IgM/IgG serology test, and mapped antibody detection patterns in association with disease progress and hospitalization. Our study supports that the rapid COVID-19 IgM/IgG test may be applied to assess the COVID-19 status both at the individual and at a population level.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yang De Marinis", - "author_inst": "Lund University" - }, - { - "author_name": "Torgny Sunnerhagen", - "author_inst": "Lund University" - }, - { - "author_name": "Pradeep Bompada", - "author_inst": "Lund University" - }, - { - "author_name": "Anna Blackberg", - "author_inst": "Lund University" - }, - { - "author_name": "Runtao Yang", - "author_inst": "Shandong University" - }, - { - "author_name": "Joel Svensson", - "author_inst": "Lund University" - }, - { - "author_name": "Ola Ekstrom", - "author_inst": "Lund University" - }, - { - "author_name": "Karl-Fredrik Eriksson", - "author_inst": "Lund University" - }, - { - "author_name": "Ola Hansson", - "author_inst": "Lund University" - }, - { - "author_name": "Leif Groop", - "author_inst": "Lund University" - }, - { - "author_name": "Isabel Goncalves", - "author_inst": "Lund University" - }, - { - "author_name": "Magnus Rasmussen", - "author_inst": "Lund University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.05.20168971", "rel_title": "Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals", @@ -1237401,6 +1233745,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.05.20169078", + "rel_title": "Transient dynamics of SARS-CoV-2 as England exited national lockdown", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169078", + "rel_abs": "Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Haowei Wang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christina J Atchison", + "author_inst": "Imperial College London" + }, + { + "author_name": "Peter Diggle", + "author_inst": "Lancaster University" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Helen Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20168963", "rel_title": "Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity", @@ -1238508,57 +1234923,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.08.05.237867", - "rel_title": "Rapid GMP-compliant expansion of SARS-CoV-2-specific T cells from convalescent donors for use as an allogeneic cell therapy for COVID-19", - "rel_date": "2020-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.237867", - "rel_abs": "COVID-19 disease caused by the SARS-CoV-2 virus is characterized by dysregulation of effector T cells and accumulation of exhausted T cells. T cell responses to viruses can be corrected by adoptive cellular therapy using donor-derived virus-specific T cells. Here we show that SARS-CoV-2-exposed blood donations contain CD4 and CD8 memory T cells specific for SARS-CoV-2 spike, nucleocapsid and membrane antigens. These peptides can be used to isolate virus-specific T cells in a GMP-compliant process. These T cells can be rapidly expanded using GMP-compliant reagents for use as a therapeutic product. Memory and effector phenotypes are present in the selected virus-specific T cells, but our method rapidly expands the desirable central memory phenotype. A manufacturing yield ranging from 1010 to 1011 T cells can be obtained within 21 days culture. Thus, multiple therapeutic doses of virus-specific T cells can be rapidly generated from convalescent donors for treatment of COVID-19 patients\n\nOne Sentence SummaryCD4+ and CD8+ T cells specific for SARS-CoV-2 can be isolated from convalescent donors and rapidly expanded to therapeutic doses at GMP standard, maintaining the desired central memory phenotype required for protective immune responses against severe COVID-19 infections.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Rachel S Cooper", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Alasdair R Fraser", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Linda Smith", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Paul Burgoyne", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Stuart N Imlach", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Lisa M Jarvis", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Sharon Zahara", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "Marc L Turner", - "author_inst": "Scottish National Blood Transfusion Service" - }, - { - "author_name": "John DM Campbell", - "author_inst": "Scottish National Blood Transfusion Service" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.05.237339", "rel_title": "Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences", @@ -1239399,6 +1235763,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.26.20154724", + "rel_title": "Interim Results of a Phase II/III Multicenter Randomized Clinical Trial of AVIFAVIR in Hospitalized Patients with COVID-19", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20154724", + "rel_abs": "In May 2020 the Russian Ministry of Health granted fast-track marketing authorization to RNA polymerase inhibitor AVIFAVIR (favipiravir) for the treatment of COVID-19 patients. In the pilot stage of Phase II/III clinical trial, AVIFAVIR enabled SARS-CoV-2 viral clearance in 62.5% of patients within 4 days, and was safe and well-tolerated.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Andrey A. Ivashchenko", + "author_inst": "ChemRar High-Tech Center, Khimki, Moscow region, Russian Federation" + }, + { + "author_name": "Kirill A. Dmitriev", + "author_inst": "Russian Direct Investment Fund, Moscow, Russian Federation" + }, + { + "author_name": "Natalia V. Vostokova", + "author_inst": "IPHARMA LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Valeria N. Azarova", + "author_inst": "IPHARMA LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Andrew A. Blinow", + "author_inst": "Chromis LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Alina N. Egorova", + "author_inst": "IPHARMA LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Ivan G. Gordeev", + "author_inst": "City Clinical Hospital n.a. O.M. Filatov, Moscow, Russian Federation" + }, + { + "author_name": "Alexey P. Ilin", + "author_inst": "Department of Chemistry and Technology, Chemical Diversity Research Institute, Khimki, Moscow region" + }, + { + "author_name": "Ruben N. Karapetian", + "author_inst": "Department of Biology, Chemical Diversity Research Institute, Khimki, Moscow region, Russian Federation" + }, + { + "author_name": "Dmitry V. Kravchenko", + "author_inst": "Department of Chemistry and Technology, Chemical Diversity Research Institute, Khimki, Moscow region" + }, + { + "author_name": "Nikita V. Lomakin", + "author_inst": "Central Clinical Hospital with Polyclinic, Moscow, Russian Federation" + }, + { + "author_name": "Elena A. Merkulova", + "author_inst": "IPHARMA LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Natalia A. Papazova", + "author_inst": "Department of finished dosage forms, Chemical Diversity Research Institute, Khimki, Moscow region, Russian Federation" + }, + { + "author_name": "Elena P. Pavlikova", + "author_inst": "Moscow State University n.a. M. V. Lomonosov, Moscow, Russian Federation" + }, + { + "author_name": "Nikolay P. Savchuk", + "author_inst": "Chemical Diversity Research Institute, Khimki, Moscow region, Russian Federation" + }, + { + "author_name": "Elena N. Simakina", + "author_inst": "Clinical Hospital No.1, Smolensk, Russian Federation" + }, + { + "author_name": "Tagir A. Sitdekov", + "author_inst": "Russian Direct Investment Fund, Moscow, Russian Federation" + }, + { + "author_name": "Elena A. Smolyarchuk", + "author_inst": "First Moscow State Medical University n.a. I.M. Sechenov, Moscow, Russian Federation" + }, + { + "author_name": "Elena G. Tikhomolova", + "author_inst": "Infectious clinical hospital No. 2, Nizhny Novgorod, Russian Federation" + }, + { + "author_name": "Elena V. Yakubova", + "author_inst": "Chromis LLC, Skolkovo Innovative Centre, Moscow, Russian Federation" + }, + { + "author_name": "Alexandre V. Ivachtchenko", + "author_inst": "Chemical Diversity Research Institute, Khimki, Moscow region, Russian Federation" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.28.20157974", "rel_title": "Therapeutic effectiveness of interferon alpha 2b treatment for COVID-19 patient recovery", @@ -1240630,37 +1237093,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20165761", - "rel_title": "The COVID-19 Consequences of College Class Continuity Calculator: A Tool to Provide Students and Administrators with Estimated Risks of Returning to Campus", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165761", - "rel_abs": "As schools prepare for the start of the Fall 2020 semester, many are struggling to make decisions regarding whether or not to return to on-campus classes or whether to remain fully online. Unfortunately, there is no one-size-fits-all answer, and schools must balance their own risks against the costs of remote learning. We present a tool that integrates information about study body composition with predictions of COVID-19 infection rates in order to provide clarity and insight into the decisions facing colleges and universities nationwide. Our tool is freely available and currently hosted at the following location: https://bewicklab.shinyapps.io/covid-1/", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sharon Bewick", - "author_inst": "Clemson University" - }, - { - "author_name": "Erika Ludden", - "author_inst": "Clemson University" - }, - { - "author_name": "Suzanne Robertson", - "author_inst": "Virginia Commonwealth University" - }, - { - "author_name": "Jeffrey Demers", - "author_inst": "University of Maryland College Park" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.31.20165126", "rel_title": "A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy", @@ -1241405,6 +1237837,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.01.20165142", + "rel_title": "A variational model for computing the effective reproduction number of SARS-CoV-2", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20165142", + "rel_abs": "The COVID-19 pandemic has undergone frequent and rapid changes in its local and global infection rates, driven by governmental measures, or the emergence of new viral variants. The reproduction number Rt indicates the average number of cases generated by an infected person at time t and is a key indicator of the spread of an epidemic. A timely estimation of Rt is a crucial tool to enable governmental organizations to adapt quickly to these changes and assess the consequences of their policies. The EpiEstim method is the most widely accepted method for estimating Rt. But it estimates Rt with a significant temporal delay. Here, we propose a new method, EpiInvert, that shows good agreement with EpiEstim, but that provides estimates of Rt several days in advance. We show that Rt can be estimated by inverting the renewal equation linking Rt with the observed incidence curve of new cases, it. Our signal processing approach to this problem yields both Rt and a restored it corrected for the \"weekend effect\" by applying a deconvolution + denoising procedure. The implementations of the EpiInvert and EpiEstim methods are fully open-source and can be run in real-time on every country in the world, and every US state through a web interface at www.ipol.im/epiinvert.\n\nSignificance StatementBased on a signal processing approach we propose a method to compute the reproduction number Rt, the transmission potential of an epidemic over time. Rt is estimated by minimizing a functional that enforces: (i) the ability to produce an incidence curve it corrected of the weekly periodic bias produced by the \"weekend effect\", obtained from Rt through a renewal equation; (ii) the regularity of Rt. A good agreement is found between our Rt estimate and the one provided by the currently accepted method, EpiEstim, except our method predicts Rt several days closer to present. We provide the mathematical arguments for this shift. Both methods, applied every day on each country, can be compared at www.ipol.im/epiinvert.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Luis Alvarez", + "author_inst": "Universidad de Las Palmas de Gran Canaria" + }, + { + "author_name": "Miguel Colom", + "author_inst": "Universite Paris-Saclay" + }, + { + "author_name": "Jean-David Morel", + "author_inst": "Laboratoire de Physiologie Integrative et Systemique. Ecole Polytechnique Federale de Lausanne, AI 1144 Station 15 CH-1015 Lausanne Switzerland" + }, + { + "author_name": "Jean-Michel Morel", + "author_inst": "Universite Paris-Saclay" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.01.20164335", "rel_title": "The Incubation Period of Severe Acute Respiratory Syndrome Coronavirus 2:A Systematic Review", @@ -1242156,57 +1238619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.01.20166330", - "rel_title": "Respiratory viral infections by Non-influenza viruses are associated with more adverse clinical outcome in patients with underlying liver disease: a single centre laboratory based study.", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166330", - "rel_abs": "BackgroundRespiratory viral infections are an important cause of acute respiratory tract infections. They are caused by both Influenza and non influenza viruses. Respiratory viral infections are known to be associated with severe clinical outcome especially in the critically ill. A constant surveillance is needed for early etiological identification which can help in timely and appropriate management and will further help in prevention of indiscriminate use of antibiotics in patients with viral etiology.\n\nMethodsIn this retrospective study, clinical records of all adult liver disease patients with clinically confirmed ARI, whose request for respiratory viral testing were received in the virology laboratory during September 2016 - March 2019 were reviewed. Respiratory viruses were identified by real time PCR on FilmArray 2.0 instrument (BioFire Diagnostics, Utah, USA) using Respiratory panel as per the manufacturers instructions.\n\nResultsOf the 603 patients of liver disease with clinically confirmed influenza like illness, over all incidence of respiratory viral infection was 24.3% (n= 147). Infections by non-influenza viruses (87, 59.1%) were more than influenza group of viruses. Mortality was higher in non influenza group (43, 49.4%) as compared to influenza (24, 40%) [p=0.015] being maximum in Rhinovirus, 22 (32.8%). Two peaks were observed in both influenza and non influenza groups, first in the months of January and February and the other one in August and October.\n\nConclusionWith the emergence of SARS-CoV-2 it has now become imperative for a constant surveillance of the non influenza viruses for early etiological identification of the respiratory viral infection for proper and timely management in the critically ill.\n\nHighlightsO_LIPatients with liver cirrhosis having Respiratory viral infections have a poor outcome in terms of morbidity and mortality.\nC_LIO_LIMortality associated with non influenza viruses (NIV) is more as compared to influenza virus infections.\nC_LIO_LICOVID-19 pandemic and higher mortality in NIVs warrants a constant monitoring of respiratory viral infections.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ekta Gupta", - "author_inst": "ILBS" - }, - { - "author_name": "Abhishek Padhi", - "author_inst": "ILBS" - }, - { - "author_name": "Kavita Agarwal", - "author_inst": "ILBS" - }, - { - "author_name": "Krithiga Ramachandran", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Reshu Aggarwal", - "author_inst": "Institute of Liver and Biliary Sciences" - }, - { - "author_name": "Samba Siva Rao Pasupuleti", - "author_inst": "ILBS" - }, - { - "author_name": "Debajyoti Bhattacharyya", - "author_inst": "INSTITUTE OF LIVER & BILIARY SCIENCES, NEW DELHI" - }, - { - "author_name": "Rakhi Maiwall", - "author_inst": "ILBS" - }, - { - "author_name": "Shiv Kumar Sarin", - "author_inst": "Institute of Liver and Biliary Sciences (ILBS)" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.03.20167692", "rel_title": "COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020", @@ -1242695,6 +1239107,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.08.02.20166785", + "rel_title": "The Lebanese Cohort for COVID-19; A Challenge for the ABO Blood Group System", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.02.20166785", + "rel_abs": "A sudden outbreak of pneumonia caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world facilitating the declaration of the resultant disease as a pandemic in March,2020. In Lebanon, the fast action of announcing a state of emergency with strict measures was among the factors that helped in achieving a successful containment of the disease in the country. Predisposing factors for acquiring COVID-19 and for developing a severe form of this disease were postulated to be related to epidemiological and clinical characteristics as well as the genomics signature of a given population or its environment. Biological markers such as the ABO blood group system was amongst those factors that were proposed to be linked to the variability in the disease course and/or the prevalence of this infection among different groups. We therefore conducted the first retrospective case-control study in the Middle-East and North Africa that tackles the association between the blood group types and the susceptibility as well as the severity of SARS-CoV2 infection. Opposing to the current acknowledged hypothesis, our results have challenged the association significance of this system with COVID-19. Herein, we highlighted the importance of studying larger cohorts using more rigorous approaches to diminish the potential confounding effect of some underlying comorbidities and genetic variants that are known to be associated with the ABO blood group system.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Athar Khalil", + "author_inst": "American University of Beirut" + }, + { + "author_name": "Mahmoud Hassoun", + "author_inst": "Rafik Hariri University Hospital" + }, + { + "author_name": "Rita Feghali", + "author_inst": "Rafik Hariri University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.08.03.20167007", "rel_title": "Severity Assessment and Progression Prediction of COVID-19 Patients based on the LesionEncoder Framework and Chest CT", @@ -1243834,25 +1240273,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.03.20167338", - "rel_title": "COVID-19 Case Mortality Rates Continue to Decline in Florida", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167338", - "rel_abs": "We studied COVID-19 case mortality in Florida among four successive cohorts of persons at least 50 years of age, each of whom we followed for 28 to 48 days from date of diagnosis. The cohorts were separated by date of diagnosis into four nonoverlapping intervals: March 29 - April 18; April 29 - May 19; May 21 - June 10; and June 14 - July 4, 2020. Case mortality rates declined consistently and significantly over the course of the four intervals: 57% among those aged 50-59 years; 62% among those aged 60-69 years; 52% among those aged 70-79 years; and 34% among those aged 80 or more years. These findings were consistent with progressive improvements in the medical care of COVID-19 patients. We further studied case mortality by hospitalization status. The case mortality rate among hospitalized patients aged 60-69 years fell significantly from the first to the third interval. During the fourth interval, an apparent rise in mortality among hospitalized patients in the same age group was mirrored by a significant decline in mortality among those not hospitalized. These findings were consistent with the out-of-hospital treatment of some patients who would have previously been hospitalized.\n\nThis study relies exclusively on publicly available, aggregate health data that contain no individual identifiers. The author has no competing interests and no funding sources to declare. This article represents to the sole opinion of its author and does not necessarily represent the opinions of the Massachusetts Institute of Technology, the National Bureau of Economic Research, Eisner Health, or any other organization.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jeffrey E Harris", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167262", "rel_title": "Altitude as a protective factor from COVID-19", @@ -1244457,6 +1240877,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.04.20167890", + "rel_title": "Hospital Admission Rates, Length of Stay and In-hospital Mortality for Common Acute Care Conditions in COVID-19 vs. Pre-COVID-19 Era", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167890", + "rel_abs": "BackgroundImpact of COVID-19 upon acute care admission rates and patterns are unknown. We sought to determine the change in rates and types of admissions to tertiary and specialty care hospitals in the COVID-19 era compared with pre-COVID-19 era.\n\nMethodsAcute care admissions to the largest tertiary care referral hospital, designated national referral centers for cardiac, cancer and maternity hospital in the State of Qatar during March 2020 (COVID-19 era) and January 2020 and March 2019 (pre-COVID-19 era) were compared. We calculated total admissions, and admissions for eight specific acute care conditions, in-hospital mortality rate and length of stay at each hospital.\n\nResultsA total of 18,889 hospital admissions were recorded. A sharp decline ranging from 9%-75% was observed in overall admissions. A decline in both elective and non-elective surgeries was observed. A decline of 9%-58% was observed in admissions for acute appendicitis, acute coronary syndrome, stroke, bone fractures, cancer and live births, while an increase in admissions due to respiratory tract infections was observed. Overall length of stay was shorter in the COVID-19 period possibly suggesting lesser overall disease severity, with no significant change in in-hospital mortality. Unadjusted mortality rate for Qatar showed marginal increase in the COVID-19 period.\n\nConclusionsWe observed a sharp decline in acute care hospital admissions, with a significant decline in admissions due to seven out of eight acute care conditions. This decline was associated with a shorter length of stay, but not associated with a change in in-hospital mortality rate.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anand B Kartha", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Naseer A Masoodi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Aftab M Azad", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Nidal A Asaad", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Mohamad U Alhomsi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Huda A Saleh", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health Qatar" + }, + { + "author_name": "Abdul-Badi Abou-Samra", + "author_inst": "Hamad Medical Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.02.20166694", "rel_title": "Assessment of multiplex digital droplet RT-PCR as an accurate diagnosis tool for SARS-CoV-2 detection in nasopharyngeal swabs and saliva samples", @@ -1245671,69 +1242142,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.08.04.235549", - "rel_title": "Hypertonic saline solution inhibits SARS-CoV-2 in vitro assay", - "rel_date": "2020-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.235549", - "rel_abs": "We are facing an unprecedented global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At this date more than 680 thousand people have died due to coronavirus disease 2019 (COVID-19). Unfortunately, until now no effective treatment to combat the virus and vaccine are available. We performed experiments to test if hypertonic saline solution is able to inhibit virus replication in vitro. Our data shows that 260 mM NaCl (1.5%) inhibits 100% SARS-CoV-2 replication in Vero cells. Furthermore, our results suggest that the virus replication inhibition is due to an intracellular mechanism and not due to the dissociation between spike SARS-CoV-2 protein and its human receptor angiotensin-converting enzyme 2 interaction. NaCl depolarizes the plasma membrane supposedly associated with the inhibition of the SARS-CoV-2 life cycle. This observation could lead to simple, safe and low cost interventions at various stages of COVID-19 treatment, improving the prognosis of infected patients, thereby mitigating the social and economic costs of the pandemic.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Rafael Rahal Guaragna Machado", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Talita Glaser", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Danielle Bastos Araujo", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Lyvia Lintzmaier Petiz", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Danielle Bruna Leal Oliveira", - "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" - }, - { - "author_name": "Giuliana Stravinskas Durigon", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Alessandra Lima Leal", - "author_inst": "Gaspar Vianna Clinic Hospital Foundation" - }, - { - "author_name": "Joao Renato R. Pinho", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Luis Carlos S. Ferreira", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Henning Ulrich", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Edison Luiz Rodrigues Durigon", - "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" - }, - { - "author_name": "Cristiane Rodrigues Guzzo", - "author_inst": "Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.30.20165035", "rel_title": "Modified SIR-model applied to covid-19, similarity solutions and projections to further development", @@ -1246690,6 +1243098,77 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.08.03.234914", + "rel_title": "De novo design of picomolar SARS-CoV-2 miniprotein inhibitors", + "rel_date": "2020-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.03.234914", + "rel_abs": "We used two approaches to design proteins with shape and chemical complementarity to the receptor binding domain (RBD) of SARS-CoV-2 Spike protein near the binding site for the human ACE2 receptor. Scaffolds were built around an ACE2 helix that interacts with the RBD, or de novo designed scaffolds were docked against the RBD to identify new binding modes. In both cases, designed sequences were optimized first in silico and then experimentally for target binding, folding and stability. Nine designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked bona fide SARS-CoV-2 infection of Vero E6 cells with IC50 values ranging from 35 pM to 35 nM; the most potent of these -- 56 and 64 residue hyperstable proteins made using the second approach -- are roughly six times more potent on a per mass basis (IC50 ~ 0.23 ng/ml) than the best monoclonal antibodies reported thus far. Cryo-electron microscopy structures of the SARS-CoV-2 spike ectodomain trimer in complex with the two most potent minibinders show that the structures of the designs and their binding interactions with the RBD are nearly identical to the computational models, and that all three RBDs in a single Spike protein can be engaged simultaneously. These hyperstable minibinders provide promising starting points for new SARS-CoV-2 therapeutics, and illustrate the power of computational protein design for rapidly generating potential therapeutic candidates against pandemic threats.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "David Baker", + "author_inst": "University of Washington" + }, + { + "author_name": "Longxing Cao", + "author_inst": "University of Washington" + }, + { + "author_name": "Inna Goreshnik", + "author_inst": "University of Washington" + }, + { + "author_name": "Brian Coventry", + "author_inst": "University of Washington" + }, + { + "author_name": "James Brett Case", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Lauren Miller", + "author_inst": "University of Washington" + }, + { + "author_name": "Lisa Kozodoy", + "author_inst": "University of Washington" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Lauren Carter", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "Lance Stewart", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2020.08.03.234005", "rel_title": "Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic", @@ -1247789,41 +1244268,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.30.20165522", - "rel_title": "Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165522", - "rel_abs": "The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. The IgG avidity assay used a novel label-free immunoassay technology. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yiqi Ruben Luo", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Indrani Chakraborty", - "author_inst": "Gator Bio" - }, - { - "author_name": "Cassandra Yun", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Alan H.B. Wu", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Kara Lake Lynch", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20165068", "rel_title": "Outpatient screening of health status and lifestyle among post-bariatric patients during the Covid-19 pandemic in Sao Paulo, Brazil.", @@ -1248640,6 +1245084,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20164681", + "rel_title": "Loss expansion of SARS-CoV-2 specific immunity is a key risk factor in fatal patients with COVID-19", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164681", + "rel_abs": "Knowledge of the dynamic immunological characteristics of patients with coronavirus disease 2019 (COVID-19) is essential for clinicians to understand the progression of the disease. Our data showed that the immune system and function gradually remodeled and declined with age, starting from age 16 until age 91 in 25,239 healthy controls. An analysis of the relationship between the number of lymphocytes and age revealed that the lymphocyte and subset counts tended to decline with age significantly. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunity declined with age and was associated with survival time in fatal cases. Loss in the expansion of SARS-CoV-2-specific immunity could be expanded in vitro. The concurrent decline in SARS-CoV-2-specific cellular and humoral immunities and prolonged SARS-CoV-2 exposure predicted fatal outcomes. Our findings provide a basis for further analysis of SARS-CoV-2-specific immunity and understanding of the pathogenesis of fatal COVID-19 cases.\n\nO_LSTHighlightsC_LSTO_LIThe immune system and function gradually remodeled and declined with age.\nC_LIO_LISARS-CoV-2-specific immunity declined with age in fatal cases.\nC_LIO_LISARS-CoV-2-specific immunity was associated with survival time in fatal cases.\nC_LIO_LILoss in the expansion of SARS-CoV-2-specific immunity could be expanded in vitro.\nC_LIO_LIA concurrent decline in SARS-CoV-2-specific cellular and humoral immunities and prolonged SARS-CoV-2 exposure predicted fatal outcomes.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Qiang Zeng", + "author_inst": "Chinese PLA General Hospital," + }, + { + "author_name": "Gang Huang", + "author_inst": "Shanghai University of Medicine and Health Sciences" + }, + { + "author_name": "Yong-zhe Li", + "author_inst": "Peking Union Medical College Hospital" + }, + { + "author_name": "Guoqiang Xu", + "author_inst": "Soochow University" + }, + { + "author_name": "Sheng-yong Dong", + "author_inst": "Chinese PLA General Hospital" + }, + { + "author_name": "Tian-yu Zhong", + "author_inst": "Gannan Medical University" + }, + { + "author_name": "Zong-tao Chen", + "author_inst": "Army Medical University" + }, + { + "author_name": "Yang Xu", + "author_inst": "Shanghai University of Medicine and Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.29.20164640", "rel_title": "Sex-specificity of mortality risk factors among hospitalized COVID-19 patients in New York City: prospective cohort study", @@ -1249659,81 +1246150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20165175", - "rel_title": "Sustained Cellular Immune Dysregulation in Individuals Recovering from SARS-CoV-2 Infection", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165175", - "rel_abs": "SARS-CoV-2 causes a wide spectrum of clinical manifestations and significant mortality. Studies investigating underlying immune characteristics are needed to understand disease pathogenesis and inform vaccine design. In this study, we examined immune cell subsets in hospitalized and non-hospitalized individuals. In hospitalized patients, many adaptive and innate immune cells were decreased in frequency compared to healthy and convalescent individuals, with the exception of B lymphocytes which increased. Our findings show increased frequencies of T-cell activation markers (CD69, Ox40, HLA-DR and CD154) in hospitalized patients, with other T-cell activation/exhaustion markers (CD25, PD-L1 and TIGIT) remaining elevated in hospitalized and non-hospitalized individuals. B cells had a similar pattern of activation/exhaustion, with increased frequency of CD69 and CD95 during hospitalization, followed by an increase in PD1 frequencies in non-hospitalized individuals. Interestingly, many of these changes were found to increase over time in non-hospitalized longitudinal samples, suggesting a prolonged period of immune dysregulation following SARS-CoV-2 infection. Changes in T-cell activation/exhaustion in non-hospitalized patients were found to positively correlate with age. Severely infected individuals had increased expression of activation and exhaustion markers. These data suggest a prolonged period of immune dysregulation following SARS-CoV-2 infection highlighting the need for additional studies investigating immune dysregulation in convalescent individuals.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Jacob K Files", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Sushma Boppana", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Mildred D Perez", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Sanghita Sarkar", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Kelsey E Lowman", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Kai Qin", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Sarah Sterrett", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Eric Carlin", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Anju Bansal", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Steffanie Sabbaj", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Dustin M Long", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Olaf Kutsch", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "James Kobie", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Paul A Goepfert", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Nathan Erdmann", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20164327", "rel_title": "Self-rated smell ability enables highly specific predictors of COVID-19 status: a case control study in Israel", @@ -1250342,6 +1246758,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.07.30.228023", + "rel_title": "The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein", + "rel_date": "2020-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.30.228023", + "rel_abs": "The multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the ~30 kb viral RNA genome to aid its packaging into the 80-90 nm membrane-enveloped virion. The N protein is composed of N-terminal RNA-binding and C-terminal dimerization domains that are flanked by three intrinsically disordered regions. Here we demonstrate that a centrally located 40 amino acid intrinsically disordered domain drives phase separation of N protein when bound to RNA, with the morphology of the resulting condensates affected by inclusion in the RNA of the putative SARS-CoV-2 packaging signal. The SARS-CoV-2 M protein, normally embedded in the virion membrane with its C-terminus extending into the virion core, independently induces N protein phase separation that is dependent on the N proteins C-terminal dimerization domain and disordered region. Three-component mixtures of N+M+RNA form condensates with mutually exclusive compartments containing N+M or N+RNA, including spherical annular structures in which the M protein coats the outside of an N+RNA condensate. These findings support a model in which phase separation of the N protein with both the viral genomic RNA and the SARS-CoV-2 M protein facilitates RNA packaging and virion assembly.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Shan Lu", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Qiaozhen Ye", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Digvijay Singh", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Elizabeth Villa", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Don W. Cleveland", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Kevin D. Corbett", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.31.230987", "rel_title": "Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates", @@ -1251245,41 +1247700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20165910", - "rel_title": "Job insecurity, financial threat and mental health in the COVID-19 context: The buffer role of perceived social support", - "rel_date": "2020-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165910", - "rel_abs": "The social distancing, confinement and quarantine adopted since March 2020 to confront the COVID-19 pandemic have affected multiple vital areas, and specially work, business and productive activities. Prior research has highlighted the relation between perceptions of risk in employment and its concomitant financial risk with a myriad of consequences for peoples well-being and health. In order to analyze the potential negative consequences of temporary layoffs, downsizing or closure of companies and businesses, and the consequent insecurity about the continuity of employment, the aim of this study is twofold. Firstly, to analyze the relations between the perceptions of job insecurity and financial threat and overall mental health during the first month of the COVID-19 pandemic in a sample of the Chilean adult population. And secondly, to identify the potential buffer effect of perceived social support on this relation. To analyze this, we carried out a cross-sectional study on a non-probabilistic sample aimed at a general Chilean adult population. The results show that both perceptions of job insecurity and financial threat are associated with a decline in perceived mental health. Additionally, results indicate a moderate buffer effect of perceived social support relative to the size of the social network. Thus, in relation to job insecurity and financial threat, the network size mitigates the association of both with the decline in perceived mental health. The theoretical and applied scope of these findings are analyzed, and their challenges and limitations are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carlos-Maria Alcover", - "author_inst": "Universidad Rey Juan Carlos" - }, - { - "author_name": "Sergio Salgado", - "author_inst": "Universidad de La Frontera" - }, - { - "author_name": "Gabriela Nazar", - "author_inst": "Universidad de Concepcion" - }, - { - "author_name": "Raul Ramirez-Vielma", - "author_inst": "Universidad de Concepcion" - }, - { - "author_name": "Carolina Gonzalez-Suhr", - "author_inst": "Universidad de La Frontera" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.07.29.20164285", "rel_title": "Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19", @@ -1252000,6 +1248420,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20161323", + "rel_title": "Model stability of COVID-19 mortality prediction with biomarkers", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20161323", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is an unprecedented and fast evolving pandemic, which has caused a large number of critically ill patients and deaths globally. It is an acute public health crisis leading to overloaded critical care capacity. Timely prediction of the clinical outcome (death/survival) of hospital-admitted COVID-19 patients can provide early warnings to clinicians, allowing improved allocation of medical resources. In a recently published paper, an interpretable machine learning model was presented to predict the mortality of COVID-19 patients with blood biomarkers, where the model was trained and tested on relatively small data sets. However, the model or performance stability was not explored and assessed. By re-analyzing the data, we reveal that the reported mortality prediction performance was likely over-optimistic and its uncertainty was underestimated or overlooked, with a large variability in predicting deaths.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chenyan Huang", + "author_inst": "Syracuse University" + }, + { + "author_name": "Xi Long", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Zhuozhao Zhan", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Edwin van den Heuvel", + "author_inst": "Eindhoven University of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.21.20157677", "rel_title": "A Non-Adaptive Combinatorial Group Testing Strategy to Facilitate Healthcare Worker Screening During the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Outbreak", @@ -1252819,81 +1249270,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.07.29.20158717", - "rel_title": "Determinants of SARS-CoV-2 infection in Italian healthcare workers: a multicenter study", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20158717", - "rel_abs": "BackgroundHealthcare workers (HCW) are at increased risk of being infected with SARS-CoV-2, yet limited information is available on risk factors of infection.\n\nMethodsWe pooled data on occupational surveillance of 10,654 HCW who were tested for SARS-CoV-2 infection in six Italian centers. Information was available on demographics, job title, department of employment, source of exposure, use of personal protective equipment (PPE), and COVID-19-related symptoms. We fitted multivariable logistic regression models to calculate odds ratios (OR) and 95% confidence intervals (CI).\n\nFindingsThe prevalence of infection varied across centers and ranged from 3.0% to 22.0%, being strongly correlated with that of the respective areas. Women were at lower risk of infection compared to men. Fever, cough, dyspnea and malaise were the symptoms most strongly associated with infection, together with anosmia and ageusia. No differences in the risk of infection were detected between job titles, or working in a COVID-19 designated department. Reported contact with a patient inside or outside the workplace was a risk factor. Use of a mask was strongly protective against risk of infection as was use of gloves. The use of a mask by the source of exposure (patient or colleague) had an independent effect in reducing infection risk.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Paolo Boffetta", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Francesco Violante", - "author_inst": "Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy" - }, - { - "author_name": "Paolo Durando", - "author_inst": "Department of Health Sciences, University of Genoa, Genoa, Italy" - }, - { - "author_name": "Giuseppe De Palma", - "author_inst": "Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy" - }, - { - "author_name": "Enrico Pira", - "author_inst": "Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" - }, - { - "author_name": "Luigi Vimercati", - "author_inst": "Interdisciplinary Department of Medicine, University of Bari, Bari, Italy" - }, - { - "author_name": "Alfonso Cristaudo", - "author_inst": "University Hospital Pisana, Pisa, Italy" - }, - { - "author_name": "Giancarlo Icardi", - "author_inst": "Department of Health Sciences, University of Genoa, Genoa, Italy" - }, - { - "author_name": "Emma Sala", - "author_inst": "University Hospital Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Maurizio Coggiola", - "author_inst": "University Hospital City of Health and Science of Turin, Turin, Italy" - }, - { - "author_name": "Silvio Tafuri", - "author_inst": "Interdisciplinary Department of Medicine, University of Bari, Bari, Italy" - }, - { - "author_name": "Vittorio Gattini", - "author_inst": "University Hospital Pisana, Pisa, Italy" - }, - { - "author_name": "Pietro Apostoli", - "author_inst": "Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy" - }, - { - "author_name": "Giovanna Spatari", - "author_inst": "Department of Biomedical and Dentistry Sciences and Morphological and Functional Imaging, University of Messina, Messina, Italy" - }, - { - "author_name": "- Working Group on SARS-CoV-2 infection in Italian healthcare workers", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.07.24.20160101", "rel_title": "Red blood cells injuries and hypersegmented neutrophils in COVID-19 peripheral blood film", @@ -1253702,6 +1250078,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.07.29.227785", + "rel_title": "Mucin-type O-glycosylation Landscapes of SARS-CoV-2 Spike Proteins", + "rel_date": "2020-07-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.29.227785", + "rel_abs": "The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 N-glycosites and site-specific N-glycans in the S protein protomer. Herein, we report the comprehensive and precise site-specific O-glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized using high-resolution mass spectrometry. Following digestion using trypsin and trypsin/Glu-C, and de-N-glycosylation using PNGase F, we determined the mucin-type (GalNAc-type) O-glycosylation pattern of S proteins, including unambiguous O-glycosites and the 6 most common O-glycans occupying them, via Byonic identification and manual validation. Finally, 43 O-glycosites were identified in the insect cell-expressed S protein. Most glycosites were modified by non-sialylated O-glycans such as HexNAc(1) and HexNAc(1)Hex(1). In contrast, 30 O-glycosites were identified in the human cell-expressed S protein S1 subunit. Most glycosites were modified by sialylated O-glycans such as HexNAc(1)Hex(1)NeuAc(1) and HexNAc(1)Hex(1)NeuAc(2). Our results are the first to reveal that the SARS-CoV-2 S protein is a mucin-type glycoprotein; clustered O-glycans often occur in the N- and the C-termini of the S protein, and the O-glycosite and O-glycan compositions vary with the host cell type. These site-specific O-glycosylation landscapes of the SARS-CoV-2 S protein are expected to provide novel insights into the viral binding mechanism and present a strategy for the development of vaccines and targeted drugs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yong Zhang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Wanjun Zhao", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yonghong Mao", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yaohui Chen", + "author_inst": "Sichuan University" + }, + { + "author_name": "Liqiang Hu", + "author_inst": "Sichuan University" + }, + { + "author_name": "Jingqiang Zhu", + "author_inst": "Sichuan University" + }, + { + "author_name": "Meng Gong", + "author_inst": "Sichuan University" + }, + { + "author_name": "Jingqiu Cheng", + "author_inst": "Sichuan University" + }, + { + "author_name": "Hao Yang", + "author_inst": "West China Hospital, Sichuan University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.30.228890", "rel_title": "EUAdb: a resource for COVID-19 test development", @@ -1254625,25 +1251052,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.07.26.20162347", - "rel_title": "A HYBRID KNOWLEDGE-BASED AND MODIFIED REGRESSION ANALYSIS APPROACH FOR COVID-19 TRACKING IN USA", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162347", - "rel_abs": "Since its appearance in 2019, the covid-19 virus deluged the world with unprecedented data in short time. Despite the countless worldwide pertinent studies and advanced technologies, the spread is neither contained nor defeated. In fact, there is a record surge in the number of confirmed new cases since July 2020. This article presents a new predictive Knowledge-based (KB) toolkit named CORVITT (Corona Virus Tracking Toolkit) and modified linear regression model. This hybrid approach uses the confirmed new cases and demographic data, implemented. CORVITT is not an epidemiological model, in the sense that it does not model disease transmission, nor does it use underlying epidemiological parameters like the reproductive rate. It forecasts the spread in order to assist the official to make proactive intervention.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rafaat Hussein", - "author_inst": "SUNY" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.26.20162248", "rel_title": "ACE2 Expression is elevated in Airway Epithelial Cells from aged and male donors but reduced in asthma", @@ -1255356,6 +1251764,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.26.20162495", + "rel_title": "Impact of the COVID-19 Pandemic on the Short-term Course of Obsessive-Compulsive Disorder", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162495", + "rel_abs": "BackgroundThere is an understandable concern that obsessive-compulsive disorder (OCD) may worsen during the COVID-19 pandemic, but there is little empirical data. We report the impact of COVID-19 pandemic on the short-term course of OCD. We also assessed for predictors of relapse and emergence of COVID-19-themed obsessive-compulsive symptoms.\n\nMethodsA cohort of patients with a primary diagnosis of OCD (n=240) who were on regular follow-up at a tertiary care specialty OCD Clinic in India were assessed telephonically, about 2 months after the declaration of the pandemic ( pandemic cohort). Data from the medical records of an independent set of patients with OCD (n=207) who were followed-up during the same period, one year prior, was used for comparison (historical controls).\n\nResultsThe pandemic group and historical controls did not differ in the trajectories of the Yale-Brown Obsessive-Compulsive Scale (YBOCS) scores (Chi-square for likelihood-ratio test of the Group x Time interaction = 2.73, p= 0.255) and relapse rate [21% vs 20%, adjusted odds ratio = 0.81 (95% CI 0.41 -1.59, p=0.535]. Pre-existing contamination symptoms and COVID-19-related health anxiety measured by the COVID-Threat Scale did not predict relapse. Only a small proportion of patients (6%) reported COVID-19-themed obsessive-compulsive symptoms.\n\nLimitationsFollow-up 2 months after pandemic declaration may be too early understand the true impact.\n\nConclusionsThe COVID-19 pandemic, at least in the short-run, did not influence the course of illness in those who were on medications. It would be pertinent to evaluate the long-term impact of the pandemic on the course of OCD.\n\nHighlights\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@15a988dorg.highwire.dtl.DTLVardef@d5880borg.highwire.dtl.DTLVardef@d68eb4org.highwire.dtl.DTLVardef@330a6dorg.highwire.dtl.DTLVardef@f18891_HPS_FORMAT_FIGEXP M_TBL C_TBL", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lavanya P Sharma", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Srinivas Balachander", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Abel Thamby", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Mahashweta Bhattacharya", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Chethana Kishore", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Vandita Shanbhag", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Jaisoorya TS", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Janardhanan C Narayanaswamy", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "Shyam Sundar Arumugham", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + }, + { + "author_name": "YC Janardhan Reddy", + "author_inst": "National Institute of Mental Health & Neuro Sciences (NIMHANS), Bangalore" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.07.27.20162610", "rel_title": "Mental Health of Medical Workers During the COVID-19 Pandemic in Russia: Results of a Cross-Sectional Study", @@ -1256411,45 +1252874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.27.20147249", - "rel_title": "Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR.", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20147249", - "rel_abs": "Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Here we compare qRT-PCR with DETECTR to diagnose COVID-19 on 378 patient samples and report a 95% reproducibility. Patient sample dilution assays suggest a higher analytical sensitivity of DETECTR compared to qRT-PCR, however, this was not confirmed in a large patient cohort. The data showed that both techniques are equally sensitive in detecting SARS-CoV-2 providing an added value of DETECTR to the currently used qRT-PCR platforms. For DETECTR, different gRNAs can be used simultaneously to obviate negative results due to mutations in N-gene. Lateral flow strips, suitable as a point of care test (POCT), showed a 100% correlation to the high-throughput DETECTR assay. Importantly, DETECTR was 100% specific for SARS-CoV-2 and did not detect other human coronaviruses. As there is no need for specialized equipment, DETECTR could be rapidly implemented as a complementary technically independent approach to qRT-PCR thereby increasing the testing capacity of medical microbiological laboratories and relieving the existent PCR-platforms for routine non-SARS-CoV-2 diagnostic testing.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Eelke Brandsma", - "author_inst": "Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Department of Hematopoiesis, Amsterdam, The Netherla" - }, - { - "author_name": "Han JMP Verhagen", - "author_inst": "Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Department of Hematopoiesis, Amsterdam, The Netherla" - }, - { - "author_name": "Thijs J.W. van de Laar", - "author_inst": "Medical Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands" - }, - { - "author_name": "Eric C.J. Claas", - "author_inst": "Department of medical microbiology, Leiden University Medical Center, Leiden, The Netherlands" - }, - { - "author_name": "Marion Cornelissen", - "author_inst": "Department of medical microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands" - }, - { - "author_name": "Emile van den Akker", - "author_inst": "Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Department of Hematopoiesis, Amsterdam, The Netherla" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.28.20162941", "rel_title": "Sensitive detection of SARS-CoV-2 seroconversion by flow cytometry reveals the presence of nucleoprotein-reactive antibodies in Covid-19-naive individuals", @@ -1256978,6 +1253402,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.27.20163188", + "rel_title": "Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20163188", + "rel_abs": "COVID-19 primarily affects the lungs, but evidence of systemic disease with multi-organ involvement is emerging. Here, we developed a blood test to broadly quantify cell, tissue, and organ specific injury due to COVID-19, using genome-wide methylation profiling of circulating cell-free DNA in plasma. We assessed the utility of this test to identify subjects with severe disease in two independent, longitudinal cohorts of hospitalized patients. Cell-free DNA profiling was performed on 104 plasma samples from 33 COVID-19 patients and compared to samples from patients with other viral infections and healthy controls. We found evidence of injury to the lung and liver and involvement of red blood cell progenitors associated with severe COVID-19. The concentration of cfDNA correlated with the WHO ordinal scale for disease progression and was significantly increased in patients requiring intubation. This study points to the utility of cell-free DNA as an analyte to monitor and study COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Alexandre Pellan Cheng", + "author_inst": "Cornell University" + }, + { + "author_name": "Matthew Pellan Cheng", + "author_inst": "McGill University" + }, + { + "author_name": "Wei Gu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joan Sesing Lenz", + "author_inst": "Cornell University" + }, + { + "author_name": "Elaine Hsu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Erwin Schurr", + "author_inst": "McGill University" + }, + { + "author_name": "Guillaume Bourque", + "author_inst": "McGill University" + }, + { + "author_name": "Mathieu Bourgey", + "author_inst": "McGill University" + }, + { + "author_name": "Jerome Ritz", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Francisco M Marty", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Donald Cuong Vinh", + "author_inst": "McGill University" + }, + { + "author_name": "Iwijn De Vlaminck", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.07.27.20163204", "rel_title": "Examining Australian's beliefs, misconceptions, and sources of information for COVID-19: A national online survey", @@ -1258113,45 +1254604,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.25.20162107", - "rel_title": "SARS-CoV-2 viral load dynamics, duration of viral shedding and infectiousness: a living systematic review and meta-analysis", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162107", - "rel_abs": "BackgroundViral load kinetics and the duration of viral shedding are important determinants for disease transmission. We aim i) to characterize viral load dynamics, duration of viral RNA, and viable virus shedding of SARS-CoV-2 in various body fluids and ii) to compare SARS-CoV-2 viral dynamics with SARS-CoV-1 and MERS-CoV.\n\nMethodsMedline, EMBASE, Europe PMC, preprint servers and grey literature were searched to retrieve all articles reporting viral dynamics and duration of SARS-CoV-2, SARS-CoV-1 and MERS-CoV shedding. We excluded case reports and case series with < 5 patients, or studies that did not report shedding duration from symptom onset. PROSPERO registration: CRD42020181914.\n\nFindingsSeventy-nine studies on SARS-CoV-2, 8 on SARS-CoV-1, and 11 on MERS-CoV were included. Mean SARS-CoV-2 RNA shedding duration in upper respiratory tract, lower respiratory tract, stool and serum were 17.0, 14.6, 17.2 and 16.6 days, respectively. Maximum duration of SARS-CoV-2 RNA shedding reported in URT, LRT, stool and serum were 83, 59, 35 and 60 days, respectively. Pooled mean duration of SARS-CoV-2 RNA shedding was positively associated with age (p=0.002), but not gender (p = 0.277). No study to date has cultured live virus beyond day nine of illness despite persistently high viral loads. SARS-CoV-2 viral load in the upper respiratory tract appears to peak in the first week of illness, while SARS-CoV-1 and MERS-CoV peak later.\n\nConclusionAlthough SARS-CoV-2 RNA shedding in respiratory and stool can be prolonged, duration of viable virus is relatively short-lived. Thus, detection of viral RNA cannot be used to infer infectiousness. High SARS-CoV-2 titers are detectable in the first week of illness with an early peak observed at symptom onset to day 5 of illness. This review underscores the importance of early case finding and isolation, as well as public education on the spectrum of illness. However, given potential delays in the isolation of patients, effective containment of SARS-CoV-2 may be challenging even with an early detection and isolation strategy.\n\nFundingNo funding was received.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Muge Cevik", - "author_inst": "Division of Infection and Global Health, School of Medicine, University of St Andrews" - }, - { - "author_name": "Matthew Tate", - "author_inst": "Respiratory Medicine, University Hospital Wishaw, Wishaw, UK" - }, - { - "author_name": "Oliver Lloyd", - "author_inst": "NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K." - }, - { - "author_name": "Alberto Enrico Maraolo", - "author_inst": "First Division of Infectious Diseases, Cotugno Hospital, AORN dei Colli, Naples, Italy" - }, - { - "author_name": "Jenna Schafers", - "author_inst": "NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, U.K." - }, - { - "author_name": "Antonia Ho", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.25.20162156", "rel_title": "30-day mortality and morbidity in COVID-19 versus influenza: A populationbased study", @@ -1258724,6 +1255176,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.26.20158550", + "rel_title": "Association of olfactory dysfunction with hospitalization for COVID-19: a multicenter study in Kurdistan", + "rel_date": "2020-07-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20158550", + "rel_abs": "ObjectiveTo evaluate the association of olfactory dysfunction (OD) with hospitalization for COVID-19.\n\nStudy DesignMulti-center cohort study.\n\nSettingEmergency departments of thirteen COVID-19-designed hospitals in Kurdistan province, Iran.\n\nSubjects and MethodsPatients presenting with flu-like symptoms who tested positive by RT-PCR for COVID-19 between May 1st and 31st, 2020. At the time of presentation and enrollment, patients were asked about the presence of OD, fever, cough, shortness of breath, headache, rhinorrhea and sore throat. The severity of OD was assessed on an 11-point scale from 0 (none) to 10 (anosmia). Patients were either hospitalized or sent home for outpatient care based on standardized criteria.\n\nResultsOf 203 patients, who presented at a mean of 6 days into the COVID-19 disease course, 25 patients (12.3%) had new OD and 138 patients (68.0%) were admitted for their COVID-19. Patients admitted for COVID-19 had a higher prevalence of all symptoms assessed, including OD (p<0.05 in all cases), and OD identified admitted patients with 84.0% sensitivity and 34.3% specificity. On univariate logistic regression, hospitalization was associated with OD (odds ratio [OR] = 2.47, 95%CI: 1.085-6.911, p=0.049). However, hospitalization for COVID-19 was not associated with OD (OR=3.22, 95% CI: 0.57-18.31, p=0.188) after controlling for confounding demographics and comorbidities.\n\nConclusionOD may be associated with hospitalization for (and therefore more severe) COVID-19. However, this association between OD and COVID-19 severity is more likely driven by patient characteristics linked to OD, such as greater numbers of COVID-19 symptoms experienced or high-risk comorbidities.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hosna Zobairy", + "author_inst": "Department of Otolaryngology, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Erfan Shamsoddin", + "author_inst": "National Institute for Medical Research Development (NIMAD), Tehran, Iran." + }, + { + "author_name": "Mohammad Aziz Rasouli", + "author_inst": "Clinical Research Development Center, Kowsar Hospital, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Nasrollah Veisi Khodlan", + "author_inst": "Prevention and Control of Communicable Diseases Management Group, Vice-Chancellor of Health Affairs, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Ghobad Moradi", + "author_inst": "Social Determinants of Health Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Bushra Zareie", + "author_inst": "Clinical Research Development Center, Kowsar Hospital, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Sara Teymori", + "author_inst": "Clinical Research Development Center, Tohid Hospital, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Jalal Asadi", + "author_inst": "Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran." + }, + { + "author_name": "Ahmad Sofi-Mahmudi", + "author_inst": "Cochrane Iran Associate Centre, National Institute for Medical Research Development (NIMAD), Tehran, Iran." + }, + { + "author_name": "Ahmad R. Sedaghat", + "author_inst": "Department of Otolaryngology - Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.07.19.20149898", "rel_title": "Mononeuritis multiplex: an unexpectedly common feature of severe COVID-19", @@ -1259823,33 +1256330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.24.20161547", - "rel_title": "Population Data-Driven Formulation of a COVID-19 Therapeutic", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161547", - "rel_abs": "This study is designed to utilize computer modeling of the US population through NHANES to reduce the need for preclinical formulation and toxicology studies of an Ebola anti-viral (BSN389) being repurposed for COVID-19, and to thereby speed the candidate therapeutic to the clinic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Heather R. Campbell", - "author_inst": "University of Kentucky" - }, - { - "author_name": "Regan P. Cecil", - "author_inst": "University of Kentucky" - }, - { - "author_name": "Robert Lodder", - "author_inst": "University of Kentucky" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.24.20161653", "rel_title": "COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2", @@ -1260510,6 +1256990,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.24.20161851", + "rel_title": "Trends in Angiotensin Receptor Blocker Use Among those at Risk for COVID-19 Morbidity and Mortality in the United States", + "rel_date": "2020-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161851", + "rel_abs": "ImportanceAssessment of the use of angiotensin receptor blockers (ARBs) in the United States provides insight into prescribing practices, and may inform guidelines, policy measures and research during the COVID-19 pandemic.\n\nObjectiveTo evaluate trends in ARB use among adults in the United States who have preexisting conditions and sociodemographic risk factors that put them at a higher risk of SARS-CoV-2 infection and COVID-19-related complications and mortality.\n\nDesign, setting and participantsThis study uses the nationally representative cross-sectional data from the 2005-2018 National Health and Nutrition Examination Survey (NHANES). Participants included 39,749 non-institutionalized U.S. civilian adults who were 20 years and older and those with the most common preexisting conditions and risk factors reported among patients with COVID-19.\n\nMain outcomes and measuresUse of ARBs in the prior 30 days from survey interview.\n\nResultsARB use ranged from 7.4% [95% CI, 6.5%-8.4%] to 26.2% [95% CI, 19.4%-34.4%] among those with one or two metabolic, renal, respiratory, and/or cardiovascular diseases. Among individuals with the three most common preexisting conditions in patients with COVID-19 including hypertension, diabetes and obesity, ARB use was higher among the elderly, females, non-Hispanic whites, and those with health insurance coverage.\n\nConclusions and relevanceIn this nationally representative survey, ARB use was found to be widespread, but unevenly distributed among individuals with conditions and sociodemographic risk factors that place them at a higher risk of COVID-19 morbidity and mortality.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the prevalence of angiotensin receptor blocker (ARB) use among individuals at higher risk of COVID-19-related complications?\n\nFindingsIn a cross-sectional study with data from 39,749 adult participants of the National Health and Nutrition Examination Survey, ARB use ranged between 7.4% and 26.2% among those with one or two respiratory, metabolic, renal and/or cardiovascular diseases. Significant disparities in ARB use were found in participants with preexisting conditions and sociodemographic factors that place them at a higher risk of COVID-19 morbidity and mortality.\n\nMeaningARB use is widespread and disproportionate in the United States among people at higher risk of COVID-19 complications.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alexandra Perez", + "author_inst": "Nova Southeastern University College of Pharmacy" + }, + { + "author_name": "Robert Speth", + "author_inst": "Nova Southeastern University College of Pharmacy" + }, + { + "author_name": "Juan Saavedra", + "author_inst": "Georgetown University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.25.20156471", "rel_title": "Using social contact data to predict and compare the impact of social distancing policies with implications for school re-opening", @@ -1261657,25 +1258164,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.07.26.222257", - "rel_title": "An antibody-dependent enhancement (ADE) activity eliminated neutralizing antibody with potent prophylactic and therapeutic efficacy against SARS-CoV-2 in rhesus monkeys", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.222257", - "rel_abs": "Efficacious interventions are urgently needed for the treatment of COVID-19. Here, we report a monoclonal antibody (mAb), MW05, showing high SARS-CoV-2 neutralizing activity by disrupting the interaction of receptor binding domain (RBD) with angiotensin-converting enzyme 2 (ACE2) receptor. Crosslinking of Fc with Fc{gamma}RIIB mediates antibody-dependent enhancement (ADE) activity by MW05. This activity was eliminated by introducing the LALA mutation to the Fc region (MW05/LALA). Most importantly, potent prophylactic and therapeutic effects against SARS-CoV-2 were observed in rhesus monkeys. A single dose of MW05/LALA completely blocked the infection of SARS-CoV-2 in a study of its prophylactic effect and totally cleared SARS-CoV-2 in three days in a treatment setting. These results pave the way for the development of MW05/LALA as an effective strategy for combating COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Xun Gui", - "author_inst": "Mabwell (Shanghai) Bioscience Co., Ltd." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.26.222232", "rel_title": "An alternative binding mode of IGHV3-53 antibodies to the SARS-CoV-2 receptor binding domain", @@ -1262412,6 +1258900,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.07.20.20157651", + "rel_title": "A Cluster-Randomized Trial of Hydroxychloroquine as Prevention of Covid-19 Transmission and Disease", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157651", + "rel_abs": "BackgroundCurrent strategies for preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are limited to non-pharmacological interventions. Hydroxychloroquine (HCQ) has been proposed as a postexposure therapy to prevent Coronavirus disease 2019 (Covid-19) but definitive evidence is lacking.\n\nMethodsWe conducted an open-label, cluster-randomized trial including asymptomatic contacts exposed to a PCR-positive Covid-19 case in Catalonia, Spain. Clusters were randomized to receive no specific therapy (control arm) or HCQ 800mg once, followed by 400mg daily for 6 days (intervention arm). The primary outcome was PCR-confirmed symptomatic Covid-19 within 14 days. The secondary outcome was SARS-CoV-2 infection, either symptomatically compatible or a PCR-positive result regardless of symptoms. Adverse events (AEs) were assessed up to 28 days.\n\nResultsThe analysis included 2,314 healthy contacts of 672 Covid-19 index cases identified between Mar 17 and Apr 28, 2020. A total of 1,198 were randomly allocated to usual care and 1,116 to HCQ therapy. There was no significant difference in the primary outcome of PCR-confirmed, symptomatic Covid-19 disease (6.2% usual care vs. 5.7% HCQ; risk ratio 0.89 [95% confidence interval 0.54-1.46]), nor evidence of beneficial effects on prevention of SARS-CoV-2 transmission (17.8% usual care vs. 18.7% HCQ). The incidence of AEs was higher in the intervention arm than in the control arm (5.9% usual care vs 51.6% HCQ), but no treatment-related serious AEs were reported.\n\nConclusionsPostexposure therapy with HCQ did not prevent SARS-CoV-2 disease and infection in healthy individuals exposed to a PCR-positive case. Our findings do not support HCQ as postexposure prophylaxis for Covid-19.\n\nClinicalTrials.gov registration numberNCT04304053", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Oriol Mitja", + "author_inst": "1. Fight AIDS and Infectious Diseases Foundation, Badalona, Spain 2. Hospital Universitari Germans Trias i Pujol, Badalona Spain 3. Lihir Medical Centre-Interna" + }, + { + "author_name": "Maria Ubals", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Marc Corbacho", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Andrea Alemany", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Clara Suner", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Cristian Tebe", + "author_inst": "Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain" + }, + { + "author_name": "Aurelio Tobias", + "author_inst": "Institute of Environmental Assessment and Water Research (IDAEA), Spanish Council for Scientific Research (CSIC), Barcelona, Spain" + }, + { + "author_name": "Judith Penafiel", + "author_inst": "Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain" + }, + { + "author_name": "Ester Ballana", + "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Carla A Perez", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Pol Admella", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Nuria Riera-Marti", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Pep Laporte", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Jordi Mitja", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Mireia Clua", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Laia Bertran", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Sergi Gavilan", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Jordi Ara", + "author_inst": "Hospital Universitari Germans Trias i Pujol, Badalona Spain" + }, + { + "author_name": "Maria Sarquella", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Josep M Argimon", + "author_inst": "Direccio-gerencia, Institut Catala de la Salut, Barcelona, Spain" + }, + { + "author_name": "Gabriel Cuatrecasas", + "author_inst": "Equip atencio primaria de Sarria, Barcelona, Spain" + }, + { + "author_name": "Paz Canadas", + "author_inst": "SYNLAB, Barcelona, Spain" + }, + { + "author_name": "Aleix Elizalde-Torrent", + "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Robert Fabregat", + "author_inst": "Direccio General de Recerca i Innovacio en Salut, Generalitat de Catalunya, Barcelona, Spain" + }, + { + "author_name": "Magi Farre", + "author_inst": "Hospital Universitari Germans Trias i Pujol, Badalona Spain" + }, + { + "author_name": "Anna Forcada", + "author_inst": "Gerencia territorial de Catalunya Central, Institut Catala de la Salut, St. Fruitos de Bages, Spain" + }, + { + "author_name": "Gemma Flores-Mateo", + "author_inst": "Xarxa Santa Tecla Sanitaria i Social. Tarragona, Spain" + }, + { + "author_name": "Cristina Lopez", + "author_inst": "TFS Clinical Contract Research Organization, Barcelona, Spain" + }, + { + "author_name": "Esteve Muntada", + "author_inst": "Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Catalan Institute of Oncology (ICO)-Departament de Salut, Generalitat de Cataluny" + }, + { + "author_name": "Nuria Nadal", + "author_inst": "Gerencia territorial de Barcelona, Institut Catala de la Salut, Barcelona, Spain" + }, + { + "author_name": "Silvia Narejos", + "author_inst": "Entitat de Base Asociativa Centelles- Atencio Primaria, Centelles, Spain" + }, + { + "author_name": "Aroa N Gil-Ortega", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Nuria Prat", + "author_inst": "Gerencia territorial de Ambit Metropolita nord, Institut Catala de la Salut, Sabadell, Spain" + }, + { + "author_name": "Jordi Puig", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Carles Quinones", + "author_inst": "Hospital Universitari Germans Trias i Pujol, Badalona Spain" + }, + { + "author_name": "Ferran Ramirez-Viaplana", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Juliana Reyes-Uruena", + "author_inst": "Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Catalan Institute of Oncology (ICO)-Departament de Salut, Generalitat de Cataluny" + }, + { + "author_name": "Eva Riveira-Munoz", + "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Lidia Ruiz", + "author_inst": "IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" + }, + { + "author_name": "Sergi Sanz", + "author_inst": "ISGlobal, Hospital Clinic - Universitat de Barcelona, Barcelona, Spain" + }, + { + "author_name": "Alexis Sentis", + "author_inst": "Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Catalan Institute of Oncology (ICO)-Departament de Salut, Generalitat de Cataluny" + }, + { + "author_name": "Alba Sierra", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Cesar Velasco", + "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS), Barcelona, Spain" + }, + { + "author_name": "Rosa Maria Vivanco-Hidalgo", + "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS), Barcelona, Spain" + }, + { + "author_name": "Juani Zamora", + "author_inst": "TFS Clinical Contract Research Organization, Barcelona, Spain" + }, + { + "author_name": "Jordi Casabona", + "author_inst": "Direccio-gerencia, Institut Catala de la Salut, Barcelona, Spain & Centro de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid," + }, + { + "author_name": "Marti Vall-Mayans", + "author_inst": "1. Fight AIDS and Infectious Diseases Foundation, Badalona, Spain 2. Hospital Universitari Germans Trias i Pujol, Badalona Spain" + }, + { + "author_name": "Camila G-Beiras", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain" + }, + { + "author_name": "Bonaventura Clotet", + "author_inst": "Fight AIDS and Infectious Diseases Foundation, Badalona, Spain & Hospital Universitari Germans Trias i Pujol, Badalona Spain & Universitat de Vic-Universitat Ce" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.20.20155390", "rel_title": "DYNAMICS OF THE COVID-19 PANDEMICS: GLOBAL PATTERN AND BETWEEN COUNTRIES VARIATIONS", @@ -1263947,85 +1260646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.20.20155507", - "rel_title": "Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20155507", - "rel_abs": "In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on peripheral blood samples across 77 timepoints from 46 subjects with COVID-19 and compared them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a conserved transcriptomic response in peripheral blood that is heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, that persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95). The transcriptome in peripheral blood reveals unique aspects of the immune response in COVID-19 and provides for novel biomarker-based approaches to diagnosis.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Micah T McClain", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Florica J Constantine", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Ricardo Henao", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Yiling Liu", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Ephraim L Tsalik", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Thomas W Burke", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Julie M Steinbrink", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Bradly P Nicholson", - "author_inst": "Durham Veterans Affairs Medical Center" - }, - { - "author_name": "Robert Rolfe", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Bryan D Kraft", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Matthew S Kelly", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Gregory D Sempowski", - "author_inst": "Duke Human Vaccine Institute" - }, - { - "author_name": "Thomas N Denny", - "author_inst": "Duke Human Vaccine Institute" - }, - { - "author_name": "Geoffrey S Ginsburg", - "author_inst": "Duke Center for Applied Genomics and Precision Medicine" - }, - { - "author_name": "Christopher W Woods", - "author_inst": "Duke University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20131664", "rel_title": "Covid19 2020 projection report: Germany, Israel, Italy and USA. Mid-July 2020", @@ -1264726,6 +1261346,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20159806", + "rel_title": "Estimating Variation of Covid-19 infection in the Population:Results from Understanding Society (UKHLS) first monthly covid-19 survey", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159806", + "rel_abs": "The analysis in this paper uses the new Understanding Society COVID-19 survey. The key advantage of these data is that they allow us to examine infection rates for people with particular characteristics. We study how reported symptoms vary in the population and relate reported symptoms to a positive Covid-19 test in the small sample in the survey who were tested. Combining these probabilities we find that the chances of infection increase with a persons education level, are lower and declining with age among those aged over 55, and were higher in the West Midlands and London and lower in the North East than in the rest of the country, and tended to increase with regional population density. There is also evidence that the infection rate was lower among those of a Caribbean origin. A suitably cautious estimate of the mean infection rate is that, during the period up to the end of April 2020, it was between 2% and 8%, with a central rate of about 5%.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Richard Breen", + "author_inst": "Nuffield College, University of Oxford" + }, + { + "author_name": "John Ermisch", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.22.20159772", "rel_title": "Projecting contact matrices in 177 geographical regions: an update and comparison with empirical data for the COVID-19 era", @@ -1265593,25 +1262236,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.07.21.20158873", - "rel_title": "An Analysis of Outbreak Dynamics and Intervention Effects for COVID-19 Transmission in Europe", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158873", - "rel_abs": "As of March 13, 2020, Europe became the center of COVID-19 pandemic. In order to prevent further spread and slow down the increase in confirmed cases and deaths, many countries in European Union have taken some interventions since mid-March. In this study, a metapopulation model was used to model the outbreak of COVID-19 in Europe and the effectiveness of these interventions were also estimated. The findings suggested that many countries successfully kept the reproduction number Rt less than 1 (e.g., Belgium, Germany, Spain, and France) while other countries exhibited Rt greater than 1 (e.g., United Kingdom, Cyprus). Based on the assumed reopen strategy, this study also revealed that a 2-week delay in response predicted approximately 2,000 deaths and 200,000 cases (daily peak value), while a 3-week delay predicted approximately 5,000 deaths and 600,000 cases (daily peak value). Therefore, a quick response upon signs of a re-emerging pandemic in the world is highly imperative to mitigate potential loss of life and to keep transmission of Covid-19 under control.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Wei Wang", - "author_inst": "R&D, Lab management, and Bioinformatics, IT, Merck Holding (China), Shanghai, China, a business of Merck KGaA, Darmstadt, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.22.20159400", "rel_title": "Weak association of coinfection by SARS-CoV-2 and other respiratory viruses with severe cases and death", @@ -1266264,6 +1262888,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.20.20158147", + "rel_title": "Acute Shortage Ventilator", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20158147", + "rel_abs": "We have implemented an \"Acute Shortage Ventilator\" (ASV) motivated by the COVID-19 pandemic and the possibility of severe ventilator shortages in the near future. The unit cost per ventilator is less than $400 US excluding the patient circuit parts. The ASV mechanically compresses a self-inflating bag resuscitator, uses a modified patient circuit, and is commanded by a microcontroller and an optional laptop. It operates in both Volume-Controlled Assist-Control mode and a Pressure-Controlled Assist-Control mode. It has been tested using an artificial lung against the EURS guidelines. The key design goals were to develop a simple device with high performance for short-term use, made primarily from common hospital parts and generally-available non-medical components, and at low cost and ease in manufacturing.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Daniel Akerib", + "author_inst": "SLAC" + }, + { + "author_name": "Andrew Ames", + "author_inst": "SLAC" + }, + { + "author_name": "Martin Breidenbach", + "author_inst": "SLAC" + }, + { + "author_name": "Michael Bressack", + "author_inst": "Stanford University school of medicine" + }, + { + "author_name": "Pieter A Breur", + "author_inst": "SLAC" + }, + { + "author_name": "Eric Charles", + "author_inst": "SLAC" + }, + { + "author_name": "David M Gaba", + "author_inst": "VA Palo Alto healthcare system and Stanford University school of medicine" + }, + { + "author_name": "Ryan Herbst", + "author_inst": "SLAC" + }, + { + "author_name": "Christina M Ignarra", + "author_inst": "SLAC" + }, + { + "author_name": "Steffen Luitz", + "author_inst": "SLAC" + }, + { + "author_name": "Eric H Miller", + "author_inst": "SLAC" + }, + { + "author_name": "Brian Mong", + "author_inst": "SLAC" + }, + { + "author_name": "Tom A Shutt", + "author_inst": "SLAC" + }, + { + "author_name": "Matthias Wittgen", + "author_inst": "SLAC" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.07.21.20158014", "rel_title": "Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020", @@ -1267039,65 +1263734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.22.20159202", - "rel_title": "Chronic Hemodialysis Patients have better outcomes with COVID-19 - a retrospective cohort study", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159202", - "rel_abs": "IntroductionSeveral comorbid conditions, have been identified as risk factors in patients with COVID-19. However, there is a dearth of data describing the impact of COVID-19 infection in patients with end-stage renal disease on hemodialysis (ESRD-HD).\n\nMethodsThis retrospective case series analyzed 362 adult patients consecutively hospitalized with confirmed COVID-19 illness between March 12, 2020 and May 13, 2020, at a teaching hospital in the New York City metropolitan area. Primary outcome was severe pneumonia as defined by the World Health Organization. Secondary outcomes were: 1) the Combined Outcome of Acute respiratory distress syndrome or in-hospital Death (COAD), and 2) the need for High-levels of Oxygen supplementation (HiO2).\n\nResultsPatients with ESRD-HD had lower odds for poor outcomes including severe pneumonia [Odds Ratio (OR) 0.4, Confidence Interval (CI) (0.2-0.9) p=.04], HiO2 [OR 0.3, CI (0.1- 0.8) p=.02] and COAD [OR 0.4, CI (0.2-1.05) p=.06], when compared to patients without ESRD. In contrast, higher odds for severe pneumonia, COAD and HiO2 were seen with advancing age. African-Americans were over-represented in the hospitalized patient cohort, when compared to their representation in the community (35% vs 18%). Hispanics had higher odds for severe-illness and HiO2 when compared to Caucasians.\n\nConclusionsPatients with ESRD-HD had a milder course of illness with a lower likelihood of severe pneumonia and a lesser need for aggressive oxygen supplementation when compared to patients not on chronic dialysis. This \"protective effect\" might have a pathophysiologic basis and needs to be further explored.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ashutossh Naaraayan", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Abhishek Nimkar", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Amrah Hasan", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Sushil Pant", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Momcilo Durdevic", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Henrik Elenius", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Corina Nava Suarez", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Prasanta Basak", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Kameswari Lakshmi", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Michael Mandel", - "author_inst": "Montefiore New Rochelle Hospital" - }, - { - "author_name": "Stephen Jesmajian", - "author_inst": "Montefiore New Rochelle Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2020.07.21.20159376", "rel_title": "Cerebral Microvascular Injury in Severe COVID-19", @@ -1267834,6 +1264470,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.23.20161240", + "rel_title": "Rhythmic components of COVID-19 daily cases in various countries", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20161240", + "rel_abs": "Not only does COVID-19 pandemic encourage scientists to look for remedies and treatment schemes, but also identify the drivers of pathogenicity and spread of the virus.\n\nThe scope of this research consisted in identifying recurrence patterns and comparing the number of daily cases between various countries. Data for countries where at least 500 daily cases were recorded at least once (17 in Europe, 3 in North America, 7 in South America, 3 in Central America, 17 in Asia and 3 in Africa).\n\nAccording to our evaluation, the dynamics recorded for 25 countries includes a 7-day statistically significant component. This statistically significant weekly component has been identified in 76% of the countries examined in Europe, 66% in North America, 71% in South America, and 18% in Asia. The range of this rhythmic component is low at the growth stage and increases at the stabilization and decrease stages.\n\nThe weekly phases feature shifting peaks depending on the country. In some cases, the phases shift, i.e. they are not limited strictly to certain days of the week. Due to range and phase variation, its explanation cannot be limited to strictly medical and social factors. In some cases, national incidence dynamics includes 3, 4, 6, 8 and 10-day periods.\n\nUnderstanding the factors of recurrence patterns in COVID-19 incidence dynamics may help in the pandemic response.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Andrew V Drozdov", + "author_inst": "The Institute for Analytical Instrumentation of the Russian Academy of Sciences" + }, + { + "author_name": "Tatiana A Zenchenko", + "author_inst": "Institute of Theoretical and Experimental Biophysics RAS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.23.20161182", "rel_title": "Cell type-specific immune dysregulation in severely ill COVID-19 patients", @@ -1268601,37 +1265260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.24.20160994", - "rel_title": "Country distancing reveals the effectiveness of travel restrictions during COVID-19", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20160994", - "rel_abs": "Travel restrictions are the current central strategy to globally stop the transmission of the novel coronavirus disease (COVID-19). Despite remarkably successful approaches in predicting the spatiotemporal patterns of the ongoing pandemic, we lack an intrinsic understanding of the travel restrictions effectiveness. We fill this gap by developing a surprisingly simple measure, country distancing, that is analogical to the effective resistance in series and parallel circuits and captures the propagation backbone tree from the outbreak locations globally. This approach enables us to map the effectiveness of travel restrictions to arrival time delay (ATD) or infected case reduction (ICR) systematically. Our method estimates that 50.8% of travel restrictions as of Apr-4 are ineffective, resulting in zero ATD or ICR worldwide. Instead, by imposing Hubeis lockdown on Jan-23 and national lockdown on Feb-8, mainland China alone leads to 11.66 [95% credible interval (CI), 9.71 to 13.92] days of ATD per geographic area and 1,012,233 (95% CI, 208,210 -4,959,094) ICR in total as of Apr-4. Our result unveils the trade-off between the country distancing increase and economic loss, offering practical guidance for strategic actsion about when and where to implement travel restrictions, tailed to the real-time national context.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lu Zhong", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Mamadou Diagne", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Weiping Wang", - "author_inst": "Beijing Jiaotong University" - }, - { - "author_name": "Jianxi Gao", - "author_inst": "Rensselaer Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.24.20161604", "rel_title": "CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia", @@ -1269244,6 +1265872,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.23.20160853", + "rel_title": "COVID-19: A Data-Driven Mean-Field-Type Game Perspective", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160853", + "rel_abs": "In this article, a class of mean-field-type games with discrete-continuous state spaces is considered. We establish Bellman systems which provide sufficiency conditions for mean-field-type equilibria in state-and-mean-field-type feedback form. We then derive unnormalized master adjoint systems (MASS). The methodology is shown to be flexible enough to capture multi-class interaction in epidemic propagation in which multiple authorities are risk-aware atomic decision-makers and individuals are risk-aware non-atomic decision-makers. Based on MASS, we present a data-driven modelling and analytics for mitigating Coronavirus Disease 2019 (COVID-19). The model integrates untested cases, age-structure, decision-making, gender, pre-existing health conditions, location, testing capacity, hospital capacity, mobility map on local areas, in-city, inter-cities, and international. It shown that the data-driven model can capture most of the reported data on COVID-19 on confirmed cases, deaths, recovered, number of testing and number of active cases in 66+ countries. The model also reports non-Gaussianity and non-exponential properties in 15+ countries.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hamidou Tembine", + "author_inst": "L&G Lab, NYUAD" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.23.20160317", "rel_title": "Infectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China", @@ -1270043,53 +1266690,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20160309", - "rel_title": "Longitudinal study about low back pain, mental health, and access to healthcare system during COVID-19 pandemic: protocol of an ambispective cohort", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160309", - "rel_abs": "This study aims to investigate the effects of physical activity before, during, and after social distancing due to the COVID-19 pandemic on low back pain (LBP), mental health and healthcare access. The PAMPA Cohort (Prospective Study About Mental and Physical Health) is a state-level ambispective longitudinal observational study that will be conducted in Rio Grande do Sul, Brazil. An online-based questionnaire will be used to assess LBP, mental health, healthcare access and physical activity at four time points: 1) pre-COVID-19 social distancing, 2) during COVID-19 social distancing, 3) 6 months and 4) 12 months after baseline. A proportional sample size calculation was conducted, and the final sample size was estimated in 1,767 people, distributed in seven state regions. Participants will be recruited by a four-arm approach: contact with universities, social media, local media and personal contacts. Descriptive analyzes will be reported as mean or proportion and respective 95% confidence interval (CI), when appropriate. Comparison between pre- and during COVID-19 social distancing, and after baseline assessments will be performed using two-way ANOVA with repeated measures. Proportions will be compared by Chi-squared test.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Natan Feter", - "author_inst": "Federal University of Pelotas; The University of Queensland" - }, - { - "author_name": "Eduardo L Caputo", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Igor R Doring", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Jayne S Leite", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Julia Cassuriaga", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Felipe F Reichert", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Marcelo C da Silva", - "author_inst": "Federal University of Pelotas" - }, - { - "author_name": "Airton J Rombaldi", - "author_inst": "Federal University of Pelotas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.22.20160184", "rel_title": "Forecasting hospitalizations due to COVID-19 in South Dakota, USA.", @@ -1270662,6 +1267262,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20160291", + "rel_title": "The collective wisdom in the COVID-19 research: comparison and synthesis of epidemiological parameter estimates in preprints and peer-reviewed articles", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160291", + "rel_abs": "SummaryO_ST_ABSBackgroundC_ST_ABSResearch papers related to COVID-19 have exploded. We aimed to explore the academic value of preprints through comparing with peer-reviewed publications, and synthesize the parameter estimates of the two kinds of literature.\n\nMethodWe collected papers regarding the estimation of four key epidemiological parameters of the COVID-19 in China: the basic reproduction number (R0), incubation period, infectious period, and case-fatality-rate (CFR). PubMed, Google Scholar, medRxiv, bioRxiv, arRxiv, and SSRN were searched by 20 March, 2020. Distributions of parameters and timeliness of preprints and peer-reviewed papers were compared. Further, four parameters were synthesized by bootstrap, and their validity was verified by susceptible-exposed-infectious-recovered-dead-cumulative (SEIRDC) model based on the context of China.\n\nFindings106 papers were included for analysis. The distributions of four parameters in two literature groups were close, despite that the timeliness of preprints was better. Four parameter estimates changed over time. Synthesized estimates of R0 (3{middle dot}18, 95% CI 2{middle dot}85-3{middle dot}53), incubation period (5{middle dot}44 days, 95% CI 4{middle dot}98-5{middle dot}99), infectious period (6{middle dot}25 days, 95% CI 5{middle dot}09-7{middle dot}51), and CFR (4{middle dot}51%, 95% CI 3{middle dot}41%-6{middle dot}29%) were obtained from the whole parameters space, all with p<0{middle dot}05. Their validity was evaluated by simulated cumulative cases of SEIRDC model, which matched well with the onset cases in China.\n\nInterpretationPreprints could reflect the changes of epidemic situation sensitively, and their academic value shouldnt be neglected. Synthesized results of literatures could reduce the uncertainty and be used for epidemic decision making.\n\nFundingThe National Natural Science Foundation of China and Beijing Municipal Natural Science Foundation.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSince its outbreak, scientific articles about the COVID-19 have greatly surged, with a significant portion as non-peer-reviewed preprints. Although preprints captured great attention, the credibility of preprints was widely debated. We searched PubMed and Google on March 20, 2020, for publications that discussed the preprints during the COVID-19 pandemic, using the terms (\"preprints\" AND \"COVID-19\"). We identified 12 papers and news, and found that scientists were skeptical of preprints mainly because rigorous peer review is absent and thus the conclusions of preprints may not be reliable. However, scientists opinions could have been biased towards limited data, and there is few knowledges about the validity of the results reported in the preprints. Further, to examine how scientists utilize results of preprints, taking the epidemiological parameter estimation as the objects, we searched reviews on Google using the terms (\"epidemiology\" AND (\"meta-analysis\" OR \"reviews\") AND \"COVID-19\") on May 23, 2020. Nine papers were identified. We found that existing meta-analysis and reviews included few preprints. This may be due to the fact that the quality of preprints was not recognized, and thus their academic value was underestimated. Overall, the validity of the results as reported in the preprints should be further examined and the potential of synthesizing preprints with formally published papers should be explored.\n\nAdded value of this studyOur study adds value in four main ways. First, we collected preprints and peer-reviewed papers on estimations of the four most important epidemiological parameters (the basic reproduction number, incubation period, infectious period, and case-fatality-rate) for the COVID-19 outbreak in China. 106 papers were included and available data were extracted. Second, we quantitatively compared the differences and timeliness between preprints and peer-reviewed publications in the estimation of the four parameters, and found that the validity of the preprints estimations was largely consistent with that of the peer-reviewed group. Third, we synthesized the estimations of the two groups of literatures using bootstrap method, and found that the values of infectious period and case-fatality-rate decreased over time, indicating that the synthesized results timely reflected the changing trend of the COVID-19 in China. Finally, the practicability of the synthesized parameter estimations was verified by the data of confirmed cases in China. The cumulative infection curve simulated using synthesized parameters fitted the real data well.\n\nImplications of all the available evidenceResults of our study indicate that the validity of the COVID-19 parameter estimations of the preprints is on par with that of peer-reviewed publications, and the preprints are relatively timelier. Further, the synthesized parameters of the two literature groups can effectively reduce the uncertainty and capture the patterns of epidemics. These results provide data-driven insights into the academic value of preprints, which have been arguably underestimated. The scientific community should actively capitalize the collective wisdom generated by the huge amount of preprints, particularly during the emerging infectious diseases like the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yuejiao Wang", + "author_inst": "Institute of Automation, Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Zhidong Cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Dajun Zeng", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Tianyi Luo", + "author_inst": "Institute of Automation, Chinese Academy of Sciences; University of Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.22.20160143", "rel_title": "The Optimal Allocation of Covid-19 Vaccines", @@ -1271561,57 +1268196,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.21.212704", - "rel_title": "Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy", - "rel_date": "2020-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.212704", - "rel_abs": "Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Herein, we report the first structure of serum albumin in complex with dexamethasone. We show that it binds to Drug Site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with our analysis of publicly available clinical data from Wuhan and suggests that an adjustment of dexamethasone regimen should be considered for patients affected by two major COVID-19 risk-factors: low albumin levels and diabetes.\n\nOne Sentence SummaryStructure of serum albumin with dexamethasone reveals why the drug may not always help COVID-19 patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ivan G. Shabalin", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA" - }, - { - "author_name": "Mateusz P. Czub", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA" - }, - { - "author_name": "Karolina A. Majorek", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA Present address: T" - }, - { - "author_name": "Dariusz Brzezinski", - "author_inst": "1Department of Molecular Physiology and Biological Physics, University of Virginia, USA; 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, Polan" - }, - { - "author_name": "Marek Grabowski", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA" - }, - { - "author_name": "David R. Cooper", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA" - }, - { - "author_name": "Mateusz Panasiuk", - "author_inst": "Medical University of Bialystok, Department of Clinical Medicine, 15-089 Bialystok, Poland" - }, - { - "author_name": "Maksymilian Chruszcz", - "author_inst": "Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA" - }, - { - "author_name": "Wladek Minor", - "author_inst": "Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.07.22.212761", "rel_title": "SARS-CoV-2-induced humoral immunity through B cell epitope analysis and neutralizing activity in COVID-19 infected individuals in Japan", @@ -1272232,6 +1268816,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.21.20158782", + "rel_title": "Real-time IP-10 measurements as a new tool for inflammation regulation within a clinical decision support protocol for managing severe COVID-19 patients", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158782", + "rel_abs": "The challenge of treating severely ill COVID-19 patients is particularly great due to the need to simultaneously manage oxygenation and the inflammatory state without compromising viral clearance. Currently, there are many tools to aid in oxygen management and in monitoring viral replication. However, predictive biomarkers for monitoring the host immune response across COVID-19 disease stages and specifically, for titrating immunomodulatory therapy are lacking. We utilized a recently cleared platform (MeMed Key) that enables rapid and easy serial measurement of IP-10, a host protein implicated in lung injury due to viral-induced hyperinflammation. A dynamic clinical decision support protocol was employed for managing SARS-CoV-2 positive patients admitted to a COVID-19 dedicated medical center run by Clalit Health Services. This is the first protocol to include real-time measurements of IP-10 as a potential aid for regulating inflammation. Overall, 502 serial real-time IP-10 measurements were performed on 52 patients recruited between 7th April 2020 to 10th May 2020, with 12 patients admitted to the intensive care unit (ICU). IP-10 levels correlated with increased COVID-19 severity score and ICU admission. Within the ICU admitted patients, the number of days with IP-10 measurements >1,000 pg/ml was associated with mortality. Upon administration of corticosteroid immunomodulatory therapy, a significant decrease in IP-10 levels was observed. Real-time IP-10 monitoring represents a new tool to aid in management and therapeutic decisions relating to the inflammatory status of COVID-19 patients.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Shaul Lev", + "author_inst": "Intensive Care Unit, Rabin Medical Center, Hasharon, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Israel" + }, + { + "author_name": "Tamar Gottesman", + "author_inst": "Intensive Care Unit, Rabin Medical Center, Hasharon, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Israel" + }, + { + "author_name": "Gal Sahaf Levin", + "author_inst": "Intensive Care Unit, Rabin Medical Center, Hasharon, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Israel" + }, + { + "author_name": "Doron Lederfein", + "author_inst": "Internal Medicine, Rabin Medical Center, Hasharon, Petah Tikva, Israel" + }, + { + "author_name": "Evgeny Berkov", + "author_inst": "Internal Medicine, Rabin Medical Center, Hasharon, Petah Tikva, Israel" + }, + { + "author_name": "Dror Diker", + "author_inst": "Internal Medicine, Rabin Medical Center, Hasharon, Petah Tikva, Israel" + }, + { + "author_name": "Aliza Zaidman", + "author_inst": "Internal Medicine, Rabin Medical Center, Hasharon, Petah Tikva, Israel" + }, + { + "author_name": "Amir Nutman", + "author_inst": "National Institute for Infection Control and Antibiotic Resistance, Tel Aviv Medical Centre, Tel-Aviv, Israel" + }, + { + "author_name": "Tahel Ilan Ber", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Alon Angel", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Lior Kellerman", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Eran Barash", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Roy Navon", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Olga Boico", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Yael Israeli", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Michal Rosenberg", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Amir Gelman", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Roy Kalfon", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Einav Simon", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Noa Avni", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Mary Hainrichson", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Oren Zarchin", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Tanya M. Gottlieb", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Kfir Oved", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Eran Eden", + "author_inst": "MeMed, Israel" + }, + { + "author_name": "Boaz Tadmor", + "author_inst": "Intensive Care Unit, Rabin Medical Center, Hasharon, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Israel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.21.20158659", "rel_title": "In-silico modeling of COVID-19 ARDS: pathophysiological insights and potential management implications", @@ -1273259,145 +1269962,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.22.215236", - "rel_title": "Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors", - "rel_date": "2020-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.215236", - "rel_abs": "The ongoing COVID-19 pandemic, caused by SARS-CoV-2 infection, has resulted in hundreds of thousands of deaths. Cellular entry of SARS-CoV-2, which is mediated by the viral spike protein and host ACE2 receptor, is an essential target for the development of vaccines, therapeutic antibodies, and drugs. Using a mammalian cell expression system, we generated a recombinant fluorescent protein (Gamillus)-fused SARS-CoV-2 spike trimer (STG) to probe the viral entry process. In ACE2-expressing cells, we found that the STG probe has excellent performance in the live-cell visualization of receptor binding, cellular uptake, and intracellular trafficking of SARS-CoV-2 under virus-free conditions. The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. This approach may also be adapted to develop a viral entry visualization system for other viruses.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Yali Zhang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Shaojuan Wang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Yangtao Wu", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Wangheng Hou", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Lunzhi Yuan", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Juan Wang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Jianghui Ye", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Qingbing Zheng", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Jian Ma", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Jingjing Xu", - "author_inst": "Fujian Medical University Union Hospital" - }, - { - "author_name": "Min Wei", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Zonglin Li", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Sheng Nian", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Hualong Xiong", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Liang Zhang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Yang Shi", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Baorong Fu", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Jiali Cao", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Chuanlai Yang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Zhiyong Li", - "author_inst": "The First Hospital of Xiamen University" - }, - { - "author_name": "Ting Yang", - "author_inst": "Fujian Medical University Union Hospital" - }, - { - "author_name": "Lei Liu", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Hai Yu", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Jianda Hu", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Shengxiang Ge", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Yixin Chen", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Tianying Zhang", - "author_inst": "Xiamen university" - }, - { - "author_name": "Jun Zhang", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Tong Cheng", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - }, - { - "author_name": "Quan Yuan", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases" - }, - { - "author_name": "Ningshao Xia", - "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.22.215731", "rel_title": "Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2", @@ -1273930,6 +1270494,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.18.20156778", + "rel_title": "COVID-19 DEATH TOLL: THE ROLE OF THE NATION'S ECONOMIC DEVELOPMENT", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156778", + "rel_abs": "BackgroundSeveral months into the novel coronavirus disease (COVID-19) pandemic, there is a limited understanding of the underlying country-specific factors associated with COVID-19 spread and mortality. This study aims to investigate the role of nations economic development in the death toll associated with COVID-19 in Europe and Israel.\n\nMethodsNumber of COVID-19 cases, deaths per million, and case fatality rate (CFR) in Israel and 39 countries in Europe were described across quintiles of gross domestic product (GDP) per capita. The association between GDP per capita and COVID-19 incidence, mortality, and CFR was investigated using generalized linear modeling adjusting for the proportion of elderly and density of the population.\n\nResultsIn countries belonging to the three lower GDP quintiles, COVID-19 incidence rates per million (range 708-1134) were substantially lower compared to countries in the fourth (3939) and fifth (3476) quintiles. Major differences were also calculated in COVID-19 mortality rates per million (25-31 vs. 222-268). There was no significant (p=0.19) differences in CFR between GDP quintiles (range: 2.79-7.62%).\n\nConclusionsCOVID-19 had a greater toll in more developed nations. Though comparisons are limited by differences in testing, reporting and lockdown policies, this association likely reflects increased spread from trade and tourism in wealthier countries, whereas limited health system capacity and lack of treatment and vaccination options contributed to higher than expected CFR in wealthier countries. This unique situation will probably encourage the stronger economies to invest the required financial capacity to respond to and recover from the current crisis.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gabriel Chodcik", + "author_inst": "Maccabitech" + }, + { + "author_name": "Clara Weil", + "author_inst": "Maccabi Healthcare Services" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20156992", "rel_title": "SARS-CoV-2 Transmission in Alberta, British Columbia, and Ontario, Canada, January 1-July 6, 2020", @@ -1274769,45 +1271356,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.20.213280", - "rel_title": "The PRRA insert at the S1/S2 site modulates cellular tropism of SARS-CoV-2 and ACE2 usage by the closely related Bat raTG13", - "rel_date": "2020-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.20.213280", - "rel_abs": "Biochemical and structural analyses suggest that SARS-CoV-2 is well-adapted to infecting human and the presence of four residues (PRRA) at the S1/S2 site within the Spike protein may lead to unexpected tissue or host tropism. Here we report that SARS-CoV-2 efficiently utilized ACE2 of 9 species except mouse to infect 293T cells. Similarly, pseudoviruses bearing spike protein derived from either the bat raTG13 or pangolin GX, two closely related animal coronaviruses, utilized ACE2 of a diverse range of animal species to gain entry. Removal of PRRA from SARS-CoV-2 Spike displayed distinct effects on pseudoviral entry into different cell types. Strikingly, insertion of PRRA into the raTG13 Spike selectively abrogated the usage of horseshoe bat and pangolin ACE2 but conferred usage of mouse ACE2 by the relevant pseudovirus to enter cells. Together, our findings identified a previously unrecognized effect of the PRRA insert on SARS-CoV-2 and raTG13 spike proteins.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shufeng Liu", - "author_inst": "CBER FDA" - }, - { - "author_name": "Prabhuanand Selvaraj", - "author_inst": "FDA" - }, - { - "author_name": "Christopher Lien", - "author_inst": "FDA" - }, - { - "author_name": "Wells W. Wu", - "author_inst": "CBER FDA" - }, - { - "author_name": "Chao-Kai Chou", - "author_inst": "CBER FDA" - }, - { - "author_name": "Tony Wang", - "author_inst": "FDA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.16.20155663", "rel_title": "Humoral Response Dynamics Following Infection with SARS-CoV-2", @@ -1275604,6 +1272152,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.07.19.20157511", + "rel_title": "Bioaersols in orthopedic surgical procedures and implications for clinical practice in the times of COVID-19 pandemic: a protocol for systematic review and meta-analysis", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20157511", + "rel_abs": "BackgroundOrthopedic surgical procedures involve a number of aerosol generating procedures; these include electrocautery, power instruments for bone cutting, burring and drilling, and tools for wound lavage. This assumes a great significance in the context of the current COVD-19 pandemic, as there are chances of aerosol-borne disease transmission in orthopedic surgical procedures. Hence, this systematic review and meta-analysis will be undertaken to assimilate and analyse the available evidence on bioaerosols in orthopedic surgical procedures and their significance with respect to SARS-CoV-2 virus transmission.\n\nObjectivesTo determine the characteristics (amount and/or density, size, infectivity, and spread etc.) of bioaerosols found in orthopaedic operating rooms (ORs) and to determine the characteristics of aerosols generated by different orthopaedic power tools and devices.\n\nMethodsA systematic review and meta-analysis will be conducted. The PRISMA guidelines will be strictly followed. The primary search will be conducted on the PubMed, EMBASE, Scopus, Cochrane Library, medRxiv, bioRxix and Lancet preprint databases, using a well-defined search strategy. Any original research study (including cohort, case-control, case series, cadaveric studies and studies, animal models, laboratory based experimental studies) looking at aerosol generation in orthopedic surgical procedures, or aerosol generation by orthopaedic power tools and devices will included. Outcome measures will include characteristics (amount and/or density, size, infectivity, and spread etc.) of bioaerosols found in orthopaedic operating rooms (ORs) and those generated by various orthopaedics power tools and devices. Metanalysis using the random-effects model will be conducted to determined pooled estimates of the outcome variables. Heterogeneity will be assessed by the I2 test. Risk of bias will be assessed by the Risk of Bias in Studies estimating Prevalence of Exposure to Occupational risk factors (RoB-SPEO) tool. The overall strength of evidence will be assessed by the GRADE approach.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Siddhartha Sharma", + "author_inst": "Postgraduate Institute of Medical Education and Research, Chandigarh, India" + }, + { + "author_name": "Rakesh John", + "author_inst": "Department of Trauma & Orthopedics, Hull University Teaching Hospitals, Hull, East Yorkshire, UK" + }, + { + "author_name": "Deepak Neradi", + "author_inst": "Postgraduate Institute of Medical Education and Research, Chandigarh, India" + }, + { + "author_name": "Sandeep Patel", + "author_inst": "Postgraduate Institute of Medical Education and Research, Chandigarh, India" + }, + { + "author_name": "Mandeep Singh Dhillon", + "author_inst": "Postgraduate Institute of Medical Education and Research, Chandigarh, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "orthopedics" + }, { "rel_doi": "10.1101/2020.07.19.20157354", "rel_title": "The Effect of GDP and Distance on Timing of COVID-19 Spread in Chinese Provinces in 2020", @@ -1276643,73 +1273226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.13.20041632", - "rel_title": "The Infectious Nature of Patient-Generated SARS-CoV-2 Aerosol", - "rel_date": "2020-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20041632", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission causing coronavirus disease 2019 (COVID-19) may occur through multiple routes. We collected aerosol samples around six patients admitted into mixed acuity wards in April of 2020 to identify the risk of airborne SARS-CoV-2. Measurements were made to characterize the size distribution of aerosol particles, and size-fractionated, aerosol samples were collected to assess the presence of infectious virus in particles sizes of >4.1 {micro}m, 1-4 {micro}m, and <1 {micro}m in the patient environment. Samples were analyzed by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), cell culture, western blot, and transmission electron microscopy (TEM). SARS-CoV-2 RNA was detected in all six rooms in all particle size fractions (>4.1 {micro}m, 1-4 {micro}m, and <1 {micro}m). Increases in viral RNA during cell culture of the virus from recovered aerosol samples demonstrated the presence of infectious, replicating virions in three <1 {micro}m aerosol samples (P<0.05). Viral replication of aerosol was also observed in the 1-4 {micro}m stage but did not reach statistical significance (0.05\nView larger version (34K):\norg.highwire.dtl.DTLVardef@a5bca3org.highwire.dtl.DTLVardef@1039176org.highwire.dtl.DTLVardef@14314f7org.highwire.dtl.DTLVardef@1159d32_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOImage 1C_FLOATNO SARS-CoV-2 infection probability progression by date. Green and orange trends: Patients with at least one risk factor. Gray trends: Patients with no risk factors.\n\nC_FIG In conclusion, we found our model could monitor accurately the probability of SARS-CoV-2 infection in relation to age, sex, and the presence of at least one risk factor. Also, because the model can be applied to any particular political region within Mexico, it could help evaluate the contagion spread in specific vulnerable populations. Further studies are needed to determine the underlying nature of the mechanisms behind such observations.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Juan Alonso Leon-Abarca", - "author_inst": "Instituto de Investigaciones de la Altura - Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Esdras Ismael Musayon", - "author_inst": "Universidad Peruana Cayetano Heredia, Instituto de Investigaciones de la Altura" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.16.20155200", "rel_title": "Gender and trust in government modify the association between mental health and stringency of social distancing related public health measures to reduce COVID-19: a global online survey", @@ -1279028,6 +1275544,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.07.16.20155382", + "rel_title": "Identifying organ dysfunction trajectory-based subphenotypes in critically ill patients with COVID-19", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155382", + "rel_abs": "RationaleCOVID-19-associated respiratory failure offers the unprecedented opportunity to evaluate the differential host response to a uniform pathogenic insult. Prior studies of Acute Respiratory Distress Syndrome (ARDS) have identified subphenotypes with differential outcomes. Understanding whether there are distinct subphenotypes of severe COVID-19 may offer insight into its pathophysiology.\n\nObjectivesTo identify and characterize distinct subphenotypes of COVID-19 critical illness defined by the post-intubation trajectory of Sequential Organ Failure Assessment (SOFA) score.\n\nMethodsIntubated COVID-19 patients at two hospitals in New York city were leveraged as development and validation cohorts. Patients were grouped into mild, intermediate, and severe strata by their baseline post-intubation SOFA. Hierarchical agglomerative clustering was performed within each stratum to detect subphenotypes based on similarities amongst SOFA score trajectories evaluated by Dynamic Time Warping. Statistical tests defined trajectory subphenotype predictive markers.\n\nMeasurements and Main ResultsDistinct worsening and recovering subphenotypes were identified within each stratum, which had distinct 7-day post-intubation SOFA progression trends. Patients in the worsening suphenotypes had a higher mortality than those in the recovering subphenotypes within each stratum (mild stratum, 29.7% vs. 10.3%, p=0.033; intermediate stratum, 29.3% vs. 8.0%, p=0.002; severe stratum, 53.7% vs. 22.2%, p<0.001). Worsening and recovering subphenotypes were replicated in the validation cohort. Routine laboratory tests, vital signs, and respiratory variables rather than demographics and comorbidities were predictive of the worsening and recovering subphenotypes.\n\nConclusionsThere are clear worsening and recovering subphenotypes of COVID-19 respiratory failure after intubation, which are more predictive of outcomes than baseline severity of illness. Organ dysfunction trajectory may be well suited as a surrogate for research in COVID-19 respiratory failure.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSCOVID-19 associated respiratory failure leads to a significant risk of morbidity and mortality. It is clear that there is heterogeneity in the viral-induced host response leading to differential outcomes, even amongst those treated with mechanical ventilation. There are many studies of COVID-19 disease which use intubation status as an outcome or an inclusion criterion. However, there is less understanding of the post intubation course in COVID-19.\n\nWhat This Study Adds to the FieldWe have developed and validated a novel subphenotyping model based on post-intubation organ dysfunction trajectory in COVID-19 patients. Specifically, we identified clear worsening and recovering organ dysfunction trajectory subphenotypes, which are more predictive of outcomes than illness severity at baseline. Dynamic inflammatory markers and ventilator variables rather than baseline severity of illness, demographics and comorbidities differentiate the worsening and recovering subphenotypes. Trajectory subphenotypes offer a potential road map for understanding the evolution of critical illness in COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Chang Su", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Zhenxing Xu", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Katherine Hoffman", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Parag Goyal", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Monika M Safford", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Jerry Lee", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Sergio Alvarez-Mulett", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Luis Gomez-Escobar", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "David R Price", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "John S Harrington", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Lisa K Torres", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Fernando J Martinez", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Thomas R Campion Jr.", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Rainu Kaushal", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Augustine M.K. Choi", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Fei Wang", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Edward J Schenck", + "author_inst": "Weill Cornell Medical College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.07.16.20155614", "rel_title": "Is it safe to lift COVID-19 travel bans? The Newfoundland story.", @@ -1279839,141 +1276438,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.07.16.205088", - "rel_title": "A single intranasal dose of chimpanzee adenovirus-vectored vaccine confers sterilizing immunity against SARS-CoV-2 infection", - "rel_date": "2020-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.16.205088", - "rel_abs": "The Coronavirus Disease 2019 pandemic has made deployment of an effective vaccine a global health priority. We evaluated the protective activity of a chimpanzee adenovirus-vectored vaccine encoding a pre-fusion stabilized spike protein (ChAd-SARS-CoV-2-S) in challenge studies with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mice expressing the human angiotensin-converting enzyme 2 receptor. Intramuscular dosing of ChAd-SARS-CoV-2-S induces robust systemic humoral and cell-mediated immune responses and protects against lung infection, inflammation, and pathology but does not confer sterilizing immunity, as evidenced by detection of viral RNA and induction of anti-nucleoprotein antibodies after SARS-CoV-2 challenge. In contrast, a single intranasal dose of ChAd-SARS-CoV-2-S induces high levels of systemic and mucosal IgA and T cell responses, completely prevents SARS-CoV-2 infection in the upper and lower respiratory tracts, and likely confers sterilizing immunity in most animals. Intranasal administration of ChAd-SARS-CoV-2-S is a candidate for preventing SARS-CoV-2 infection and transmission, and curtailing pandemic spread.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Ahmed O Hassan", - "author_inst": "Washington University" - }, - { - "author_name": "Natasha M Kafai", - "author_inst": "Washington University" - }, - { - "author_name": "Igor P Dmitriev", - "author_inst": "Washington University" - }, - { - "author_name": "Julie M Fox", - "author_inst": "Washington University" - }, - { - "author_name": "Brittany Smith", - "author_inst": "Washington University" - }, - { - "author_name": "Ian B Harvey", - "author_inst": "Washington University" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Washington University" - }, - { - "author_name": "Emma S Winkler", - "author_inst": "Washington University" - }, - { - "author_name": "Alex W Wessel", - "author_inst": "Washington University" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University" - }, - { - "author_name": "Elena Kashentseva", - "author_inst": "Washington University" - }, - { - "author_name": "Broc T McCune", - "author_inst": "Washington University" - }, - { - "author_name": "Adam L Bailey", - "author_inst": "Washington University" - }, - { - "author_name": "Haiyan Zhao", - "author_inst": "Washington University" - }, - { - "author_name": "Laura A VanBlargan", - "author_inst": "Washington University" - }, - { - "author_name": "Yanan Dai", - "author_inst": "Washington University" - }, - { - "author_name": "Meisheng Ma", - "author_inst": "Washington University" - }, - { - "author_name": "Lucas J Adams", - "author_inst": "Washington University" - }, - { - "author_name": "Swathi Shrihari", - "author_inst": "Washington University" - }, - { - "author_name": "Lisa E Gralinski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Yixuan J Hou", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Alexandra Schaefer", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Arthur S Kim", - "author_inst": "Washington University" - }, - { - "author_name": "Shamus P Keeler", - "author_inst": "Washington University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Michael J Holtzman", - "author_inst": "Washington University" - }, - { - "author_name": "Daved H Fremont", - "author_inst": "Washington University" - }, - { - "author_name": "David T Curiel", - "author_inst": "Washington University" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.16.206847", "rel_title": "Longitudinal analysis of the humoral response to SARS-CoV-2 spike RBD in convalescent plasma donors", @@ -1280742,6 +1277206,301 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.07.15.20152967", + "rel_title": "Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20152967", + "rel_abs": "RationaleThe impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established.\n\nObjectivesTo assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population.\n\nMethodsAn international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death.\n\nMeasurements and Main ResultsData from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC [≥]80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13-3.46).\n\nConclusionsPatients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.", + "rel_num_authors": 70, + "rel_authors": [ + { + "author_name": "Gisli Jenkins", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Tom Drake", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX" + }, + { + "author_name": "Annemarie B Docherty", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Ewan Harrison", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jennifer Quint", + "author_inst": "Imperial College London" + }, + { + "author_name": "Huzaifa Adamali", + "author_inst": "Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB." + }, + { + "author_name": "Sarah Agnew", + "author_inst": "Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK." + }, + { + "author_name": "Suresh Babu", + "author_inst": "Queen Alexandra Hospital, Portsmouth, UK." + }, + { + "author_name": "Christopher Barber", + "author_inst": "Northern General Hospital, Sheffield, S5 7AU, UK" + }, + { + "author_name": "Shaney Barratt", + "author_inst": "Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Southmead Hospital, Bristol, UK, BS10 5NB." + }, + { + "author_name": "Elisabeth Bendstrup", + "author_inst": "Centre for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99,8200 Aarhus N, Denmar" + }, + { + "author_name": "Stephen Bianchi", + "author_inst": "Northern General Hospital, Sheffield, S5 7AU, UK." + }, + { + "author_name": "Diego Castillo", + "author_inst": "ILD Unit, Respiratory Medicine Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain." + }, + { + "author_name": "Nazia Chaudhuri", + "author_inst": "ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK" + }, + { + "author_name": "Felix Chua", + "author_inst": "Royal Brompton Hospital" + }, + { + "author_name": "Robina Coker", + "author_inst": "Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK" + }, + { + "author_name": "William Chang", + "author_inst": "Nottingham University Hospital" + }, + { + "author_name": "Anjali Cranshaw", + "author_inst": "Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK." + }, + { + "author_name": "Louise Crowley", + "author_inst": "Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK." + }, + { + "author_name": "Davinder Dosanjh", + "author_inst": "Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK." + }, + { + "author_name": "Christine Fiddler", + "author_inst": "Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK" + }, + { + "author_name": "Ian A Forrest", + "author_inst": "Department of Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK." + }, + { + "author_name": "Peter George", + "author_inst": "Royal Brompton Hospital" + }, + { + "author_name": "Michael Gibbons", + "author_inst": "South West Peninsula ILD Network, Royal Devon & Exeter Foundation NHS Trust Barrack Road, Exeter EX2 5DW, UK" + }, + { + "author_name": "Katherine Groom", + "author_inst": "Respiratory Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK" + }, + { + "author_name": "Sarah Haney", + "author_inst": "Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ" + }, + { + "author_name": "Simon Hart", + "author_inst": "Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, UK, HU16 5JQ" + }, + { + "author_name": "Emily Heiden", + "author_inst": "University Hospitals Southampton NHS Foundation Trust, Southampton, UK" + }, + { + "author_name": "Michael Henry", + "author_inst": "Cork University Hospital, Cork, Ireland" + }, + { + "author_name": "Ling-Pei Ho", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rachel Hoyles", + "author_inst": "Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK" + }, + { + "author_name": "John Hutchinson", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Killian Hurley", + "author_inst": "Beaumont Hospital, Dublin, Ireland." + }, + { + "author_name": "Mark Jones", + "author_inst": "NIHR Southampton Biomedical Research Centre & Clinical and Experimental Sciences, University of Southampton, Southampton, UK" + }, + { + "author_name": "Steve Jones", + "author_inst": "Action for Pulmonary Fibrosis" + }, + { + "author_name": "Maria Kokosi", + "author_inst": "Guys and St Thomas' Hospital" + }, + { + "author_name": "Michael Kreuter", + "author_inst": "Center for interstitial and rare lung diseases, Pneumology, Thoraxklinik, University of Heidelberg, Germany and German Center for Lung Research, 69126 Heidelber" + }, + { + "author_name": "Laura Mackay", + "author_inst": "Northumbria Specialist Emergency Care Hospital, Northumbria Way, Northumbria Healthcare NHS Foundation Trust, Cramlington, NE23 6NZ" + }, + { + "author_name": "Siva Mahendran", + "author_inst": "Kingston Hospital NHS Foundation Trust. Galsworthy Road, Kingston upon Thames, Surrey KT2 7QB, UK." + }, + { + "author_name": "Georgios Margaritopoulos", + "author_inst": "ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK" + }, + { + "author_name": "Maria Molina-Molina", + "author_inst": "ILD Unit, Respiratory Department, University Hospital of Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain." + }, + { + "author_name": "Philip Molyneaux", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aidan D O'Brien", + "author_inst": "University Hospital Limerick, Dooradoyle, Limerick, Ireland." + }, + { + "author_name": "Katherine O'Reilly", + "author_inst": "Department of Respiratory Medicine, Mater Misericordiae University Hospital, Dublin, Ireland." + }, + { + "author_name": "Alice Packham", + "author_inst": "Birmingham Interstitial Lung Disease Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK." + }, + { + "author_name": "Helen Parfrey", + "author_inst": "Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK" + }, + { + "author_name": "Venerino Poletti", + "author_inst": "Department of Diseases of the Thorax, Morgagni Hospital, Forli, Italy." + }, + { + "author_name": "Joanna Porter", + "author_inst": "University College London" + }, + { + "author_name": "Elisabetta Renzoni", + "author_inst": "Royal Brompton Hospital" + }, + { + "author_name": "Pilar Rivera-Ortega", + "author_inst": "ILD Unit, Manchester University Hospital NHS FT, Wythenshawe Hospital, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK" + }, + { + "author_name": "Anne-Marie Russell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gauri Saini", + "author_inst": "Nottingham University Hospitals" + }, + { + "author_name": "Lisa G Spencer", + "author_inst": "Liverpool Interstitial Lung Disease Service, Aintree site, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L9 7AL, UK." + }, + { + "author_name": "Giulia Stella", + "author_inst": "Laboratory of Biochemistry and Genetics, Pneumology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy." + }, + { + "author_name": "Helen Stone", + "author_inst": "University Hospital North Midlands NHS Trust, Royal Stoke University Hospital, Newcastle Road, Stoke-on-Trent, ST4 6QG, UK." + }, + { + "author_name": "Sharon Sturney", + "author_inst": "Royal United Hospitals Bath NHS Foundation Trust, Combe Park, Bath BA1 3NG, UK" + }, + { + "author_name": "David Thickett", + "author_inst": "University of Birmingham, Birmingham, UK." + }, + { + "author_name": "Muhunthan Thillai", + "author_inst": "Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK" + }, + { + "author_name": "Timothy Wallis", + "author_inst": "University of Southampton" + }, + { + "author_name": "Katie Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Athol U Wells", + "author_inst": "Royal Brompton Hospital" + }, + { + "author_name": "Alex West", + "author_inst": "Guys and St Thomas' Hospital" + }, + { + "author_name": "Melissa Wickremasinghe", + "author_inst": "Imperial Healthcare NHS Trust, St Mary's Hospital, The Bays, S Wharf Rd, Paddington, London W2 1NY, UK." + }, + { + "author_name": "Felix Woodhead", + "author_inst": "Glenfield Hospital Leicester" + }, + { + "author_name": "Glenn Herson", + "author_inst": "Nottingham University Hospitals Trust" + }, + { + "author_name": "Lucy Howard", + "author_inst": "Nottingham University Hospitals Trust" + }, + { + "author_name": "Peter JM Openshaw", + "author_inst": "Imperial College London" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Malcolm Gracie Semple", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Iain Stewart", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.07.14.20153528", "rel_title": "Calming the Cytokine Storm - Splenic Ultrasound for Treating Inflammatory Disorders and Potentially COVID-19", @@ -1281885,61 +1278644,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.15.20149195", - "rel_title": "Reconciling model predictions with low reported cases of COVID-19 in Sub-Saharan Africa: Insights from Madagascar", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20149195", - "rel_abs": "The COVID-19 pandemic has wreaked havoc globally, and there has been a particular concern for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers high burdens of other infectious diseases: ecology, socio-economic conditions, lack of water and sanitation infrastructure, and weak health systems. However, so far SSA has reported lower incidence and fatalities compared to the predictions of standard models and the experience of other regions of the world. There are three leading explanations, each with very different implications for the final epidemic burden: (1) low case detection, (2) differences in COVID-19 epidemiology (e.g. low R0), and (3) policy interventions. The low number of cases to date have led some SSA governments to relax these policy interventions. Will this result in a resurgence of cases? To understand how to interpret the lower-than-expected COVID-19 case data in Madagascar, we use a simple age-structured model to explore each of these explanations and predict the epidemic impact associated with them. We show that the current incidence of COVID-19 cases can be explained by any combination of the late introduction of first imported cases, early implementation of non-pharmaceutical interventions (NPIs), and low case detection rates. This analysis reinforces that Madagascar, along with other countries in SSA, remains at risk of an impending health crisis. If NPIs remain enforced, up to 50,000 lives may be saved. Even with NPIs, without vaccines and new therapies, COVID-19 could infect up to 30% of the population, making it the largest public health threat in Madagascar until early 2021, hence the importance of conducting clinical trials and continually improving access to healthcare.\n\nResumeLa pandemie de COVID-19 a eu des consequences nefastes partout dans le monde, et il y a une preoccupation particuliere pour lAfrique subsaharienne (ASS), ou des modeles suggerent que la majorite de la population sera infectee. Il est craint que le continent supportera un fardeau plus elevee de COVID-19 pour les memes raisons quil souffre davantage dautres maladies infectieuses: ecologie, conditions socio-economiques, manque dinfrastructures deau et dassainissement, et faiblesse des systemes de sante. Cependant, jusqua present, lASS a rapporte une incidence et une mortalite bien inferieure a celle des previsions des modeles pour cette region, ainsi quau nombre observe dans dautres regions du monde. Il y a trois explications principales pour ce phenomene, chacune ayant des implications tres differentes pour le fardeau epidemique final: (1) detection faible des cas, (2) differences dans lepidemiologie COVID-19 (par exemple faible R0), et (3) interventions et politiques mises en place. Le faible nombre de cas a ce jour a conduit certains gouvernements dASS a assouplir ces interventions. Cela entrainera-t-il une resurgence de cas? Pour comprendre comment interpreter le fait que les cas COVID-19 rapportes sont plus faibles que prevu a Madagascar, nous utilisons un modele de transmission structure par groupe dage pour explorer chacune de ces explications et predire limpact epidemique qui leur est associe. Nous montrons que lincidence actuelle des cas de COVID-19 peut sexpliquer par leffet cumule de lintroduction tardive des premiers cas importes, la mise en uvre rapide dinterventions non pharmaceutiques (INP) et de faibles taux de detection des cas. Cette analyse renforce le fait que Madagascar, ainsi que dautres pays dAfrique subsaharienne, reste a risque dune crise sanitaire imminente. Si les INP restent appliques, jusqua 50 000 vies pourraient etre sauvees. Meme avec des INP, tant quil ny aura pas des vaccins ni des nouvelles therapies efficaces, COVID-19 pourrait infecter jusqua 30% de la population, ce qui constituerait la plus grande menace pour la sante publique a Madagascar jusquau debut de 2021, dou limportance de la realisation des essais cliniques et de lamelioration continuelle de lacces aux soins.\n\nSummary BoxO_LIThe lower-than-expected number of reported cases of COVID-19 in Madagascar can be explained by a combination of the relatively late introduction of the disease, low detection rates, and low transmission rates due to the early and effective implementation of non-pharmaceutical interventions that reduced contact rates.\nC_LIO_LICOVID-19 is predicted to be the largest public health problem in Madagascar in 2020, but non-pharmaceutical interventions at an effectiveness similar to those seen in the first few months could save up to 50,000 lives.\nC_LIO_LIHealth systems in SSA remain at risk of an impending health crisis due to COVID-19, stressing the importance of ongoing clinical trials and improving health care access.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michelle V Evans", - "author_inst": "University of Georgia" - }, - { - "author_name": "Andres V Garchitorena", - "author_inst": "Institut de Recherche pour le Developpement" - }, - { - "author_name": "Rado JL Rakotonanahary", - "author_inst": "Pivot" - }, - { - "author_name": "John M Drake", - "author_inst": "University of Georgia" - }, - { - "author_name": "Benjamin Andriamihaja", - "author_inst": "Pivot" - }, - { - "author_name": "Elinambinina Rajaonarifara", - "author_inst": "Universite de Montpellier, CNRS, IRD, France" - }, - { - "author_name": "Calistus N Ngonghala", - "author_inst": "University of Florida" - }, - { - "author_name": "Benjamin ROCHE", - "author_inst": "IRD" - }, - { - "author_name": "Matthew H Bonds", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Julio Rakotonirina", - "author_inst": "University of Antananarivo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.14.20151126", "rel_title": "SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months", @@ -1282552,6 +1279256,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2020.07.05.20146589", + "rel_title": "COVID-19 national lockdown in Morocco: impacts on air quality and public health", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146589", + "rel_abs": "On the 20th April 2020, the end date of the first strict lockdown period in Morocco, 2 403 410 cases of the corona Virus were confirmed globally. The number of Morocco confirmed cases attended 2990, while 12 746 were suspected and 143 deaths were recorded. Due to the pandemic of coronavirus disease 2019 worldwide and in Morocco, almost all avoidable activities in the country were prohibited since the kingdom announced activities reduction on March 16, 2020 and then general lockdown with reduced industrial activities on March 20, 2020.\n\nThis study aims at comparing the air quality status in Casablanca and Marrakech, two large cities from Morocco, before the pandemic and during the lockdown situation to show whether COVID-19 compelled-anthropogenic activities lockdown may have saved lives by restraining ambient air pollution than by preventing infection.\n\nWe found that, during the quarantine, NO2 dropped by -12 g/m3 in Casablanca and -7 g/m3 in Marrakech. PM2{middle dot}5 dropped by -18 g/m3 in Casablanca and -14 g/m3 in Marrakech. CO dropped by -0.04 mg/m3 in Casablanca and -0.12 mg/m3 in Marrakech. This air pollution reduction had created human health benefits and had reduced mortality and saved lives mainly from cardiovascular diseases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "kenza khomsi", + "author_inst": "General Directorate of Meteoroloy Morocco" + }, + { + "author_name": "Houda Najmi", + "author_inst": "General Directorate of Meteorology Morocco" + }, + { + "author_name": "Hassan Amghar", + "author_inst": "General Directorate of Meteorology" + }, + { + "author_name": "Youssef Chelhaoui", + "author_inst": "General Directorate of Meteorology" + }, + { + "author_name": "Zineb Souhaili", + "author_inst": "Faculty of Medicine and Pharmacy" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.07.16.20153437", "rel_title": "Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19", @@ -1283727,157 +1280466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20156000", - "rel_title": "Going beyond clinical routine in SARS-CoV-2 antibody testing - A multiplex corona virus antibody test for the evaluation of cross-reactivity to endemic coronavirus antigens", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156000", - "rel_abs": "Given the importance of the humoral immune response to SARS-CoV-2 as a global benchmark for immunity, a detailed analysis is needed to monitor seroconversion in the general population, understand manifestation and progression of COVID-19 disease, and ultimately predict the outcome of vaccine development. In contrast to currently available serological assays, which are only able to resolve the SARS-CoV-2 antibody response on an individual antigen level, we developed a multiplex immunoassay, for which we included spike and nucleocapsid proteins of SARS-CoV-2 and the endemic human coronaviruses (NL63, OC43, 229E, HKU1) in an expanded antigen panel. Compared to three commercial in vitro diagnostic tests, our MULTICOV-AB assay achieved the highest sensitivity and specificity when analyzing a well-characterized sample set of SARS-CoV-2 infected and uninfected individuals. Simultaneously, high IgG responses against endemic coronaviruses became apparent throughout all samples, but no consistent cross-reactive IgG response patterns could be defined. In summary, we have established and validated, a robust, high-content-enabled, and antigen-saving multiplex assay MULTICOV-AB, which is highly suited to monitor vaccination studies and will facilitate epidemiologic screenings for the humoral immunity toward pandemic as well as endemic coronaviruses.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Matthias Becker", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Monika Strengert", - "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; TWINCORE GmbH, Centre for Experimental and Clinical Infection Resear" - }, - { - "author_name": "Daniel Junker", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Tobias Kerrinnes", - "author_inst": "Helmholtz-Institute for RNA-based Infection Research (HIRI), Wuerzburg, Germany" - }, - { - "author_name": "Philipp D. Kaiser", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Bjoern Traenkle", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany; Pharmaceutical Biotechnology, University of Tuebingen, Germany" - }, - { - "author_name": "Heiko Dinter", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany; Pharmaceutical Biotechnology, University of Tuebingen, Germany" - }, - { - "author_name": "Julia Haering", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Anne Zeck", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Frank Weise", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Andreas Peter", - "author_inst": "Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany; Instit" - }, - { - "author_name": "Sebastian Hoerber", - "author_inst": "Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany; Instit" - }, - { - "author_name": "Simon Fink", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Felix Ruoff", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Tamam Bakchoul", - "author_inst": "Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Armin Baillot", - "author_inst": "Niedersaechsisches Landesgesundheitsamt, Department of Virology/Serology, Hannover, Germany" - }, - { - "author_name": "Stefan Lohse", - "author_inst": "Institute of Virology, Saarland University Medical Center, Homburg/Saar, Germany" - }, - { - "author_name": "Markus Cornberg", - "author_inst": "Department of Gastroenterology, Hepatology, Endocrinology, Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine (CiiM), Hann" - }, - { - "author_name": "Thomas Illig", - "author_inst": "Hannover Unified Biobank (HUB), Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Jens Gottlieb", - "author_inst": "Clinic for Pneumonology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Sigrun Smola", - "author_inst": "Institute of Virology, Saarland University Medical Center, Homburg/Saar, Germany" - }, - { - "author_name": "Andre Karch", - "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" - }, - { - "author_name": "Klaus Berger", - "author_inst": "Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany" - }, - { - "author_name": "Hans-Georg Rammensee", - "author_inst": "Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Ce" - }, - { - "author_name": "Katja Schenke-Layland", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany; Department of Womens Health, Research Institute for Womens Health, Eberhard-" - }, - { - "author_name": "Annika Nelde", - "author_inst": "Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC2180) Image-Guided and Functio" - }, - { - "author_name": "Melanie Maerklin", - "author_inst": "Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen" - }, - { - "author_name": "Jonas S. Heitmann", - "author_inst": "Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen" - }, - { - "author_name": "Juliane S. Walz", - "author_inst": "Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC2180) Image-Guided and Functio" - }, - { - "author_name": "Markus F. Templin", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Thomas O. Joos", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - }, - { - "author_name": "Ulrich Rothbauer", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany; Pharmaceutical Biotechnology, University of Tuebingen, Germany" - }, - { - "author_name": "Gerard Krause", - "author_inst": "Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; TWINCORE GmbH, Centre for Experimental and Clinical Infection Resear" - }, - { - "author_name": "Nicole Schneiderhan-Marra", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.17.20155929", "rel_title": "Role of intermediate care unit admission and non-invasive respiratory support during the COVID-19 pandemic: a retrospective cohort study", @@ -1284702,6 +1281290,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.15.20154823", + "rel_title": "SARS-COV-2 THREE FORCING SEASONALITIES: POLICIES, ENVIRONMENT AND URBAN SPACES", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154823", + "rel_abs": "This research investigated if pandemic of SARS-COV-2 follows the Earth seasonality{varepsilon} comparing countries cumulative daily new infections incidence over Earth periodic time of interest for north and south hemisphere. It was found that no seasonality in this form{varepsilon} occurs as far as a seasonality forcing behavior{varepsilon} ' assumes most of the influence in SARS-COV-2 spreading patterns. Putting in order{varepsilon} ' of influence, there were identified three main forms of SARS-COV-2 of transmission behavior: during epidemics growth, policies are the main stronger seasonality forcing behavior of the epidemics followed by secondary and weaker environmental and urban spaces driving patterns of transmission. At outbreaks and control phase, environmental and urban spaces are the main seasonality forcing behavior due to policies/ALE limitations to address heterogeneity and confounding scenario of infection. Finally regarding S and R compartments of SIR model equations, control phases are the most reliable phase to predictive analysis.\n\nThese seasonality forcing behaviors cause environmental driven seasonality researches to face hidden or false observations due to policy/ALE interventions for each country and urban spaces characteristics. And also, it causes policies/ALE limitations to address urban spaces and environmental seasonality instabilities, thus generating posterior waves or uncontrolled patterns of transmission (fluctuations).\n\nAll this components affect the SARS-COV-2 spreading patterns simultaneously being not possible to observe environmental seasonality not associated intrinsically with policies/ALE and urban spaces, therefore conferring to these three forms of transmission spreading patterns, specific regions of analysis for time series data extraction.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Charles Roberto Telles", + "author_inst": "Secretary of State for Education and Sport of Parana" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.16.20155077", "rel_title": "Estimating the burden of COVID-19 on mortality, life expectancy and lifespan inequality in England and Wales: A population-level study", @@ -1285521,37 +1282128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.15.20154757", - "rel_title": "Space-time patterns, change, and propagation of COVID-19 risk relative to the intervention scenarios in Bangladesh", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154757", - "rel_abs": "The novel coronavirus (COVID-19) pandemic continues to be a significant public health threat worldwide. As of mid-June 2020, COVID-19 has spread worldwide with more than 7.7 million confirmed cases and more than 400,000 deaths. The impacts are substantial particularly in developing and densely populated countries like Bangladesh with inadequate health care facilities, where COVID-19 cases are currently surging. While early detection and isolation were identified as important non-pharmaceutical intervention (NPI) measures for containing the disease spread, this may not be pragmatically implementable in developing countries primarily due to social and economic reasons (i.e. poor education, less public awareness, massive unemployment). To shed light on COVID-19 transmission dynamics and impacts of NPI scenarios - e.g. social distancing, this study conducted emerging pattern analysis using the space-time scan statistic at district and thana (i.e. a sub-district or upazila with at least one police station) levels in Bangladesh and its capital - Dhaka city, respectively. We found that the central and south eastern regions in Bangladesh are currently exhibiting a high risk of COVID-19 transmission. Dhaka megacity remains as the highest risk \"active\" cluster since early April. The space-time progression of COVID-19 infection, when validated against the chronicle of government press releases and newspaper reports, suggests that Bangladesh have experienced a community level transmission at the early phase (i.e., March, 2020) primarily introduced by Bangladeshi citizens returning from coronavirus-affected countries in the Europe and the Middle East. A linkage is evident between the violation of NPIs and post-incubation period emergence of new clusters with elevated exposure risk around Bangladesh. This study provides novel insights into the space-time patterns of COVID-19 transmission dynamics and recommends pragmatic NPI implementation for reducing disease transmission and minimizing impacts in a resource-scarce country with Bangladesh as a case-study example.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arif Masrur", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Manzhu Yu", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Wei Luo", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Ashraf Dewan", - "author_inst": "Curtin University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.15.20154765", "rel_title": "Controlling COVID-19 via test-trace-quarantine", @@ -1286116,6 +1282692,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.14.20154005", + "rel_title": "A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20154005", + "rel_abs": "With the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, there is need for sensitive, specific and affordable diagnostic tests to identify infected individuals, not all of whom are symptomatic. The most sensitive test involves the detection of viral RNA using RT-qPCR, with many commercial kits now available for this purpose. However, these are expensive and supply of such kits in sufficient numbers cannot always be guaranteed. We therefore developed a multiplex assay using well-established SARS-CoV-2 targets alongside internal controls that monitor sample quality and nucleic acid extraction efficiency. Here, we establish that this test performs as well as widely used commercial assays, but at substantially reduced cost. Furthermore, we demonstrate >1,000-fold variability in material routinely collected by nose-and-throat swabbing. The inclusion of a human control probe in our assay provides additional information that could help reduce false negative rates.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Martin AM Reijns", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Louise Thompson", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "Juan Carlos Acosta", + "author_inst": "Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Holly A Black", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "Francisco J Sanchez-Luque", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Austin Diamond", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "David A Parry", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Alison Daniels", + "author_inst": "Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh" + }, + { + "author_name": "Carolina Uggenti", + "author_inst": "Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Maria C Sanchez", + "author_inst": "Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh" + }, + { + "author_name": "Alan O'Callaghan", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Michelle LL McNab", + "author_inst": "Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh" + }, + { + "author_name": "Martyna Adamowicz", + "author_inst": "Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Elias T Friman", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Toby Hurd", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Edward J Jarman", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Frederic Li Mow Chee", + "author_inst": "Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Jacqueline K Rainger", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Marion Walker", + "author_inst": "Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Camilla Drake", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Dasa Longman", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Christine Mordstein", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Sophie J Warlow", + "author_inst": "Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Stewart McKay", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Louise Slater", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "Morad Ansari", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "Ian PM Tomlinson", + "author_inst": "Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "David Moore", + "author_inst": "NHS Lothian, The South East of Scotland Clinical Genetic Service" + }, + { + "author_name": "Nadine Wilkinson", + "author_inst": "NHS Lothian, Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh" + }, + { + "author_name": "Jill Shepherd", + "author_inst": "NHS Lothian, Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh" + }, + { + "author_name": "Kate Templeton", + "author_inst": "NHS Lothian, Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh" + }, + { + "author_name": "Ingolfur Johannessen", + "author_inst": "NHS Lothian, Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh" + }, + { + "author_name": "Christine Tait-Burkard", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh" + }, + { + "author_name": "J\u00fcrgen G Haas", + "author_inst": "Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh" + }, + { + "author_name": "Nick Gilbert", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Ian R Adams", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + }, + { + "author_name": "Andrew P Jackson", + "author_inst": "MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.14.20153825", "rel_title": "Obesity has an impact on COVID-19 susceptibility and severity: a two-sample Mendelian randomization study", @@ -1286947,49 +1283686,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.14.20152629", - "rel_title": "Covid-19 infection and attributable mortality in UK Long Term Care Facilities: Cohort study using active surveillance and electronic records (March-June 2020)", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20152629", - "rel_abs": "BackgroundEpidemiological data on COVID-19 infection in care homes are scarce. We analysed data from a large provider of long-term care for older people to investigate infection and mortality during the first wave of the pandemic.\n\nMethodsCohort study of 179 UK care homes with 9,339 residents and 11,604 staff.We used manager-reported daily tallies to estimate the incidence of suspected and confirmed infection and mortality in staff and residents. Individual-level electronic health records from 8,713 residents were used to model risk factors for confirmed infection, mortality, and estimate attributable mortality.\n\nResults2,075/9,339 residents developed COVID-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory-confirmed infections. The incidence of confirmed infection was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days in residents and staff respectively. 121/179 (67.6%) care homes had at least one COVID-19 infection or COVID-19-related death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection.\n\n217/607 residents with confirmed infection died (case-fatality rate: 35.7% [31.9%; 39.7%]). Mortality in residents with no direct evidence of infection was two-fold higher in care homes with outbreaks versus those without (adjusted HR 2.2 [1.8; 2.6]).\n\nConclusionsFindings suggest many deaths occurred in people who were infected with COVID-19, but not tested. Higher occupancy and lower staffing levels were independently associated with risks of infection. Protecting staff and residents from infection requires regular testing for COVID-19 and fundamental changes to staffing and care home occupancy.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Peter F Dutey-Magni", - "author_inst": "University College London" - }, - { - "author_name": "Haydn Williams", - "author_inst": "Four Seasons Healthcare Group" - }, - { - "author_name": "Arnoupe Jhass", - "author_inst": "UCL" - }, - { - "author_name": "Greta Rait", - "author_inst": "University College London" - }, - { - "author_name": "Harry Hemingway", - "author_inst": "University College London" - }, - { - "author_name": "Andrew C Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.13.20153049", "rel_title": "Mechanistic Transmission Modeling of COVID-19 on the Diamond Princess Cruise Ship Demonstrates the Importance of Aerosol Transmission", @@ -1287626,6 +1284322,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.13.20152983", + "rel_title": "Smart Pooling: AI-powered COVID-19 testing", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152983", + "rel_abs": "BackgroundCOVID-19 is an acute respiratory illness caused by the novel coronavirus SARS-CoV-2. The disease has rapidly spread to most countries and territories and has caused 14{middle dot}2 million confirmed infections and 602,037 deaths as of July 19th 2020. Massive molecular testing for COVID-19 has been pointed as fundamental to moderate the spread of the disease. Pooling methods can enhance testing efficiency, but they are viable only at very low incidences of the disease. We propose Smart Pooling, a machine learning method that uses clinical and sociodemographic data from patients to increase the efficiency of pooled molecular testing for COVID-19 by arranging samples into all-negative pools.\n\nMethodsWe developed machine learning methods that estimate the probability that a sample will test positive for SARS-Cov-2 based on complementary information from the sample. We use these predictions to exclude samples predicted as positive from pools. We trained our machine learning methods on samples from more than 8,000 patients tested for SARS-Cov-2 from April to July in Bogota, Colombia.\n\nFindingsOur method, Smart Pooling, shows efficiency of 306% at a disease prevalence of 5% and efficiency of 107% at disease a prevalence of up to 50%, a regime in which two-stage pooling offers marginal efficiency gains compared to individual testing (see Figure 1). Additionally, we calculate the possible efficiency gains of one- and two-dimensional two-stage pooling strategies, and present the optimal strategies for disease prevalences up to 25%. We discuss practical limitations to conduct pooling in the laboratory.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC=\"FIGDIR/small/20152983v2_fig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@13980eforg.highwire.dtl.DTLVardef@3fd3beorg.highwire.dtl.DTLVardef@668b2eorg.highwire.dtl.DTLVardef@3bb6c3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Efficiency of Smart Pooling compared to standard testing methods on Patient Dataset. Smart pooling achieves higher efficiencies than two-stage pooling and individual testing for prevalences of the disease of up to 50% on the Patient Dataset. The average efficiency measures the overall efficiency of each method in the complete prevalence range.\n\nC_FIG InterpretationPooled testing has been a theoretically alluring option to increase the coverage of diagnostics since its proposition by Dorfmann during World War II. Although there are examples of successfully using pooled testing to reduce the cost of diagnostics, its applicability has remained limited because efficiency drops rapidly as prevalence increases. Not only does our method provide a cost-effective solution to increase the coverage of testing amid the COVID-19 pandemic, but it also demonstrates that artificial intelligence can be used complementary with well-established techniques in the medical praxis.\n\nFundingFaculty of Engineering, Universidad de los Andes, Colombia.\n\n1 Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThe acute respiratory illness COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The World Health Organization (WHO) labeled COVID-19 as a pandemic in March 2020. Reports from February 2020 indicated the possibility of asymptomatic transmission of the virus, which has called for molecular testing to identify carriers of the disease and prevent them from spreading it. The dramatic rise in the global need for molecular testing has made reagents scarce. Pooling strategies for massive diagnostics were initially proposed to diagnose syphilis during World War II, but have not yet seen widespread use mainly because their efficiency falls even at modest disease prevalence.\n\nWe searched PubMed, BioRxiv, and MedRxiv for articles published in English from inception to July 15th 2020 for keywords \"pooling\", \"testing\" AND \"COVID-19\", AND \"machine learning\" OR \"artificial intelligence\". Early studies for pooled molecular testing of SARS-CoV-2 revealed the possibility of detecting single positive samples in dilutions of samples from up to 32 individuals. The first reports of pooled testing came in March from Germany and the USA. These works suggested that it was feasible to conduct pooled testing as long as the prevalence of the disease was low. Numerous theoretical works have focused only on finding or adapting the ideal pooling strategy to the prevalence of the disease. Nonetheless, many do not consider other practical limitations of putting these strategies into practice. Reports from May 2020 indicated that it was feasible to predict an individuals status with machine learning methods based on reported symptoms.\n\nAdded value of this studyWe show how artificial intelligence methods can be used to enhance, but not replace, existing well-proven methods, such as diagnostics by qPCR. We show that in this fashion, pooled testing can yield efficiency gains even as prevalence increases. Our method does not compromise the sensitivity or specificity of the diagnostics, as these are still given by the molecular test. The artificial intelligence models are simple, and we make them free to use. Remarkably, artificial intelligence methods can continuously learn from every set of samples and thus increase their performance over time.\n\nImplications of all the available evidenceUsing artificial intelligence to enhance rather than replace molecular testing can make pooling testing feasible, even as disease incidence rises. This approach could make pooled testing an effective tool to tackle the diseases progression, particularly in territories with limited resources.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Mar\u00eda Escobar", + "author_inst": "Universidad de Los Andes" + }, + { + "author_name": "Guillaume Jeanneret", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Laura Bravo-S\u00e1nchez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Angela Castillo", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Catalina G\u00f3mez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Diego Valderrama", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Maria F. Roa", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Juli\u00e1n Mart\u00ednez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Jorge Madrid-Wolff", + "author_inst": "\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne" + }, + { + "author_name": "Martha Cepeda", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Marcela Guevara-Suarez", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Olga L. Sarmiento", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Andr\u00e9s L. Medaglia", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Manu Forero-Shelton", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Mauricio Velasco", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Juan Manuel Pedraza-Leal", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Silvia Restrepo", + "author_inst": "Universidad de los Andes" + }, + { + "author_name": "Pablo Arbelaez", + "author_inst": "Universidad de los Andes" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.13.20153163", "rel_title": "Estimating the seroprevalence of SARS-CoV-2 infections: systematic review", @@ -1288629,57 +1285412,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.07.15.203489", - "rel_title": "Prophylactic and Therapeutic Inhibition of In Vitro SARS-CoV-2 Replication by Oleandrin", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.203489", - "rel_abs": "With continued expansion of the COVID-19 pandemic, antiviral drugs are desperately needed to treat patients at high risk of life-threatening disease and even to limit spread if administered early during infection. Typically, the fastest route to identifying and licensing a safe and effective antiviral drug is to test those already shown safe in early clinical trials for other infections or diseases. Here, we tested in vitro oleandrin, derived from the Nerium oleander plant and shown previously to have inhibitory activity against several viruses. Using Vero cells, we found that prophylactic oleandrin administration at concentrations down to 0.05 g/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1 g/ml dose resulted in a greater than 3,000-fold reduction in infectious virus production. The EC50 values were 11.98ng/ml when virus output was measured at 24 hours post-infection, and 7.07ng/ml measured at 48 hours post-infection. Therapeutic (post-infection) treatment up to 24 hours after infection of Vero cells also reduced viral titers, with the 0.1 g/ml dose causing greater than 100-fold reductions as measured at 48 hours, and the 0.05 g/ml dose resulting in a 78-fold reduction. The potent prophylactic and therapeutic antiviral activities demonstrated here strongly support the further development of oleandrin to reduce the severity of COVID-19 and potentially also to reduce spread by persons diagnosed early after infection.\n\nIMPORTANCECOVID-19, a pandemic disease caused by infection with SARS-CoV-2, has swept around the world to cause millions of infections and hundreds-of-thousands of deaths due to the lack of vaccines and effective therapeutics. We tested oleandrin, derived from the Nerium oleander plant and shown previously to reduce the replication of several viruses, against SARS-CoV-2 infection of Vero cells. When administered both before and after virus infection, nanogram doses of oleandrin significantly inhibited replication by up to 3,000-fold, indicating the potential to prevent disease and virus spread in persons recently exposed to SARS-CoV-2, as well as to prevent severe disease in persons at high risk. These results indicate that oleandrin should be tested in animal models and in humans exposed to infection to determine its medical usefulness in controlling the pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Diana Fernandez", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Divya Mirchandani", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Nathen E Bopp", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Patricia V Aguilar", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "K Jagannadha Sastry", - "author_inst": "University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Robert A Newman", - "author_inst": "University of Texas MD Anderson Cancer Center, Phoenix Biotechnology, Inc." - }, - { - "author_name": "Scott C Weaver", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.15.204404", "rel_title": "A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells", @@ -1289332,6 +1286064,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.12.20151084", + "rel_title": "Prehospitalization Proton Pump Inhibitor (PPI) use and Clinical Outcomes in COVID-19", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151084", + "rel_abs": "Background and AimGastric acid has shown to neutralize many viruses. The working receptor of SARS-CoV-2 is angiotensin-converting enzyme-2 (ACE-2), which has shown to be omnipresent in the gastrointestinal tract. There is a theoretical concern that SARS-CoV-2 can escape the neutralization by gastric acid because of hypochlorhydria caused by the use of proton pump inhibitors (PPI) and can predispose the patients for severe COVID-19.\n\nMethodsWe studied the association between prehospitalization PPI use and clinical outcomes among hospitalized COVID-19 patients.\n\nResultsIn our study, 15.6% of hospitalized COVID-19 patients were on PPIs at home. Mortality among PPI-users was 2.3 times higher than non-users, along with 2.5 times higher risk of mechanical ventilation. This relationship existed even after adjusting for confounding variables.\n\nConclusionThese results warrant further investigation in prospective studies to evaluate if PPI-induced hypochlorhydria is associated with worse outcomes, including mortality because of the omnipresence of ACE-2 in the gastrointestinal tract.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Preethi Ramachandran", + "author_inst": "Brookdale UniversityHospital and Medical Center" + }, + { + "author_name": "Abhilash Perisetti", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Mahesh Gajendran", + "author_inst": "TTUHSC El Paso" + }, + { + "author_name": "Farla Jean-Louise", + "author_inst": "Brookdale University Hospital and Medical center" + }, + { + "author_name": "Alok Kumar Dwivedi", + "author_inst": "Texas Tech University, Paul L Foster School of Medicine" + }, + { + "author_name": "Hemant Goyal", + "author_inst": "Wright Center for Graduate Medical Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2020.07.12.20152165", "rel_title": "Clinical Ordering Practices of the SARS-CoV-2 Antibody Test at a Large Academic Medical Center", @@ -1290231,53 +1287002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.07.13.20152736", - "rel_title": "Who is wearing a mask? Gender-, age-, and location-related differences during the COVID-19 pandemic", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152736", - "rel_abs": "Masks are an effective tool in combatting the spread of COVID-19, but some people still resist wearing them and mask-wearing behavior has not been experimentally studied in the United States. To understand the demographics of mask wearers and resistors, and the impact of mandates on mask-wearing behavior, we observed shoppers (n = 9935) entering retail stores during periods of June, July, and August 2020. Approximately 41% of the June sample wore a mask. At that time, the odds of an individual wearing a mask increased significantly with age and was also 1.5x greater for females than males. Additionally, the odds of observing a mask on an urban or suburban shopper were ~4x that for rural areas. Mask mandates enacted in late July and August increased mask-wearing compliance to over 90% in all groups, but a small percentage of resistors remained. Thus, gender, age, and location factor into whether shoppers in the United States wear a mask or face covering voluntarily. Additionally, mask mandates are necessary to increase mask wearing among the public to a level required to mitigate the spread of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Michael H Haischer", - "author_inst": "Marquette University" - }, - { - "author_name": "Rachel Beilfuss", - "author_inst": "Marquette University" - }, - { - "author_name": "Meggie Rose Hart", - "author_inst": "Marquette University" - }, - { - "author_name": "Lauren Opielinski", - "author_inst": "Marquette University" - }, - { - "author_name": "David Wrucke", - "author_inst": "Marquette University" - }, - { - "author_name": "Gretchen Zirgaitis", - "author_inst": "Marquette University" - }, - { - "author_name": "Toni D Uhrich", - "author_inst": "Marquette University" - }, - { - "author_name": "Sandra K Hunter", - "author_inst": "Marquette University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.05.20146043", "rel_title": "Luminore CopperTouch\u2122 surface coating effectively inactivates SARS-CoV-2, Ebola and Marburg viruses in vitro", @@ -1291026,6 +1287750,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.11.20151597", + "rel_title": "Effectiveness of COCOA, a COVID-19 contact notification application, in Japan", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151597", + "rel_abs": "BackgroundCOCOA, a contact reporting application in Japan, was launched at the end of June 2020.\n\nObjectWe assessed effectiveness of COCOA.\n\nMethodAfter developing a simple susceptible-infected-recovery model with COCOA and voluntary restrictions against going out (VRG), we assumed that COCOA can reduce infectiousness by 10-50% points through self-quarantine at home after receiving notification from COCOA.\n\nResultsCOCOA alone is insufficient to halt an outbreak. Even if the entire population were to use COCOA, the reproduction number would be 1.31. However, if VRG were 15%, about half of the maximum VRG effectiveness under the emergency state declaration, then 10% COCOA use by a population can reduce the reproduction number to less than one.\n\nConclusionSignificant effects of COCOA for reducing the reproduction number were found. However, without VRG, COCOA alone is insufficient to control an outbreak.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.11.20151563", "rel_title": "Identification of Vulnerable Populations and Areas at Higher Risk of COVID-19 Related Mortality in the U.S.", @@ -1291993,73 +1288744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.13.20151233", - "rel_title": "Predictive performance of international COVID-19 mortality forecasting models", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20151233", - "rel_abs": "BackgroundForecasts and alternative scenarios of the COVID-19 pandemic have been critical inputs into a range of important decisions by healthcare providers, local and national government agencies and international organizations and actors. Hundreds of COVID-19 models have been released. Decision-makers need information about the predictive performance of these models to help select which ones should be used to guide decision-making.\n\nMethodsWe identified 383 published or publicly released COVID-19 forecasting models. Only seven models met the inclusion criteria of: estimating for five or more countries, providing regular updates, forecasting at least 4 weeks from the model release date, estimating mortality, and providing date-versioned sets of previously estimated forecasts. These models included those produced by: a team at MIT (Delphi), Youyang Gu (YYG), the Los Alamos National Laboratory (LANL), Imperial College London (Imperial) the USC Data Science Lab (SIKJalpha), and three models produced by the Institute for Health Metrics and Evaluation (IHME). For each of these models, we examined the median absolute percent error--compared to subsequently observed trends--for weekly and cumulative death forecasts. Errors were stratified by weeks of extrapolation, world region, and month of model estimation. For locations with epidemics showing a clear peak, each models accuracy was also evaluated in predicting the timing of peak daily mortality.\n\nResultsAcross models, the median absolute percent error (MAPE) on cumulative deaths for models released in June rose with increased weeks of extrapolation, from 2.3% at one week to 32.6% at ten weeks. Globally, ten-week MAPE values were lowest for IHME-MS-SEIR (20.3%) and YYG (22.1). Across models, MAPE at six weeks were the highest in Sub-Saharan Africa (55.6%), and the lowest in high-income countries (7.7%). Median absolute errors (MAE) for peak timing also rose with increased forecasting weeks, from 14 days at one week to 30 days at eight weeks. Peak timing MAE at eight weeks ranged from 24 days for the IHME Curve Fit model, to 48 days for LANL.\n\nInterpretationFive of the models, from IHME, YYG, Delphi, SIKJalpha and LANL, had less than 20% MAPE at six weeks. Despite the complexities of modelling human behavioural responses and government interventions related to COVID-19, predictions among these better-performing models were surprisingly accurate. Forecasts and alternative scenarios can be a useful input to decision-makers, although users should be aware of increasing errors with a greater amount of extrapolation time, and corresponding steadily widening uncertainty intervals further in the future. The framework and publicly available codebase presented can be routinely used to evaluate the performance of all publicly released models meeting inclusion criteria in the future, and compare current model predictions.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Joseph Friedman", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Patrick Liu", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Christopher E Troeger", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Austin Carter", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Robert C Reiner", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Ryan M Barber", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "James Collins", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Stephen Lim", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "David M Pigott", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Theo Vos", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Simon I Hay", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Christopher JL Murray", - "author_inst": "Institute For Health Metrics and Evaluation" - }, - { - "author_name": "Emmanuela Gakidou", - "author_inst": "Institute For Health Metrics and Evaluation" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152637", "rel_title": "Modelling suggests blood group incompatibility may substantially reduce SARS-CoV-2 transmission", @@ -1292604,6 +1289288,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.12.199588", + "rel_title": "Cold sensitivity of the SARS-CoV-2 spike ectodomain", + "rel_date": "2020-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.12.199588", + "rel_abs": "The SARS-CoV-2 spike (S) protein, a primary target for COVID-19 vaccine development, presents its Receptor Binding Domain in two conformations: receptor-accessible \"up\" or receptor-inaccessible \"down\" conformations. Here, we report that the commonly used stabilized S ectodomain construct \"2P\" is sensitive to cold temperature, and that this cold sensitivity is resolved in a \"down\" state stabilized spike. Our results will impact structural, functional and vaccine studies that use the SARS-CoV-2 S ectodomain.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Robert J Edwards", + "author_inst": "Duke University" + }, + { + "author_name": "Katayoun Mansouri", + "author_inst": "Duke University" + }, + { + "author_name": "Victoria Stalls", + "author_inst": "Duke University" + }, + { + "author_name": "Kartik Manne", + "author_inst": "Duke University" + }, + { + "author_name": "Brian Watts", + "author_inst": "Duke University" + }, + { + "author_name": "Rob Parks", + "author_inst": "Duke University" + }, + { + "author_name": "Katarzyna Janowska", + "author_inst": "Duke University" + }, + { + "author_name": "Sophie M.C. Gobeil", + "author_inst": "Duke University" + }, + { + "author_name": "Megan Kopp", + "author_inst": "Duke University" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "Xiaozhi Lu", + "author_inst": "Duke University" + }, + { + "author_name": "Zekun Mu", + "author_inst": "Duke University" + }, + { + "author_name": "Margaret Deyton", + "author_inst": "Duke University" + }, + { + "author_name": "Thomas Oguin III", + "author_inst": "Duke University" + }, + { + "author_name": "Jordan Sprenz", + "author_inst": "Duke University" + }, + { + "author_name": "Wilton Williams", + "author_inst": "Duke University" + }, + { + "author_name": "Kevin Saunders", + "author_inst": "Duke University" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "Greogory D Sempowski", + "author_inst": "Duke University" + }, + { + "author_name": "Rory Henderson", + "author_inst": "Duke University" + }, + { + "author_name": "Munir Alam", + "author_inst": "Duke University" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Priyamvada Acharya", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.13.190140", "rel_title": "Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses", @@ -1293579,81 +1290370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150565", - "rel_title": "Magnitude and time-course of excess mortality during COVID-19 outbreak: population-based empirical evidence from highly impacted provinces in northern Italy", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150565", - "rel_abs": "BackgroundThe real impact of SARS-CoV-2 on overall mortality remains uncertain and surveillance reports attributed to COVID-19 a limited amount of deaths during the outbreak. Aim of this study is to assess the excess mortality (EM) during COVID-19 outbreak in highly impacted areas of northern Italy.\n\nMethodsWe analyzed data on deaths occurred in the first four months of 2020 in health protection agencies (HPA) of Bergamo and Brescia (Lombardy), building a time-series of daily number of deaths and predicting the daily standardized mortality ratio (SMR) and cumulative number of excess deaths (ED) through a Poisson generalized additive model of the observed counts in 2020, using 2019 data as a reference.\n\nResultsWe estimated 5740 (95% Credible Set (CS): 5552-5936) ED in the HPA of Bergamo and 3703 (95% CS: 3535 - 3877) in Brescia, corresponding to 2.55 (95% CS: 2.50-2.61) and 1.93 (95% CS: 1.89-1.98) folds increase in the number of deaths. The ED wave started a few days later in Brescia, but the daily estimated SMR peaked at the end of March in both HPAs, roughly two weeks after the introduction of lock-down measures, with significantly higher estimates in Bergamo (9.4, 95% CI: 9.1-9.7).\n\nConclusionEM was significantly larger than that officially attributed to COVID-19, disclosing its hidden burden likely due to indirect effects on health system. Time-series analyses highlighted the impact of lockdown restrictions, with a lower EM in the HPA where there was a smaller delay between the epidemic outbreak and their enforcement.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Sara Conti", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Pietro Ferrara", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Giampiero Mazzaglia", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Marco I D'Orso", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Roberta Ciampichini", - "author_inst": "ATS Bergamo" - }, - { - "author_name": "Carla Fornari", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Fabiana Madotto", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Michele Magoni", - "author_inst": "ATS Brescia" - }, - { - "author_name": "Giuseppe Sampietro", - "author_inst": "ATS Bergamo" - }, - { - "author_name": "Andrea Silenzi", - "author_inst": "ATS Brescia" - }, - { - "author_name": "Claudio V Sileo", - "author_inst": "ATS Brescia" - }, - { - "author_name": "Andrea Zucchi", - "author_inst": "ATS Bergamo" - }, - { - "author_name": "Giancarlo Cesana", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - }, - { - "author_name": "Lamberto Manzoli", - "author_inst": "University of Ferrara" - }, - { - "author_name": "Lorenzo G Mantovani", - "author_inst": "Center for Public Health Research, University of Milano Bicocca, Monza, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20150508", "rel_title": "ICU admissions and in-hospital deaths linked to covid-19 in the Paris region are correlated with previously observed ambient temperature", @@ -1294046,6 +1290762,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.10.20150680", + "rel_title": "Addition of Tocilizumab to the standard of care reduces mortality in severe COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150680", + "rel_abs": "IntroductionTocilizumab is an anti-interleukin-6 antibody that has been used for the treatment of severe coronavirus disease 2019 (COVID-19). However, the concrete evidence of its benefit in reducing the mortality in severe COVID-19 is lacking. Therefore, we performed a systematic review and meta-analysis of relevant studies that compared the efficacy of Tocilizumab in severe COVID-19 vs. standard of care alone.\n\nMethodsLiterature search for studies that compared Tocilizumab and Standard of care in the treatment of COVID-19 was done using major online databases from December 2019 to June 14th, 2020. Search words Tocilizumab, anti-interleukin-6 antibody, and COVID-19 or coronavirus 2019 in various combinations were used. Articles in the form of abstracts, letters without original data, case reports, and reviews were excluded. Data was gathered on an excel sheet, and statistical analysis was performed using Review Manager 5.3.\n\nResultsSixteen studies were eligible from 693 initial studies, including 3,641 patients (64% males). There were thirteen retrospective studies and three prospective studies. There were 2,488 patients in the standard of care group (61.7%) and 1,153 patients (68.7%) in the Tocilizumab group. The death rate in the tocilizumab group, 22.4% (258/1153), was lower than the standard of care group, 26.21% (652/2,488) (Pooled odds ratio 0.57 [95% CI 0.36-0.92] p=0.02). There was a significant heterogeneity (Inconsistency index= 80%) among the included studies.\n\nConclusionThe addition of Tocilizumab to the standard of care might reduce the mortality in severe COVID-19. Larger randomized clinical trials are needed to validate these findings.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Umesha Boregowda", + "author_inst": "Bassett Medical Center" + }, + { + "author_name": "Abhilash Perisetti", + "author_inst": "University of Arkansas for Medical Sciences" + }, + { + "author_name": "Arpitha Nanjappa", + "author_inst": "Bassett Medical Center" + }, + { + "author_name": "Mahesh Gajendran", + "author_inst": "Texas Tech University, Paul L Foster School of Medicine," + }, + { + "author_name": "Gurusaravanan Kutti Sridharan", + "author_inst": "University of Arizona, Banner University Medical Center" + }, + { + "author_name": "Hemant Goyal", + "author_inst": "Wright Center for Graduate Medical Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.11.20151324", "rel_title": "Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders", @@ -1294993,25 +1291748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.09.20149245", - "rel_title": "Dynamics of RT-qPCR SARS-CoV-2 Detection Rates Prior to and After Symptom Onset", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149245", - "rel_abs": "Effective RT-qPCR testing for SARS-CoV-2 is essential for treatment, surveillance and control of the COVID-19 pandemic. A recent meta-analysis 1 suggested that testing prior to the onset of symptoms is likely to miss the majority of infected individuals. These findings cast severe doubts on the effectiveness of mass screening efforts intended to detect SARS-CoV-2 prior to the onset of symptoms and decrease community transmissions from pre-/asymptomatic individuals2-4. However, alternative analyses and additional data described herein refine these estimates and suggest that many SARS-CoV-2 infections could potentially be detected prior to symptom onset.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Scott Sherrill-Mix", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20149013", "rel_title": "The Age Pattern of the Male- to- Female Ratio in Mortality from COVID-19 Mirrors that of Cardiovascular Disease but not Cancer in the General Population", @@ -1295540,6 +1292276,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.09.20149633", + "rel_title": "Antibody dynamics to SARS-CoV-2 in Asymptomatic and Mild COVID-19 patients", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149633", + "rel_abs": "ImportanceAsymptomatic COVID-19 infections have a long duration of viral shedding and contribute substantially to disease transmission. However, the missing asymptomatic cases have been significantly overlooked because of imperfect sensitivity of nucleic acid testing. We aimed to investigate the humoral immunity in asymptomatics, which will help us develop serological tests and improve early identification, understand the humoral immunity to COVID-19, and provide more rational control strategies for the pandemic.\n\nObjectiveTo better control the pandemic of COVID-19, dynamics of IgM and IgG responses to 23 proteins of SARS-CoV-2 and neutralizing antibody in asymptomatic COVID-19 infections after exposure time were investigated.\n\nDesign, setting, and participants63 asymptomatic individuals were screened by RT-qPCR and ELISA for IgM and IgG from 11,776 personnel returning to work, and close contacts with the confirmed cases in different communities of Wuhan by investigation of clusters and tracing infectious sources. 63 healthy contacts with both negative results for NAT and antibodies were selected as negative controls. 51 mild patients without any preexisting conditions were also screened as controls from 1056 patients during hospitalization in Tongji Hospital. A total of 177 participants were enrolled in this study and serial serum samples (n=213) were collected. The research was conducted between 17 February 2020 and 28 April 2020. Serum IgM and IgG profiles of 177 participants were further probed using a SARS-CoV-2 proteome microarray. Neutralizing antibody responses in different population were detected by a pseudotyped virus neutralization assay system. The dynamics of IgM and IgG antibodies and neutralizing antibodies were analyzed with exposure time or symptoms onset.\n\nResultsAsymptomatics were classified into four subgroups based on NAT and serological tests. In particular, only 19% had positive NAT results while approximately 81% detected positive IgM/IgG responses. Comparative SARS-CoV-2 proteome microarray further demonstrated that there was a significantly difference of antibody dynamics responding to S1 or N proteins among three populations, although IgM and IgG profiles could not be used to differentiate them. S1 specific IgM responses were elicited in asymptomatic individuals as early to the seventh day after exposure and peaked on days from 17d to 25d, which might be used as an early diagnostic biomarker and give an additional 36.5% seropositivity. Mild patients produced stronger both S1 specific IgM and neutralizing antibody responses than asymptomatic individuals. Most importantly, S1 specific IgM/IgG responses and the titers of neutralizing antibody in asymptomatic individuals gradually vanished in two months.\n\nConclusions and relevanceOur findings might have important implications for the definition of asymptomatic COVID-19 infections, diagnosis, serological survey, public health and immunization strategies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Qing Lei", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Yang Li", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Hongyan Hou", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Feng Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yandi Zhang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Danyun Lai", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Banga Ndzouboukou Jo-Lewis", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Zhaowei Xu", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Bo Zhang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hong Chen", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Zhuqing Ouyang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Junbiao Xue", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Xiaosong Lin", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Yunxiao Zheng", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Zhongjie Yao", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Xuening Wang", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Caizheng Yu", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Jeremy Jiang", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Hainan Zhang", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Huan Qi", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Shujuan Guo", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Shenghai Huang", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Ziyong Sun", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Sheng-ce Tao", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Xionglin Fan", + "author_inst": "Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.09.20148429", "rel_title": "Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection", @@ -1296587,97 +1293438,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.08.20148841", - "rel_title": "A Multicenter, randomized, open-label, controlled trial to evaluate the efficacy and tolerability of hydroxychloroquine and a retrospective study in adult patients with mild to moderate Coronavirus disease 2019 (COVID-19)", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148841", - "rel_abs": "ObjectiveIn this study, we evaluated the efficacy of hydroxychloroquine (HCQ) against coronavirus disease 2019 (COVID-19) via a randomized controlled trial (RCT) and a retrospective study.\n\nMethodsSubjects admitted to 11 designated public hospitals in Taiwan between April 1 and May 31, 2020, with COVID-19 diagnosis confirmed by pharyngeal real-time RT-PCR for SARS-CoV-2, were randomized at a 2:1 ratio and stratified by mild or moderate illness. HCQ 400 mg twice for 1 d and HCQ 200 mg twice daily for 6 days were administered. Both study group and controlled group received standard of care (SOC). Pharyngeal swabs and sputum were collected every other day. The proportion and time to negative viral PCR were assessed on day 14. In the retrospective study, medical records were reviewed for patients admitted before March 31, 2020.\n\nResultsThere were 33 and 37 cases in the RCT and retrospective study, respctively. In the RCT, the median times to negative rRT-PCR from randomization to hospital day 14 were 5 days (95% CI; 1-9 days) and 10 days (95% CI; 2-12 days) for the HCQ and SOC groups, respectively (p = 0.40). On day 14, 81.0% (17/21) and 75.0% (9/12) of the subjects in the HCQ and SOC groups, respectively, had undetected virus (p = 0.36). In the retrospective study, 12 (42.9%) in the HCQ group and 5 (55.6%) in the control group had negative rRT-PCR results on hospital day 14 (p = 0.70).\n\nConclusionsNeither study demonstrated that HCQ shortened viral shedding in mild to moderate COVID-19 subjects.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Cheng-Pin Chen", - "author_inst": "Taoyuan General Hospital, Ministry of Health and Welfare, Taiwan" - }, - { - "author_name": "Yi-Chun Lin", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Tsung-Chia Chen", - "author_inst": "Taichung Hospital" - }, - { - "author_name": "Ting-Yu Tseng", - "author_inst": "Taichung Hospital" - }, - { - "author_name": "Hon-Lai Wong", - "author_inst": "Keelung Hospital" - }, - { - "author_name": "Cheng-Yu Kuo", - "author_inst": "Pingtung Hospital" - }, - { - "author_name": "Wu-Pu Lin", - "author_inst": "Taipei Hospital" - }, - { - "author_name": "Sz-Rung Huang", - "author_inst": "Miaoli General Hospital" - }, - { - "author_name": "Wei-Yao Wang", - "author_inst": "Feng Yuan Hospital" - }, - { - "author_name": "Jia-Hung Liao", - "author_inst": "Nantou Hospital" - }, - { - "author_name": "Chung-Shin Liao", - "author_inst": "Chia Yi Hospital" - }, - { - "author_name": "Yuan-Pin Hung", - "author_inst": "Tainan Hospital" - }, - { - "author_name": "Tse-Hung Lin", - "author_inst": "Chang Hua Hospital" - }, - { - "author_name": "Tz-Yan Chang", - "author_inst": "Chang Hua Hospital" - }, - { - "author_name": "Chin-Fu Hsiao", - "author_inst": "National Health Research Institutes" - }, - { - "author_name": "Yi-Wen Huang", - "author_inst": "Chang Hua Hospital" - }, - { - "author_name": "Wei-Sheng Chung", - "author_inst": "Taichung Hospital" - }, - { - "author_name": "Chien-Yu Cheng", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Shu-Hsing Cheng", - "author_inst": "Taoyuan General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.08.20148999", "rel_title": "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2", @@ -1297446,6 +1294206,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.07.08.20148171", + "rel_title": "Sleep quality, mental health and circadian rhythms during COVID lockdown: Results from the SleepQuest Study", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148171", + "rel_abs": "Behavioural responses to COVID-19 lockdown will define the long-term impact of psychological stressors on sleep and brain health. Here we tease apart factors that help protect against sleep disturbance. We capitalise on the unique restrictions during COVID-19 to understand how time of day of daylight exposure and outside exercise interact with chronotype and sleep quality. 3474 people from the UK (median age 62, range 18-91) completed our online SleepQuest Study between 29th April and 13th May 2020 - a set of validated questionnaires probing sleep quality, depression, anxiety and attitudes to sleep alongside bespoke questions on the effect of COVID-19 lockdown on sleep, time spent outside and exercising and self-help sleep measures. Significantly more people (n=1252) reported worsened than improved sleep (n=562) during lockdown (p<0.0001). Factors significantly associated with worsened sleep included low mood (p<0.001), anxiety (p<0.001) and suspected, proven or at risk of COVID-19 symptoms (all p<0.03). Sleep improvement was related to the increased length of time spent outside (P<0.01). Older peoples sleep quality was less affected than younger people by COVID lockdown (p<0.001). Better sleep quality was associated with going outside and exercising earlier, rather than later, in the day. However, the benefit of being outside early is driven by improved sleep in owl (p=0.0002) and not lark (p=0.27) chronotype, whereas, the benefit of early exercise (inside or outside) did not depend on chronotype. Defining the interaction between chronotype, mental health and behaviour will be critical for targeted lifestyle adaptations to protect brain health through current and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Neil Carrigan", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alfie R Wearn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Saba Meky", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "James Selwood", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hugh Piggins", + "author_inst": "University of Bristol" + }, + { + "author_name": "Nicholas Turner", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rosemary Greenwood", + "author_inst": "University Hospitals Bristol and Weston NHS Foundation Trust" + }, + { + "author_name": "Elizabeth Coulthard", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.09.20149591", "rel_title": "IN-UTERO MOTHER-TO-CHILD SARS-CoV-2 TRANSMISSION: viral detection and fetal immune response", @@ -1298509,41 +1295316,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.09.196378", - "rel_title": "Molecular analysis of binding region of an ACE2 as a receptor for SARS-CoV-2 between humans and mammals", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196378", - "rel_abs": "In June 2020, a second wave of coronavirus disease-2019 (COVID-19) infections raised concern in Beijing, where salmon sold a fresh fish wholesale market was suspected of being the source of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. It has raised questions in the press and elsewhere about the scientific basis of salmon as a source of infection. With the number of cases growing, the surface of a salmon chopping board in the market was examined for the presence of SARS-CoV-2 and a positive reaction was observed. Following these test results, there has been debate over whether salmon can be infected with SARS-CoV-2. To find assess this, we investigated the structural homology of angiotensin-converting enzyme 2 (ACE2), a host-side receptor for SARS-CoV-2, between humans and other species including salmon and mink. As a result, a high structural homology between ACE2 and mink, which has reportedly transmitted SARS-CoV-2 to humans, was confirmed. However, a non-high structural homology of ACE2 between salmon and humans was observed. Further experiments are needed to find the source of SARS-CoV-2 transmission to the salmon.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Takuma Hayashi", - "author_inst": "National Hospital Organization Kyoto Medical Center" - }, - { - "author_name": "Kaoru Abiko", - "author_inst": "National Hospital Organization Kyoto Medical Center" - }, - { - "author_name": "Masaki Mandai", - "author_inst": "Kyoto University School of Medicine" - }, - { - "author_name": "Ikuo Konishi", - "author_inst": "Kyoto Medical Center Kyoto University School of Medicine" - }, - { - "author_name": "Nobuo Yaegashi", - "author_inst": "Tohoku University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.07.09.196188", "rel_title": "SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation, immune cell infiltration, and compromised respiratory function", @@ -1299356,6 +1296128,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.08.20148700", + "rel_title": "G6PD Deficiency Overrepresented Among Pediatric COVID-19 Cases in One Saudi Children Hospital", + "rel_date": "2020-07-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148700", + "rel_abs": "Fluorescent spot test for glucose-6-phosphate dehydrogenase (G6PD) deficiency was performed in 5 boys and 14 girls who had confirmed COVID-19. Out of those, 4 (80%) boys and 5 (36%) girls were found to be G6PD deficient.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Maryam Al-Aamri", + "author_inst": "Department of Pediatrics, King Abdulaziz Hospital, Ministry of the National Guard-Health Affairs, Al-Ahsa, Saudi Arabia." + }, + { + "author_name": "Fatima Al-Khalifa", + "author_inst": "Department of Pediatrics, King Abdulaziz Hospital, Ministry of the National Guard-Health Affairs, Al-Ahsa, Saudi Arabia." + }, + { + "author_name": "Fawatim Al-Nahwi", + "author_inst": "Department of Pediatrics, Maternity and Children Hospital, Al-Ahsa, Ministry of Health, Saudi Arabia" + }, + { + "author_name": "Heba Al-Ameer", + "author_inst": "Department of Pediatrics, Maternity and Children Hospital, Al-Ahsa, Ministry of Health, Saudi Arabia" + }, + { + "author_name": "Sameer Al-Abdi", + "author_inst": "Department of Pediatrics, Maternity and Children Hospital, Al-Ahsa, Ministry of Health, Saudi Arabia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.08.20148775", "rel_title": "Air recirculation role in the infection with COVID-19, lessons learned from Diamond Princess cruise ship", @@ -1300750,93 +1297557,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.07.08.192104", - "rel_title": "Molecular architecture of the SARS-CoV-2 virus", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.192104", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins and the complexes of the spike (S) proteins with the cellular receptor ACE2 or neutralizing antibodies, detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in both pre- and postfusion conformations were determined to average resolutions of 8.7-11 [A]. Compositions of the N-linked glycans from the native spikes were analyzed by mass-spectrometry, which revealed highly similar overall processing states of the native glycans to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNP) and its higher-order assemblies were revealed. Overall, these characterizations have revealed the architecture of the SARS-CoV-2 virus in unprecedented detail, and shed lights on how the virus packs its [~]30 kb long single-segmented RNA in the [~]80 nm diameter lumen.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Hangping Yao", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Yutong Song", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Yong Chen", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Nanping Wu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Jialu Xu", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Chujie Sun", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Jiaxing Zhang", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Tianhao Weng", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Zheyuan Zhang", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Zhigang Wu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Linfang Cheng", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Danrong Shi", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Xiangyun Lu", - "author_inst": "Zhejiang University School of Medicine First Affiliated Hospital" - }, - { - "author_name": "Jianlin Lei", - "author_inst": "School of Life Sciences, Tsinghua University, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure and " - }, - { - "author_name": "Max Crispin", - "author_inst": "University of Southampton" - }, - { - "author_name": "Yigong Shi", - "author_inst": "School of Life Sciences, Tsinghua University, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure and " - }, - { - "author_name": "Lanjuan Li", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases and National Clinical Research Center for Infectious Diseases, First Affiliated Hospital" - }, - { - "author_name": "Sai Li", - "author_inst": "School of Life Sciences, Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.08.193045", "rel_title": "A single-dose live-attenuated YF17D-vectored SARS-CoV2 vaccine candidate", @@ -1301665,6 +1298385,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.05.20140343", + "rel_title": "The COVID-19 mortality effects of underlying health conditions in India: a modelling study", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20140343", + "rel_abs": "ObjectiveTo model how known COVID-19 comorbidities will affect mortality rates and the age distribution of mortality in a large lower middle income country (India), as compared with a high income country (England), and to identify which health conditions drive any differences.\n\nDesignModelling study.\n\nSettingEngland and India.\n\nParticipants1,375,548 respondents aged 18 to 99 to the District Level Household Survey-4 and Annual Health Survey in India. Additional information on health condition prevalence on individuals aged 18 to 99 was obtained from the Health Survey for England and the Global Burden of Diseases, Risk Factors, and Injuries Studies (GBD).\n\nMain outcome measuresThe primary outcome was the proportional increase in age-specific mortality in each country due to the prevalence of each COVID-19 mortality risk factor (diabetes, hypertension, obesity, chronic heart disease, respiratory illness, kidney disease, liver disease, and cancer, among others). The combined change in overall mortality and the share of deaths under 60 from the combination of risk factors was estimated in each country.\n\nResultsRelative to England, Indians have higher rates of diabetes (10.6% vs. 8.5%), chronic respiratory disease (4.8% vs. 2.5%), and kidney disease (9.7% vs. 5.6%), and lower rates of obesity (4.4% vs. 27.9%), chronic heart disease (4.4% vs. 5.9%), and cancer (0.3% vs. 2.8%). Population COVID-19 mortality in India relative to England is most increased by diabetes (+5.4%) and chronic respiratory disease (+2.3%), and most reduced by obesity (-9.7%), cancer (-3.2%), and chronic heart disease (-1.9%). Overall, comorbidities lower mortality in India relative to England by 9.7%. Accounting for demographics and population health explains a third of the difference in share of deaths under age 60 between the two countries.\n\nConclusionsKnown COVID-19 health risk factors are not expected to have a large effect on aggregate mortality or its age distribution in India relative to England. The high share of COVID-19 deaths from people under 60 in low- and middle-income countries (LMICs) remains unexplained. Understanding mortality risk associated with health conditions prevalent in LMICs, such as malnutrition and HIV/AIDS, is essential for understanding differential mortality.\n\nSUMMARY BOXO_ST_ABSWhat is already known on this topicC_ST_ABSCOVID-19 infections in low- and middle-income countries (LMICs) are rising rapidly, with the burden of mortality concentrated at much younger ages than in rich countries.\n\nA range of pre-existing health conditions can increase the severity of COVID-19 infections.\n\nIt is feared that poor population health may worsen the severity of the pandemic in LMICs.\n\nWhat this study addsThe COVID-19 comorbidities that have been studied to date may have only a very small effect on aggregate mortality in India relative to England and do not shift the mortality burden toward lower ages at all.\n\nIndias younger demographics can explain only a third of the substantial difference in the share of deaths under age 60 between India and England.\n\nHowever, mortality risk associated with health conditions prevalent in LMICs, such as malnutrition and HIV/AIDS, is unknown and research on this topic is urgently needed.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Paul Novosad", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Radhika Jain", + "author_inst": "Stanford University" + }, + { + "author_name": "Alison Campion", + "author_inst": "Development Data Lab" + }, + { + "author_name": "Sam Asher", + "author_inst": "Johns Hopkins University SAIS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.04.20146209", "rel_title": "Ultrametric model for covid-19 dynamics: an attempt to explain slow approaching herd immunity in Sweden", @@ -1302708,73 +1299459,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.07.20148460", - "rel_title": "Reconstructing the global dynamics of under-ascertained COVID-19 cases and infections", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148460", - "rel_abs": "BackgroundAsymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.\n\nMethodsUsing reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever >= 37.5{degrees}C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the case fatality ratio (CFR) as an assumed baseline. We then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.\n\nResultsWe estimate that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.38% (Bangladesh) to 99.6% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 17.8 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. Despite low case detection in some countries, our results that adjust for this still suggest that all countries have had only a small fraction of their populations infected as of July 2020.\n\nConclusionsWe found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each countrys population infected with SARS-CoV-2 worldwide is generally low.\n\nFundingWellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Timothy W Russell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nick Golding", - "author_inst": "Telethon Kids Institute and Curtin University" - }, - { - "author_name": "Joel Hellewell", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Lawrence Wright", - "author_inst": "Defence Science and Technology Laboratory/Sopra Steria, Fareham, United Kingdom" - }, - { - "author_name": "Carl A B Pearson", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Hamish Gibbs", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Yang Liu", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "John W Edmunds", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.03.179028", "rel_title": "Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations", @@ -1303547,6 +1300231,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.06.20147272", + "rel_title": "Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147272", + "rel_abs": "BackgroundUniversity campuses present an ideal environment for viral spread and are therefore at extreme risk of serving as a hotbed for a COVID-19 outbreak. While active surveillance throughout the semester such as widespread testing, contact tracing, and case isolation, may assist in detecting and preventing early outbreaks, these strategies will not be sufficient should a larger outbreak occur. It is therefore necessary to limit the initial number of active cases at the start of the semester. We examine the impact of pre-semester NAT testing on disease spread in a university setting.\n\nMethodsWe implement simple dynamic transmission models of SARS-CoV-2 infection to explore the effects of pre-semester testing strategies on the number of active infections and occupied isolation beds throughout the semester. We assume an infectious period of 3 days and vary R0 to represent the effectiveness of disease mitigation strategies throughout the semester. We assume the prevalence of active cases at the beginning of the semester is 5%. The sensitivity of the NAT test is set at 90%.\n\nResultsIf no pre-semester screening is mandated, the peak number of active infections occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections when effective mitigation strategies (R0 = 1.25) are implemented to over 15,000 active infections for less effective strategies (R0 = 3). When one NAT test is mandated within one week of campus arrival, effective (R0 = 1.25) and less effective (R0 = 3) mitigation strategies delay the onset of the peak to 40 days and 17 days, respectively, and result in peak size ranging from 1,000 to over 15,000 active infections. When two NAT tests are mandated, effective (R0 = 1.25) and less effective (R0 = 3) mitigation strategies delay the onset of the peak through the end of fall semester and 20 days, respectively, and result in peak size ranging from less than 1,000 to over 15,000 active infections. If maximum occupancy of isolation beds is set to 2% of the student population, then isolation beds would only be available for a range of 1 in 2 confirmed cases (R0 = 1.25) to 1 in 40 confirmed cases (R0 = 3) before maximum occupancy is reached.\n\nConclusionEven with highly effective mitigation strategies throughout the semester, inadequate pre-semester testing will lead to early and large surges of the disease and result in universities quickly reaching their isolation bed capacity. We therefore recommend NAT testing within one week of campus return. While this strategy is sufficient for delaying the timing of the outbreak, pre-semester testing would need to be implemented in conjunction with effective mitigation strategies to reduce the outbreak size.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Lior Rennert", + "author_inst": "Clemson University" + }, + { + "author_name": "Corey Andrew Kalbaugh", + "author_inst": "Clemson University" + }, + { + "author_name": "Lu Shi", + "author_inst": "Clemson University" + }, + { + "author_name": "Christopher McMahan", + "author_inst": "Clemson University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.05.20146910", "rel_title": "Near Term Predictions of Covid-19 Cases in West Bengal, Maharashtra, Delhi and Tamil Nadu in India Based on Basu Model", @@ -1304250,45 +1300965,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.07.07.191429", - "rel_title": "Genes Encoding ACE2, TMPRSS2 and Related Proteins Mediating SARS-CoV-2 Viral Entry are Upregulated with Age in Human Cardiomyocytes", - "rel_date": "2020-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.191429", - "rel_abs": "Age is an independent risk factor for adverse outcome in patients following COVID-19 infection. We hypothesised that differential expression of genes encoding proteins proposed to be required for entry of SARS-Cov-2 in aged compared to younger cardiomyocytes might contribute to the susceptibility of older individuals to COVID-19-associated cardiovascular complications.We generated strand-specific RNA-sequencing libraries from RNA isolated from flow-sorted cardiomyocyte nuclei from left ventricular tissue. RNASeq data were compared between five young (19-25yr) and five older (63-78yr) Caucasian males who had not been on medication or exhibited evidence of cardiovascular disease post-mortem.Expression of relevant genes encoding ACE2, TMPRSS2, TMPRS11D, TMPRS11E, FURIN, CTSL, CTSB and B0AT1/SLC6A19 were upregulated in aged cardiomyocytes and the combined relative cardiomyocyte expression of these genes correlated positively with age. Genes encoding proteins in the RAAS and interferon/interleukin pathways were also upregulated such as ACE, AGTR1, MAS1 and IL6R.Our results highlight SARS-CoV-2 related genes that have higher expression in aged compared with young adult cardiomyocytes. These data may inform studies using selective enzyme inhibitors/antagonists, available as experimental compounds or clinically approved drugs e.g. remdesivir that has recently been rapidly accepted for compassionate use, to further understand the contribution of these pathways in human cardiomyocytes to disease outcome in COVID-19 patients.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Emma L Robinson", - "author_inst": "Maastricht University" - }, - { - "author_name": "Kanar Alkass", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Olaf Bergmann", - "author_inst": "TU-Dresden" - }, - { - "author_name": "Janet J Maguire", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Llewelyn Roderick", - "author_inst": "KU Leuven" - }, - { - "author_name": "Anthony P Davenport", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.07.05.20140467", "rel_title": "Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation.", @@ -1304865,6 +1301541,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20145375", + "rel_title": "Risk Factors for Mortality of COVID-19 Patients", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145375", + "rel_abs": "BackgroundLethality rates of COVID-19 are so different between countries and continents. This lethality seems to be very low in Africa and Asia, but exceedingly high in western Europe and North America. Many factors could have a role in this disparity such as comorbidities. Advanced age, obesity, cardiovascular disease, diabetes and cancer were the most frequently cited in the reported COVID-19 data. The main objective was to analyze and evaluate the association between the COVID-19 mortality and the mentioned factors in 164 countries.\n\nMethodsThe Data of COVID-19 deaths, latitude degrees, population age distribution, cardiovascular diseases, obesity, diabetes and cancer were extracted from different online sources. For the statistical analysis, we used Spearman to measure the correlation coefficient between numbers of deaths and the mentioned factors until June 29, 2020.\n\nResultsThe correlation between COVID-19 mortality and latitude, high age, obesity, CVD and number of cancer patients per 100,000 is significant at 0.01 level with r = 0.489, r=0.511, r=0.489, r=0.561 and r=0.536 respectively. The correlation between the number of deaths and diabetes is less strong than the previous ones, and the correlation coefficient is r= 0.154.\n\nConclusionThe great lethality of COVID-19 in western Europe and North America can be explained in part by the highest of age, cancer and CVD percentage in these regions. It seems also plausible that the increased obesity in the USA and vitamin D deficiency in Europe may contribute to increasing the number of COVID-19 deaths.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ouail Ouchetto", + "author_inst": "Hassan II University - Casablanca" + }, + { + "author_name": "Asmaa Drissi Bourhanbour", + "author_inst": "Faculty of Medicine and Pharmacy, Hassan II University of Casablanca" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.28.20141911", "rel_title": "Characteristics and outcomes of Acute Respiratory Distress Syndrome related to COVID-19 in Belgian and French Intensive Care Units according to antiviral strategies. The COVADIS multicenter observational study.", @@ -1305544,45 +1302243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.06.20147868", - "rel_title": "Projections and early-warning signals of a second wave of the COVID-19 epidemic in Illinois", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147868", - "rel_abs": "We present two different scenarios for a second wave of the COVID-19 epidemic in Illinois and simulate them using our previously described age-of-infection model, calibrated to real-time hospital and deaths data. In the first scenario we assume that the parameters of the second wave in Illinois would be similar to those currently observed in other states such as Arizona, Florida, and Texas. We estimate doubling times of hospitalizations and test positivity in all states with relevant publicly available data and calculate the corresponding effective reproduction numbers for Illinois. These parameters are remarkably consistent in states with rapidly growing epidemics. We conjecture that the emergence of the second wave of the epidemic in these states can be attributed to superspreading events at large parties, crowded bars, and indoor dining. In our second, more optimistic scenario we assume changes in Illinois state policy would result in successful mitigation of superspreading events and thus would lower the effective reproduction number to the value observed in late June 2020. In this case our calculations show effective suppression of the second wave in Illinois. Our analysis also suggests that the logarithmic time derivatives of COVID-19 hospitalizations and case positivity can serve as a simple but strong early-warning signal of the onset of a second wave.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zach Weiner", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "George Wong", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Ahmed Elbanna", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Alexei Tkachenko", - "author_inst": "Brookhaven National Laboratory" - }, - { - "author_name": "Sergei Maslov", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Nigel Goldenfeld", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.07.20140996", "rel_title": "Modelling interventions to control COVID-19 outbreaks in a refugee camp", @@ -1306075,6 +1302735,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.04.20142752", + "rel_title": "Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.04.20142752", + "rel_abs": "Initially, the global outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spared children from severe disease. However, after the initial wave of infections, clusters of a novel hyperinflammatory disease have been reported in regions with ongoing SARS-CoV-2 epidemics. While the characteristic clinical features are becoming clear, the pathophysiology remains unknown. Herein, we report on the immune profiles of eight Multisystem Inflammatory Syndrome in Children (MIS-C) cases. We document that all MIS-C patients had evidence of prior SARS-CoV-2 exposure, mounting an antibody response with normal isotype-switching and neutralization capability. We further profiled the secreted immune response by high-dimensional cytokine assays, which identified elevated signatures of inflammation (IL-18 and IL-6), lymphocytic and myeloid chemotaxis and activation (CCL3, CCL4, and CDCP1) and mucosal immune dysregulation (IL-17A, CCL20, CCL28). Mass cytometry immunophenotyping of peripheral blood revealed reductions of mDC1 and non-classical monocytes, as well as both NK- and T-lymphocytes, suggesting extravasation to affected tissues. Markers of activated myeloid function were also evident, including upregulation of ICAM1 and Fc{gamma}R1 in neutrophil and non-classical monocytes, well-documented markers in autoinflammation and autoimmunity that indicate enhanced antigen presentation and Fc-mediated responses. Finally, to assess the role for autoimmunity secondary to infection, we profiled the auto-antigen reactivity of MIS-C plasma, which revealed both known disease-associated autoantibodies (anti-La) and novel candidates that recognize endothelial, gastrointestinal and immune-cell antigens. All patients were treated with anti-IL6R antibody or IVIG, which led to rapid disease resolution tracking with normalization of inflammatory markers.\n\nOne Sentence SummaryThis study maps the cellular and serological immune dysfunction underlying a novel pediatric inflammatory syndrome associated with SARS-CoV-2.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Conor Gruber", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Roosheel Patel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebecca Trachman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lauren Lepow", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Karen M. Wilson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kenan Onel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel Geanon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kevin Tuballes", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Manishkumar Patel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Konstantinos Mouskas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicole Simons", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Vanessa Barcessat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Diane Del Valle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Samantha Udondem", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Gurpawan Kang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sandeep Gangadharan", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "George Ofori-Amanfo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adeeb Rahman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Seunghee Kim-Schulze", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bruce Gelb", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dusan Bogunovic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.04.20146084", "rel_title": "A County-Level Susceptibility Index and Coronavirus Disease 2019 Mortality in the United States: A Socioecological Study", @@ -1306866,37 +1303645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.04.20146100", - "rel_title": "Associations between state-level healthcare access and COVID-19 case trajectories in the United States", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.04.20146100", - "rel_abs": "IntroductionWe conducted an ecological study to determine if state-level healthcare access is associated with trajectories of daily reported COVID-19 cases in the United States. Our focus is on trajectories of daily reported COVID-19 cases, rather than cumulative cases, as trajectories help us identify trends in how the pandemic naturally develops over time, and study the shapes of the curve in different states.\n\nMethodsWe analyzed data on daily reported confirmed and probable COVID-19 cases from January 21 to June 16, 2020 in 50 states, adjusted for the population size of each state. Cluster analysis for time-series data was used to split the states into clusters that have distinct trajectories of daily cases. Differences in socio-demographic characteristics and healthcare access between clusters were tested. Adjusted models were used to determine if healthcare access is associated with reporting a high trajectory of COVID-19 cases.\n\nResultsTwo clusters of states were identified. One cluster had a high trajectory of population- adjusted COVID-19 cases, and comprised of 19 states, including New York and New Jersey. The other cluster of states (n=31) had a low trajectory of population-adjusted COVID-19 cases.\n\nThere were significantly more Black residents (p=0.027) and more nursing facility residents (p=0.001) in states reporting high trajectory of COVID-19 cases. States reporting a high trajectory of COVID-19 cases also had fewer uninsured persons (p=0.005), fewer persons who reported having to forgo medical care due to cost (p=0.016), more registered physicians (p=0.002) and more nurses (p=0.03), higher health spending per capita (p=0.01), fewer residents in Health Professional Shortage Areas per 100,000 population (p=0.027), and higher adoption of Medicaid Expansion (p=0.05).\n\nIn adjusted models, a higher proportion of uninsured persons (OR: 0.51 [0.25-0.85]; p=0.032), higher proportion of patients who had to forgo medical care due to cost (OR: 0.55 [0.28-0.95]; p=0.048), and no adoption of Medicaid expansion (OR: 0.05 [0 - 0.59]; p=0.04), were associated with reporting a low trajectory of COVID-19 cases.\n\nConclusionOur findings from adjusted models suggest that healthcare access can partially explain variations in COVID-19 case trajectories by state.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shelley H. Liu", - "author_inst": "Icahn School of Medicine at Mount SInai" - }, - { - "author_name": "Bian Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Agnes Norbury", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Yan Li", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.03.20145409", "rel_title": "Split ventilation with pressure regulators for patient-specific tidal volumes", @@ -1307445,6 +1304193,37 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.07.06.190348", + "rel_title": "SARS-CoV-2 contributes to altering the post-transcriptional regulatory networks across human tissues by sponging RNA binding proteins and micro-RNAs", + "rel_date": "2020-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.190348", + "rel_abs": "The outbreak of a novel coronavirus SARS-CoV-2 responsible for COVID-19 pandemic has caused worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2 mediated alteration on post-transcriptional gene regulation across human tissues remains elusive. In this study, we analyze publicly available genomic datasets to systematically dissect the crosstalk and dysregulation of human post-transcriptional regulatory networks governed by RNA binding proteins (RBPs) and micro-RNAs (miRs), due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2 encoded proteins directly interact with 51 human RBPs of which majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed a functional analysis of differentially expressed genes in mock-treated versus SARS-CoV-2 infected lung cells that revealed enrichment for immune response, cytokine-mediated signaling, and metabolism associated genes. This study also characterized the alternative splicing events in SARS-CoV-2 infected cells compared to control demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to viral infection. Motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed the enrichment for RBPs such as SRSFs, PCBPs, ELAVs, and HNRNPs suggesting the sponging of RBPs by SARS-CoV-2 genome. A similar analysis to study the interactions of miRs with SARS-CoV-2 revealed functionally important miRs that were highly expressed in immune cells, suggesting that these interactions may contribute to the progression of the viral infection and modulate host immune response across other human tissues. Given the need to understand the interactions of SARS-CoV-2 with key post-transcriptional regulators in the human genome, this study provides a systematic computational analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs, across tissues types during SARS-CoV-2 infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rajneesh Srivastava", + "author_inst": "Indiana University Purdue University Indianapolis (IUPUI)" + }, + { + "author_name": "Swapna Vidhur Daulatabad", + "author_inst": "Indiana University Purdue University Indianapolis (IUPUI)" + }, + { + "author_name": "Mansi Srivastava", + "author_inst": "Indiana University Purdue University Indianapolis (IUPUI)" + }, + { + "author_name": "Sarath Chandra Janga", + "author_inst": "Indiana University Purdue University Indianapolis (IUPUI)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.02.20144543", "rel_title": "The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis", @@ -1308232,109 +1305011,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.04.187757", - "rel_title": "SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain", - "rel_date": "2020-07-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.04.187757", - "rel_abs": "The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and cells rendered permissive by ectopic expression of various mammalian ACE2 orthologs. Nonetheless, D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts a critical interprotomer contact and that this dramatically shifts the S protein trimer conformation toward an ACE2-binding and fusion-competent state. Consistent with the more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated. These results indicate that D614G adopts conformations that make virion membrane fusion with the target cell membrane more probable but that D614G retains susceptibility to therapies that disrupt interaction of the SARS-CoV-2 S protein with the ACE2 receptor.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Leonid Yurkovetskiy", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Xue Wang", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Kristen E Pascal", - "author_inst": "Regeneron Pharmaceutical, Inc." - }, - { - "author_name": "Christopher Tompkins-Tinch", - "author_inst": "Harvard University" - }, - { - "author_name": "Thomas Nyalile", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Yetao Wang", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Alina Baum", - "author_inst": "Regeneron Pharmaceutical, Inc" - }, - { - "author_name": "William E Diehl", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Ann Dauphin", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Claudia Carbone", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Kristen Veinotte", - "author_inst": "University of Massachetts Med School" - }, - { - "author_name": "Shawn B Egri", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Stephen F Schaffner", - "author_inst": "Broad Institute" - }, - { - "author_name": "Jacob E Lemieux", - "author_inst": "Broad Institute" - }, - { - "author_name": "James Munro", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Ashique Rafique", - "author_inst": "Regeneron Pharmaceutical, Inc." - }, - { - "author_name": "Abhi Barve", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Pardis C Sabeti", - "author_inst": "Broad Institute" - }, - { - "author_name": "Christos Kyratsous", - "author_inst": "Regeneron Pharmaceutical, Inc" - }, - { - "author_name": "Natalya Dudkina", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Kuang Shen", - "author_inst": "University of Massachusetts Med School" - }, - { - "author_name": "Jeremy Luban", - "author_inst": "University of Massachusetts Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.03.20146134", "rel_title": "Timing of PCR and Antibody Testing in Patients with COVID-19 associated dermatologic manifestations", @@ -1308835,6 +1305511,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.20145615", + "rel_title": "Laboratory-based surveillance of COVID-19 in the Greater Helsinki area, Finland, February-June 2020", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145615", + "rel_abs": "Laboratory registry data (80,791 specimens, 70,517 individuals) was used to characterise age- and sex-specific SARS-CoV-2 RT-PCR sampling frequency and positivity rate, and laboratory capacity building in Greater Helsinki, Finland during February-June 2020. While the number of positive cases was similar in males and females, the positivity rate was significantly higher in males. The highest incidence/100,000 was observed in those aged [≥]80 years. The proportion of young adults in positive cases increased in late May 2020.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Hanna Jarva", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Maija Lappalainen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Oskari Luomala", + "author_inst": "Finnish Institute for Health and Welfare (THL), Helsinki, Finland" + }, + { + "author_name": "Pia Jokela", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Anu E Jaaskelainen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Anne J Jaaskelainen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Hannimari Kallio-Kokko", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Eliisa Kekalainen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Laura Mannonen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Hanna Soini", + "author_inst": "Finnish Institute for Health and Welfare (THL), Helsinki, Finland" + }, + { + "author_name": "Satu Suuronen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Anne Toivonen", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + }, + { + "author_name": "Carita Savolainen-Kopra", + "author_inst": "Finnish Institute for Health and Welfare (THL), Helsinki, Finland" + }, + { + "author_name": "Raisa Loginov", + "author_inst": "Finnish Institute for Health and Welfare (THL), Helsinki, Finland" + }, + { + "author_name": "Satu Kurkela", + "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.03.20145581", "rel_title": "Prior diagnoses and medications as risk factors for COVID-19 in a Los Angeles Health System", @@ -1309550,57 +1306301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.03.20144949", - "rel_title": "The projected impact of mitigation and suppression strategies on the COVID-19 epidemic in Senegal: A modelling study", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20144949", - "rel_abs": "BackgroundPhysical distancing measures that reduce social contacts have formed a key part of national COVID-19 containment and mitigation strategies. Many Sub-Saharan African nations are now facing increasing numbers of cases of COVID-19 and there is a need to understand what levels of measures may be required to successfully reduce transmission.\n\nMethodsWe collated epidemiological data along with information on key COVID-19 specific response policies and health system capacity estimates for services needed to treat COVID-19 patients in Senegal. We calibrated an age-structured SEIR model to these data to capture transmission dynamics accounting for demography, contact patterns, hospital capacity and disease severity. We simulated the impact of mitigation and suppression strategies focussed on reducing social contact rates.\n\nResultsSenegal acted promptly to contain the spread of SARS-CoV-2 and as a result has reduced the reproduction number from 1.9 (95% CI 1.7-2.2) to 1.3 (95% CI 1.2-1.5), which has slowed but not fully interrupted transmission. We estimate that continued spread is likely to peak in October, and to overwhelm the healthcare system with an estimated 77,400 deaths (95% CI 55,270-100,700). Further reductions in contact rates to suppress transmission (Rt<1) could significantly reduce this burden on healthcare services and improve overall health outcomes.\n\nConclusionsOur results demonstrate that Senegal has already significantly reduced transmission. Enhanced physical distancing measures and rapid scale up of hospital capacity is likely to be needed to reduce mortality and protect healthcare infrastructure from high levels of demand.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hayley A Thompson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Aminata Mboup", - "author_inst": "IRESSEF: Institut de Recherche en Sante de Surveillance Epidemiologique et de Formations" - }, - { - "author_name": "Badara Cisse", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Shevanthi Nayagam", - "author_inst": "Imperial College London" - }, - { - "author_name": "Oliver J Watson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Charles Whittaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick G T Walker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Azra C Ghani", - "author_inst": "Imperial College London" - }, - { - "author_name": "Souleymane Mboup", - "author_inst": "IRESSEF: Institut de Recherche en Sante de Surveillance Epidemiologique et de Formations" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.03.20144931", "rel_title": "Psychiatric symptoms, risk, and protective factors among university students in quarantine during the COVID-19 pandemic in China", @@ -1310297,6 +1306997,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.06.30.20143289", + "rel_title": "Hydroxychloroquine has no effect on SARS-CoV-2 load in nasopharynx of patients with mild form of COVID-19", + "rel_date": "2020-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143289", + "rel_abs": "Due to the urgent need to stop the spread of the COVID-19 attempts to find the drug with anti SARS-CoV-2 effects among ones already available on a market are actively being made. A number of in vitro as well as in vivo model animal studies have shown that widely used compound hydroxychloroquine (HCQ) is able to cause anti-viral effect on SARS-CoV-2. While there is no enough clinical data to support the use of HCQ, several countries including Russia have already approved HCQ as treatment and prophylactic option. In the current study we analyzed the dynamics of the SARS-CoV-2 RNA quantity change in nasopharynx swabs of infected patients in mild condition and compared that of patients receiving HCQ and receiving no antiviral pharmacological therapy. We found that most of the patients demonstrated gradual decrease in the number of SARS-CoV-2 RNA copies in the swab regardless of the HCQ receiving. Noteworthy that patients with RNA load higher than 106 copies were hospitalized due to condition deteriorating significantly more frequently compared to those with RNA load below 106 copies even with HCQ administration. In addition, the results of the current study indicate that recovering patients may produce viruses at least during 18 days from the onset of symptoms and HCQ therapy does not block or reduce it.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Alexey Komissarov", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky" + }, + { + "author_name": "Ivan Molodtsov", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Oxana Ivanova", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Elena Maryukhnich", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Svetlana Kudryavtseva", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Alexey Mazus", + "author_inst": "Moscow City Center for AIDS Prevention and Control, Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Evgeniy Nikonov", + "author_inst": "Moscow Department of Healthcare, Moscow, Russia" + }, + { + "author_name": "Elena Vasilieva", + "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, Moscow, Russia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.30.20143115", "rel_title": "Chopping the tail: how preventing superspreading can help to maintain COVID-19 control", @@ -1311104,37 +1307851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.02.20144378", - "rel_title": "Comparison of Multimorbidity in COVID-19 infected and general population in Portugal", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20144378", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWUnderstanding COVID-19 and its risk factors in the Portuguese population is critical to the struggle against this infectious disease. To study the impact of multimorbidity in the population with COVID-19 infection, we performed a descriptive analysis of a dataset extracted from all reported confirmed cases of COVID-19 in Portugal until June 30, 2020. We observed a prevalence of multimorbidity in 6.77% of the 36,244 infected patients. These patients showed an increased risk of hospitalization, ICU admission, and mortality with OR 2.22 (CI 95%: 2.13-2.32) for every additional morbidity. Further studies should confirm these findings and special attention should be made on data collection, to ensure proper recording of patient comorbidities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Miguel T Froes", - "author_inst": "INESC-ID" - }, - { - "author_name": "Bernardo Duque Neves", - "author_inst": "Hospital da Luz" - }, - { - "author_name": "Bruno Martins", - "author_inst": "INESC-ID" - }, - { - "author_name": "Mario J Silva", - "author_inst": "INESC-ID" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.02.20143206", "rel_title": "Navigating hospitals safely through the COVID-19 epidemic tide: predicting case load for adjusting bed capacity", @@ -1311711,6 +1308427,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.01.20144295", + "rel_title": "Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144295", + "rel_abs": "ImportancePopulation-wide serological testing is an essential component in understanding the COVID-19 pandemic. The logistical challenges of undertaking widespread serological testing could be eased through use of a reliable dried blood spot (DBS) sampling method.\n\nObjectiveTo validate the use of dried blood spot sampling for the detection of SARS-CoV-2-specific antibodies.\n\nDesign, setting and participantsEighty-seven matched DBS and serum samples were obtained from eighty individuals, including thirty-one who were previously PCR-positive for SARS-CoV-2. DBS eluates and sera were used in an ELISA to detect antibodies to the viral spike protein.\n\nResultsSpecific anti-SARS-Cov-2 spike glycoprotein antibodies were detectable in both serum and DBS eluate and there was a significant correlation between the antibody levels detected in matched samples (r = 0.96, p<0.0001). Using serum as the gold standard in the assay, matched DBS samples achieved a Cohens kappa coefficient of 0.975 (near-perfect agreement), a sensitivity of 98.1% and specificity of 100%, for detecting anti-spike glycoprotein antibodies.\n\nConclusions and relevanceEluates from DBS samples are a reliable and reproducible source of antibodies to be used for the detection of SARS-CoV-2-specific antibodies. The use of DBS sampling could complement the use of venepuncture in the immunosurveillance of COVID-19 in both low and high income settings.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Gabriella L Morley", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Stephen Taylor", + "author_inst": "Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, U.K." + }, + { + "author_name": "Sian Jossi", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Marisol Perez-Toledo", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Sian E Faustini", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Edith Marcial-Juarez", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Adrian M Shields", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Margaret Goodall", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Joel D Allen", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K." + }, + { + "author_name": "Yasunori Watanabe", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K." + }, + { + "author_name": "Maddy L Newby", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K." + }, + { + "author_name": "Max Crispin", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K." + }, + { + "author_name": "Mark T Drayson", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Adam F Cunningham", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Alex G Richter", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + }, + { + "author_name": "Matthew K O'Shea", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, U.K." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144436", "rel_title": "Injury-Prone: Peripheral nerve injuries associated with prone positioning for COVID-19-related acute respiratory distress syndrome", @@ -1312702,37 +1309497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.30.20143636", - "rel_title": "Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of COVID-19 in the United States", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143636", - "rel_abs": "The SARS-CoV-2 pandemic has caused significant mortality and morbidity worldwide, sparing almost no community. As the disease will likely remain a threat for years to come, an understanding of the precise influences of human demographics and settlement, as well as the dynamic factors of climate, susceptible depletion, and intervention, on the spread of localized epidemics will be vital for mounting an effective response. We consider the entire set of local epidemics in the United States; a broad selection of demographic, population density, and climate factors; and local mobility data, tracking social distancing interventions, to determine the key factors driving the spread and containment of the virus. Assuming first a linear model for the rate of exponential growth (or decay) in cases/mortality, we find that population-weighted density, humidity, and median age dominate the dynamics of growth and decline, once interventions are accounted for. A focus on distinct metropolitan areas suggests that some locales benefited from the timing of a nearly simultaneous nationwide shutdown, and/or the regional climate conditions in mid-March; while others suffered significant outbreaks prior to intervention. Using a first-principles model of the infection spread, we then develop predictions for the impact of the relaxation of social distancing and local climate conditions. A few regions, where a significant fraction of the population was infected, show evidence that the epidemic has partially resolved via depletion of the susceptible population (i.e., \"herd immunity\"), while most regions in the United States remain overwhelmingly susceptible. These results will be important for optimal management of intervention strategies, which can be facilitated using our online dashboard.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Niayesh Afshordi", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Benjamin Holder", - "author_inst": "Grand Valley State University" - }, - { - "author_name": "Mohammad Bahrami", - "author_inst": "Wolfram Research Inc" - }, - { - "author_name": "Daniel Lichtblau", - "author_inst": "Wolfram Research Inc" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.30.20143586", "rel_title": "Does Lockdown Decrease the Protective Role of ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths?", @@ -1313201,6 +1309965,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.184481", + "rel_title": "Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission", + "rel_date": "2020-07-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.02.184481", + "rel_abs": "The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Nicolae Sapoval", + "author_inst": "Department of Computer Science, Rice University, Houston, TX 77005" + }, + { + "author_name": "Medhat Mahmoud", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Michael D. Jochum", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Yunxi Liu", + "author_inst": "Department of Computer Science, Rice University, Houston, TX 77005" + }, + { + "author_name": "R.A. Leo Elworth", + "author_inst": "Department of Computer Science, Rice University, Houston,TX 77005" + }, + { + "author_name": "Qi Wang", + "author_inst": "Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX, 77005" + }, + { + "author_name": "Dreycey Albin", + "author_inst": "Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Houston, TX 77005" + }, + { + "author_name": "Huw Ogilvie", + "author_inst": "Department of Computer Science, Rice University, Houston, TX 77005" + }, + { + "author_name": "Michael D. Lee", + "author_inst": "Exobiology Branch, NASA Ames Research Center, Mountain View, CA" + }, + { + "author_name": "Sonia Villapol", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "Kyle Hernandez", + "author_inst": "Department of Medicine, University of Chicago, Chicago, IL" + }, + { + "author_name": "Irina Maljkovic Berry", + "author_inst": "Walter Reed Army Institute of Research" + }, + { + "author_name": "Jon Foox", + "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York" + }, + { + "author_name": "Afshin Beheshti", + "author_inst": "KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA" + }, + { + "author_name": "Krista Ternus", + "author_inst": "Signature Science, LLC, 8329 North Mopac Expressway, Austin TX 78759" + }, + { + "author_name": "Kjersti M. Aagaard", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "David Posada", + "author_inst": "University of Vigo" + }, + { + "author_name": "Christopher Mason", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Todd J Treangen", + "author_inst": "Rice University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.01.183020", "rel_title": "6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro protease activities", @@ -1314256,69 +1311115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.29.20142851", - "rel_title": "Modeling the early phase of the Belgian COVID-19 epidemic using a stochastic compartmental model and studying its implied future trajectories", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142851", - "rel_abs": "Following the onset of the ongoing COVID-19 pandemic throughout the world, a large fraction of the global population is or has been under strict measures of physical distancing and quarantine, with many countries being in partial or full lockdown. These measures are imposed in order to reduce the spread of the disease and to lift the pressure on healthcare systems. Estimating the impact of such interventions as well as monitoring the gradual relaxing of these stringent measures is quintessential to understand how resurgence of the COVID-19 epidemic can be controlled for in the future. In this paper we use a stochastic age-structured discrete time compartmental model to describe the transmission of COVID-19 in Belgium. Our model explicitly accounts for age-structure by integrating data on social contacts to (i) assess the impact of the lockdown as implemented on March 13, 2020 on the number of new hospitalizations in Belgium; (ii) conduct a scenario analysis estimating the impact of possible exit strategies on potential future COVID-19 waves. More specifically, the aforementioned model is fitted to hospital admission data, data on the daily number of COVID-19 deaths and serial serological survey data informing the (sero)prevalence of the disease in the population while relying on a Bayesian MCMC approach. Our age-structured stochastic model describes the observed outbreak data well, both in terms of hospitalizations as well as COVID-19 related deaths in the Belgian population. Despite an extensive exploration of various projections for the future course of the epidemic, based on the impact of adherence to measures of physical distancing and a potential increase in contacts as a result of the relaxation of the stringent lockdown measures, a lot of uncertainty remains about the evolution of the epidemic in the next months.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Steven Abrams", - "author_inst": "Data Science Institute, Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt & Global Health Institute (GHI), Depart" - }, - { - "author_name": "James Wambua", - "author_inst": "Data Science Institute, Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Eva Santermans", - "author_inst": "Data Science Institute, Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Lander Willem", - "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp" - }, - { - "author_name": "Elise Kuylen", - "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp" - }, - { - "author_name": "Pietro Coletti", - "author_inst": "Data Science Institute, Interuniversity Institute of Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Pieter Libin", - "author_inst": "Data Science Institute, Interuniversity Institute of Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Christel Faes", - "author_inst": "Data Science Institute, Interuniversity Institute of Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Oana Petrof", - "author_inst": "Data Science Institute, Interuniversity Institute of Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt" - }, - { - "author_name": "Sereina A. Herzog", - "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp" - }, - { - "author_name": "Philippe Beutels", - "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp" - }, - { - "author_name": "Niel Hens", - "author_inst": "Data Science Institute, Interuniversity Institute of Biostatistics and statistical Bioinformatics (I-BioStat), UHasselt & Centre for Health Economic Research an" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.30.20142935", "rel_title": "A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust", @@ -1315087,6 +1311883,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.30.20142877", + "rel_title": "Quantifying the impact of US state non-pharmaceutical interventions on COVID-19 transmission", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20142877", + "rel_abs": "COVID-19 is an ongoing public health emergency. Without a vaccine or effective antivirals, non-pharmaceutical interventions form the foundation of current response efforts. Quantifying the efficacy of these interventions is crucial. Using mortality data and a classification guide of state level responses, we relate the intensity of interventions to statistical estimates of transmission, finding that more stringent control measures are associated with larger reductions in disease proliferation. Additionally, we observe that transmission increases with population density, but not population size. These results may help inform future response efforts.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hannah M Korevaar", + "author_inst": "Princeton University" + }, + { + "author_name": "Alexander David Becker", + "author_inst": "Princeton University" + }, + { + "author_name": "Ian F Miller", + "author_inst": "Princeton University" + }, + { + "author_name": "Bryan T Grenfell", + "author_inst": "Princeton University" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.01.182741", "rel_title": "SARS-CoV-2 reactive T cells in uninfected individuals are likely expanded by beta-coronaviruses", @@ -1316170,141 +1313005,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.29.178509", - "rel_title": "SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.178509", - "rel_abs": "The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd immunity to control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length spike (S) protein, stabilized in the prefusion conformation. Purified NVX-CoV2373 S form 27.2nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). NVX-CoV2373 vaccine also elicits multifunctional CD4+ and CD8+ T cells, CD4+ T follicular helper T cells (Tfh), and the generation of antigen-specific germinal center (GC) B cells in the spleen. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2327 with Matrix-M (NCT04368988).", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Jing-Hui Tian", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Nita Patel", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Robert Haupt", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Haixia Zhou", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Stuart Weston", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Holly Hammond", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "James Lague", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Alyse D Portnoff", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "James Norton", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Mimi Guebre-Xabier", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Bin Zhou", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Kelsey Jacobson", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Sonai Maciejewski", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Rafia Khatoon", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Malgorzata Wisniewska", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Will Mottitt", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Stenfanie Kluepfel-Stahl", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Betty Ekechukwu", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "James Papin", - "author_inst": "University of Oklahoma, Health Sciences Center, Department of Pathology, Division of Comparative Medicine" - }, - { - "author_name": "Sarathi Boddapati", - "author_inst": "Catalent Paragon Gene Therapy" - }, - { - "author_name": "C. Jason Wong", - "author_inst": "Catalent Paragon Gene Therapy" - }, - { - "author_name": "Pedro A Piedra", - "author_inst": "Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine" - }, - { - "author_name": "Matthew B Frieman", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Michael J Massare", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Louis Fries", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Karin Lovgren Bengtsson", - "author_inst": "Novavax, AB" - }, - { - "author_name": "Linda Stertman", - "author_inst": "Novavax, AB" - }, - { - "author_name": "Larry R Ellingsworth", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Gregory Glenn", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Gale Smith", - "author_inst": "Novavax, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.29.179192", "rel_title": "Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen", @@ -1317041,6 +1313741,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.06.29.20142661", + "rel_title": "COVID-19, smoking, vaping and quitting: A representative population survey in England", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142661", + "rel_abs": "AimsTo explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home.\n\nDesignCross-sectional household surveys of a representative sample of the population in England from April-May 2020.\n\nParticipantsThe sample included 3,285 adults aged [≥]18 years.\n\nMeasurementsParticipants who reported they definitely or think they had coronavirus were classified as having a suspected SARS-CoV-2 infection. Participants were asked how often they wash their hands after returning home, before eating, before preparing foods or before touching their face. They were also asked whether, due to COVID-19, they had i) attempted to quit smoking, ii) attempted to quit vaping, and iii) changed the amount they smoke inside the home.\n\nFindingsOdds of suspected SARS-CoV-2 infection were significantly greater among current smokers (20.9%, adjusted odds ratio [ORadj]=1.34, 95% confidence interval [CI]=1.04-1.73) and long-term (>1-year) ex-smokers (16.1%, ORadj=1.33, 95%CI=1.05-1.68) than never smokers (14.5%). Recent (<1-year) ex-smokers had non-significantly greater odds of suspected infection (22.2%, ORadj=1.50, 95%CI=0.85-2.53, Bayes factor= 0.55-1.17). Bayes factors indicated there was sufficient evidence to rule out large differences in suspected SARS-CoV-2 infection by NRT use and medium differences by e-cigarette use. With the exception of hand washing before face touching, engagement in hand washing behaviours was high (>85%) regardless of nicotine use. A minority (12.2%) of past-year smokers who made a quit attempt in the past three months were triggered by COVID-19, and approximately one-in-ten current e-cigarette users reported attempting to quit vaping because of COVID-19. Most people reported smoking the same amount inside the home.\n\nConclusionsIn a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In general, engagement in hand washing was high regardless of nicotine or tobacco use. A minority of past-year smokers and current e-cigarette users, respectively, attempted to quit smoking/vaping due to COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Harry Tattan-Birch", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + }, + { + "author_name": "Olga Perski", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + }, + { + "author_name": "Sarah E Jackson", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + }, + { + "author_name": "Lion Shahab", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + }, + { + "author_name": "Robert West", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + }, + { + "author_name": "Jamie Brown", + "author_inst": "Institute of Epidemiology and Health Care, University College London, London, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.29.20142596", "rel_title": "Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children", @@ -1318168,89 +1314907,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.25.20140178", - "rel_title": "SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140178", - "rel_abs": "BackgroundThe extent of SARS-CoV-2 transmission among pupils in primary schools and their families is unknown.\n\nMethodsBetween 28-30 April 2020, a retrospective cohort study was conducted among pupils, their parents and relatives, and staff of primary schools exposed to SARS-CoV-2 in February and March 2020 in a city north of Paris, France. Participants completed a questionnaire that covered sociodemographic information and history of recent symptoms. A blood sample was tested for the presence of anti-SARS-CoV-2 antibodies using a flow-cytometry-based assay.\n\nResultsThe infection attack rate (IAR) was 45/510 (8.8%), 3/42 (7.1%), 1/28 (3.6%), 76/641 (11.9%) and 14/119 (11.8%) among primary school pupils, teachers, non-teaching staff, parents, and relatives, respectively (P = 0.29). Prior to school closure on February 14, three SARS-CoV-2 infected pupils attended three separate schools with no secondary cases in the following 14 days among pupils, teachers and non-teaching staff of the same schools. Familial clustering of cases was documented by the high proportion of antibodies among parents and relatives of infected pupils (36/59 = 61.0% and 4/9 = 44.4%, respectively). In children, disease manifestations were mild, and 24/58 (41.4%) of infected children were asymptomatic.\n\nInterpretationIn young children, SARS-CoV-2 infection was largely mild or asymptomatic and there was no evidence of onwards transmission from children in the school setting.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Arnaud Fontanet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Rebecca Grant", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Tondeur", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Yoann Madec", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludivine Grzelak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Isabelle Cailleau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marie-Noelle Ungeheuer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Charlotte Renaudat", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sandrine Fernandes Pellerin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Lucie Kuhmel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Isabelle Staropoli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Timothee Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Bruno Hoen", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.24.20139386", "rel_title": "Electrocardiographic safety of daily Hydroxychloroquine 400mg plus Azithromycin 250mg as an ambulatory treatment for COVID-19 patients in Cameroon.", @@ -1319015,6 +1315671,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.06.29.20142364", + "rel_title": "Estimation of COVID-19 dynamics in the different states of the United States using Time-Series Clustering", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142364", + "rel_abs": "Estimation of COVID-19 dynamics and its evolution is a multidisciplinary effort, which requires the unification of heterogeneous disciplines (scientific, mathematics, epidemiological, biological/bio-chemical, virologists and health disciplines to mention the most relevant) to work together in a better understanding of this pandemic. Time series analysis is of great importance to determine both the similarity in the behavior of COVID-19 in certain countries/states and the establishment of models that can analyze and predict the transmission process of this infectious disease. In this contribution, an analysis of the different states of the United States will be carried out to measure the similarity of COVID-19 time series, using dynamic time warping distance (DTW) as a distance metric. A parametric methodology is proposed to jointly analyze infected and deceased persons. This metric allows to compare time series that have a different time length, making it very appropriate for studying the United States, since the virus did not spread simultaneously in all the states/provinces. After a measure of the similarity between the time series of the states of United States was determined, a hierarchical cluster was created, which makes it possible to analyze the behavioral relationships of the pandemic between different states and to discover interesting patterns and correlations in the underlying data of COVID-19 in the United States. With the proposed methodology, nine different clusters were obtained, showing a different behavior in the eastern zone and western zone of the United States. Finally, to make a prediction of the evolution of COVID-19 in the states, Logistic, Gompertz and SIR model was computed. With these mathematical model it is possible to have a more precise knowledge of the evolution and forecast of the pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ignacio Rojas", + "author_inst": "University of Granada" + }, + { + "author_name": "Fernando Rojas", + "author_inst": "University of Granada" + }, + { + "author_name": "Olga Valenzuela", + "author_inst": "University of Granada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.26.20139923", "rel_title": "Macropahge expression and prognostic significance of the long pentraxin PTX3 in COVID-19", @@ -1320106,53 +1316789,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.27.20141440", - "rel_title": "A Modelling Study for Designing a Multi-layered Surveillance Approach to Detect the Potential Resurgence of SARS-CoV-2", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141440", - "rel_abs": "BackgroundCountries achieving control of COVID-19 after an initial outbreak will continue to face the risk of SARS-CoV-2 resurgence. This study explores surveillance strategies for COVID-19 containment based on polymerase chain reaction tests.\n\nMethodsUsing a dynamic SEIR-type model to simulate the initial dynamics of a COVID-19 introduction, we investigate COVID-19 surveillance strategies among healthcare workers, hospital patients, and community members. We estimate surveillance sensitivity as the probability of COVID-19 detection using a hypergeometric sampling process. We identify test allocation strategies that maximise the probability of COVID-19 detection across different testing capacities. We use Beijing, China as a case study.\n\nFindingsSurveillance subgroups are more sensitive in detecting COVID-19 transmission when they are defined by more COVID-19 specific symptoms. In this study, fever clinics have the highest surveillance sensitivity, followed by respiratory departments. With a daily testing rate of 0.07/1000 residents, via exclusively testing at fever clinic and respiratory departments, there would have been 598 [95% eCI: 35, 2154] and 1373 [95% eCI: 47, 5230] cases in the population by the time of first case detection, respectively. Outbreak detection can occur earlier by including non-syndromic subgroups, such as younger adults in the community, as more testing capacity becomes available.\n\nInterpretationA multi-layer approach that considers both the surveillance sensitivity and administrative constraints can help identify the optimal allocation of testing resources and thus inform COVID-19 surveillance strategies.\n\nFundingBill & Melinda Gates Foundation, National Institute of Health Research (UK), National Institute of Health (US), the Royal Society, and Wellcome Trust.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yang Liu", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Wenfeng Gong", - "author_inst": "Bill & Melinda Gates Foundation" - }, - { - "author_name": "Samuel Clifford", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Maria E Sundaram", - "author_inst": "Rollins School of Public Health, Emory University" - }, - { - "author_name": "- CMMID COVID19 Working Group", - "author_inst": "" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Petra Klepac", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.27.20141424", "rel_title": "Incubation Period and Reproduction Number for novel coronavirus (COVID-19) infections in India", @@ -1320649,6 +1317285,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.28.20141986", + "rel_title": "Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141986", + "rel_abs": "IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases.\n\nMethods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available.\n\nEthics and disseminationThe project has ethical approval and the results will be submitted for publication in a peer-reviewed journal.\n\nStrengths and limitations of the studyO_LIThe individual-level linkage of general practice, Public Health England testing, Hospital Episode Statistics and Office of National Statistics death register datasets enable a robust and accurate ascertainment of outcomes\nC_LIO_LIThe models will be trained and evaluated in population-representative datasets of millions of individuals\nC_LIO_LIShielding for clinically extremely vulnerable was advised and in place during the study period, therefore risk predictions influenced by the presence of some shielding conditions may require careful consideration\nC_LI", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Julia Hippisley-Cox", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ashley Kieran Clift", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carol AC Coupland", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Ruth Keogh", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Karla Diaz-Ordaz", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Elizabeth Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ewen Harrison", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Andrew Hayward", + "author_inst": "University College London" + }, + { + "author_name": "Harry Hemingway", + "author_inst": "University College London" + }, + { + "author_name": "Peter Horby", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nisha Mehta", + "author_inst": "Department of Health and Social Care" + }, + { + "author_name": "Jonathan Kieran Benger", + "author_inst": "NHS Digital" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "David Spiegelhalter", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jonathan Valabhji", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ronan A Lyons", + "author_inst": "Swansea University" + }, + { + "author_name": "John Robson", + "author_inst": "Queen Mary University London" + }, + { + "author_name": "Malcolm Gracie Semple", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Frank Kee", + "author_inst": "Queen's University Belfast" + }, + { + "author_name": "Peter Johnson", + "author_inst": "University of Southampton" + }, + { + "author_name": "Susan Jebb", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tony Williams", + "author_inst": "Working Fit, Ltd." + }, + { + "author_name": "David Coggon", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.28.20136168", "rel_title": "SARS-CoV-2 & Pediatric Mental Health: A Review of Recent Evidence", @@ -1321392,45 +1318139,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.28.176248", - "rel_title": "Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein", - "rel_date": "2020-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.28.176248", - "rel_abs": "The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell1\u20133. The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder4. Phosphorylation of the central disordered region is required for normal viral genome transcription5,6, which occurs in a cytoplasmic structure called the replication transcription complex (RTC)7\u201311. It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates12\u201315. Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Christopher R. Carlson", - "author_inst": "UCSF" - }, - { - "author_name": "Jonathan B. Asfaha", - "author_inst": "UCSF" - }, - { - "author_name": "Chloe M. Ghent", - "author_inst": "UCSF" - }, - { - "author_name": "Conor J. Howard", - "author_inst": "UCSF" - }, - { - "author_name": "Nairi Hartooni", - "author_inst": "UCSF" - }, - { - "author_name": "David O. Morgan", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.29.174623", "rel_title": "SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery", @@ -1322123,6 +1318831,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.26.20141150", + "rel_title": "Social media and smartphone app use predicts maintenance of physical activity during Covid-19 enforced isolation in psychiatric outpatients", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20141150", + "rel_abs": "Public health professionals have raised concerns that the social and physical distancing measures implemented in response to the Covid-19 pandemic may negatively impact health in other areas, via both decreased physical activity and increased social isolation. Here, we investigated whether increased engagement with digital social tools may help mitigate effects of enforced isolation on physical activity and mood, in a naturalistic study of at-risk individuals. Passively sensed smartphone app use and actigraphy data, collected from a sample of psychiatric outpatients both before and during imposition of strict lockdown conditions (N=163), were analysed using Gaussian graphical models: a form of network analysis which gives insight into the predictive relationships between measures across timepoints. Within-individuals, we found evidence of a positive predictive path between digital social engagement, general smartphone use, and physical activity - selectively under lockdown conditions. Further, we observed a positive relationship between social media use and total daily steps across individuals during (but not prior to) lockdown. We interpret these findings in terms of individuals using these digital tools to harness online social support structures, which may help guard against negative effects of in-person social deprivation and other pandemic-related stress. Monitoring of these measures is low burden and unintrusive and therefore, given appropriate consent, could potentially help identify individuals who are failing to engage this mechanism, providing a route to early intervention in this and other vulnerable populations.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Agnes Norbury", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shelley H Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan Jos\u00e9 Campa\u00f1a-Montes", + "author_inst": "Universidad Carlos III de Madrid" + }, + { + "author_name": "Lorena Romero-Medrano", + "author_inst": "Universidad Carlos III de Madrid" + }, + { + "author_name": "Maria L Barrigon", + "author_inst": "University Hospital Jimenez Diaz Foundation" + }, + { + "author_name": "Emma Smith", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "- MEmind Study Group", + "author_inst": "" + }, + { + "author_name": "Antonio Artes", + "author_inst": "Universidad Carlos III de Madrid" + }, + { + "author_name": "Enrique Baca-Garcia", + "author_inst": "University Hospital Jimenez Diaz Foundation" + }, + { + "author_name": "M. Mercedes Perez-Rodriguez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.26.20141044", "rel_title": "Cost Benefit Analysis of Limited Reopening Relative to a Herd Immunity Strategy or Shelter in Place for SARS-CoV-2 in the United States", @@ -1322978,101 +1319741,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.26.20139873", - "rel_title": "Secondary pneumonia in critically ill ventilated patients with COVID-19", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20139873", - "rel_abs": "BackgroundPandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive artificial ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP).\n\nObjectivesTo study the incidence of VAP, as well as differences in secondary infections, and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients.\n\nMethodsIn this prospective observational study, we compared the incidence of VAP and secondary infections using a combination of a TaqMan multi-pathogen array and microbial culture. In addition, we determined the lung microbime composition using 16S RNA analyisis. The study involved eighteen COVID-19 and seven non-COVID-19 patients receiving invasive ventilation in three ICUs located in a single University teaching hospital between April 13th 2020 and May 7th 2020.\n\nResultsWe observed a higher percentage of confirmed VAP in COVID-19 patients. However, there was no statistical difference in the detected organisms or pulmonary microbiome when compared to non-COVID-19 patients.\n\nConclusionCOVID-19 makes people more susceptible to developing VAP, partly but not entirely due to the increased duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the array of secondary infections observed are similar to that seen in critically ill patients ventilated for other reasons.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Mailis Maes", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Ellen Higginson", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Joana Pereira Dias", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Martin D Curran", - "author_inst": "Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Surendra Parmar", - "author_inst": "Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Fahad Khokhar", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Delphine Cuchet-Louren\u00e7o", - "author_inst": "Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Janine Lux", - "author_inst": "Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Sapna Sharma-Hajela", - "author_inst": "John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Benjamin Ravenhill", - "author_inst": "John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Razeen Mahroof", - "author_inst": "John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Amelia Solderholm", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Sally Forrest", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Sushmita Sridhar", - "author_inst": "Wellcome Sanger Insitute, Hinxton, United Kingdom" - }, - { - "author_name": "Nicholas M Brown", - "author_inst": "Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Stephen Baker", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Vilas Navapurkar", - "author_inst": "John Farman ICU, Addenbrookes Hospital, Cambridge, United Kingdom" - }, - { - "author_name": "Gordon Dougan", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Josefin Bartholdson Scott", - "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Andrew Conway Morris", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.25.20139022", "rel_title": "Problem drinking before and during the COVID-19 crisis in US and UK adults: Evidence from two population-based longitudinal studies", @@ -1323605,6 +1320273,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.06.23.20138370", + "rel_title": "Novel coronavirus (COVID-19) Outbreak in Iraq: The First Wave and Future Scenario", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138370", + "rel_abs": "The first patient with COVID-19 was reported in Iraq on 24 February 2020 for the Iranian student came from Iran. As of 24 May 2020, the confirmed cases of COVID-19 infections reached 4469, with 160 deaths and 2738 patients were recovered from the infection. Significant public health strategies have been implemented by the authorities to contain the outbreak nationwide. Nevertheless however, the number of cases is still rising dramatically. Here, we aim to describe a comprehensive and epidemiological study of all cases diagnosed in Iraq by 24 May 2020. Most of the cases were recorded in Baghdad followed by Basra and Najaf. About 45% of the patients were female (with 31% deaths of the total cases) and 55% were male (with 68% deaths of the total cases). Most cases are between the ages of (20-59) years old, and (30-39) years are the most affected range (19%) Approximately (8%) of cases are children under 10 years old. Iraq has shown a cure rate lower than those reported by Iran, Turkey and Jordan; and higher than Saudi Arabia and Kuwait. Healthcare workers represented about (5%) of the total confirmed cases. These findings enable us to understand COVID-19 epidemiology and prevalence in Iraq that can alert the our community to the risk of this novel coronavirus and serve as a baseline for future studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Adil R. Sarhan", + "author_inst": "Nasiriyah Technical Institute" + }, + { + "author_name": "Mohammed H. Flaih", + "author_inst": "Nasiriyah Technical Institute" + }, + { + "author_name": "Thaer A. Hussein", + "author_inst": "Nasiriyah Technical Institute" + }, + { + "author_name": "Khwam R. Hussein", + "author_inst": "Nasiriyah Technical Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20139287", "rel_title": "Epidemiological model with anomalous kinetics - The Covid-19 pandemics", @@ -1324452,93 +1321151,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.24.20139303", - "rel_title": "COVID-19-associated ARDS treated with DEXamethasone (CoDEX): Study design and rationale for a randomized trial.", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139303", - "rel_abs": "OBJECTIVESThe infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) spreads worldwide and is considered a pandemic. The most common manifestation of SARS-CoV2 infection (Coronavirus disease 2019 - COVID-19) is viral pneumonia with varying degrees of respiratory compromise and up to 40% of hospitalized patients might develop Acute Respiratory Distress Syndrome (ARDS). Several clinical trials evaluated the role of corticosteroids in non-COVID-19 ARDS with conflicting results. We designed a trial to evaluate the effectiveness of early intravenous dexamethasone administration on the number of days alive and free of mechanical ventilation within 28 days after randomization in adult patients with moderate or severe ARDS due to confirmed or probable COVID-19.\n\nMETHODSThis is a pragmatic, prospective, randomized, stratified, multicenter, open-label, controlled trial including 350 patients with early-onset (less than 48h before randomization) moderate or severe ARDS, defined by the Berlin criteria, due to COVID-19. Eligible patients will be randomly allocated to either standard treatment plus dexamethasone (intervention group) or standard treatment without dexamethasone (control group). Patients in the intervention group will receive dexamethasone 20mg IV once daily for 5 days, followed by dexamethasone 10mg IV once daily for additional 5 days or until Intensive Care Unit (ICU) discharge, whichever occurs first. The primary outcome is ventilator-free days within 28 days after randomization, defined as days alive and free from invasive mechanical ventilation. Secondary outcomes are all-cause mortality rates at day 28, evaluation of the clinical status at day 15 assessed with a 6-level ordinal scale, mechanical ventilation duration from randomization to day 28, Sequential Organ Failure Assessment (SOFA) Score evaluation at 48h, 72h and 7 days and ICU-free days within 28.\n\nETHICS AND DISSEMINATIONThis trial was approved by the Brazilian National Committee of Ethics in Research (Comissao Nacional de Etica em Pesquisa - CONEP) and National Health Surveillance Agency (ANVISA). An independent data monitoring committee will perform interim analyses and evaluate adverse events throughout the trial. Results will be submitted for publication after enrolment and follow-up are complete.\n\nClinicalTrials.gov identifierNCT04327401", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Bruno Martins Tomazini", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Israel S. Maia", - "author_inst": "HCor Research Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Flavia R. Bueno", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Maria Vitoria A. O. Silva", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Franca P. Baldassare", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Eduardo Leite V. Costa", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Ricardo A. B. Moura", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Michele Honorato", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Andre N. Costa", - "author_inst": "Hospital Sirio-Libanes" - }, - { - "author_name": "Alexandre B. Cavalcanti", - "author_inst": "HCor Research Institute" - }, - { - "author_name": "Regis Rosa", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Alvaro Avezum", - "author_inst": "Hospital Alemao Oswaldo Cruz" - }, - { - "author_name": "Viviane C. Veiga", - "author_inst": "BP A Beneficencia Portuguesa de Sao Paulo" - }, - { - "author_name": "Renato D. Lopes", - "author_inst": "Brazilian Clinical Research Institute (BCRI)" - }, - { - "author_name": "Lucas P. Damiani", - "author_inst": "HCor Research Institute" - }, - { - "author_name": "Flavia R. Machado", - "author_inst": "Brazilian Research in Intensive Care Network" - }, - { - "author_name": "Otavio Berwanger", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Luciano C. P. Azevedo", - "author_inst": "Hospital Sirio-Libanes" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.24.20139634", "rel_title": "Shut and re-open: the role of schools in the spread of COVID-19 in Europe", @@ -1325079,6 +1321691,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.25.20137323", + "rel_title": "Factors Associated with Hospitalization and Disease Severity in a Racially and Ethnically Diverse Population of COVID-19 Patients", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20137323", + "rel_abs": "BackgroundThe coronavirus disease (COVID-19) first identified in Wuhan in December 2019 became a pandemic within a few months of its discovery. The impact of COVID-19 is due to both its rapid spread and its severity, but the determinants of severity have not been fully delineated.\n\nObjectiveIdentify factors associated with hospitalization and disease severity in a racially and ethnically diverse cohort of COVID-19 patients.\n\nMethodsWe analyzed data from COVID-19 patients diagnosed at the University of Cincinnati health system from March 13, 2020 to May 31, 2020. Severe COVID-19 was defined as admission to intensive care unit or death. Logistic regression modeling adjusted for covariates was used to identify the factors associated with hospitalization and severe COVID-19.\n\nResultsAmong the 689 COVID-19 patients included in our study, 29.2% were non-Hispanic White, 25.5% were non-Hispanic Black, 32.5% were Hispanic, and 12.8% were of Other race/ethnicity. About 31.3% of patients were hospitalized and 13.2% had severe disease. In adjusted analyses, the sociodemographic factors associated with hospitalization and/or disease severity included older age, non-Hispanic Black or Hispanic race/ethnicity (compared non-Hispanic White), and smoking. The following comorbidities: diabetes, hypercholesterolemia, asthma, chronic obstructive pulmonary disease (COPD), chronic kidney disease, cardiovascular diseases, osteoarthritis, and vitamin D deficiency, were associated with hospitalization and/or disease severity. Hematological disorders such as anemia, coagulation disorders, and thrombocytopenia were associated with higher odds of both hospitalization and disease severity.\n\nConclusionThis study confirms race and ethnicity as predictors of severe COVID-19 and identifies clinical risk factors not previously reported such a vitamin D deficiency, hypercholesterolemia, osteoarthritis, and anemia.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Angelico Mendy", + "author_inst": "Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, USA" + }, + { + "author_name": "Senu Apewokin", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Cincinnati College of Medicine" + }, + { + "author_name": "Anjanette A Wells", + "author_inst": "School of Social Work, College of Allied Health Sciences, University of Cincinnati" + }, + { + "author_name": "Ardythe L Morrow", + "author_inst": "Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.25.20140442", "rel_title": "Population heterogeneity is a critical factor of the kinetics of the COVID-19 epidemics", @@ -1325898,153 +1322541,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.06.25.171009", - "rel_title": "Swarm Learning as a privacy-preserving machine learning approach for disease classification", - "rel_date": "2020-06-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.171009", - "rel_abs": "Identification of patients with life-threatening diseases including leukemias or infections such as tuberculosis and COVID-19 is an important goal of precision medicine. We recently illustrated that leukemia patients are identified by machine learning (ML) based on their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed because of privacy legislation. To facilitate integration of any omics data from any data owner world-wide without violating privacy laws, we here introduce Swarm Learning (SL), a decentralized machine learning approach uniting edge computing, blockchain-based peer-to-peer networking and coordination as well as privacy protection without the need for a central coordinator thereby going beyond federated learning. Using more than 14,000 blood transcriptomes derived from over 100 individual studies with non-uniform distribution of cases and controls and significant study biases, we illustrate the feasibility of SL to develop disease classifiers based on distributed data for COVID-19, tuberculosis or leukemias that outperform those developed at individual sites. Still, SL completely protects local privacy regulations by design. We propose this approach to noticeably accelerate the introduction of precision medicine.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Stefanie Warnat-Herresthal", - "author_inst": "Life and Medical Science Institute, University of Bonn, Germany" - }, - { - "author_name": "Hartmut Schultze", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Krishna Prasad Lingadahalli Shastry", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Sathyanarayanan Manamohan", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Saikat Mukherjee", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Vishesh Garg", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Ravi Sarveswara", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Kristian Haendler", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "Peter Pickkers", - "author_inst": "Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6500HB, The Netherland" - }, - { - "author_name": "N Ahmad Aziz", - "author_inst": "\"Population Health Sciences, German Center for Neurodegenerative diseases (DZNE), Bonn, 53127 Bonn, Germany; Department of Neurology, Faculty of Medicine, Unive" - }, - { - "author_name": "Sofia Ktena", - "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece" - }, - { - "author_name": "Christian Siever", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Michael Kraut", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "Milind Desai", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Bruno Monet", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Maria Saridaki", - "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece" - }, - { - "author_name": "Charles Martin Siegel", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Anna Drews", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "Melanie Nuesch-Germano", - "author_inst": "Life and Medical Science Institute, University of Bonn, Germany" - }, - { - "author_name": "Heidi Theis", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "Mihai G Netea", - "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen 6500HB, The Netherlands" - }, - { - "author_name": "Fabian J Theis", - "author_inst": "Helmholtz Center Munich" - }, - { - "author_name": "Anna C Aschenbrenner", - "author_inst": "Life and Medical Science Institute, University of Bonn, Germany and Radboud UMC, Nijmegen, The Netherlands" - }, - { - "author_name": "Thomas Ulas", - "author_inst": "Life and Medical Science Institute, University of Bonn, Germany, PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative " - }, - { - "author_name": "Monique M.B. Breteler", - "author_inst": "\"Population Health Sciences, German Center for Neurodegenerative diseases (DZNE), Bonn, 53127 Bonn, Germany; Institute for Medical Biometry, Informatics and Epi" - }, - { - "author_name": "Evangelos J Giamarellos-Bourboulis", - "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece" - }, - { - "author_name": "Matthijs Kox", - "author_inst": "Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands" - }, - { - "author_name": "Matthias Becker", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "Sorin Cheran", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Michael S Woodacre", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Eng Lim Goh", - "author_inst": "Hewlett Packard Enterprise" - }, - { - "author_name": "Joachim L. Schultze", - "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" - }, - { - "author_name": "- German COVID-19 OMICS Initiative (DeCOI)", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.25.172510", "rel_title": "Nanotrap(R) particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free medium methods", @@ -1326613,6 +1323109,77 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.06.26.152520", + "rel_title": "Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2", + "rel_date": "2020-06-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.152520", + "rel_abs": "Pathogens (bacteria, fungus and virus) are becoming a potential threat to the health of human beings and environment worldwide. They widely exist in the environment, with characteristics of variety, spreading quickly and easily causing adverse reactions. In this work, an Ag-based material is used to be incorporated and functionalized in polycotton fabrics using pad-dry-cure method. This composite proved to be effective for inhibiting the SARS-CoV-2 virus, decreasing the number of replicates in 99.99% after an incubation period of 2 minutes. In addition, it caused 99.99% inhibition of the pathogens S. aureus, E. coli and C. albicans, preventing cross-infections and does not cause allergies or photoirritation processes, demonstrating the safety of its use.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Guilherme Carvalho Tremiliosi", + "author_inst": "Nanox Tecnologia SA" + }, + { + "author_name": "Luiz Gustavo Pagotto Simoes", + "author_inst": "Nanox Tecnologia SA" + }, + { + "author_name": "Daniel Tamassia Minozzi", + "author_inst": "Nanox Tecnologia SA" + }, + { + "author_name": "Renato Ignacio Santos", + "author_inst": "Nanox Tecnologia SA" + }, + { + "author_name": "Daiane Barboza Vilela", + "author_inst": "Nanox Tecnologia SA" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Rafael Rahal Guaragna Machado", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Douglas Sales Medina", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, ICB, University of Sao Paulo, Brazil" + }, + { + "author_name": "Lara Kelly Ribeiro", + "author_inst": "Center for the Development of Functional Materials, CDMF, Federal University of Sao Carlos, Brazil" + }, + { + "author_name": "Ieda Lucia Viana Rosa", + "author_inst": "Center for the Development of Functional Materials, CDMF, Federal University of Sao Carlos, Brazil" + }, + { + "author_name": "Marcelo Assis", + "author_inst": "Center for the Development of Functional Materials, CDMF, Federal University of Sao Carlos, Brazil" + }, + { + "author_name": "Juan Manuel Andres Bort", + "author_inst": "Laboratory of Theoretical and Computational Chemistry, Department of Analytical and Physical Chemistry, University Jaume I, Spain" + }, + { + "author_name": "Elson Longo", + "author_inst": "Center for the Development of Functional Materials, CDMF, Federal University of Sao Carlos, Brazil" + }, + { + "author_name": "Lucio H. Freitas-Junior", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, ICB, University of Sao Paulo, Brazil" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.25.149427", "rel_title": "Elucidation of the antiviral mechanism of cystine and theanine through transcriptome analysis of mice and comparison with COVID-19 gene set data", @@ -1327324,85 +1323891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.24.20139006", - "rel_title": "Evaluation of two commercial and two non-commercial immunoassays for the detection of prior infection to SARS-CoV-2", - "rel_date": "2020-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139006", - "rel_abs": "BackgroundSeroepidemiology is an important tool to characterize the epidemiology and immunobiology of SARS-CoV-2 but many immunoassays have not been externally validated raising questions about reliability of study findings. To ensure meaningful data, particularly in a low seroprevalence population, assays need to be rigorously characterized with high specificity.\n\nMethodsWe evaluated two commercial (Roche Diagnostics and Epitope Diagnostics IgM/IgG) and two non-commercial (Simoa and Ragon/MGH IgG) immunoassays against 68 confirmed positive and 232 pre-pandemic negative controls. Sensitivity was stratified by time from symptom onset. The Simoa multiplex assay applied three pre-defined algorithm models to determine sample result.\n\nResultsThe Roche and Ragon/MGH IgG assays each registered 1/232 false positive, the primary Simoa model registered 2/232 false positives, and the Epitope registered 2/230 and 3/230 false positives for the IgG and IgM assays respectively. Sensitivity >21 days post symptom-onset was 100% for all assays except Epitope IgM, but lower and/or with greater variability between assays for samples collected 9-14 days (67-100%) and 15-21 days (69-100%) post-symptom onset. The Simoa and Epitope IgG assays demonstrated excellent sensitivity earlier in the disease course. The Roche and Ragon/MGH assays were less sensitive during early disease, particularly among immunosuppressed individuals.\n\nConclusionsThe Epitope IgG demonstrated good sensitivity and specificity. The Roche and Ragon/MGH IgG assays registered rare false positives with lower early sensitivity. The Simoa assay primary model had excellent sensitivity and few false positives.\n\nSummarySARS-CoV-2 immunoassays can be valuable tools for informing the global response, but many currently available assays have not been independently validated. We conducted a performance assessment of four assays including the Roche Diagnostics and Epitope Diagnostics immunoassays.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Eric J. Nilles", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Elizabeth W. Karlson", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Maia Norman", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Tal Gilboa", - "author_inst": "Brigham and Women's Hospital & Harvard medical school" - }, - { - "author_name": "Stephanie Fischinger", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA" - }, - { - "author_name": "Caroline Atyeo", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA" - }, - { - "author_name": "Guohai Zhou", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Christopher L. Bennett", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Nicole V. Tolan", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Karina Oganezova", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "David R. Walt", - "author_inst": "Brigham and Women's Hospital, Wyss Institute for Biologically Inspired Engineering at Harvard University, Harvard Medical School" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Daimon P. Simmons", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Peter Schur", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Petr Jarolim", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Lindsey R. Baden", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.25.171975", "rel_title": "Increased Expression of Chondroitin Sulfotransferases following AngII may Contribute to Pathophysiology Underlying Covid-19 Respiratory Failure: Impact may be Exacerbated by Decline in Arylsulfatase B Activity", @@ -1327958,6 +1324446,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.24.20138313", + "rel_title": "Practical recommendations for staying physically active during the COVID-19 pandemic: A systematic literature review", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138313", + "rel_abs": "BackgroundDue to home-confinement and social isolation of during the Covid-19 pandemic, reductions in performing physical activities were observed. A main consequence of inactivity is a poorer general health and a higher mortality rate. Therefore, it is important to inform the public about practical recommendations for staying physically active, especially during the current Covid-19 pandemic.\n\nMethodsThrough a systematic review of literature in two databases (Pubmed/Medline; Web of Science), studies were analysed which include practical recommendations for staying active during Covid-19 (Q1), or if they did not explicitly deal with Covid-19, research with useful results regarding the adaption to the present situation (Q2).\n\nResultsCurrently, there are 6 studies published which are related to the first research question. In total, 26 papers, were found to correlate to the second one.\n\nConclusionResearchers need to be more specific in the exact recommendations for different age-groups and various health statuses. Key sources are the websites of the World Health Organization and the American Heart Association. In addition, exergames need to be adaptable to restrictions by product designers and to integrate social interaction-functions. Furthermore, it is essential that governmental actions need to be taken, with the help of researchers, to inform citizens about possible physical activities, with precise examples, clarification of benefits of the exercises, the exact exercise with duration, intensity and other substitute tasks for different age-groups and for people with diseases.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ellen Bentlage", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Achraf Ammar", + "author_inst": "Otto-von-Guericke University, Germany" + }, + { + "author_name": "Hamdi Chtourou", + "author_inst": "Observatoire National du Sport; Universite de Sfax, Tunisie" + }, + { + "author_name": "Khaled Trabelsi", + "author_inst": "Universite de Sfax, ; Sport et Sante, Tunisie" + }, + { + "author_name": "Daniella How", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Mona Ahmed", + "author_inst": "University of Muenster, Germany" + }, + { + "author_name": "Michael Brach", + "author_inst": "University of Muenster, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.24.20138230", "rel_title": "Incidence, risk factors and mortality outcome in patients with acute kidney injury in COVID-19: a single-center observational study", @@ -1328933,45 +1325464,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.21.20136523", - "rel_title": "Breath-borne VOC Biomarkers for COVID-19", - "rel_date": "2020-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136523", - "rel_abs": "Rapid diagnosis of COVID-19 is key to controlling the pandemic. Here we report the potential breath-borne volatile organic compound (VOC) biomarkers for COVID-19. Higher levels of ethyl butanoate were detected in exhaled breath of COVID-19 patients (N=10) than healthy controls/health care workers (N=21), lung cancer (LC) patients (N=7) and backgrounds. In contrast, breath-borne butyraldehyde and isopropanol (an efficient SARS-CoV-2 inactivation agent) were significantly higher for non-COVID-19 respiratory infections (URTI) (N=22) than COVID-19, HC, LC patients and backgrounds. Breath-borne isopropanol emission from COVID-19 patients varied greatly up to [~]100-fold difference. COVID-19 patients had lower acetone levels than other subjects, except LC patients. The monitoring of ethyl butanoate, butyraldehyde and isopropanol could lend considerable support in rapidly screening COVID-19; and alerting the presence of COVID-19 patient in particular environments.\n\nOne Sentence SummaryCOVID-19 patients emit distinctive VOC profiles", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Haoxuan Chen", - "author_inst": "Peking University" - }, - { - "author_name": "Xiao Qi", - "author_inst": "Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, China." - }, - { - "author_name": "Jianxin Ma", - "author_inst": "Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, China" - }, - { - "author_name": "Chunyang Zhang", - "author_inst": "Respiratory Department of the Sixth Medical Center of PLA General Hospital" - }, - { - "author_name": "Huasong Feng", - "author_inst": "Respiratory Department of the Sixth Medical Center of PLA General Hospital" - }, - { - "author_name": "Maosheng Yao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.23.20138289", "rel_title": "Longitudinal immunological analyses reveal inflammatory misfiring in severe COVID-19 patients", @@ -1329567,6 +1326059,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.06.24.20138818", + "rel_title": "Transmission of Respiratory Infectious Diseases between Neighboring Cities using Agent-based Model and Compartmental Model", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138818", + "rel_abs": "We formulate an agent-based model and a compartmental model (SEIR) that simulate the spread of a respiratory infectious disease between two neighboring cities. We consider preventive measures such as implementation of social distancing and lockdown in a city, as well as the effect of protective gears or practices. The chance of travelling to another city and within the city during lockdown, and initial percentage of exposed and infected individuals on both cities influence the increase in the number of newly-infected individuals on both models. Our simulations show that (i) increase in exposed individuals results in increase in number of new infections, hence the need for increased testing-isolation efforts; (ii) protection level of 75-100% effectiveness impedes disease transmission; (iii) travelling within city or to other city can be an option given that strict preventive measures (e.g., non-pharmaceutical interventions) are observed; and (iv) the ideal set-up for neighboring cities is to implement lockdown when there is high risk of disease local transmission while individuals observe social distancing, maximizing protective measures, and isolating those that are exposed. The results of the agent-based and compartmental models show similar qualitative dynamics; the differences are due to different spatio-temporal heterogeneity and stochasticity. These models can aid decision makers in designing infectious disease-related policies to protect individuals while continuing population movement.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christian Alvin H Buhat", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Destiny SM Lutero", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Yancee H Olave", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Monica C Torres", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Jomar F Rabajante", + "author_inst": "University of the Philippines Los Banos" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20138891", "rel_title": "Knowledge, Attitude, Perceptions and Practice towards COVID-19: A systematic review and Meta-analysis", @@ -1330334,157 +1326861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.21.20132944", - "rel_title": "Clinical predictors of donor antibody titer and correlation with recipient antibody response in a COVID-19 convalescent plasma clinical trial", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20132944", - "rel_abs": "BackgroundConvalescent plasma therapy for COVID-19 relies on the transfer of anti-viral antibody from donors to recipients via plasma transfusion. The relationship between clinical characteristics and antibody response to COVID-19 is not well defined. We investigated predictors of convalescent antibody production and quantified recipient antibody response in a convalescent plasma therapy clinical trial.\n\nMethodsMultivariable analysis of clinical and serological parameters in 103 confirmed COVID-19 convalescent plasma donors 28 days or more following symptom resolution was performed. Mixed effects regression models with piecewise linear trends were used to characterize serial antibody responses in 10 convalescent plasma recipients with severe COVID-19.\n\nFindingsMean symptom duration of plasma donors was 11.9{+/-}5.9 days and 7.8% (8/103) had been hospitalized. Antibody titers ranged from 0 to 1:3,892 (anti-receptor binding domain (RBD)) and 0 to 1:3,289 (anti-spike). Multivariable analysis demonstrated that higher anti-RBD and anti-spike titer were associated with increased age, hospitalization for COVID-19, fever, and absence of myalgia (all p<0.05). Fatigue was significantly associated with anti-RBD (p=0.03) but not anti-spike antibody titer (p=0.11). In pairwise comparison among ABO blood types, AB donors had higher anti-RBD titer than O negative donors (p=0.048) and higher anti-spike titer than O negative (p=0.015) or O positive (p=0.037) donors. Eight of the ten recipients were discharged, one remains on ECMO and one died on ECMO. No toxicity was associated with plasma transfusion. After excluding two ECMO patients and adjusting for donor antibody titer, recipient anti-RBD antibody titer increased on average 31% per day during the first three days post-transfusion (p=0.01) and anti-spike antibody titer by 40.3% (p=0.02).\n\nInterpretationAdvanced age, fever, absence of myalgia, fatigue, blood type and hospitalization were associated with higher convalescent antibody titer to COVID-19. Despite variability in donor titer, 80% of convalescent plasma recipients showed significant increase in antibody levels post-transfusion. A more complete understanding of the dose-response effect of plasma transfusion among COVID-19 patients is needed to determine the clinical efficacy of this therapy.\n\nTrial RegistrationNCT04340050\n\nFundingDepartment of Surgery University of Chicago, National Institute of Allergy and Infectious Diseases (NIAID) Collaborative Influenza Vaccine Innovation Centers (CIVIC) contract 75N93019C00051", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Maria Lucia L Madariaga", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jenna Guthmiller", - "author_inst": "University of Chicago" - }, - { - "author_name": "Stephen Schrantz", - "author_inst": "University of Chicago" - }, - { - "author_name": "Maud Jansen", - "author_inst": "University of Chicago" - }, - { - "author_name": "Chancey Christenson", - "author_inst": "University of Chicago" - }, - { - "author_name": "Madan Kumar", - "author_inst": "University of Chicago" - }, - { - "author_name": "Micah Prochaska", - "author_inst": "University of Chicago" - }, - { - "author_name": "Geoffrey Wool", - "author_inst": "University of Chicago" - }, - { - "author_name": "Amy Durkin", - "author_inst": "University of Chicago" - }, - { - "author_name": "Won Hee Oh", - "author_inst": "University of Chicago" - }, - { - "author_name": "Laura Trockman", - "author_inst": "University of Chicago" - }, - { - "author_name": "Janani Vigneswaran", - "author_inst": "University of Chicago" - }, - { - "author_name": "Robert Keskey", - "author_inst": "University of Chicago" - }, - { - "author_name": "Dustin G Shaw", - "author_inst": "University of Chicago" - }, - { - "author_name": "Haley Dugan", - "author_inst": "Unviversity of Chicago" - }, - { - "author_name": "Nai Zheng", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mari Cobb", - "author_inst": "University of Chicago" - }, - { - "author_name": "Henry Utset", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jiaolong Wang", - "author_inst": "University of Chicago" - }, - { - "author_name": "Olivia Stovicek", - "author_inst": "University of Chicago" - }, - { - "author_name": "Cindy Bethel", - "author_inst": "University of Chicago" - }, - { - "author_name": "Scott Matushek", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mihai Giurcanu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kathleen Beavis", - "author_inst": "University of Chicago" - }, - { - "author_name": "Diego diSabato", - "author_inst": "University of Chicago" - }, - { - "author_name": "David Meltzer", - "author_inst": "The University of Chicago" - }, - { - "author_name": "Mark Ferguson", - "author_inst": "University of Chicago" - }, - { - "author_name": "John P Kress", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kumaran Shanmugarajah", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jeffrey Matthews", - "author_inst": "University of Chicago" - }, - { - "author_name": "John Fung", - "author_inst": "University of Chicago" - }, - { - "author_name": "Patrick Wilson", - "author_inst": "University of Chicago" - }, - { - "author_name": "John C Alverdy", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jessica Donington", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.21.20136580", "rel_title": "Estimation of Undetected Symptomatic and Asymptomatic cases of COVID-19 Infection and prediction of its spread in USA", @@ -1330909,6 +1327285,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.21.20136903", + "rel_title": "Low serum 25-hydroxyvitamin D (25D) levels in patients hospitalised with COVID-19 are associated with greater disease severity: results of a local audit of practice.", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136903", + "rel_abs": "ObjectivesTo audit implementation of a local protocol for the treatment of vitamin D deficiency (VDD) among patients hospitalized for Coronavirus Disease 2019 (COVID-19), including an assessment of the prevalence of VDD in these patients, and of potential associations with disease severity and fatality.\n\nDesignThis was not a study or clinical trial, but rather a retrospective interim audit (Newcastle-upon-Tyne Hospitals Registration No. 10075) of a local clinical care pathway for hospitalized patients with COVID-19-related illness. The Information (Caldicott) Guardian permitted these data to be shared beyond the confines of our institution.\n\nSettingA large tertiary academic NHS Foundation Trust in the North East of England, UK, providing care to COVID-19 patients.\n\nParticipantsOne hundred thirty-four hospitalized patients with documented COVID-19 infection.\n\nMain outcome measuresAdherence to local investigation and treatment protocol; prevalence of VDD, and relationship of baseline serum 25(OH)D with markers of COVID-19 severity and inpatient fatality versus recovery.\n\nResults55.8% of eligible patients received Colecalciferol replacement, albeit not always loaded as rapidly as our protocol suggested, and no cases of new hypercalcaemia occurred following treatment. Patients admitted to ITU were younger than those managed on medical wards (61.1 years {+/-} 11.8 vs. 76.4 years {+/-} 14.9, p<0.001), with greater prevalence of hypertension, and higher baseline respiratory rate, National Early Warning Score-2 and C-reactive protein level. While mean serum 25(OH)D levels were comparable [i.e. ITU: 33.5 nmol/L {+/-} 16.8 vs. Non-ITU: 48.1 nmol/L {+/-} 38.2, mean difference for Ln-transformed-25(OH)D: 0.14, 95% Confidence Interval (CI) (-0.15, 0.41), p=0.3], only 19% of ITU patients had 25(OH)D levels greater than 50 nmol/L vs. 39.1% of non-ITU patients (p=0.02). However, we found no association with fatality, potentially due to small sample size, limitations of no-trial data and, potentially, the prompt diagnosis and treatment of VDD.\n\nConclusionsSubject to the inherent limitations of observational (non-trial) audit data, analysed retrospectively, we found that patients requiring ITU admission were more frequently vitamin D deficient than those managed on medical wards, despite being significantly younger. Larger prospective studies and/or clinical trials are needed to elucidate the role of vitamin D as a preventive and/or therapeutic strategy for mitigating the effects of COVID-19 infection in patients with VDD.\n\nWhat is already known on this topicO_LIVitamin D deficiency (VDD) is associated with increased risk for acute respiratory tract infections\nC_LIO_LIA link between VDD and severity of COVID-19 pathophysiology has been proposed\nC_LIO_LITwo recent (non-peer-reviewed) studies have reported crude associations between VDD in defined geographic populations and COVID-19 severity and mortality\nC_LI\n\nWhat this study addsO_LIThese data do not arise from a clinical study; rather from an audit of a local replacement protocol for VDD in COVID-19 inpatients in a large UK centre, which found a significantly higher prevalence of VDD among ITU patients compared to non-ITU patients, despite the ITU patients being significantly younger.\nC_LIO_LIPrompt treatment of VDD following a local protocol did not result in any adverse events, such as hypercalcaemia.\nC_LIO_LIWhilst by no means conclusive, these data suggest an important association between VDD and COVID-19 severity; hence our report of interim findings in advance of achieving completed outcomes (fatality vs. recovery) for all patients.\nC_LIO_LIThere is an urgent need for larger studies exploring vitamin D as a potential preventative measure and/or treatment of Covid-19-related illness among individuals with VDD.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Grigorios Panagiotou", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Su Ann Tee", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Yasir Ihsan", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Waseem Athar", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Gabriella Marchitelli", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Donna Kelly", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Christopher S. Boot", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Nadia Stock", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Jim Macfarlane", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Adrian R. Martineau", + "author_inst": "Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom" + }, + { + "author_name": "Graham Paul Burns", + "author_inst": "Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + }, + { + "author_name": "Richard Quinton", + "author_inst": "University of Newcastle-upon-Tyne and Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.06.22.20136994", "rel_title": "Management and Clinical Characteristics in Children with SARS-CoV-2 Infection: Experience in a highly complex public hospital in the city of Sao Paulo", @@ -1331660,29 +1328099,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.22.20137208", - "rel_title": "Understanding the Bias between the Number of Confirmed Cases and Actual Number of Infections in the COVID-19 Pandemic", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137208", - "rel_abs": "The number of positive cases confirmed in the viral tests is a probe of the actual number of infections of COVID-19. The bias between these two quantities is a key element underlying the determination of some important parameters of this disease and the policy-making during the pandemic. To study the dependence of this bias on measured variables, we introduce a parameterization model that motivates a method of organizing the daily data of the numbers of the total tests, confirmed cases, hospitalizations and fatalities. After comparing with the historical data of the USA in the past few months, we find a simple formula relating these four variables. As a few applications, we show, among other things, how this formula can be used to project the number of actual infections, to provide guidance on how the test volume should be adjusted, and to derive an upper bound on the overall infection fatality rate of COVID-19 (< 0.64%, 95% C.L.) and a theoretical estimate of its value.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Xingang Chen", - "author_inst": "Institute for Theory and Computation, Harvard-Smithsonian Center for Astrophysics" - }, - { - "author_name": "Dhiraj Kumar Hazra", - "author_inst": "The Institute of Mathematical Sciences, Chennai, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.23.20137992", "rel_title": "Hydroxychloroquine serum concentrations in non-critical care patients infected with SARS CoV 2", @@ -1332435,6 +1328851,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.22.20137588", + "rel_title": "The impact of COVID-19 non-pharmaceutical interventions on the future dynamics of endemic infections", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137588", + "rel_abs": "Non-pharmaceutical interventions (NPIs) have been employed to reduce the transmission of SARS-CoV-2, yet these measures are already having similar effects on other directly-transmitted, endemic diseases. Disruptions to the seasonal transmission patterns of these diseases may have consequences for the timing and severity of future outbreaks. Here we consider the implications of SARS-CoV-2 NPIs for two endemic infections circulating in the United States of America (USA): respiratory syncytial virus (RSV) and seasonal influenza. Using laboratory surveillance data from 2020, we estimate that RSV transmission declined by at least 20% in the USA at the start of the NPI period. We simulate future trajectories of both RSV and influenza, using an epidemic model. As susceptibility increases over the NPI period, we find that substantial outbreaks of RSV may occur in future years, with peak outbreaks likely occurring in the winter of 2021-2022. Results for influenza broadly echo this picture, but are more uncertain; future outbreaks are likely dependent on the transmissibility and evolutionary dynamics of circulating strains.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rachel E. Baker", + "author_inst": "Princeton University" + }, + { + "author_name": "Sang Woo Park", + "author_inst": "Princeton University" + }, + { + "author_name": "Wenchang Yang", + "author_inst": "Princeton University" + }, + { + "author_name": "Gabriel A. Vecchi", + "author_inst": "Princeton University" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Bryan T. Grenfell", + "author_inst": "Princeton University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.23.20138016", "rel_title": "Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay", @@ -1333198,81 +1329653,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.06.22.165712", - "rel_title": "A nanoluciferase SARS-CoV-2 for rapid neutralization testing and screening of anti-infective drugs for COVID-19", - "rel_date": "2020-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.165712", - "rel_abs": "A high-throughput platform would greatly facilitate COVID-19 serological testing and antiviral screening. Here we report a nanoluciferase SARS-CoV-2 (SARS-CoV-2-Nluc) that is genetically stable and replicates similarly to the wild-type virus in cell culture. We demonstrate that the optimized reporter virus assay in Vero E6 cells can be used to measure neutralizing antibody activity in patient sera and produces results in concordance with a plaque reduction neutralization test (PRNT). Compared with the low-throughput PRNT (3 days), the SARS-CoV-2-Nluc assay has substantially shorter turnaround time (5 hours) with a high-throughput testing capacity. Thus, the assay can be readily deployed for large-scale vaccine evaluation and neutralizing antibody testing in humans. Additionally, we developed a high-throughput antiviral assay using SARS-CoV-2-Nluc infection of A549 cells expressing human ACE2 receptor (A549-hACE2). When tested against this reporter virus, remdesivir exhibited substantially more potent activity in A549-hACE2 cells compared to Vero E6 cells (EC50 0.115 vs 1.28 M), while this difference was not observed for chloroquine (EC50 1.32 vs 3.52 M), underscoring the importance of selecting appropriate cells for antiviral testing. Using the optimized SARS-CoV-2-Nluc assay, we evaluated a collection of approved and investigational antivirals and other anti-infective drugs. Nelfinavir, rupintrivir, and cobicistat were identified as the most selective inhibitors of SARS-CoV-2-Nluc (EC50 0.77 to 2.74 M). In contrast, most of the clinically approved antivirals, including tenofovir alafenamide, emtricitabine, sofosbuvir, ledipasvir, and velpatasvir were inactive at concentrations up to 10 M. Collectively, this high-throughput platform represents a reliable tool for rapid neutralization testing and antiviral screening for SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Antonio E. Muruato", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kumari G. Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Camila R. Fontes-Garfias", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jianying Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Ping Ren", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Mini Balakrishnan", - "author_inst": "Gilead Sciences, Inc., Foster City, CA, USA" - }, - { - "author_name": "Tomas Cihlar", - "author_inst": "Gilead Sciences, Inc., Foster City, CA, USA" - }, - { - "author_name": "Chien-Te K. Tseng", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Shinji Makino", - "author_inst": "Texas Univ" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "John P. Bilello", - "author_inst": "Gilead Sciences, Inc., Foster City, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.22.165803", "rel_title": "CD209L/L-SIGN and CD209/DC-SIGN act as receptors for SARS-CoV-2 and are differentially expressed in lung and kidney epithelial and endothelial cells", @@ -1333969,6 +1330349,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.06.22.165035", + "rel_title": "Oral epithelial expression of angiotensin converting enzyme-2: Implications for COVID-19 diagnosis and prognosis.", + "rel_date": "2020-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.165035", + "rel_abs": "The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) uses the angiotensin converting enzyme (ACE)-2 as the host receptor for target cell entry. The extent and distribution of ACE-2 has been associated with the clinical symptoms of coronavirus disease (COVID)-19. Here we show by immunofluorescence analysis that the ACE2 is abundantly expressed in oral mucosa, particularly in the surface epithelial cells suggesting that these cells could represent sites of entry for SARS-CoV-2. Further, together with the reports on ACE2 ectodomain shedding, we discuss the rationale for the hypothesis that the ACE-2 measurement in saliva could be a marker for COVID-19 infection during early phase following SARS-CoV-2 exposure.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mythily Srinivasan", + "author_inst": "Indiana University School of Dentistry" + }, + { + "author_name": "Susan L Zunt", + "author_inst": "Indiana University School of Dentistry" + }, + { + "author_name": "Lawrence I Goldblatt", + "author_inst": "Indiana University School of Dentistry" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.23.166421", "rel_title": "Modeling the effect of COVID-19 disease on the cardiac function: a computational study", @@ -1334796,33 +1331203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.18.20134916", - "rel_title": "Management strategies and prediction of COVID-19 by a fractional order generalized SEIR model", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134916", - "rel_abs": "In this project, we study a class of fractional order generalized SEIR epidemic models. Based on the public data from Jan. 22th to May 15th, 2020, we reliably estimate key epidemic parameters and make predictions on the peak point and possible ending time for the target region. We analyze the current management strategy and predict the future implementation of different management strategies. Numerical simulations which support our analysis are also given.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lihong Guo", - "author_inst": "Jilin University, China" - }, - { - "author_name": "Yanting Zhao", - "author_inst": "University of Science and Technology of China" - }, - { - "author_name": "YangQuan Chen", - "author_inst": "University of California Merced" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.18.20135004", "rel_title": "The long term predictions from Imperial College CovidSim Report 9", @@ -1335283,6 +1331663,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.22.20137273", + "rel_title": "Effect of Dexamethasone in Hospitalized Patients with COVID-19: Preliminary Report", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137273", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is associated with diffuse lung damage. Corticosteroids may modulate immune-mediated lung injury and reducing progression to respiratory failure and death.\n\nMethodsThe Randomised Evaluation of COVID-19 therapy (RECOVERY) trial is a randomized, controlled, open-label, adaptive, platform trial comparing a range of possible treatments with usual care in patients hospitalized with COVID-19. We report the preliminary results for the comparison of dexamethasone 6 mg given once daily for up to ten days vs. usual care alone. The primary outcome was 28-day mortality.\n\nResults2104 patients randomly allocated to receive dexamethasone were compared with 4321 patients concurrently allocated to usual care. Overall, 454 (21.6%) patients allocated dexamethasone and 1065 (24.6%) patients allocated usual care died within 28 days (age-adjusted rate ratio [RR] 0.83; 95% confidence interval [CI] 0.74 to 0.92; P<0.001). The proportional and absolute mortality rate reductions varied significantly depending on level of respiratory support at randomization (test for trend p<0.001): Dexamethasone reduced deaths by one-third in patients receiving invasive mechanical ventilation (29.0% vs. 40.7%, RR 0.65 [95% CI 0.51 to 0.82]; p<0.001), by one-fifth in patients receiving oxygen without invasive mechanical ventilation (21.5% vs. 25.0%, RR 0.80 [95% CI 0.70 to 0.92]; p=0.002), but did not reduce mortality in patients not receiving respiratory support at randomization (17.0% vs. 13.2%, RR 1.22 [95% CI 0.93 to 1.61]; p=0.14).\n\nConclusionsIn patients hospitalized with COVID-19, dexamethasone reduced 28-day mortality among those receiving invasive mechanical ventilation or oxygen at randomization, but not among patients not receiving respiratory support.\n\nTrial registrationsThe RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFundingMedical Research Council and National Institute for Health Research (Grant ref: MC_PC_19056).", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Peter Horby", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom." + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom" + }, + { + "author_name": "Jonathan Emberson", + "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Marion Mafham", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Jennifer Bell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Louise Linsell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Natalie Staplin", + "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Christopher Brightling", + "author_inst": "Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom" + }, + { + "author_name": "Andrew Ustianowski", + "author_inst": "Regional Infectious Diseases Unit, North Manchester General Hospital & University of Manchester, Manchester, United Kingdom" + }, + { + "author_name": "Einas Elmahi", + "author_inst": "Research and Development Department, Northampton General Hospital, Northampton, United Kingdom" + }, + { + "author_name": "Benjamin Prudon", + "author_inst": "Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom" + }, + { + "author_name": "Christopher Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust and Institute of Microbiology & Infection, University of Birmingham, Birmingham, United Kingdom" + }, + { + "author_name": "Timothy Felton", + "author_inst": "University of Manchester and Manchester University NHS Foundation Trust, Manchester, United Kingdom" + }, + { + "author_name": "David Chadwick", + "author_inst": "Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom" + }, + { + "author_name": "Kanchan Rege", + "author_inst": "North West Anglia NHS Foundation Trust, Peterborough, United Kingdom" + }, + { + "author_name": "Christopher Fegan", + "author_inst": "Department of Research and Development, Cardiff and Vale University Health Board, Cardiff, United Kingdom" + }, + { + "author_name": "Lucy C Chappell", + "author_inst": "School of Life Course Sciences, Kings College London, London, United Kingdom" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " + }, + { + "author_name": "Thomas Jaki", + "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Kathryn Rowan", + "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" + }, + { + "author_name": "Richard Haynes", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Martin J Landray", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "- RECOVERY Collaborative Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.20.163097", "rel_title": "Female reproductive tract has low concentration of SARS-CoV2 receptors", @@ -1336329,117 +1332832,6 @@ "type": "confirmatory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.20.163188", - "rel_title": "Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: moving toward a universal vaccine for the \"confined virus\"?", - "rel_date": "2020-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.163188", - "rel_abs": "The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from December 24, 2019, to May 13, 2020, according to the GISAID database. Our analysis revealed the presence of 3,206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (> 10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein and one in each of three proteins: spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the RBD of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with mutational frequency dissimilarity and intra-genomic divergence of SARS-CoV-2 could indicate that the SARS-CoV-2 is not yet adapted to its host. Unlike the influenza virus or HIV viruses, the low mutation rate of SARS-CoV-2 makes the development of an effective global vaccine very likely.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Tarek Alouane", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Meriem Laamarti", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Abdelomunim Essabbar", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Mohammed Hakmi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "El Mehdi Bouricha", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "M.W. Chemao-Elfihri", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Souad Kartti", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Nasma Boumajdi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Houda Bendani", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Rokia Laamarti", - "author_inst": "MASCIR, Rabat Design, Rabat, Morocco." - }, - { - "author_name": "Fatima Ghrifi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Loubna Allam", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Tarik Aanniz", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Mouna Ouadghiri", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Naima El Hafidi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Rachid El Jaoudi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Houda Benrahma", - "author_inst": "Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco." - }, - { - "author_name": "Jalil El Attar", - "author_inst": "Laboratoire Riad, hay Riad, Rabat, Morocco." - }, - { - "author_name": "Rachid Mentag", - "author_inst": "Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco." - }, - { - "author_name": "Laila Sbabou", - "author_inst": "Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University o" - }, - { - "author_name": "Chakib Nejjari", - "author_inst": "International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco." - }, - { - "author_name": "Saaid Amzazi", - "author_inst": "Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco." - }, - { - "author_name": "Lahcen Belyamani", - "author_inst": "Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - }, - { - "author_name": "Azeddine Ibrahimi", - "author_inst": "Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.20.162933", "rel_title": "A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution", @@ -1337068,6 +1333460,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.06.19.20135723", + "rel_title": "Clinical Sensitivity and Interpretation of PCR and Serological COVID-19 Diagnostics for Patients Presenting to the Hospital", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135723", + "rel_abs": "IntroductionThe diagnosis of COVID-19 requires integration of clinical and laboratory data. SARS-CoV-2 diagnostic assays play a central role in diagnosis and have fixed technical performance metrics. Interpretation becomes challenging because the clinical sensitivity changes as the virus clears and the immune response emerges. Our goal was to examine the clinical sensitivity of two most common SARS-CoV-2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital.\n\nMethodsA single-center, retrospective study. To derive clinical sensitivity of PCR, we identified 209 PCR-positive SARS-CoV-2 patients with multiple PCR test results (624 total PCR tests) and calculated daily sensitivity from date of symptom onset or first positive test. To calculate daily clinical sensitivity by serology, we utilized 157 PCR- positive patients with a total of 197 specimens tested by enzyme-linked immunosorbent assay for IgM, IgG, and IgA anti-SARS-CoV-2 antibodies.\n\nResultsClinical sensitivity of PCR decreased with days post symptom onset with >90% clinical sensitivity during the first 5 days after symptom onset, 70-71% from days 9-11, and 30% at day 21. In contrast, serological sensitivity increased with days post symptom onset with >50% of patients seropositive by at least one antibody isotype after day 7, >80% after day 12, and 100% by day 21.\n\nConclusionPCR and serology are complimentary modalities that require time- dependent interpretation. Superimposition of sensitivities over time indicate that serology can function as a reliable diagnostic aid indicating recent or prior infection.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Tyler E Miller", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Wilfredo F. Garcia Beltran", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Adam Z. Bard", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Tasos Gogakos", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Melis N Anahtar", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Michael G. Astudillo", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Diane Yang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Julia Thierauf", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Adam S. Fisch", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Grace K. Mahowald", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Megan J. Fitzpatrick", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Valentina Nardi", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jared Feldman", + "author_inst": "The Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Blake M. Hauser", + "author_inst": "The Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Timothy M. Caradonna", + "author_inst": "The Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Hetal D. Marble", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Lauren L. Ritterhouse", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Sarah E. Turbett", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Julie Batten", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Nicholas Z. Georgantas", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Galit Alter", + "author_inst": "The Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Aaron G. Schmidt", + "author_inst": "The Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Jason B. Harris", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey A. Gelfand", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mark C. Poznansky", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Bradley E. Bernstein", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "David N. Louis", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Anand Dighe", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Richelle C. Charles", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Edward T. Ryan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "John A. Branda", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Virginia M. Pierce", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mandakolathur R. Murali", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "A. John Iafrate", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric S Rosenberg", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jochen Lennerz", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.18.20135277", "rel_title": "Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India", @@ -1337859,109 +1334410,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.18.20134791", - "rel_title": "Design and clinical validation of a 3D-printed nasopharyngeal swab for COVID-19 testing", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134791", - "rel_abs": "We describe the development and validation of a novel 3D-printed nasopharyngeal swab for the identification of SARS-CoV-2. We subjected the novel swab to mechanical and fluid absorption testing ex-vivo, and confirmed its ability to retain and release murine coronavirus and SARS-CoV-2. Compared to the Copan FLOQSwab, the novel swab displayed excellent correlation of RT-PCR cycle threshold values on paired clinical testing in COVID-19 patients, at r = 0.918 and 0.943 for the SARS-CoV-2 ORF1/a and sarbecovirus E-gene respectively. Overall positive and negative percent agreement was 90.6% and 100% respectively on a dual-assay RT-PCR platform, with discordant samples observed only at high cycle thresholds. When carefully designed and tested, 3D-printed swabs are a viable alternative to traditional swabs and will help mitigate strained resources in the escalating COVID-19 pandemic.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Joshua K Tay", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Gail B Cross", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Chun Kiat Lee", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Benedict Yan", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Jerold Loh", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Zhen Yu Lim", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Nicholas Ngiam", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Jeremy Chee", - "author_inst": "National University Hospital Singapore" - }, - { - "author_name": "Soo Wah Gan", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Anmol Saraf", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Wai Tung Eason Chow", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Han Lee Goh", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Chor Hiang Siow", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Derrick WQ Lian", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Woei Shyang Loh", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Kwok Seng Loh", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Vincent TK Chow", - "author_inst": "National University of Singapore" - }, - { - "author_name": "De Yun Wang", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Jerry YH Fuh", - "author_inst": "National University of Singapore" - }, - { - "author_name": "Ching-Chiuan Yen", - "author_inst": "National University of Singapore" - }, - { - "author_name": "John EL Wong", - "author_inst": "National University of Singapore" - }, - { - "author_name": "David M Allen", - "author_inst": "National University of Singapore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.18.20135053", "rel_title": "Short-term Forecasting of Cumulative Confirmed Cases of Covid-19 Pandemic in Somalia", @@ -1338486,6 +1334934,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.18.20134627", + "rel_title": "Kidney function on admission predicts in-hospital mortality in COVID-19", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134627", + "rel_abs": "BackgroundRecent data have reinforced the concept of a reciprocal relationship between COVID-19 and kidney function. However, most studies have focused on the effect of COVID-19 on kidney function, whereas data regarding kidney function on the COVID-19 prognosis is scarce. Therefore, in this study, we aimed to investigate the association between eGFR on admission and the mortality rate of COVID-19.\n\nMethodsWe recruited 336 adult consecutive patients (male 57.1%, mean age 55.0{+/-}15.9) that were hospitalized with the diagnosis of COVID-19 in the tertiary care university hospital. Data were collected from the electronic health records of the hospital. On admission, eGFR was calculated using the CKD-EPI formula. Acute kidney injury was defined according to the KDIGO criteria. Binary logistic regression and Cox regression analyses were used to assess the relationship between eGFR on admission and in-hospital mortality of COVID-19.\n\nResultsBaseline eGFR was under 60 mL/min/1.73m2 in 61 patients (18.2%). Acute kidney injury occurred in 29.1% of the patients. In-hospital mortality was calculated as 12.8%. Age-adjusted and multivariate logistic regression analysis (p:0.005, odds ratio:0.974, CI:0.956-0.992) showed that baseline eGFR was independently associated with mortality. Additionally, age-adjusted Cox regression analysis revealed a higher mortality rate in patients with an eGFR under 60 mL/min/1.73m2.\n\nConclusionsOn admission eGFR seems to be a prognostic marker for mortality in patients with COVID-19; We recommend to determine eGFR in all patients on admission and use it as an additional tool for risk stratification. Close follow-up should be warranted in patients with reduced eGFR.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sinan Trabulus", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Cebrail Karaca", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Ilker Inanc Balkan", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Mevlut Tamer Dincer", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Ahmet Murt", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Seyda Gul Ozcan", + "author_inst": "Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Ridvan Karaali", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Bilgul Mete", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Alev Bakir", + "author_inst": "Halic University, Department of Biostatistics and Medical Informatics" + }, + { + "author_name": "Mert Ahmet Kuskucu", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Mehmet Riza Altiparmak", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Fehmi Tabak", + "author_inst": "Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty" + }, + { + "author_name": "Nurhan Seyahi", + "author_inst": "Istanbul University- Cerrahpasa, Cerrahpasa Medical Faculty" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2020.06.18.20134718", "rel_title": "A Combined Deep CNN-LSTM Network for the Detection of Novel Coronavirus (COVID-19) Using X-ray Images", @@ -1339313,33 +1335828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.06.19.20135251", - "rel_title": "Distress among Brazilian university students due to the Covid-19 pandemic: survey results and reflections", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135251", - "rel_abs": "The first case of infection with the new coronavirus was identified in December 2019 in Wuhan, China. In March, the World Health Organization (WHO) defined the disease epidemic as a pandemic. Thus, a quarantine was imposed by many governments. As a consequence, and given that epidemiological outbreaks of infectious diseases, such as Covid-19, are associated with psychological disorders and symptoms of mental illness, researchers at the Shanghai Mental Health Center have created the Covid-19 Peritraumatic Distress Index (CPDI), in which the results are obtained: normal, mild/moderate distress and severe distress. The main objective of the study was based on the application of CPDI, in order to identify the health and well-being of Brazilian students from different undergraduate courses at the Pontifical Catholic University of Sao Paulo (PUC/SP) during the Covid-19 pandemic and to test the hypothesis that medical students suffer more than students from other courses. The research is based on a cross-sectional observational study, in which we applied, using Google FormsR, the questions contained in CPDI, among with demographic data: age, sex, educational institution, undergraduate course and school year. The Index was applied online for seven days in which a total of 654 valid responses were obtained: 501 (76.6%) female and 149 (22.8%) male. Regarding age, 333 students (50.91%) were 17-20 years old, 279 (42.66%) between 21-25, 30 (4.59%) between 26-30 and 12 (1.84%) between 31-50. The results indicate that the participants reported significant psychological distress, according to the CPDI score. Practically 90% (87.92%) of the students experienced suffering, while only 12.08% did not suffer. The study provides the first empirical evidence on the level of psychological distress in Brazilian university students during the Covid-19 pandemic. Also, it suggests support and monitoring of university students during and after the pandemic, with effective and efficient intervention in their mental health.\n\nSummary boxesO_ST_ABSSECTION 1C_ST_ABSResearchers at the Shanghai Mental Health Center have created the Covid-19 Peritraumatic Distress Index (CPDI), to measure the amount of psychological suffering of the population, due to the pandemic of Coronavirus. Before our research, the survey had been applicated in China and Iran. The main objective of the study was to identify with the survey, the health and well-being of Brazilian students from different undergraduate courses at the Pontifical Catholic University of Sao Paulo (PUC/SP) during the Covid-19 pandemic and to test the hypothesis that medical students suffer more than students from other courses.\n\nSECTION 2The study provides the first empirical evidence on the level of psychological distress in Brazilian university students during the Covid-19 pandemic, practically 90% (87.92%) of the students experienced some suffering.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Carlos von Krakauer Hubner Sr.", - "author_inst": "Pontifical Catholic University of Sao Paulo" - }, - { - "author_name": "Marcella Lima Bruscatto", - "author_inst": "Pontifical Catholic University of Sao Paulo" - }, - { - "author_name": "Rafaella Dourado Lima", - "author_inst": "Pontifical Catholic University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.17.20133595", "rel_title": "Clozapine treatment and risk of COVID-19.", @@ -1340468,6 +1336956,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20132407", + "rel_title": "Comparative efficacy and safety of pharmacological interventions for the treatment of COVID-19: A systematic review and network meta-analysis of confounder-adjusted 20212 hospitalized patients", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20132407", + "rel_abs": "ObjectiveTo evaluate the comparative efficacy and safety of pharmacological interventions used in treating COVID-19 and form a basis for an evidence-based guideline of COVID-19 management by evaluating the level of evidence behind each treatment regimen in different clinical settings.\n\nDesignSystematic review and network meta-analysis\n\nData SourcesPubMed, Google Scholar, MEDLINE, the Cochrane Library, medRxiv, SSRN, WHO International Clinical Trials Registry Platform, and ClinicalTrials.gov up to June 9th, 2020.\n\nStudy SelectionPublished and unpublished randomized controlled trials (RCTs) and baseline-adjusted observational studies which met our predefined eligibility criteria.\n\nMain Outcome MeasuresThe outcomes of interest were mortality, progression to severe disease (severe pneumonia or admission to intensive care unit (ICU)), time to viral clearance, QT prolongation, fatal cardiac complications, and non-cardiac serious adverse events. The level of evidence behind each outcome was also measured using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) framework.\n\nResults49 studies with a total of 20212 confounder-adjusted patients were included for analysis. The risk of progression to severe pneumonia or ICU admission was significantly reduced with tocilizumab (GRADE low), anakinra (GRADE very low), and remdesivir (GRADE high) compared to standard care. Tocilizumab was shown to reduce mortality rate for both moderate-severe patients in the non-ICU setting at admission (Odds ratio (OR) 0.31, 95% confidence interval (CI) 0.18 to 0.54, GRADE low) and critically ill patients in the ICU setting (OR 0.67, 95% CI 0.50 to 0.91, GRADE low). High dose IVIG reduced death rate (GRADE low) while corticosteroids increased mortality for critically ill patients (GRADE moderate). Convalescent plasma and hydroxychloroquine were shown to promote viral clearance (OR 11.39, 95% CI 3.91 to 33.18, GRADE low and OR 6.08, 95% CI 2.74 to 13.48, GRADE moderate, respectively) while not altering mortality or progression to the severe courses. The combination of hydroxychloroquine and azithromycin was shown to be associated with increased QT prolongation incidence (OR 1,85, 95% CI 1.05 to 3.26, GRADE low) and fatal cardiac complications in cardiac-impaired populations (OR 2.26, 95% CI 1.26 to 4.05, GRADE low). High-dose (>600mg/day) hydroxychloroquine monotherapy was significantly associated with increased non-cardiac serious adverse events (GRADE moderate).\n\nConclusionAnti-inflammatory agents (tocilizumab, anakinra, and IVIG) and remdesivir may safely and effectively improve outcomes of hospitalized COVID-19 patients. Widely used hydroxychloroquine provides marginal clinical benefit in improving viral clearance rates whilst posing both cardiac and non-cardiac safety risks, especially in the vulnerable population. Only 20% of current evidence on pharmacological management of COVID-19 is on moderate and high evidence certainty and can be considered in practice and policy; remaining 80% are of low or very low certainty and warrant further studies to establish firm conclusions.\n\nSystematic Review RegistrationPROSPERO 2020: CRD42020186527.\n\nSummary BoxO_ST_ABSSection 1: What is already known on this topicC_ST_ABS- Numerous clinical trials and observational studies have investigated various pharmacological agents as potential treatment for COVID-19.\n- Results from numerous studies are heterogeneous and sometimes even contradictory to one another, making it difficult for clinicians to determine which treatments are truly effective.\n- Level of evidence behind each outcome from diverse studies remains unknown.\n\n\nSection 2: What this study adds- Anti-inflammatory agents (tocilizumab, anakinra, and IVIG) and remdesivir may safely and effectively improve clinical outcomes of COVID-19.\n- Widely used hydroxychloroquine provides marginal clinical benefit in improving viral clearance rates whilst posing both cardiac and non-cardiac safety risks.\n- Only 20% of current evidence on pharmacological management of COVID-19 is on moderate/high evidence certainty and can be considered in practice and policy; remaining 80% are of low or very low certainty and warrant further studies to establish firm conclusions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Min Seo Kim", + "author_inst": "Korea Uinversity, College of Medicine" + }, + { + "author_name": "Min Ho An", + "author_inst": "Wando county health center and hospital" + }, + { + "author_name": "Won Jun Kim", + "author_inst": "Gangneung Prison Medical Department, Ministry of Justice, Republic of Korea" + }, + { + "author_name": "Tae-Ho Hwang", + "author_inst": "Department of pharmacology, Pusan National University, School of Medicine, Yangsan, Republic of Korea" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.17.20133793", "rel_title": "Development of a SARS-CoV-2 total antibody assay and the dynamics of antibody response over time in hospitalized and non-hospitalized patients with COVID-19", @@ -1341803,57 +1338322,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.17.20124396", - "rel_title": "A new system in qualitative RT-PCR detecting SARS-CoV-2 in biological samples: an Italian experience.", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20124396", - "rel_abs": "In the last moths the world was faced with the pandemic of a new severe acute respiratory syndrome coronavirus (SARS-CoV) and the majority of the Nations have yet to come out of it. Numerous assays have emerged to meet SARS-CoV-2 diagnostic needs. A clear knowledge of these assays parameters is essential to choose the proper test by clinical microbiologists. Unfortunately, the latter cannot be the unique criterion that guides test selection as - given the great demand - shortcomings of commercial kits is also a great issue. Aimed by the intention of overcoming both difficulties we have developed a new qualitative RT-PCR probe based for COVID-19 detection. The system detects three genes of SARS-CoV-2: RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N) and {beta}-actin gene used as endogenous internal control. The results of our assay show a total agreement with those obtained using a commercially available kit, with the exception of two specimens which did not pass the endogenous internal control. Moreover, our kit was designed to be open either for nucleic acid extraction step or on the RT-PCR assay to be carried out on several instruments. Thus, it is free from the industrial production logics of closed systems and conversely it is hypothetically available for distribution on large numbers in any microbiological laboratories. Presently, the kit is currently distributed worldwide", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Marco Favaro", - "author_inst": "University of Rome Tor Vergata" - }, - { - "author_name": "Walter Mattina", - "author_inst": "LifeGeneMap. Messina, Italy" - }, - { - "author_name": "Enrico Salvatore Pistoia", - "author_inst": "University of Rome Tor Vergata" - }, - { - "author_name": "Roberta Gaziano", - "author_inst": "University of Rome Tor Vergata" - }, - { - "author_name": "Paolo Di Francesco", - "author_inst": "University of Rome Tor Vergata" - }, - { - "author_name": "Simon Middleton", - "author_inst": "Adaltis R&D s.r.l. Via Luigi Einaudi 7, 00012, Guidonia Montecelio, Italy" - }, - { - "author_name": "Silvia D'Angelo", - "author_inst": "Adaltis R&D s.r.l. Via Luigi Einaudi 7, 00012, Guidonia Montecelio, Italy" - }, - { - "author_name": "Tullio Altarozzi", - "author_inst": "Adaltis R&D s.r.l. Via Luigi Einaudi 7, 00012, Guidonia Montecelio, Italy" - }, - { - "author_name": "Carla Fontana", - "author_inst": "Tor Vergata University of Rome" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.17.158105", "rel_title": "Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs", @@ -1342386,6 +1338854,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2020.06.16.20131243", + "rel_title": "SARS-CoV-2 qRT-PCR Ct value distribution in Japan and possible utility of rapid antigen testing kit", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20131243", + "rel_abs": "The exact pathology of COVID-19 remains mostly unclear, and accurate epidemiological understanding and rapid testing are crucial to overcome this disease. Several types of nucleic acid tests (NAT) have been used in Japan, but information about the viral RNA load, determined by Ct values, of the patients is limited due to the small number of patients tested in each clinical institution and lack of standardization of the testing kits. We have been performing the qRT-PCR tests established by NIID, and the mean Ct value distribution of 62 cases, which are deemed \"first-visit\" patients, among the total of 88 positive cases tested in a 4-day window of early April, was 24.9 with SD=5.45. Recently approved antigen testing kits were also used in the same samples (62 positives) along with 100 negative cases, and it revealed the positive predictive value of 80.6% and negative predictive value of 100%, with an overall agreement rate of 92.6%. These results indicate that a certain number of patients with lower Ct values, existed in Japan when SARS-CoV-2 virus started to spread. The newly approved rapid antigen testing kit will be a useful tool to identify such populations rapidly.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kazuya Omi", + "author_inst": "SRL inc." + }, + { + "author_name": "Yuta Takeda", + "author_inst": "SRL inc." + }, + { + "author_name": "Masatoshi Mori", + "author_inst": "SRL inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.16.20132001", "rel_title": "Progression / remission of Coronavirus disease 2019: Data driven recommendations for repeating SARS-CoV-2 nucleic acid amplification tests.", @@ -1343201,53 +1339696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20132902", - "rel_title": "Distinct genetic spectrums and evolution patterns of SARS-CoV-2", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132902", - "rel_abs": "Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains. Some SNVs predominated but were mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguishable evolution patterns over time. A few hundred patients were detected with multiple viral strain-representing mutations simultaneously, which may stand for possible co-infection or potential homogenous recombination of SARS-CoV-2 in environment or within the viral host. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tended to switch between bat RaTG13 coronavirus sequence and Wuhan-Hu-1 genome, indicating the higher genetic instability or tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sheng Liu", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "JIKUI SHEN", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Shuyi Fang", - "author_inst": "Indiana University Purdue University at Indianapolis" - }, - { - "author_name": "Kailing Li", - "author_inst": "Indiana University Purdue University at Indianapolis" - }, - { - "author_name": "Juli Liu", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Lei Yang", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Chang-Deng Hu", - "author_inst": "Purdue University" - }, - { - "author_name": "Jun Wan", - "author_inst": "Indiana University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.17.20106302", "rel_title": "Standardized Testing Demonstrates Altered Odor Detection Sensitivity and Hedonics in Asymptomatic College Students as SARS-CoV-2 Emerged Locally", @@ -1343788,6 +1340236,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.17.20133702", + "rel_title": "Statistical Issues and Lessons Learned from COVID-19 Clinical Trials with Lopinavir-Ritonavir and Remdesivir", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133702", + "rel_abs": "BackgroundSince the outbreak of the novel coronavirus disease 2019 (COVID-19) in December 2019, it has rapidly spread in more than 200 countries or territories with over 8 million confirmed cases and 440,000 deaths by June 17, 2020. Recently, three randomized clinical trials on COVID-19 treatments were completed, one for lopinavir-ritonavir and two for remdesivir. One trial reported that remdesivir was superior to placebo in shortening the time to recovery, while the other two showed no benefit of the treatment under investigation. However, several statistical issues in the original design and analysis of the three trials are identified, which might shed doubts on their findings and the conclusions should be evaluated with cautions.\n\nObjectiveFrom statistical perspectives, we identify several issues in the design and analysis of three COVID-19 trials and reanalyze the data from the cumulative incidence curves in the three trials using more appropriate statistical methods.\n\nMethodsThe lopinavir-ritonavir trial enrolled 39 additional patients due to insignificant results after the sample size reached the planned number, which led to inflation of the type I error rate. The remdesivir trial of Wang et al. failed to reach the planned sample size due to a lack of eligible patients, while the bootstrap method was used to predict the quantity of clinical interest conditionally and unconditionally if the trial had continued to reach the originally planned sample size. Moreover, we used a terminal (or cure) rate model and a model-free metric known as the restricted mean survival time or the restricted mean time to improvement (RMTI) in this context to analyze the reconstructed data due to the existence of death as competing risk and a terminal event. The remdesivir trial of Beigel et al. reported the median recovery time of the remdesivir and placebo groups and the rate ratio for recovery, while both quantities depend on a particular time point representing local information. We reanalyzed the data to report other percentiles of the time to recovery and adopted the bootstrap method and permutation test to construct the confidence intervals as well as the P values. The restricted mean time to recovery (RMTR) was also computed as a global and robust measure for efficacy.\n\nResultsFor the lopinavir-ritonavir trial, with the increase of sample size from 160 to 199, the type I error rate was inflated from 0.05 to 0.071. The difference of terminal rates was -8.74% (95% CI [-21.04, 3.55]; P=.16) and the hazards ratio (HR) adjusted for terminal rates was 1.05 (95% CI [0.78, 1.42]; P=.74), indicating no significant difference. The difference of RMTIs between the two groups evaluated at day 28 was -1.67 days (95% CI [-3.62, 0.28]; P=.09) in favor of lopinavir-ritonavir but not statistically significant. For the remdesivir trial of Wang et al., the difference of terminal rates was -0.89% (95% CI [-2.84, 1.06]; P=.19) and the HR adjusted for terminal rates was 0.92 (95% CI [0.63, 1.35]; P=.67). The difference of RMTIs at day 28 was -0.89 day (95% CI [-2.84, 1.06]; P=.37). The planned sample size was 453, yet only 236 patients were enrolled. The conditional prediction shows that the HR estimates would reach statistical significance if the target sample size had been maintained, and both conditional and unconditional prediction delivered significant HR results if the trial had continued to double the target sample size. For the remdesivir trial of Beigel et al., the difference of RMTRs between the remdesivir and placebo groups up to day 30 was -2.7 days (95% CI [-4.0, -1.2]; P<.001), confirming the superiority of remdesivir. The difference in recovery time at the 25th percentile (95% CI [-3, 0]; P=.65) was insignificant, while the differences manifested to be statistically significant at larger percentiles.\n\nConclusionsBased on the statistical issues and lessons learned from the recent three clinical trials on COVID-19 treatments, we suggest more appropriate approaches for the design and analysis for ongoing and future COVID-19 trials.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Guosheng Yin", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Chenyang Zhang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Huaqing Jin", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.17.20134015", "rel_title": "Analysis of Genetic Host Response Risk Factors in Severe COVID-19 Patients", @@ -1344751,133 +1341226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20133025", - "rel_title": "Detection of antibodies to the SARS-CoV-2 spike glycoprotein in both serum and saliva enhances detection of infection", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133025", - "rel_abs": "BackgroundDetecting antibody responses during and after SARS-CoV-2 infection is essential in determining the seroepidemiology of the virus and the potential role of antibody in disease. Scalable, sensitive and specific serological assays are essential to this process. The detection of antibody in hospitalized patients with severe disease has proven straightforward; detecting responses in subjects with mild disease and asymptomatic infections has proven less reliable. We hypothesized that the suboptimal sensitivity of antibody assays and the compartmentalization of the antibody response may contribute to this effect.\n\nMethodsWe systemically developed an ELISA assay, optimising different antigens and amplification steps, in serum and saliva from symptomatic and asymptomatic SARS-CoV-2-infected subjects.\n\nResultsUsing trimeric spike glycoprotein, rather than nucleocapsid enabled detection of responses in individuals with low antibody responses. IgG1 and IgG3 predominate to both antigens, but more anti-spike IgG1 than IgG3 was detectable. All antigens were effective for detecting responses in hospitalized patients. Anti-spike, but not nucleocapsid, IgG, IgA and IgM antibody responses were readily detectable in saliva from non-hospitalized symptomatic and asymptomatic individuals. Antibody responses in saliva and serum were largely independent of each other and symptom reporting.\n\nConclusionsDetecting antibody responses in both saliva and serum is optimal for determining virus exposure and understanding immune responses after SARS-CoV-2 infection.\n\nFundingThis work was funded by the University of Birmingham, the National Institute for Health Research (UK), the NIH National Institute for Allergy and Infectious Diseases, the Bill and Melinda Gates Foundation and the University of Southampton.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Sian E Faustini", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Sian E. Jossi", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Marisol Perez-Toledo", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Adrian Shields", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Joel D. Allen", - "author_inst": "University of Southampton" - }, - { - "author_name": "Yasunori Watanabe", - "author_inst": "University of Southampton" - }, - { - "author_name": "Maddy L. Newby", - "author_inst": "University of Southampton" - }, - { - "author_name": "Alex Cook", - "author_inst": "Binding Site group Ltd" - }, - { - "author_name": "Carrie R. Willcox", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Mahboob Salim", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Margaret Goodall", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Jennifer L. Heaney", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Edith Marcial-Juarez", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Gabriella L. Morley", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Barbara Torlinska", - "author_inst": "University of Birmingham" - }, - { - "author_name": "David C. Wraith", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Tonny Veenith", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Stephen Harding", - "author_inst": "Binding Site group Ltd." - }, - { - "author_name": "Stephen Jolles", - "author_inst": "Immunodeficiency Centre for Wales" - }, - { - "author_name": "Ponsford J Mark", - "author_inst": "Mr" - }, - { - "author_name": "Tim Plant", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Aarnoud Huissoon", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Matthew K. O'Shea", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Benjamin E. Willcox", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Mark T. Drayson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Max Crispin", - "author_inst": "University of Southampton" - }, - { - "author_name": "Adam F. Cunningham", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Alex G. Richter", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20133157", "rel_title": "Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.", @@ -1345602,6 +1341950,97 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.06.17.156471", + "rel_title": "The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins", + "rel_date": "2020-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.156471", + "rel_abs": "SARS-CoV-2 emerged in late 2019, leading to the COVID-19 pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus we demonstrate that, in addition to human ACE2, the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the twenty-two different hosts we investigated, ACE2 proteins from dog, cat and rabbit were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the three genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Interestingly, while SARS-CoV-2 pseudoparticle entry was inefficient in cells bearing the ACE2 receptor from bats or birds the live virus was still able to enter these cells, albeit with markedly lower efficiency. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock and wildlife.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Carina Conceicao", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Nazia Thakur", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Stacey Human", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "James T Kelly", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Leanne Logan", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Dagmara Bialy", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Sushant Bhat", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Phoebe Stevenson-Leggett", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Adrian Zagrajek", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Philippa Hollinghurst", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Michal Varga", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Christina Tsirigoti", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "John Hammond", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Helena J Maier", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Erica Bickerton", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Holly J Shelton", + "author_inst": "The Pirbright institute" + }, + { + "author_name": "Isabelle Dietrich", + "author_inst": "The Pirbright Institute" + }, + { + "author_name": "Stephen C Graham", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Dalan Bailey", + "author_inst": "The Pirbright Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.18.158584", "rel_title": "Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein", @@ -1346653,61 +1343092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.15.20131482", - "rel_title": "The effect of serological screening for SARS-CoV-2 antibodies to participants' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131482", - "rel_abs": "Rapid serological tests for SARS-CoV-2 antibodies have been questioned by scientists and the public because of unexplored effects of negative test results on behaviour and attitudes, that could lower the level of adherence to protective measures. Therefore, our study aimed to investigate the changes in personal attitudes and behaviour before and after negative serological test results for SARS-CoV-2 antibodies. We conducted a survey questionnaire on 200 industry workers (69% males and 31% females) that have been previously tested negative. The survey examined participants self-reported general attitudes towards COVID-19, sense of fear, as well as their behaviour related to protective measures before and after the testing. The participants perceived the disease as a severe health threat and acknowledged the protective measures as appropriate. They reported a high level of adherence to measures and low level of fear both before and after the testing. Although those indicators were statistically significantly reduced after the test (P < 0.004), they did not result in risk behaviour. Therefore, the serological tests are not an additional threat regarding the risk behaviour in an environment where protective measures are efficient. In contrast, they might contribute to reducing the fear in the society and working environment.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Toni Ljubic", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Ana Banovac", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Ivan Buljan", - "author_inst": "Department of Research in Biomedicine and Health, University of Split, School of Medicine, Split, Croatia" - }, - { - "author_name": "Ivan Jerkovic", - "author_inst": "University Department of Forensic Sciences" - }, - { - "author_name": "Zeljana Basic", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Ivana Kruzic", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Andrea Kolic", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Rino Rivi Kolombatovic", - "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" - }, - { - "author_name": "Ana Marusic", - "author_inst": "Department of Research in Biomedicine and Health, University of Split, School of Medicine, Split, Croatia" - }, - { - "author_name": "Simun Andjelinovic", - "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Split; University of Split, School of Medicine, Split, Croatia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.15.20131516", "rel_title": "National Early Warning Scores (NEWS / NEWS2) and COVID-19 deaths in care homes: a longitudinal ecological study", @@ -1347416,6 +1343800,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20131706", + "rel_title": "Deregulated cellular circuits driving immunoglobulins and complement consumption associate with the severity of COVID-19", + "rel_date": "2020-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131706", + "rel_abs": "BackgroundSARS-CoV-2 infection causes an abrupt response by the host immune system, which is largely responsible for the pathogenesis and outcome of COVID-19. We aimed to investigate which specific responses from either cellular or humoral immunity associate to severity and progression of COVID-19.\n\nMethodsA cohort of 276 patients classified in mild, moderate and severe, was studied. Peripheral blood lymphocyte subpopulations were quantified by flow cytometry, and immunoglobulins and complement proteins by nephelometry.\n\nResultsAt admission, dramatic lymphopenia of T, B and NK cells associated to severity. However, only the proportion of B cells increased, while T and NK cells appeared unaffected. Accordingly, the number of plasma cells and circulating follicular helper T cells (cTfh) increased, but levels of IgM, IgA and IgG were unaffected. When degrees of severity were considered, IgG was lower in severe patients, suggesting an IgG consumption by complement activation or antibody-dependent cellular cytotoxicity (ADCC). Activated CD56-CD16+ NK-cells, which mediate ADCC, were increased. Regarding complement, C3 and C4 protein levels were higher in mild and moderate, but not in severe patients, compared to healthy donors. Moreover, IgG and C4 decreased from day 0 to day 10 in patients who were hospitalized for more than two weeks, but not in patients who were discharged earlier.\n\nConclusionOur study provides important clues to understand the immune response observed in COVID-19 patients, which is probably related to viral clearance, but also underlies its pathogenesis and severity. This study associates for the first time COVID-19 severity with an imbalanced humoral immune response characterized by excessive consumption of IgG and C4, identifying new targets for therapeutic intervention.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Ana Marcos-Jimenez", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Santiago Sanchez-Alonso", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Ana Alcaraz-Serna", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Laura Esparcia", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Celia Lopez-Sanz", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Miguel Sampedro-Nunez", + "author_inst": "University Hospital La Princesa; School of Medicine, Department of Medicine, Universidad Autonoma of Madrid, Madrid, Spain" + }, + { + "author_name": "Tamara Mateu-Albero", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Ildefonso Sanchez-Cerrillo", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Pedro Martinez-Fleta", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Ligia Gabrie", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Luciana Del Campo", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Margarita Lopez-Trascasa", + "author_inst": "School of Medicine, Department of Medicine, Universidad Autonoma of Madrid, Madrid, Spain" + }, + { + "author_name": "Enrique Martin-Gayo", + "author_inst": "Universidad Autonoma de Madrid" + }, + { + "author_name": "Maria Calzada", + "author_inst": "University Hospital La Princesa; School of Medicine, Department of Medicine, Universidad Autonoma of Madrid, Madrid, Spain" + }, + { + "author_name": "Santos Castaneda", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Hortensia de la Fuente", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Isidoro Gonzalez-Alvaro", + "author_inst": "University Hospital La Princesa" + }, + { + "author_name": "Francisco Sanchez-Madrid", + "author_inst": "University Hospital La Princesa; School of Medicine, Department of Medicine, Universidad Autonoma of Madrid, Madrid, Spain" + }, + { + "author_name": "Cecilia Munoz-Calleja", + "author_inst": "University Hospital La Princesa; School of Medicine, Department of Medicine, Universidad Autonoma of Madrid, Madrid, Spain" + }, + { + "author_name": "Arantzazu Alfranca", + "author_inst": "University Hospital La Princesa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.16.20132464", "rel_title": "Human food consumption patterns concerning COVID-19 pandemic", @@ -1348311,25 +1344790,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.17.155200", - "rel_title": "Pervasive RNA secondary structure in the genomes of SARS-CoV-2 and other coronaviruses - an endeavour to understand its biological purpose", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.155200", - "rel_abs": "The ultimate outcome of the COVID-19 pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility and population immunity. In the current study, SARS coronavirus 2 (SARS-CoV-2) was investigated for the presence of large scale internal RNA base pairing in its genome. This property, termed genome scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as HCV (MFED 7-9%). High MFED values were shared with all coronavirus genomes analysed created by several hundred consecutive energetically favoured stem-loops throughout the genome. In contrast to replication-association RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses - even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base-paired in SARS-CoV-2 showed substantially less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus which is potentially restrictive to its longer evolution. Although functionally uncharacterised, GORS in SARS-CoV-2 and other coronaviruses represent important elements in their cellular interactions that may contribute to their persistence and transmissibility.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter Simmonds", - "author_inst": "Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK." - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.17.156455", "rel_title": "Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV", @@ -1348914,6 +1345374,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.06.13.20130211", + "rel_title": "Risk and severity of COVID-19 and ABO blood group in transcatheter aortic valve patients", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130211", + "rel_abs": "BackgroundAlthough cardiovascular disease has been associated with an increased risk of coronavirus disease 2019 (COVID-19), no studies have reported its clinical course in patients with aortic stenosis who had undergone transcatheter aortic valve replacement (TAVR).\n\nSeveral observational studies have found an association between the A blood group and an increased susceptibility to SARS-CoV-2 infection, whereas the O blood group appears to be protective.\n\nObjectiveTo investigate the frequency and clinical course of COVID-19 in a large sample of patients who had undergone TAVR and to determine the associations of the ABO blood group with disease occurrence and outcomes.\n\nMethodsPatients who had undergone TAVR between 2010 and 2019 were included in this study and followed-up through the recent COVID-19 outbreak. The main outcomes were the occurrence and severity (hospitalization and/or death) of COVID-19 and their association with the ABO blood group.\n\nResultsOf the 1125 patients who had undergone TAVR, 403 (36%) died before January 1, 2020, and 20 (1.8%) were lost to follow-up. The study sample therefore consisted of 702 patients. Among them, we identified 22 cases (3.1%) with COVID-19. Fourteen patients (63.6%) were hospitalized or died of disease. Multivariate analysis identified the A blood group (versus others) as the only independent predictor of COVID-19 in patients who had undergone TAVR (odds ratio [OR] = 6.32; 95% confidence interval [CI] = 2.11-18.92; p=0.001). The A blood group (versus others; OR = 8.27; 95% CI = 1.83-37.43, p=0.006) and a history of cancer (OR = 4.99; 95% CI = 1.64-15.27, p = 0.005) were significantly and independently associated with disease severity (hospitalization and/or death).\n\nConclusionsPatients who had undergone TAVR are vulnerable to COVID-19. The subgroup with the A blood group was especially prone to develop the disease and showed unfavorable outcomes.\n\nCondensed abstractAmong 702 patients who had undergone TAVR between 2010 and 2019 and who were alive on January 1, 2020, 22 patients developed COVID-19. Fourteen patients (63.6%) were hospitalized or died of disease. The A blood group (versus others) was the only independent predictor of COVID-19. The A blood group and a history of cancer were significantly and independently associated with disease severity (hospitalization and/or death). Altogether these findings suggest that patients who had undergone TAVR are vulnerable to COVID-19. The subgroup with the A blood group was especially prone to develop the disease and showed unfavorable outcomes.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Marion Kibler", + "author_inst": "University Hospital Strasbourg" + }, + { + "author_name": "Adrien Carmona", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Benjamin Marchandot", + "author_inst": "University Hospital Of Strasbourg" + }, + { + "author_name": "Kensuke Matsushita", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Antonin Trimaille", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Mohamad Kanso", + "author_inst": "University Hospital Of Strasbourg" + }, + { + "author_name": "Laurent Dietrich", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Cecile How-Choong", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Albane Odier", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Gabrielle Gennesseaux", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Ophelie Schramm", + "author_inst": "ophelie.schramm@chru-strasbourg.fr" + }, + { + "author_name": "Anne Claire Reydel", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Michel Kindo", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Minh Hoang", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Sebastien Hess", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Chisato Sato", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Sophie Ohlmann", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Laurence Jesel", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Olivier Morel", + "author_inst": "University Hospital of Strasbourg" + }, + { + "author_name": "Patrick Ohlmann", + "author_inst": "University Hospital of Strasbourg" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129866", "rel_title": "Covid-19 rapid test by combining a random forest based web system and blood tests", @@ -1349713,25 +1346268,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.06.13.20130468", - "rel_title": "Random time transformation analysis of Covid19 2020", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130468", - "rel_abs": "The SIR epidemiological equations model new affected and removed cases as roughly proportional to the current number of infected cases. The present report adopts an alternative that has been considered in the literature, in which the number of new affected cases is proportional to the [≤] 1 power of the number of infected cases. After arguing that = 1 models exponential growth while < 1 models polynomial growth, a simple method for parameter estimation in differential equations subject to noise, the random-time transformation RTT of Bassan, Meilijson, Marcus and Talpaz 1997, will be reviewed and compared with stochastic differential equations. Both methods are applied in an attempt to uncover the growth pattern of Covid19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Isaac Meilijson", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.14.20130518", "rel_title": "An Extended Laboratory Validation Study and Comparative Performance Evaluation of the Abbott ID NOW COVID-19 Assay in a Coastal California Tertiary Care Medical Center", @@ -1350180,6 +1346716,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.13.20130658", + "rel_title": "Global and local mobility as a barometer for COVID-19 dynamics", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130658", + "rel_abs": "The spreading of infectious diseases including COVID-19 depends on human interactions. In an environment where behavioral patterns and physical contacts are constantly evolving according to new governmental regulations, measuring these interactions is a major challenge. Mobility has emerged as an indicator for human activity and, implicitly, for human interactions. Here we study the coupling between mobility and COVID-19 dynamics and show that variations in global air traffic and local driving mobility can be used to stratify different disease phases. For ten European countries, our study shows maximal correlation between driving mobility and disease dynamics with a time lag of 14.6 {+/-} 5.6 days. Our findings suggests that local mobility can serve as a quantitative metric to forecast future reproduction numbers and identify the stages of the pandemic when mobility and reproduction become decorrelated.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kevin Linka", + "author_inst": "Stanford University" + }, + { + "author_name": "Alain Goriely", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ellen Kuhl", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.13.20130575", "rel_title": "Seroprevalence against COVID-19 and follow-up of suspected cases in primary health care in Spain", @@ -1351091,45 +1347654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.14.20131102", - "rel_title": "Detecting space-time clusters of COVID-19 in Brazil: mortality, inequality, socioeconomic vulnerability, and the relative risk of the disease in Brazilian municipalities", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20131102", - "rel_abs": "The first case of COVID-19 in South America occurred in Brazil on February 25th, 2020. By June 7th, 2020, there were 691,758 confirmed cases, 36,455 confirmed deaths, and a mortality rate of 5.3%. To assist with the establishment of measures for the strategic planning to combat the COVID-19 pandemic in Brazil, we present the first Brazilian geographic study with the aims to examine \"active\" hand \"emerging\" space-time clusters of COVID-19. We examine the associations between clusters and mortality rate, vulnerability, and social inequality. We used the prospective space-time scan statistic to detect daily COVID-19 clusters and examine the relative risk from February 25th - June 7th, 2020 in 5,570 Brazilian municipalities. We apply a Spearmans statistic to measure correlation between the relative risk of each cluster and mortality rate, GINI index, and social inequality. We detected 11 emerging space-time clusters of COVID-19 occurring in all Brazilian regions, with seven of them with a relative risk greater than one, and the highest in the Amapa state in the northern region of Brazil. We observed a positive and significant correlation between the relative risk and mortality rate, Brazilian Social Vulnerability Index, and GINI Index. The results can be utilized to improve COVID-19 response and planning in all Brazilian states.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marcos Roberto Martines", - "author_inst": "Federal University of Sao Carlos" - }, - { - "author_name": "Ricardo Vicente Ferreira", - "author_inst": "Federal University of Triangulo Mineiro" - }, - { - "author_name": "Rogerio H Toppa", - "author_inst": "Federal University of Sao Carlos" - }, - { - "author_name": "Luiza Assuncao", - "author_inst": "State University of Minas Gerais" - }, - { - "author_name": "Michael Richard Desjardins", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Eric M Delmelle", - "author_inst": "University of North Carolina at Charlotte" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.15.20131136", "rel_title": "Modelling the Occurrence of the Novel Pandemic COVID-19 Outbreak; A Box and Jenkins Approach", @@ -1351826,6 +1348350,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.06.14.20131128", + "rel_title": "Innate immune signaling in the olfactory epithelium reduces odorant receptor levels: modeling transient smell loss in COVID-19 patients", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20131128", + "rel_abs": "Post-infectious anosmias typically follow death of olfactory sensory neurons (OSNs) with a months-long recovery phase associated with parosmias. While profound anosmia is the leading symptom associated with COVID-19 infection, many patients regain olfactory function within days to weeks without distortions. Here, we demonstrate that sterile induction of anti-viral type I interferon signaling in the mouse olfactory epithelium is associated with diminished odor discrimination and reduced odor-evoked local field potentials. RNA levels of all class I, class II, and TAAR odorant receptors are markedly reduced in OSNs in a non-cell autonomous manner. We find that people infected with COVID-19 rate odors with lower intensities and have odor discrimination deficits relative to people that tested negative for COVID-19. Taken together, we propose that inflammatory-mediated loss of odorant receptor expression with preserved circuit integrity accounts for the profound anosmia and rapid recovery of olfactory function without parosmias caused by COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Steve Rodriguez", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Luxiang Cao", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Gregory T. Rickenbacher", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric G. Benz", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Colin Magdamo", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Liliana A Ramirez Gomez", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric Holbrook", + "author_inst": "Mass Eye and Ear" + }, + { + "author_name": "Alefiya Dhilla Albers", + "author_inst": "Endicott College / Massachusetts General Hospital" + }, + { + "author_name": "Rose Gallagher", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "M. Brandon Westover", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kyle E. Evans", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Daniel Tatar", + "author_inst": "The ADK Group" + }, + { + "author_name": "Shibani Mukerji", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Ross Zafonte", + "author_inst": "Spaulding Rehabilitation Hospital" + }, + { + "author_name": "Edward W. Boyer", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "C. Ron Yu", + "author_inst": "Stowers Institute of Medical Research" + }, + { + "author_name": "Mark W Albers", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.06.15.151761", "rel_title": "Cumulative effect of aging and SARS-CoV2 infection on poor prognosis in the elderly: Insights from transcriptomic analysis of lung and blood", @@ -1352801,49 +1349408,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.16.154708", - "rel_title": "Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154708", - "rel_abs": "The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike-ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure binding of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3,384 small molecule drugs and pre-clinical compounds was performed, yielding 25 high-quality, small-molecule hits that can be evaluated in cell-based models. This established AlphaLISA RBD-ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral-host interaction to further the development of interventions to address the global health pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Quinlin M Hanson", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Kelli M Wilson", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Min Shen", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Zina Itkin", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Rich T Eastman", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Paul Shinn", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - }, - { - "author_name": "Matthew D Hall", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.16.154591", "rel_title": "Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity", @@ -1353556,6 +1350120,157 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.14.150607", + "rel_title": "Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis", + "rel_date": "2020-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.14.150607", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and there is a critical need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells, two different cell lines selected for increased expression of secreted glycoproteins. We show that ExpiCHO-S cells produce enhanced yields of both SARS-CoV-2 S proteins. Biochemical, biophysical, and structural (cryo-EM) characterization of the SARS-CoV-2 S proteins produced in both cell lines demonstrate that the reported purification strategy yields high quality S protein (non-aggregated, uniform material with appropriate biochemical and biophysical properties). Importantly, we show that multiple preparations of these two recombinant S proteins from either cell line exhibit identical behavior in two different serology assays. We also evaluate the specificity of S protein-mediated host cell binding by examining interactions with proposed binding partners in the human secretome. In addition, the antigenicity of these proteins is demonstrated by standard ELISAs, and in a flexible protein microarray format. Collectively, we establish an array of metrics for ensuring the production of high-quality S protein to support clinical, biological, biochemical, structural and mechanistic studies to combat the global pandemic caused by SARS-CoV-2.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Natalia G Herrera", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Nicholas C Morano", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Alev Celikgil", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "George I Georgiev", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Ryan J Malonis", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "James H Lee", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Karen Tong", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Olivia Vergnolle", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Aldo B Massimi", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Laura Y Yen", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Alex J Noble", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Mykhailo Kopylov", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Jeffrey B Bonanno", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Sarah C Garrett-Thomson", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "David B Hayes", + "author_inst": "Intl Solidarity of Scientists LLC" + }, + { + "author_name": "Robert H Bortz", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Ariel S Wirchniaski", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Catalina Florez", + "author_inst": "United States Military Academy at West Point" + }, + { + "author_name": "Ethan Laudermilch", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Denise Haslwanter", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "J Maximilian Fels", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "M Eugenia Dieterle", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Rohit K Jangra", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Jason Barnhill", + "author_inst": "United States Military Academy at West Point" + }, + { + "author_name": "Amanda Mengotto", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Duncan Kimmel", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Johanna P Daily", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Liise-anne Pirofski", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Kartik Chandran", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Michael Brenowitz", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Scott J Garforth", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Edward T Eng", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Jonathan R Lai", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Steven C Almo", + "author_inst": "Albert Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.15.150912", "rel_title": "The SARSCoV2 spike protein alters barrier function in 2D static and 3D microfluidic in vitro models of the human blood-brain barrier", @@ -1354439,81 +1351154,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.06.12.20129247", - "rel_title": "Multiplex Isothermal Amplification Coupled with Nanopore Sequencing for Rapid Detection and Mutation Surveillance of SARS-CoV-2", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129247", - "rel_abs": "Molecular testing and surveillance of the spread and mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical public health measures to combat the pandemic. There is an urgent need for methods that can rapidly detect and sequence SARS-CoV-2 simultaneously. Here we describe a method for multiplex isothermal amplification of the SARS-CoV-2 genome in 20 minutes. Based on this, we developed NIRVANA (Nanopore sequencing of Isothermal Rapid Viral Amplification for Near real-time Analysis) to detect viral sequences and monitor mutations in multiple regions of SARS-CoV-2 genome for up to 96 patients at a time. NIRVANA uses a newly developed algorithm for on-the-fly data analysis during Nanopore sequencing. The whole workflow can be completed in as short as 3.5 hours, and all reactions can be done in a simple heating block. NIRVANA provides a rapid field-deployable solution of SARS-CoV-2 detection and surveillance of pandemic strains.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Chongwei Bi", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Gerardo Ramos-Mandujano", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Sharif Hala", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Jinna Xu", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Sara Mfarrej", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Yeteng Tian", - "author_inst": "King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Concepcion Rodriguez Esteban", - "author_inst": "The Salk Institute for Biological Studies" - }, - { - "author_name": "Estrella Nunez Delicado", - "author_inst": "Universidad Catolica San Antonio de Murcia" - }, - { - "author_name": "Fadwa S Alofi", - "author_inst": "Infectious Diseases Department, King Fahad Hospital, Madinah, Saudi Arabia" - }, - { - "author_name": "Asim Khogeer", - "author_inst": "Plan and Research Department, General Directorate of Health Affairs Makkah Region, MOH, Saudi Arabia" - }, - { - "author_name": "Anwar M Hashem", - "author_inst": "Vaccines and Immunotherapy Unit, King Fahd Medical Research Center" - }, - { - "author_name": "Naif A.M. Almontashiri", - "author_inst": "College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia" - }, - { - "author_name": "Arnab Pain", - "author_inst": "Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)" - }, - { - "author_name": "Juan Carlos Izpisua Belmonte", - "author_inst": "The Salk Institute for Biological Studies" - }, - { - "author_name": "Mo Li", - "author_inst": "King Abdullah University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20129007", "rel_title": "COVID-19 Deaths: Which Explanatory Variables Matter the Most?", @@ -1355302,6 +1351942,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.12.20129460", + "rel_title": "Cross-reactivity of neutralizing antibody and its correlation with circulating T follicular cells in recovered COVID-19 individuals", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129460", + "rel_abs": "Seroconversion appeared early after COVID-19 onset, and convalescent sera therapy benefit some critical patients. However, neutralizing antibody (nAb) in convalescents is largely unknown. We found that 97.01% (65/67) of COVID-19 convalescents maintained IgG antibodies with high binding and avidity to SARS-CoV-2 spike subunits S1 and S2, and 95.52% (64/67) had neutralization activity against SARS-CoV-2 pesudovirus, one month after discharge (median ID50, 2.75; IQR, 2.34-3.08). Some sera exhibited cross-neutralization against SARS-CoV (76.12%), MERS-CoV (17.91%), or both (10.45%). Interestingly, individuals recovered from severe disease (severe group) had nAbs with binding and neutralization titers higher than non-severe group. Severe group appeared a rapid increase of lymphocytes and a high proportion of circulating CXCR3+ Tfh cells. Interestingly, the later were spike-specific and positively correlated with SARS-CoV-2 nAb titers. All subjects had no autoimmunity. Our findings provide novel insights into nAb responses in COVID-19 convalescents and facilitate treatment and vaccine development for SARS-CoV-2 infection.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jian Zhang", + "author_inst": "Translational Medicine Institute, The First Peoples Hospital of Chenzhou, University of South China" + }, + { + "author_name": "Xiaowang Qu", + "author_inst": "Translational Medicine Institute, The First Peoples Hospital of Chenzhou, University of South China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129619", "rel_title": "Healthcare Worker COVID-19 Cases in Ontario, Canada: A Cross-sectional Study", @@ -1355921,77 +1352584,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.12.148916", - "rel_title": "Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4+ T cells", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.148916", - "rel_abs": "The contribution of CD4+ T cells to protective or pathogenic immune responses to SARS-CoV-2 infection remains unknown. Here, we present large-scale single-cell transcriptomic analysis of viral antigen-reactive CD4+ T cells from 32 COVID-19 patients. In patients with severe disease compared to mild disease, we found increased proportions of cytotoxic follicular helper (TFH) cells and cytotoxic T helper cells (CD4-CTLs) responding to SARS-CoV-2, and reduced proportion of SARS-CoV-2 reactive regulatory T cells. Importantly, the CD4-CTLs were highly enriched for the expression of transcripts encoding chemokines that are involved in the recruitment of myeloid cells and dendritic cells to the sites of viral infection. Polyfunctional T helper (TH)1 cells and TH17 cell subsets were underrepresented in the repertoire of SARS-CoV-2-reactive CD4+ T cells compared to influenza-reactive CD4+ T cells. Together, our analyses provide so far unprecedented insights into the gene expression patterns of SARS-CoV-2 reactive CD4+ T cells in distinct disease severities.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Benjamin J Meckiff", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Ciro Ramirez-Suastegui", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Vicente Fajardo", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Serena J Chee", - "author_inst": "Faculty of Medicine, University of Southampton, Southampton, UK" - }, - { - "author_name": "Anthony Kusnadi", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Hayley Simon", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Emanuela Pelosi", - "author_inst": "Southampton Specialist Virology Center, University Hospitals NHS Foundation Trust, Southampton, UK." - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA. Department of Medicine, University of California San Diego, La Jolla, CA, US." - }, - { - "author_name": "Ferhat Ay", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Gregory Seumois", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA" - }, - { - "author_name": "Christian Ottensmeier", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA. Faculty of Medicine, University of Southampton, Southampton, UK. Institute of Translational Medicine, Depa" - }, - { - "author_name": "Pandurangan Vijayanand", - "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, USA. Faculty of Medicine, University of Southampton, Southampton, UK. Department of Medicine, University of Cal" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.06.12.148387", "rel_title": "Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient", @@ -1356688,6 +1353280,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.13.20130096", + "rel_title": "Nearly Perfect Forecasting of the Total COVID-19 Cases in India: A Numerical Approach", + "rel_date": "2020-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130096", + "rel_abs": "There are standard computational and statistical techniques of forecasting the spread pattern of a pandemic. In this article, we are going to show how close the forecasts can be if we use a simple numerical approach that can be worked out using just a scientific calculator. Using a few recent data, short term forecasts can be found very easily. In this numerical technique, we need not make any assumptions, unlike in the cases of using computational and statistical methods. Such numerical forecasts would be nearly perfect unless the pandemic suddenly starts retarding during the period of the forecasts naturally or otherwise.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.12.20129916", "rel_title": "ARB/ACEI use and severe COVID-19: a nationwide case-control study", @@ -1357407,61 +1354018,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20122036", - "rel_title": "Differences in antibody kinetics and functionality between severe and mild SARS-CoV-2 infections.", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20122036", - "rel_abs": "We determined and compared the humoral immune response in severe, hospitalized and mild, non-hospitalized COVID-19 patients. Severe patients (n=38) develop a robust antibody response to SARS-CoV-2, including IgG and IgA antibodies. The geometric mean 50% virus neutralization titer is 1:240. SARS-CoV-2 infected hospital personnel (n=24), who developed mild symptoms necessitating leave of absence, self-isolation, but not hospitalization, 75 % develop antibodies, but with low/absent virus neutralization (60% < 1:20).\n\nWhile severe COVID-19 patients develop a strong antibody response, mild SARS-CoV-2 infections induce a modest antibody response. Long term monitoring will show whether these responses predict protection against future infections.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ger Rijkers", - "author_inst": "Department of Medical Microbiology and Immunology, Admiral De Ruyter Hospital, 4462 RA Goes, The Netherlands" - }, - { - "author_name": "Jean-Luc Murk", - "author_inst": "Microvida, location St. Elisabeth-Tweesteden Hospital, 5022 GC Tilburg, The Netherlands" - }, - { - "author_name": "Bas Wintermans", - "author_inst": "Department of Medical Microbiology, Bravis Hospital, 4708 AE Roosendaal, The Netherlands" - }, - { - "author_name": "Bieke van Looy", - "author_inst": "Department of Medical Microbiology and Immunology, Admiral De Ruyter Hospital, 4462 RA Goes, The Netherlands" - }, - { - "author_name": "Marcel van den Berge", - "author_inst": "Department of Internal Medicine, Admiral De Ruyter Hospital, 4462 RA Goes, The Netherlands" - }, - { - "author_name": "Jacobien Veenemans", - "author_inst": "Department of Medical Microbiology and Immunology, Admiral De Ruyter Hospital, 4462 RA Goes, The Netherlands" - }, - { - "author_name": "Joep Stohr", - "author_inst": "Microvida, location St. Elisabeth-Tweesteden Hospital, 5022 GC Tilburg, The Netherlands" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "WHO COVID-19 Reference Laboratory, Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, Th" - }, - { - "author_name": "Pieter van der Pol", - "author_inst": "Department of Medical Microbiology and Immunology, Admiral De Ruyter Hospital, 4462 RA Goes, The Netherlands" - }, - { - "author_name": "Johan Reimerink", - "author_inst": "WHO COVID-19 Reference Laboratory, Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, Th" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20123836", "rel_title": "Point of care lung ultrasound is useful when screening for CoVid-19 in Emergency Department patients.", @@ -1358026,6 +1354582,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.09.20125286", + "rel_title": "Clinical characteristics and factors associated with admission to intensive care units inhospitalized COVID-19 patients in Lyon University Hospitals, France", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20125286", + "rel_abs": "IntroductionA new respiratory virus, SARS-CoV-2, has emerged and spread worldwide since late 2019. This study aims at analyzing clinical presentation on admission and the determinants associated with direct admission or transfer to intensive care units (ICUs) in hospitalized COVID-19 patients.\n\nPatients and MethodsIn this prospective hospital-based study, socio-demographic, clinical and biological characteristics, on admission, of adult COVID-19 hospitalized patients were prospectively collected and analyzed. The outcome was admission/transfer to intensive care units compared with total hospital stay in medical wards according to patient characteristics.\n\nResultsOf the 412 patients included, 325 were discharged and 87 died in hospital. Multivariable regression showed increasing odds of admission/transfer to ICUs with male gender (OR, 1.99 [95%CI, 1.07-3.73]), temperature (OR, 1.37 [95% CI, 1.01-1.88] per degree Celsius increase), abnormal lung auscultation on admission (OR, 2.62 [95% CI, 1.40-4.90]), elevated level of CRP (OR, 6.96 [95% CI, 1.45-33.35 for CRP>100mg/L vs CRP<10mg/L). Increased time was observed between symptom onset and hospital admission (OR, 4.82 [95% CI, 1.61-14.43] for time >10 days vs time <3 days) and monocytopenia (OR, 2.49 [95% CI, 1.29-4.82]). Monocytosis was associated with lower risk of admission/transfer to ICUs (OR, 0.25 [95% CI, 0.05-1.13]).\n\nConclusionsClinical and biological features on admission and time until admission were associated with admission to ICUs. Signs to predict worsening on admission could be partially associated with the time until admission. This finding reinforces the need for appropriate guidelines to manage COVID-19 patients in this time window.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Philippe Vanhems", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Marie-Paule Gustin", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Christelle ELIAS", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Laetitia HENAFF", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Cedric DANANCHE", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Beatrice GRISI", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Elodie MUNIER-MARION", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Nagham KHANAFER", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Delphine HILLIQUIN", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Sophie GARDES", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Solweig GERBIER-COLOMBAN", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Selilah AMOUR", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Elisabetta KUCZEWSKI", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Vanessa ESCURET", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Bruno LINA", + "author_inst": "Lyon University Hospitals" + }, + { + "author_name": "Mitra SAADATIAN-ELAHI", + "author_inst": "Lyon University Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.10.20125013", "rel_title": "Successful contact tracing systems for COVID-19 rely on effective quarantine and isolation", @@ -1358717,61 +1355352,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20126359", - "rel_title": "Chemoprophylaxis of COVID-19 with hydroxychloroquine: Astudy of health care workers attitude, adherence to regimeand side effects", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20126359", - "rel_abs": "BackgroundThere are apprehensions amongst healthcare worker (HCWs) about COVID-19. The HCWs have been given hydroxychloroquine (HCQ) chemoprophylaxis for seven weeks as per Government of India guidelines.\n\nObjectivesTo assess the apprehensions amongst HCWs about COVID-19 and to document accessibility, adherence and side effects related to HCQ prophylaxis in HCWs.\n\nMethodsA longitudinal follow up study was conducted in a tertiary care hospital. HCQ was given in the dose of 400 mg twice on day one, and then 400 mg weekly for seven weeks. 391 HCWs were interviewed using semi structured questionnaire.\n\nResults62.2% HCWs expressed perceived danger posted by COVID-19 infection. Doctors (54%) showed least acceptance and paramedics (88%) showed highest acceptance to chemoprophylaxis. 17.5% participants developed at least one of the side effects to HCQ. Females and nursing profession were significantly associated with adverse effects. Common side effects were gastro-intestinal symptoms, headache and abnormal mood change. Most of these were mild, not requiring any intervention. Gender, professions and perceived threat of COVID-19 were significantly associated with acceptance and adherence to HCQ prophylaxis.\n\nConclusionTwo third of HCWs had perceived danger due to COVID-19. Three fourth of the HCWs accepted chemoprophylaxis and four out of five who accepted had complete adherence to prophylaxis schedule. One out of five had developed at least one of side effects; however, most of these were mild not requiring any intervention.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Debajyoti Bhattacharyya", - "author_inst": "INSTITUTE OF LIVER & BILIARY SCIENCES, NEW DELHI" - }, - { - "author_name": "Neeraj Raizada", - "author_inst": "Institute of Liver and Biliary Sciences, Delhi, India" - }, - { - "author_name": "Bharathnag Nagappa", - "author_inst": "Institute of Liver and Biliary Sciences, Delhi, India" - }, - { - "author_name": "Arvind Tomar", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Prateek Maurya", - "author_inst": ", Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Ashok Chaudhary", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Mini George", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Deepty Katiyal", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Srishti Rajora", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - }, - { - "author_name": "Nikky Singh", - "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, Delhi, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20125849", "rel_title": "Renin-angiotensin system blockers and susceptibility to COVID-19: a multinational open science cohort study", @@ -1359456,6 +1356036,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.06.11.20127415", + "rel_title": "Even one metre seems generous. A reanalysis of data in: Chu et al. (2020) Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19.", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127415", + "rel_abs": "Re-examination of the large dataset collected and meta-analysed by Dr Chu and his colleagues contradicts their conclusions about the effects of separation distance on infection risk. Their conclusion was based on misunderstandings of the datasets. Each of these estimated risk relative to that incurred when touching infected individuals. Allowing for this suggests that the main advantage of social distancing, a perhaps 78% (95% CI 24, 92) reduction in risk of infection, occurs at distances below 1m. The data imply an 11% chance of further distances reducing the risk, with any effects likely to be small. However the limitations of the dataset do limit the strength of these conclusions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mike Lonergan", + "author_inst": "University of Dundee" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.06.10.20127738", "rel_title": "The origin and early spread of SARS-CoV-2 in Europe", @@ -1360279,49 +1356878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.06.11.20128199", - "rel_title": "Asymptomatic carriage rates and case-fatality of SARS-CoV-2 infection in residents and staff in Irish nursing homes", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128199", - "rel_abs": "BackgroundSARS-CoV-2 has disproportionately affected nursing home (NH) residents. In Ireland, the first NH case of COVID-19 occurred on 16/03/2020. A national point-prevalence testing program of all NH residents and staff took place from 18/04/2020-05/05/2020.\n\nAimsTo examine characteristics of NHs across three Community Health Organisations (CHOs) in Ireland, proportions with COVID-19 outbreaks, staff and resident, symptom-profile and resident case-fatality.\n\nMethodsForty-five NHs surveyed across three CHOs requesting details on occupancy, size, COVID-19 outbreak, timing of outbreak, total symptomatic/asymptomatic cases, and outcomes for residents from 29/02/2020-22/05/2020.\n\nResultsSurveys were returned from (62.2%, 28/45) of NHs (2043 residents, 2303 beds). Three-quarters (21/28) had COVID-19 outbreaks (1741 residents, 1972 beds). Median time from first case of COVID-19 in Ireland to first case in these NHs was 27.0 days. Resident COVID-19 incidence was (43.9%, 764/1741): laboratory-confirmed (40.1%, 710/1741) with (27.2%, 193/710 asymptomatic), and clinically-suspected (3.1%, 54/1741). Resident case-fatality was (27.6%, 211/764) for combined laboratory-confirmed/clinically-suspected COVID-19. Similar proportions of residents in NH with an \"early\" outbreak (<28days) versus a later outbreak developed confirmed/suspected COVID-19. A lower proportion of residents in NHs with \"early\" outbreaks had recovered compared to those with \"late\" outbreaks (37.4% vs 61.7%; {chi}2=56.9, p<0.001). Among 675 NH staff across twenty-four sites who had confirmed/suspected COVID-19 (23.6%, 159/675) were asymptomatic. There was a significant correlation between the proportion of staff with symptomatic COVID-19 and resident numbers with confirmed/suspected COVID-19 (Spearmans rho=0.81, p<0.001).\n\nConclusionThis study demonstrates COVID-19 impact on NH residents and staff. High infection rates lead to challenges in care provision.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sean P Kennelly", - "author_inst": "Department of Age-Related Healthcare, Tallaght University Hospital, Dublin 24, Ireland" - }, - { - "author_name": "Adam H Dyer", - "author_inst": "Department of Age-Related Healthcare, Tallaght University Hospital, Dublin 24, Ireland" - }, - { - "author_name": "Ruth Martin", - "author_inst": "Department of Medicine for the Elderly, Connolly Hospital, Blanchardstown, Dublin 15, Ireland" - }, - { - "author_name": "Siobhan M Kennelly", - "author_inst": "Department of Medicine for the Elderly, Connolly Hospital, Blanchardstown, Dublin 15, Ireland" - }, - { - "author_name": "Alan Martin", - "author_inst": "Department of Geriatric and Stroke Medicine, Beaumont Hospital, Dublin 9, Ireland" - }, - { - "author_name": "Desmond O'Neill", - "author_inst": "Department of Age-Related Healthcare, Tallaght University Hospital, Dublin 24, Ireland" - }, - { - "author_name": "Aoife Fallon", - "author_inst": "Department of Age-Related Heathcare, Tallaght University Hospital, Dublin 24, Ireland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2020.06.11.20128934", "rel_title": "SARS-CoV-2 Viral Load Predicts COVID-19 Mortality", @@ -1360838,6 +1357394,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.10.20128025", + "rel_title": "Mortality Attributed to COVID-19 in High-Altitude Populations", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20128025", + "rel_abs": "BackgroundSince partial oxygen pressure decreases as altitude increases, environmental hypoxia could worsen COVID-19 patients hypoxemia. We compared COVID-19 mortality at different altitudes.\n\nMethodsRetrospective analysis of population-level data on COVID-19 deaths in the U.S. (1,016 counties) and Mexico (567 municipalities). Mixed-model Poisson regression analysis of the association between altitude and COVID-19 mortality using individual-level data from 40,168 Mexican subjects with COVID-19, adjusting for multiple covariates.\n\nResultsBetween January 20 and April 13, 2020, mortality rates were higher in U.S. counties located at [≥]2,000 m elevation vs. those located below 1,500 m (12.3 vs. 3.2 per 100,000; P<0.001). In Mexico, between March 13 and May 13, 2020, mortality rates were higher in municipalities located at [≥]2,000 m vs. <1,500 m (5.3 vs. 3.9 per 100,000; P<0.001). Among Mexican subjects <65 years old, the risk of death was 36% higher in those living at [≥]2,000 m vs. <1,500 m (adjusted incidence rate ratio: 1.36; 95% CI, 1.05-1.78; P=0.022). Among men, the risk of death was 31% higher at [≥]2,000 m vs. <1,500 m (adjusted IRR: 1.31; 95% CI, 1.03-1.66; P=0.025). No association was found among women.\n\nConclusionAltitude is associated with COVID-19 mortality in men younger than 65 years.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Orison O Woolcott", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Richard N Bergman", + "author_inst": "Cedars-Sinai Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.11.20128603", "rel_title": "COVID-19 and children with cancer: Parents' experiences, anxieties, and support needs", @@ -1361649,53 +1358228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.11.20128520", - "rel_title": "COVID-19 pandemic-related lockdown: response time is more important than its strictness", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128520", - "rel_abs": "The rapid spread of SARS-CoV-2 and its threat to health systems worldwide have led governments to take acute actions to enforce social distancing. Previous studies used complex epidemiological models to quantify the effect of lockdown policies on infection rates. However, these rely on prior assumptions or on official regulations. Here, we use country-specific reports of daily mobility from people cellular usage to model social distancing. Our data-driven model enabled the extraction of mobility characteristics which were crossed with observed mortality rates to show that: (1) the time at which social distancing was initiated is of utmost importance and explains 62% of the number of deaths, while the lockdown strictness or its duration are not as informative; (2) a delay of 7.49 days in initiating social distancing would double the number of deaths; and (3) the expected time from infection to fatality is 25.75 days and significantly varies among countries.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Gil Loewenthal", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Shiran Abadi", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Oren Avram", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Keren Halabi", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Noa Ecker", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Natan Nagar", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Itay Mayrose", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Tal Pupko", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.10.20127365", "rel_title": "Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): Promoting piecewise smoothness via convex optimization", @@ -1362604,6 +1359136,85 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.06.11.147199", + "rel_title": "Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate", + "rel_date": "2020-06-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.11.147199", + "rel_abs": "A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Christiane Iserman", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Christine Anne Roden", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Mark Boerneke", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Rachel Sealfon", + "author_inst": "Flatiron Institute, Simons Foundation, New York, NY" + }, + { + "author_name": "Grace McLaughlin", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Irwin Jungreis", + "author_inst": "Broad Institute, MIT, Cambridge, MA," + }, + { + "author_name": "Christopher Y Park", + "author_inst": "Flatiron Institute, Simons Foundation" + }, + { + "author_name": "Avinash Boppana", + "author_inst": "Princeton Department of Computer Science" + }, + { + "author_name": "Ethan Fritch", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Yixuan Hou", + "author_inst": "UNC Chapel Hill" + }, + { + "author_name": "Chandra Theesfeld", + "author_inst": "Princeton University" + }, + { + "author_name": "Olga Troyanskaya", + "author_inst": "Princeton University, Flatiron Institute, Simons Foundation" + }, + { + "author_name": "Ralph S. G. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Timothy P Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kevin Weeks", + "author_inst": "Univ. North Carolina" + }, + { + "author_name": "Amy Gladfelter", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.11.147389", "rel_title": "Whole blood immunophenotyping uncovers immature neutrophil-to-VD2 T-cell ratio as an early prognostic marker for severe COVID-19", @@ -1363683,117 +1360294,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.10.20126532", - "rel_title": "IgA dominates the early neutralizing antibody response to SARS-CoV-2", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20126532", - "rel_abs": "A major dogma in immunology has it that the IgM antibody response precedes secondary memory responses built on the production of IgG, IgA and, occasionaly, IgE. Here, we measured acute humoral responses to SARS-CoV-2, including the frequency of antibody-secreting cells and the presence of specific, neutralizing, antibodies in serum and broncho-alveolar fluid of 145 patients with COVID-19. Surprisingly, early SARS-CoV-2-specific humoral responses were found to be typically dominated by antibodies of the IgA isotype. Peripheral expansion of IgA-plasmablasts with mucosal-homing potential was detected shortly after the onset of symptoms and peaked during the third week of the disease. While the specific antibody response included IgG, IgM and IgA, the latter contributed to a much larger extent to virus neutralization, as compared to IgG. However, specific IgA serum levels notably decrease after one month of evolution. These results represent a challenging observation given the present uncertainty as to which kind of humoral response would optimally protect against re-infection, and whether vaccine regimens should consider boosting a potent, although, at least in blood, fading IgA response.\n\nOne sentence SummaryWhile early specific antibody response included IgG, IgM and IgA, the latter contributed to a much larger extent to virus neutralization.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Delphine Sterlin", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Alexis Mathian", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Makoto Miyara", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Audrey Mohr", - "author_inst": "Centre Immunologie et des Maladies Infectieuses, Paris" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur, Paris" - }, - { - "author_name": "Laetitia Claer", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Paul Quentric", - "author_inst": "Centre d'Immunologie et des Maladies Infectieuses, Paris" - }, - { - "author_name": "Jehane Fadlallah", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pacale Ghillani", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Cary Gunn", - "author_inst": "Genalyte Inc." - }, - { - "author_name": "Rick Hockett", - "author_inst": "Genalyte Inc." - }, - { - "author_name": "Sasi Mudumba", - "author_inst": "Genlayte Inc" - }, - { - "author_name": "Amelie Guihot", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Charles-Edouard Luyt", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Julien Mayaux", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Alexandra Beurton", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Salma Fourati", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Jean-Marc Lacorte", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Hans Yssel", - "author_inst": "Centre d Immunologie et des Maladies Infectieuses" - }, - { - "author_name": "Christophe Parizot", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Karim Dorgham", - "author_inst": "Centre d Immunologie et des Maladies Infectieuses" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur Paris" - }, - { - "author_name": "Zahir Amoura", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Guy Gorochov", - "author_inst": "Assistance Publique Hopitaux de Paris" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20127092", "rel_title": "Antibody response to infectious diseases and other factors accurately predict COVID-19 infection and severity risk 10-14 years later: a retrospective UK Biobank cohort study", @@ -1364382,6 +1360882,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.09.20126334", + "rel_title": "Modeling the Transmission of Respiratory Infectious Diseases in Mass Transportation Systems", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126334", + "rel_abs": "Mass transportation is one of the areas that are badly hit by respiratory infectious disease outbreaks due to moderate to high exposure risk to pathogens brought about by the interaction among commuters. Here, we formulate agent-based models that simulate the spread of a respiratory infectious disease in a train wagon in the Manila Light Rail Transit System, and in a 49-seater public utility bus. We consider preventive measures such as implementation of social distancing, and limitation of interaction or movement among the commuters to investigate how these measures will inhibit disease transmission. We also consider the effect of protective gears and practices, crowd density, and prevalence of disease in the community on the possible number of newly-infected individuals. Our simulations show that (i) individuals must have protection with more than 90% effectiveness to inhibit transmission of the disease; (ii) social or physical distancing by more than 1m distance reduces the risk of being infected; (iii) minimizing movement or interaction with other passengers reduces the risk of transmission by 50%; (iv) passenger capacity should be less than 10-50% of the maximum seating capacity to reduce the number of infections depending on the level of imposed social distancing and passenger interaction; (v) vehicles with greater number of occupied seating capacity generate higher number of infections but vehicles with smaller dimensions have faster disease transmissions; and (vi) ideal set-up for a 24-seater train wagon (49-seater bus) is to allow a maximum of 12 (24) passengers, with little to no interaction among passengers, with social distancing of more than 1m distance apart, and each person has a protection with 90% effectiveness as much as possible. These results can aid policy makers in determining optimal strategies to minimize infections while maintaining transportation services during pandemics or disease outbreaks.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christian Alvin H Buhat", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Destiny SM Lutero", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Yancee H Olave", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Monica C Torres", + "author_inst": "University of the Philippines Los Banos" + }, + { + "author_name": "Jomar Fajardo Rabajante", + "author_inst": "University of the Philippines Los Banos" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.09.20126318", "rel_title": "Evaluation of the number of COVID-19 undiagnosed infected using source of infection measurements", @@ -1365389,113 +1361924,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.10.145144", - "rel_title": "Hydroxychloroquine Proves Ineffective in Hamsters and Macaques Infected with SARS-CoV-2", - "rel_date": "2020-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.145144", - "rel_abs": "We remain largely without effective prophylactic/therapeutic interventions for COVID-19. Although many human clinical trials are ongoing, there remains a deficiency of supportive preclinical drug efficacy studies. Here we assessed the prophylactic/therapeutic efficacy of hydroxychloroquine (HCQ), a drug of interest for COVID-19 management, in two animal models. When used for prophylaxis or treatment neither the standard human malaria dose (6.5 mg/kg) nor a high dose (50 mg/kg) of HCQ had any beneficial effect on clinical disease or SARS-CoV-2 kinetics (replication/shedding) in the Syrian hamster disease model. Similarly, HCQ prophylaxis/treatment (6.5 mg/kg) did not significantly benefit clinical outcome nor reduce SARS-CoV-2 replication/shedding in the upper and lower respiratory tract in the rhesus macaque disease model. In conclusion, our preclinical animal studies do not support the use of HCQ in prophylaxis/treatment of COVID-19.One Sentence Summary Hydroxychloroquine prophylaxis/treatment showed no beneficial effect in SARS-CoV-2 hamster and macaque disease models.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Kyle Rosenke", - "author_inst": "NIAID" - }, - { - "author_name": "Michael Jarvis", - "author_inst": "University of Plymouth" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID" - }, - { - "author_name": "Benjamin Schwarz", - "author_inst": "NIAID" - }, - { - "author_name": "Atsushi Okumura", - "author_inst": "NIAID" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "NIAID" - }, - { - "author_name": "Greg Saturday", - "author_inst": "NIAID" - }, - { - "author_name": "Patrick Hanley", - "author_inst": "NIAID" - }, - { - "author_name": "Kimberly Meade-White", - "author_inst": "NIAID" - }, - { - "author_name": "Brandi Williamson", - "author_inst": "NIAID" - }, - { - "author_name": "Frederick Hansen", - "author_inst": "NIAID" - }, - { - "author_name": "Lizzette Perez-Perez", - "author_inst": "NIAID" - }, - { - "author_name": "Shanna Leventhal", - "author_inst": "NIAID" - }, - { - "author_name": "Tsing-Lee Tang-Huau", - "author_inst": "NIAID" - }, - { - "author_name": "Martha Nason", - "author_inst": "NIAID" - }, - { - "author_name": "Julie Callison", - "author_inst": "NIAID" - }, - { - "author_name": "Elaine Haddock", - "author_inst": "NIAID" - }, - { - "author_name": "Dana Scott", - "author_inst": "NIAID" - }, - { - "author_name": "Graham Sewell", - "author_inst": "NIAID" - }, - { - "author_name": "Catherine Bosio", - "author_inst": "NIAID" - }, - { - "author_name": "David Hawman", - "author_inst": "NIAID" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Heinz Feldmann", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.06.09.20076646", "rel_title": "Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study", @@ -1366236,6 +1362664,45 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.06.09.142315", + "rel_title": "Designed peptides as potential fusion inhibitors against SARA-CoV-2 coronavirus infection", + "rel_date": "2020-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.142315", + "rel_abs": "Inspired by fusion-inhibitory peptides from heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains from human immuno-deficiency virus type 1 (HIV-1) envelope glycoprotein gp41 and severe acute respiratory syndrome-coronavirus (SARS-CoV) based on viral fusogenic mechanism in the present work, we provided a similar approach to design the synthesized peptides against the entry into host cells of SARA-CoV-2 virus that causes 2019 novel coronavirus disease (COVID-19). These peptides derived from HR1 and HR2 of SARA-CoV-2 spike protein were further tested for their interaction and potential fusion possibility through circular dichroism spectrum. Here we used the peptide COVID-2019-HR1P1 (40 amino acids) as the target, which was derived from HR1 of SARA-CoV-2 spike protein, while the designed peptides including COVID-2019-HR2P1 (37 amino acids), COVID-2019-HR2P2 (32 amino acids) and others derived from HR2 of SARA-CoV-2 were tested for their binding to COVID-2019-HR1P1. Interestingly, results showed that both COVID-2019-HR2P1 and COVID-2019-HR2P2 can form the complex with COVID-2019-HR1P1, respectively. This implied that these designed peptides could play an important role in blocking SARA-CoV-2 entry into mammalian host cells via viral fusogenic mechanism, and thus could be used for preventing SARA-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ke Chen", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Shihao Bai", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Xin Zou", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Jie Hao", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Lin-tai Da", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Ze-Guang Han", + "author_inst": "Shanghai Jiao Tong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.09.142570", "rel_title": "Comparative analysis of non structural protein 1 of SARS-COV2 with SARS-COV1 and MERS-COV: An in silico study", @@ -1366943,29 +1363410,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.08.20125419", - "rel_title": "Effectiveness of stay-in-place-orders during COVID-19 pandemic: Evidence from US border counties.", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125419", - "rel_abs": "Recent studies on US counties, with varying effect sizes, show that stay-in-place-orders (SIPOs) are associated with a decline in new COVID-19 cases. Our estimation approach relies on county-pairs across state-borders where one state has SIPO whereas the other state does not, controls for matched county-pair fixed effects and day of observation fixed-effects. The county-pair sample from southern, mid-western, and mountain region states (from March 1, 2020 to April 25, 2020) shows that daily COVID-19 incidence case growth rate is 1.994 percentage points lower for counties in SIPO states relative to those bordering in non-SIPO states. Specifically, we find SIPO reduced daily growth rates by 1.97, 2.14, 2.03, and 2.27 percentage points after 1 to 5 days, 6 to 10 days, 11 to 15 days, and 16 to 20 days, respectively. Our effect sizes are much smaller than in the previous studies with the caveat that states in the northeast and on the west coast could not be included in the border county-pair specification. We find limited evidence of heterogeneous effects in counties with a higher population density, percentage of black or Hispanic residents, proportion of population over 65 years, and social association rates in a county. Nor do we find evidence of meaningful differences in effects of SIPO by county Gini index, unemployment, or GDP. The results of this study could further inform policymakers in making decisions on SIPO extensions or lifting of such orders.\n\nJELH75; I18", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Srikant Devaraj", - "author_inst": "Ball State University" - }, - { - "author_name": "Pankaj C Patel", - "author_inst": "Villanova University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.08.20125708", "rel_title": "A web survey to assess the use efficacy of personnel protective materials among allied health care workers during COVID-19 pandemic at North-East India", @@ -1367870,6 +1364314,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.138990", + "rel_title": "Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.138990", + "rel_abs": "Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer [≥]160 was 80% or greater with anti-RBD or anti-ECD titers of [≥]1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers [≥]160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of [≥]1:1350, and evidence of VN [≥]1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of [≥]1:1350 may provide critical information about protection against COVID-19 disease.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Eric Salazar", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Suresh V Kuchipudi", + "author_inst": "Pennsylvania State University University Park : Penn State" + }, + { + "author_name": "Paul A Christensen", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Todd N Eagar", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Xin Yi", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Picheng Zhao", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Zhicheng Jin", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "S. Wesley Long", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Randall J Olsen", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Jian Chen", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Brian Castillo", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Christopher Leveque", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "Dalton M Towers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jason Lavinder", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Jimmy D Gollihar", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jose Cardona", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Gregory C Ippolito", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Ruth H Nissly", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Ian M Bird", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Denver Greenawalt", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Randall M Rossi", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Abinhay Gontu", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Sreenidhi Srinivasan", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Indira B Poojary", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Isabella M Cattadori", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Peter J Hudson", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Nicole Joselyn", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "Laura Prugar", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "Kathleen Huie", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "Andrew Herbert", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "David W Bernard", + "author_inst": "Houston Methodist Hospital" + }, + { + "author_name": "John Dye", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "Vivek Kapur", + "author_inst": "USAMRIID (United States Army Medical Research Institute of Infectious Diseases)" + }, + { + "author_name": "James M. Musser", + "author_inst": "Houston Methodist Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.08.140871", "rel_title": "Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses", @@ -1369104,77 +1365699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.03.20121525", - "rel_title": "Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121525", - "rel_abs": "BackgroundSARS-CoV-2 infection can be detected indirectly by measuring the host immune response. Anti-viral antibody concentrations generally correlate with host protection and viral neutralization, but in rare cases, antibodies can promote disease progression. Elucidation of the kinetics and magnitude of the SARS-CoV-2 antibody response is essential to understand the pathogenesis of COVID-19 and identify potential therapeutic targets.\n\nMethodsSera (n=533) from patients with RT-PCR confirmed COVID-19 (n=153) were tested using a high-throughput quantitative IgM and IgG assay that detects antibodies to the spike protein receptor binding domain and nucleocapsid protein. Individual and serial samples covered the time of initial diagnosis, during the disease course, and following recovery. We evaluated antibody kinetics and correlation between magnitude of the response and disease severity.\n\nResultsPatterns of SARS-CoV-2 antibody production varied considerably. Among 52 patients with 3 or more serial specimens, 44 (84.6%) and 42 (80.8%) had observed IgM and IgG seroconversion at a median of 8 and 10 days, respectively. Compared to those with milder disease, peak measurements were significantly higher for patients admitted to the intensive care unit for all time intervals between 6 and 20 days for IgM, and all intervals after 5 days for IgG.\n\nConclusionsHigh sensitivity assays with a robust dynamic range provide a comprehensive picture of host antibody response to SARS-CoV-2. IgM and IgG responses were significantly higher in patients with severe than mild disease. These differences may affect strategies for seroprevalence studies, therapeutics and vaccine development.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kara Lake Lynch", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Jeffrey D. Whitman", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Noreen P Lacanienta", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Erica W Beckerdite", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Shannon A Kastner", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Brian R Shy", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Gregory M Goldgof", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Andrew G Levine", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Sagar P Bapat", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Susan L Stramer", - "author_inst": "American Red Cross" - }, - { - "author_name": "Jonathan H Esensten", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Allen W Hightower", - "author_inst": "Independent Consultant" - }, - { - "author_name": "Caryn Bern", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Alan HB Wu", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20119636", "rel_title": "No Evidence for Reduced Hospital Admissions or Increased Deaths from Stroke or Heart Attack During COVID-19", @@ -1369795,6 +1366319,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.07.20125047", + "rel_title": "Survival and predictors of deaths of patients hospitalized due to COVID-19 from a retrospective and multicenter cohort study in Brazil", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20125047", + "rel_abs": "The epidemic caused by COVID-19 in Brazil is associated with an unfavorable political scenario, aggravated by intense social inequality and low number of available hospital beds. Therefore, this study aimed to analyze the survival of patients admitted to Brazilian hospitals due to the COVID-19 and estimate prognostic factors. This is a retrospective, multicenter cohort study, based on data from 46285 hospitalizations for COVID-19 in Brazil. Survival functions were calculated using the Kaplan-Meiers method. The Log-rank test compared the survival functions for each variable and from that, hazard ratios were calculated and the proportional hazards model was used in Cox multiple regression. The smallest survival curves were the ones for patients at the age of 68 years or more, black / brown race, illiterate, living in the countryside, dyspnea, respiratory distress, influenza-like outbreak, O2 saturation <95%, X-ray change, length of stay in the ICU, invasive ventilatory support, previous heart disease, pneumopathy, diabetes, downs syndrome, neurological disease and kidney disease. Better survival was observed in the symptoms and in an asthmatic patient. The multiple model for increased risk of death when they were admitted to the ICU HR 1.28 (95% CI 1.21-1.35), diabetes HR 1.17 (95% CI 1.11-1.24), neurological disease HR 1.34 (95% CI 1.22-1.46), kidney disease HR 1.11 (95% CI 1.02-1.21), heart disease HR 1.14 (95% CI 1.08-1.20), black or brown race of HR 1.50 (95% CI 1.43-1.58), asthma HR 0.71 (95% CI 0.61-0.81) and pneumopathy HR 1.12 (95% CI 1.02-1.23). The overall survival time was low in hospitalizations for COVID-19 and this reinforces the importance of sociodemographic and clinical factors as a prognosis for death. The lack of a protocol for scientific clinical management puts a greater risk of death for about 80 million Brazilians, who are chronically ill or living in poverty. COVID-19 can promote selective mortality that borders the eugenics of specific social segments in Brazil.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marquiony Santos", + "author_inst": "UERN" + }, + { + "author_name": "Eudes ES Lucena", + "author_inst": "UFRN" + }, + { + "author_name": "Kenio C Lima", + "author_inst": "UFRN" + }, + { + "author_name": "Andiara AC Brito", + "author_inst": "UFERSA" + }, + { + "author_name": "Monica B Bay", + "author_inst": "UFRN" + }, + { + "author_name": "Diego Bonfada", + "author_inst": "UFRN" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20124834", "rel_title": "Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence", @@ -1370770,41 +1367333,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.04.20122093", - "rel_title": "Case Study: Using Facebook Data to Monitor Adherence to Stay-at-home Orders in Colorado and Utah", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122093", - "rel_abs": "In the absence of effective treatments, social distancing has been the only public health measure available to combat the COVID-19 pandemic. In the US, implementing this response has been left to state, county, and city officials, and many localities have issued some form of a stay-at-home order. Without existing tools and with limited resources, localities struggled to understand how their orders changed behavior. In response, several technology companies opened access to their users location data. As part of the COVID-19 Data Mobility Network, we obtained access to Facebook User data and developed four key metrics and visualizations to monitor various aspects of adherence to stay at home orders. These metrics were carefully incorporated into static and interactive visualizations for dissemination to local officials.\n\nAll code is open source and freely available at https://github.com/ryanlayer/COvid19", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ryan M Layer", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Bailey Fosdick", - "author_inst": "Colorado State University" - }, - { - "author_name": "Daniel B Larremore", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Michael Bradshaw", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Paul Doherty", - "author_inst": "National Alliance for Public Safety GIS Foundation" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.05.20123307", "rel_title": "Reduced ICU demand with early CPAP and proning in COVID-19 at Bradford: a single centre cohort", @@ -1371261,6 +1367789,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.05.20109637", + "rel_title": "Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20109637", + "rel_abs": "An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital system following the emergency use authority (EUA) guidance issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=124) using newly designed dual-target rRT-PCR (altona RealStar(R) SARS-CoV-2 Reagent) for detecting of SARS-CoV-2 in upper respiratory and lower respiratory tract specimens, including bronchoalveolar lavage and tracheal aspirates. Accuracy testing demonstrated excellent assay agreement between expected and observed values. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 tests from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Our findings demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarizes clinical data from early in the epidemic in New York City.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Priya Velu", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Arryn Craney", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Phyllis Ruggiero", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "John Sipley", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lin Cong", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Erika Hissong", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Massimo Loda", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lars F Westblade", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Melissa Cushing", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hanna Rennert", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20083980", "rel_title": "Nano short peptide nutrition intervention on the prognosis of patients with COVID-19", @@ -1372116,45 +1368699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.06.07.20124610", - "rel_title": "Relationship Between Blood Group and Risk of Infection and Death in COVID-19: a live Meta-Analysis", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124610", - "rel_abs": "IntroductionThe relationship between ABO blood group and the incidence of COVID-19 infection and death has been investigated in several studies. The reported results were controversial, so the objective of the present study is to assess the relationship between different blood groups and the onset and mortality of COVID-19 infection using meta-analysis method.\n\nMethodsWe searched the databases using appropriate MeSH terms. We screened articles on the basis of titles, abstracts, and full texts and the articles that met the inclusion criteria were selected. Quality assessment was done with the Newcastle-Ottawa Scale checklist. The estimated frequency of COVID-19 infection and death in terms of ABO blood group and the overall estimate of the odd ratio between blood group with COVID-19 infection and death was done with 95% confidence interval.\n\nResultsThe pooled frequency of blood groups A, B, O, and AB among COVID-19 infected individuals was estimated as 36.22%, 24.99%, 29.67%, and 9.29% respectively. The frequency of blood groups A, B, O, and AB among the dead cases due to COVID-19 infection was estimated as 40%, 23%, 29%, and 8% respectively. The odd ratio of COVID-19 infection for blood group A versus the other blood groups was estimated 1.16 (CI 95%: 1.02-1.33). The corresponding figures for blood groups O and AB versus other blood groups were estimated as 0.73 (CI 95%: 0.60-0.88) and 1.25(CI 95%: 0.84-1.86) respectively.\n\nConclusionThis meta-analysis showed that individuals with blood group A are at higher risk for COVID-19 infection while those with blood group O are at lower risk. Although the odds ratio of death for AB blood group was non-significant, it was considerable.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fateme Pourali", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Mahdi Afshari", - "author_inst": "Zabol University of Medical Sciences" - }, - { - "author_name": "Reza Alizadeh-Navaei", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Javad Javidnia", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Mahmood Moosazadeh", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Amirhossein Hessami", - "author_inst": "Mazandaran University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.07.20124594", "rel_title": "Early Detection of Coronavirus Cases Using Chest X-ray Images Employing Machine Learning and Deep Learning Approaches", @@ -1372999,6 +1369543,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.08.140236", + "rel_title": "Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives", + "rel_date": "2020-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.140236", + "rel_abs": "Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused a pandemic of historic proportions and continues to spread globally, with enormous consequences to human health. Currently there is no vaccine, effective therapeutic or prophylactic. Like other betacoronaviruses, attachment and entry of SARS-CoV-2 is mediated by the spike glycoprotein (SGP). In addition to its well-documented interaction with its receptor, human angiotensin converting enzyme 2 (hACE2), SGP has been found to bind to glycosaminoglycans like heparan sulfate, which is found on the surface of virtually all mammalian cells. Here, we pseudotyped SARS-CoV-2 SGP on a third generation lentiviral (pLV) vector and tested the impact of various sulfated polysaccharides on transduction efficiency in mammalian cells. The pLV vector pseudotyped SGP efficiently and produced high titers on HEK293T cells. Various sulfated polysaccharides potently neutralized pLV-S pseudotyped virus with clear structure-based differences in anti-viral activity and affinity to SGP. Concentration-response curves showed that pLV-S particles were efficiently neutralized by a range of concentrations of unfractionated heparin (UFH), enoxaparin, 6-O-desulfated UFH and 6-O-desulfated enoxaparin with an IC50 of 5.99 {micro}g/L, 1.08 mg/L, 1.77 {micro}g/L, and 5.86 mg/L respectively. The low serum bioavailability of intranasally administered UFH, along with data suggesting that the nasal epithelium is a portal for initial infection and transmission, suggest that intranasal administration of UFH may be an effective and safe prophylactic treatment.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ritesh Tandon", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Joshua S. Sharp", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Fuming Zhang", + "author_inst": "Rensselaer Polytechnic Institute" + }, + { + "author_name": "Vitor H. Pomin", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Nicole M. Ashpole", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Dipanwita Mitra", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Weihua Jin", + "author_inst": "Rensselaer Polytechnic Institute" + }, + { + "author_name": "Hao Liu", + "author_inst": "University of Mississippi" + }, + { + "author_name": "Poonam Sharma", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Robert J. Linhardt", + "author_inst": "Rensselaer Polytechnic Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.08.140244", "rel_title": "Cross-sectional evaluation of humoral responses against SARS-CoV-2 Spike", @@ -1373894,49 +1370493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.06.20124016", - "rel_title": "Risk and protective factors of SARS-CoV-2 infection - Meta-regression of data from worldwide nations", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124016", - "rel_abs": "Although it has been reported that coexistent chronic diseases are strongly associated with COVID-19 severity, investigations of predictors for SARS-CoV-2 infection itself have been seldom performed. To screen potential risk and protective factors for SARS-CoV-2 infection, meta-regression of data from worldwide nations were herein conducted. We extracted total confirmed COVID-19 cases in worldwide 180 nations (May 31, 2020), nation total population, population ages 0-14/[≥]65, GDP/GNI per capita, PPP, life expectancy at birth, medical-doctor and nursing/midwifery-personnel density, hypertension/obesity/diabetes prevalence, annual PM2.5 concentrations, daily ultraviolet radiation, population using safely-managed drinking-water/sanitation services and hand-washing facility with soap/water, inbound tourism, and bachelors or equivalent (ISCED 6). Restricted maximum-likelihood meta-regression in the random-effects model was performed using Comprehensive Meta-Analysis version 3. To adjust for other covariates, we conducted the hierarchical multivariate models. A slope (coefficient) of the meta-regression line for the COVID-19 prevalence was significantly negative for population ages 0-14 (-0.0636; P = .0021) and positive for obesity prevalence (0.0411; P = .0099) and annual PM2.5 concentrations in urban areas (0.0158; P = .0454), which would indicate that the COVID-19 prevalence decreases significantly as children increase and that the COVID-19 prevalence increases significantly as the obese and PM2.5 increase. In conclusion, children (negatively) and obesity/PM2.5 (positively) may be independently associated with SARS-CoV-2 infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hisato Takagi", - "author_inst": "Shizuoka Medical Center" - }, - { - "author_name": "Toshiki Kuno", - "author_inst": "Mount Sinai Beth Israel Medical Center" - }, - { - "author_name": "Yujiro Yokoyama", - "author_inst": "Easton Hospital" - }, - { - "author_name": "Hiroki Ueyama", - "author_inst": "Mount Sinai Beth Israel Medical Center" - }, - { - "author_name": "Takuya Matsushiro", - "author_inst": "Shizuoka Medical Center" - }, - { - "author_name": "Yosuke Hari", - "author_inst": "Shizuoka Medical Center" - }, - { - "author_name": "Tomo Ando", - "author_inst": "New York Presbyterian Hospital/Columbia University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.05.20123752", "rel_title": "Changes in non-linear and time-domain heart rate variability indices between critically ill COVID-19 and all-cause sepsis patients -a retrospective study", @@ -1374377,6 +1370933,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.04.20122838", + "rel_title": "ENVIRONMENTAL SAFETY EVALUATION OF THE PROTECTION AND ISOLATION SYSTEM FOR PATIENTS WITH COVID-19.", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122838", + "rel_abs": "BackgroundSARS-CoV-2 has high transmissibility through respiratory droplets and aerosol, making COVID-19 a worldwide pandemic. In its severe form, patients progress to respiratory failure. Non-invasive mechanical ventilation restrictions and early orotracheal intubation have collapsed health systems due to insufficient intensive care unit beds and mechanical ventilators. COVID-19 dedicated healthcare professionals have high infection rates. This publication describes experimental testing of the Protection and Isolation System for Patients with COVID-19 (PISP/COVID-19).\n\nMethodPISP/COVID-19 is a disposable transparent polyethylene plastic that covers the patients entire hospital bed, with its internal air aspirated by the hospitals vacuum system attached to a microparticle filter. Experiments validated PISP/COVID-19s ability to block aerosolized microparticles dissemination. Caffeine was used as a molecular marker, with leakage evaluation through sensors analysis using nuclear magnetic resonance spectroscopy. The biological marker was synthetic SARS-CoV-2 RNA, using Reverse Transcription Polymerase Chain Reaction (RT-PCR) as the detection method.\n\nResultsPISP/COVID-19 was effective against molecular and biological markers environmental dispersion in simulations of non-invasive ventilation, high-flow nasal cannula oxygen and mechanical ventilation isolation. Caffeine was not detected in any of the sensors positioned at points outside the PISP/COVID-19. The ability of PISP/COVID-19 to retain virus particles and protect the surrounding environment was confirmed by detection and gradients quantification of synthetic SARS-CoV-2 RNA by RT-PCR.\n\nConclusionPISP/COVID-19 was effective in the retention of the molecular and biological markers in all tested simulations. Considering the current pandemic, PISP/COVID-19 might increase the use of non-invasive ventilation, high-flow nasal cannula oxygen and provide additional protection to healthcare professionals.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Claudio Almeida Quadros", + "author_inst": "University of Bahia State, Department of Life Sciences" + }, + { + "author_name": "Maria Carolina BDM Leal", + "author_inst": "Sao Carlos Federal University, Department of Chemistry" + }, + { + "author_name": "Carlos A Baptista-Sobrinho", + "author_inst": "University Center of Planalto Central Aparecido dos Santos" + }, + { + "author_name": "Carolina KV Nonaka", + "author_inst": "Center for Biotechnology and Cell Therapy, Sao Rafael Hospital. D'Or Institute for Research and Education." + }, + { + "author_name": "Bruno SF Souza", + "author_inst": "Center for Biotechnology and Cell Therapy, Sao Rafael Hospital. D'Or Institute for Research and Education. Goncalo Moniz Instituto, FIOCRUZ" + }, + { + "author_name": "Juliana Cristina Milan-Mattos", + "author_inst": "Sao Carlos Federal University, Department of Physiotherapy" + }, + { + "author_name": "Aparecida Maria Catai", + "author_inst": "Sao Carlos Federal University, Department of Physiotherapy" + }, + { + "author_name": "Valeria AP Lorenzo", + "author_inst": "Sao Carlos Federal University, Department of Physiotherapy" + }, + { + "author_name": "Antonio Gilberto Ferreira", + "author_inst": "Sao Carlos Federal University, Department of Chemistry" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.06.04.20122614", "rel_title": "A rapid systematic review and case study on test, contact tracing, testing, and isolation policies for Covid-19 prevention and control", @@ -1375196,45 +1371803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.04.20112417", - "rel_title": "Human mobility and poverty as key factors in strategies against COVID-19", - "rel_date": "2020-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20112417", - "rel_abs": "BackgroundApplying heavy nationwide restrictions is a powerful method to curtail COVID-19 transmission but poses a significant humanitarian and economic crisis. Thus, it is essential to improve our understanding of COVID-19 transmission and develop more focused and effective strategies. As human mobility drives transmission, data from cell phone devices can be utilized to achieve these goals.\n\nMethodsWe analyzed aggregated and anonymized mobility data from the cell-phone devices of>3 million users between February 1, 2020, to May 16, 2020 - in which several movement restrictions were applied and lifted in Israel. We integrated these mobility patterns into age-, risk- and region-structured transmission model. Calibrated to coronavirus incidence in 250 regions covering Israel, we evaluated the efficacy and effectiveness in decreasing mortality of applying localized and temporal lockdowns (stay-at-home order).\n\nResultsPoorer regions exhibited lower and slower compliance with the restrictions. Our transmission model further indicated that individuals from poverty areas were associated with high transmission rates. Model projections suggested that, counterintuitively, school closure has an adverse effect and increases COVID-19 mortality in the long run, while interventions focusing on the elderly are the most efficient. We also found that applying localized and temporal lockdowns during regional outbreaks reduce mortality compared to nationwide lockdowns. These trends were consistent across vast ranges of epidemiological parameters, possible seasonal forcing, and even when we assumed that vaccination would be commercially available in 1-3 years.\n\nConclusionsMore resources should be devoted to helping impoverished regions. Utilizing cellphone data despite being anonymized and aggregated can help policymakers worldwide identify hotspots and apply designated strategies against future COVID-19 outbreaks.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matan Yechezkel", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Amit Weiss", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Idan Rejwan", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Edan Shahmoon", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Shahaf Ben Gal", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Dan Yamin", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.05.137349", "rel_title": "Synthetic Antibodies neutralize SARS-CoV-2 infection of mammalian cells", @@ -1376087,6 +1372655,273 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20119818", + "rel_title": "Suppressive myeloid cells are a hallmark of severe COVID-19", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20119818", + "rel_abs": "Severe Acute Respiratory Syndrome - Coronavirus-2 (SARS-CoV-2) infection causes Coronavirus Disease 2019 (COVID-19), a mild to moderate respiratory tract infection in the majority of patients. A subset of patients, however, progresses to severe disease and respiratory failure with acute respiratory distress syndrome (ARDS). Severe COVID-19 has been associated with increased neutrophil counts and dysregulated immune responses. The mechanisms of protective immunity in mild forms and the pathogenesis of dysregulated inflammation in severe courses of COVID-19 remain largely unclear. Here, we combined two single-cell RNA-sequencing technologies and single-cell proteomics in whole blood and peripheral blood mononuclear cells (PBMC) to determine changes in immune cell composition and activation in two independent dual-center patient cohorts (n=46+n=54 COVID-19 samples), each with mild and severe cases of COVID-19. We observed a specific increase of HLA-DRhiCD11chi inflammatory monocytes that displayed a strong interferon (IFN)-stimulated gene signature in patients with mild COVID-19, which was absent in severe disease. Instead, we found evidence of emergency myelopoiesis, marked by the occurrence of immunosuppressive pre-neutrophils and immature neutrophils and populations of dysfunctional and suppressive mature neutrophils, as well as suppressive HLA-DRto monocytes in severe COVID-19. Our study provides detailed insights into systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the peripheral myeloid cell compartment associated with severe courses of COVID-19.", + "rel_num_authors": 63, + "rel_authors": [ + { + "author_name": "Jonas Schulte-Schrepping", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Nico Reusch", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Daniela Paclik", + "author_inst": "Institute of Medical Immunology, Charit\u00e9, Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Kevin Ba\u00dfler", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Stephan Schlickeiser", + "author_inst": "Institute of Medical Immunology, Charit\u00e9, Universit\u00e4tsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charit\u00e9 and Berlin Institute of H" + }, + { + "author_name": "Bowen Zhang", + "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" + }, + { + "author_name": "Benjamin Kr\u00e4mer", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany" + }, + { + "author_name": "Tobias Krammer", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), W\u00fcrzburg, Germany" + }, + { + "author_name": "Sophia Brumhard", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Lorenzo Bonaguro", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Elena De Domenico", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" + }, + { + "author_name": "Daniel Wendisch", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Martin Grasshoff", + "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" + }, + { + "author_name": "Theodore S. Kapellos", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Michael Beckstette", + "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" + }, + { + "author_name": "Tal Pecht", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Adem Saglam", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" + }, + { + "author_name": "Oliver Dietrich", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), W\u00fcrzburg, Germany" + }, + { + "author_name": "Henrik E. Mei", + "author_inst": "Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany" + }, + { + "author_name": "Axel R. Schulz", + "author_inst": "Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany" + }, + { + "author_name": "Claudia Conrad", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "D\u00e9sir\u00e9e Kunkel", + "author_inst": "Flow & Mass Cytometry Core Facility, Charit\u00e9 Universit\u00e4tsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany" + }, + { + "author_name": "Ehsan Vafadarnejad", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), W\u00fcrzburg, Germany" + }, + { + "author_name": "Cheng-Jian Xu", + "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" + }, + { + "author_name": "Arik Horne", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Miriam Herbert", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Anna Drews", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" + }, + { + "author_name": "Charlotte Thibeault", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Moritz Pfeiffer", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Stefan Hippenstiel", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)" + }, + { + "author_name": "Andreas Hocke", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)" + }, + { + "author_name": "Holger M\u00fcller-Redetzky", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Katrin-Moira Heim", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Felix Machleidt", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Alexander Uhrig", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Laure Bousquillon de Jarcy", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Linda J\u00fcrgens", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Miriam Stegemann", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Christoph R. Gl\u00f6senkamp", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Hans-Dieter Volk", + "author_inst": "Institute of Medical Immunology, Charit\u00e9, Universit\u00e4tsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charit\u00e9 and Berlin Institute of He" + }, + { + "author_name": "Christine Goffinet", + "author_inst": "Institute of Virology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; Berlin Institute of Health, 10178 Berlin" + }, + { + "author_name": "Jan Raabe", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany" + }, + { + "author_name": "Kim Melanie Kaiser", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany" + }, + { + "author_name": "Michael To Vinh", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany" + }, + { + "author_name": "Gereon Rieke", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany" + }, + { + "author_name": "Christian Meisel", + "author_inst": "Institute of Virology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Thomas Ulas", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany" + }, + { + "author_name": "Matthias Becker", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" + }, + { + "author_name": "Robert Geffers", + "author_inst": "Genome Analytics, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany" + }, + { + "author_name": "Martin Witzenrath", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Infection Research (DZIF)" + }, + { + "author_name": "Norbert Suttorp", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)" + }, + { + "author_name": "Christof von Kalle", + "author_inst": "Clinical Study Center (CSC), Berlin Institute of Health (BIH), and Charit\u00e9 Universit\u00e4tsmedizin Berlin, Germany" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Kristian H\u00e4ndler", + "author_inst": "PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, Bonn, Germany and University of Bonn, Bonn Germany" + }, + { + "author_name": "Joachim L. Schultze", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegene" + }, + { + "author_name": "Anna C. Aschenbrenner", + "author_inst": "Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany and Radboud UMC, Nijmegen, The Netherlands" + }, + { + "author_name": "Yang Li", + "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" + }, + { + "author_name": "Jacob Nattermann", + "author_inst": "Department of Internal Medicine I, University Hospital Bonn, Bonn Germany; German Center for Infection Research (DZIF)" + }, + { + "author_name": "Birgit Sawitzki", + "author_inst": "Institute of Medical Immunology, Charit\u00e9, Universit\u00e4tsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Antoine-Emmanuel Saliba", + "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), W\u00fcrzburg, Germany" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)" + }, + { + "author_name": "- Deutsche COVID-19 OMICS Initiative (DeCOI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.01.20119750", "rel_title": "SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication", @@ -1376798,49 +1373633,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.02.20116830", - "rel_title": "Calculated grades, predicted grades, forecasted grades and actual A-level grades: Reliability, correlations and predictive validity in medical school applicants, undergraduates, and postgraduates in a time of COVID-19", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20116830", - "rel_abs": "Calculated A-level grades will replace actual, attained A-levels and other Key Stage 5 qualifications in 2020 in the UK as a result of the COVID-19 pandemic. This paper assesses the likely consequences for medical schools in particular, beginning with an overview of the research literature on predicted grades, concluding that calculated grades are likely to correlate strongly with the predicted grades that schools currently provide on UCAS applications. A notable absence from the literature is evidence on whether predicted grades are better or worse than actual grades in predicting university outcomes. This paper provides such evidence on the reduced predictive validity of predicted A-level grades in comparison with actual A-level grades.\n\nThe present study analyses the extensive data on predicted and actual grades which are available in UKMED (United Kingdom Medical Education Database), a large-scale administrative dataset containing longitudinal data from medical school application, through undergraduate and then postgraduate training. In particular, predicted A-level grades as well as actual A-level grades are available, along with undergraduate outcomes and postgraduate outcomes which can be used to assess predictive validity of measures collected at selection. This study looks at two UKMED datasets. In the first dataset we compare actual and predicted A-level grades in 237,030 A-levels taken by medical school applicants between 2010 and 2018. 48.8% of predicted grades were accurate, grades were over-predicted in 44.7% of cases and under-predicted in 6.5% of cases. Some A-level subjects, General Studies in particular, showed a higher degree of over-estimation. Similar over-prediction was found for Extended Project Qualifications, and for SQA Advanced Highers.\n\nThe second dataset considered 22,150 18-year old applicants to medical school in 2010 to 2014, who had both predicted and actual A-level grades. 12,600 students entered medical school and had final year outcomes available. In addition there were postgraduate outcomes for 1,340 doctors. Undergraduate outcomes are predicted significantly better by actual, attained A-level grades than by predicted A-level grades, as is also the case for postgraduate outcomes.\n\nModelling the effect of selecting only on calculated grades suggests that because of the lesser predictive ability of predicted grades, medical school cohorts for the 2020 entry year are likely to under-attain, with 13% more gaining the equivalent of the current lowest decile of performance, and 16% fewer gaining the equivalent of the current top decile, effects which are then likely to follow through into postgraduate training. The problems of predicted/calculated grades can to some extent, although not entirely, be ameliorated, by taking U(K)CAT, BMAT, and perhaps other measures into account to supplement calculated grades. Medical schools will probably also need to consider whether additional teaching is needed for entrants who are struggling, or might have missed out on important aspects of A-level teaching, with extra support being needed, so that standards are maintained.\n\n\"... the ... exam hall [is] a level playing field for all abilities, races and genders to get the grades they truly worked hard for and in true anonymity (as the examiners marking dont know you). [... Now we] are being given grades based on mere predictions.\" Yasmin Hussein, letter to The Guardian, March 29th 2020 [1].\n\n\"[Lets] be honest, this year group will always be different.\" Dave Thomson, blogpost on FFT Educational Lab [2]\n\n\"One headmistress commented that entrance to university on teachers estimates may be fraught with unimagined difficulties. ... If there is in the future considerable emphasis on school assessment, some work of calibration is imperatively called for.\" James Petch, December 1964[3].", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ian Christopher McManus", - "author_inst": "University College London" - }, - { - "author_name": "Katherine Woolf", - "author_inst": "University College London" - }, - { - "author_name": "Dave Harrison", - "author_inst": "University College London" - }, - { - "author_name": "Paul Tiffin", - "author_inst": "University of York" - }, - { - "author_name": "Lewis Paton", - "author_inst": "University of York" - }, - { - "author_name": "Kevin Yet Fong Cheung", - "author_inst": "Cambridge Assessment" - }, - { - "author_name": "Daniel Smith", - "author_inst": "General Medical Council, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.06.02.20116855", "rel_title": "The attitudes, perceptions and experiences of medical school applicants following the closure of schools and cancellation of public examinations in 2020 due to the COVID-19 pandemic", @@ -1377489,6 +1374281,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.03.20120691", + "rel_title": "Modeling COVID-19 dynamics in Illinois under non-pharmaceutical interventions", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120691", + "rel_abs": "We present modeling of the COVID-19 epidemic in Illinois, USA, capturing the implementation of a Stay-at-Home order and scenarios for its eventual release. We use a non-Markovian age-of-infection model that is capable of handling long and variable time delays without changing its model topology. Bayesian estimation of model parameters is carried out using Markov Chain Monte Carlo (MCMC) methods. This framework allows us to treat all available input information, including both the previously published parameters of the epidemic and available local data, in a uniform manner. To accurately model deaths as well as demand on the healthcare system, we calibrate our predictions to total and in-hospital deaths as well as hospital and ICU bed occupancy by COVID-19 patients. We apply this model not only to the state as a whole but also its sub-regions in order to account for the wide disparities in population size and density. Without prior information on non-pharmaceutical interventions (NPIs), the model independently reproduces a mitigation trend closely matching mobility data reported by Google and Unacast. Forward predictions of the model provide robust estimates of the peak position and severity and also enable forecasting the regional-dependent results of releasing Stay-at-Home orders. The resulting highly constrained narrative of the epidemic is able to provide estimates of its unseen progression and inform scenarios for sustainable monitoring and control of the epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "George N Wong", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Zachary J Weiner", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Alexei Tkachenko", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Ahmed Elbanna", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Sergei Maslov", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Nigel Goldenfeld", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.03.20121194", "rel_title": "Identification of spatial variations in COVID-19 epidemiological data using K-Means clustering algorithm: a global perspective", @@ -1378172,125 +1375003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.03.20121426", - "rel_title": "Detection of SARS-Coronavirus-2 in wastewater, using the existing environmental surveillance network: An epidemiological gateway to an early warning for COVID-19 in communities.", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121426", - "rel_abs": "BackgroundThe ongoing COVID-19 pandemic caused by SARs-CoV-2 was transmitted person to person via droplet infections and fecal-oral transmission. This illustrates the probability of environmentally facilitated transmission, mainly the sewage.\n\nMethodWe used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value.\n\nResultsA total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID patients and COVID 19 patient quarantine center drainage strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater.\n\nDiscussionThis study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as early warning system to monitor viral tracking and circulation in cities with lower COVID-19 disease burden or heavily populated areas where door-to-door tracing may not be possible. However, attention needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Salmaan Sharif Sr.", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Aamer Ikram Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan" - }, - { - "author_name": "Adnan Khurshid Sr.", - "author_inst": "National Institute of Health, Islamabad, Paksitan" - }, - { - "author_name": "Muhammad Salman Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Nayab Mehmood Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Yasir Arshad Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Jamal Ahmad Sr.", - "author_inst": "World Health Organization" - }, - { - "author_name": "Mehar Angez Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Muhammad Masroor Alam Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Lubna Rehman Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Ghulam Mujtaba", - "author_inst": "National Institute of Health, Islamabad, Pakistan" - }, - { - "author_name": "Jaffar Hussain Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan" - }, - { - "author_name": "Johar Ali Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan" - }, - { - "author_name": "RIbqa Akthar Sr.", - "author_inst": "National Institute of Health Islamabad, Pakistan" - }, - { - "author_name": "Muhammad Wasif Malik Sr.", - "author_inst": "National Institute of Health, Islamabad, Paksitan." - }, - { - "author_name": "Zeeshan Iqbal Baig Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Muhammad Suleman Rana Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Muhammad Usman Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Muhammad Qasir Ali Sr.", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Abdul Ahad Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Nazish Badar Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan" - }, - { - "author_name": "Massab Umair Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Sana Tamim Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Asiya Ashraf", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Faheem Tahir Sr.", - "author_inst": "National Institute of Health, Islamabad, Pakistan." - }, - { - "author_name": "Nida Ali Sr.", - "author_inst": "World Health Organization" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.03.20121392", "rel_title": "Modulation of COVID-19 Epidemiology by UV-B and -A Photons from the Sun", @@ -1379311,6 +1376023,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.04.135608", + "rel_title": "Design of a Novel Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection", + "rel_date": "2020-06-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.04.135608", + "rel_abs": "Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 386,000 deaths globally as of June 4, 2020. In this study, we developed a novel multiplex real time reverse transcription (RT)-PCR test for detection of SARS-CoV-2, with primers designed to amplify a 108 bp target on the spike surface glycoprotein (S gene) of SARS-CoV-2 and a hydrolysis Taqman probe designed to specifically detect SARS-CoV-2. Following our design, we evaluated the Limit of detection (LOD) and clinical performance of this laboratory-developed test (LDT). A LOD study with inactivated whole virus exhibited equal performance to that seen in the modified CDC assay with a final LOD of 1,301 \u00b1 13 genome equivalents/ml for our assay vs 1,249 \u00b1 14 genome equivalents/ml for the modified CDC assay. In addition, a clinical evaluation with 270 nasopharyngeal (NP) swab specimens exhibited 98.5% positive percent agreement and 99.3% negative percent agreement with the modified CDC assay. The multiplex design of this assay allows the testing of 91 patients per plate, versus a maximum of 29 patients per plate on the modified CDC assay, providing the benefit of testing significantly more patients per run and saving reagents during a time when both of these parameters have been critical. Our results demonstrate that our multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and is therefore adequate for use as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2.View Full Text", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Wei Zhen", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Gregory J Berry", + "author_inst": "Northwell Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.06.04.135616", "rel_title": "Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type.", @@ -1380333,41 +1377068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.04.20122481", - "rel_title": "Characteristics and risk factors for COVID-19 diagnosis and adverse outcomes in Mexico: an analysis of 89,756 laboratory-confirmed COVID-19 cases", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122481", - "rel_abs": "BackgroundThere is insufficient information about risk factors for COVID-19 diagnosis and adverse outcomes from low and middle-income countries (LMICs).\n\nObjectivesWe estimated the association between patients characteristics and COVID-19 diagnosis, hospitalization and adverse outcome in Mexico.\n\nMethodsThis retrospective case series used a publicly available nation-level dataset released on May 31, 2020 by the Mexican Ministry of Health, with patients classified as suspected cases of viral respiratory disease. Patients with COVID-19 were laboratory-confirmed. Their profile was stratified by COVID-19 diagnosis or not. Differences among COVID-19 patients based on two separate clinical endpoints, hospitalization and adverse outcome, were examined. Multivariate logistic regressions examined the associations between patient characteristics and hospitalization and adverse outcome.\n\nResultsOverall, 236,439 patients were included, with 89,756 (38.0%) being diagnosed with COVID-19. COVID-19 patients were disproportionately older, males and with increased prevalence of one or more comorbidities, particularly diabetes, obesity, and hypertension. Age, male gender, diabetes, obesity and having one or more comorbidities were independently associated with laboratory-confirmed COVID-19. Current smokers were 23% less likely to be diagnosed with COVID-19 compared to non-smokers. Of all COVID-19 patients, 34.8% were hospitalized and 13.0% experienced an adverse outcome. Male gender, older age, having one or more comorbidities, and chronic renal disease, diabetes, obesity, COPD, immunosuppression and hypertension were associated with hospitalization and adverse outcome. Current smoking was not associated with adverse outcome.\n\nConclusionThis largest ever case series of COVID-19 patients identified risk factors for COVID-19 diagnosis, hospitalization and adverse outcome. The findings could provide insight for the priorities the need to be set, especially by LMICs, to tackle the pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Theodoros Giannouchos", - "author_inst": "Pharmacotherapy Outcomes Research Center, University of Utah Health, USA" - }, - { - "author_name": "Roberto Sussman", - "author_inst": "Institute of Nuclear Sciences, National Autonomous University of Mexico, Mexico" - }, - { - "author_name": "Jose Manuel Mier", - "author_inst": "Institute of Minimally Invasive Thoracic Surgery, Angeles Lomas Hospital, Mexico" - }, - { - "author_name": "Konstantinos Poulas", - "author_inst": "Laboratory of Molecular Biology and Immunology, University of Patras, Greece" - }, - { - "author_name": "Konstantinos Farsalinos", - "author_inst": "Laboratory of Molecular Biology and Immunology, University of Patras, Greece" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.04.20122044", "rel_title": "ACE2 levels are altered in comorbidities linked to severe outcome in COVID-19", @@ -1380884,6 +1377584,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.05.134114", + "rel_title": "Neuropilin-1 is a host factor for SARS-CoV-2 infection", + "rel_date": "2020-06-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.134114", + "rel_abs": "SARS-CoV-2 is the causative agent of COVID-19, a coronavirus disease that has infected more than 6.6 million people and caused over 390,000 deaths worldwide1,2. The Spike (S) protein of the virus forms projections on the virion surface responsible for host cell attachment and penetration. This viral glycoprotein is synthesized as a precursor in infected cells and, to be active, must be cleaved to two associated polypeptides: S1 and S2(3,4). For SARS-CoV-2 the cleavage is catalysed by furin, a host cell protease, which cleaves the S protein precursor at a specific sequence motif that generates a polybasic Arg-Arg-Ala-Arg (RRAR) C-terminal sequence on S1. This sequence motif conforms to the C-end rule (CendR), which means that the C-terminal sequence may allow the protein to associate with cell surface neuropilin-1 (NRP1) and neuropilin-2 (NRP2) receptors5. Here we demonstrate using immunoprecipitation, site-specific mutagenesis, structural modelling, and antibody blockade that, in addition to engaging the known receptor ACE2, S1 can bind to NRP1 through the canonical CendR mechanism. This interaction enhances infection by SARS-CoV-2 in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection, and provides a therapeutic target for COVID-19.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "James L Daly", + "author_inst": "University of Bristol" + }, + { + "author_name": "Boris Simonetti", + "author_inst": "University of Bristol" + }, + { + "author_name": "Carlos Anton Plagaro", + "author_inst": "University of Bristol" + }, + { + "author_name": "Maia Kavanagh Williamson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Deborah K Shoemark", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lorena Simon-Gracia", + "author_inst": "University of Tartu" + }, + { + "author_name": "Katja Klein", + "author_inst": "University of Bristol" + }, + { + "author_name": "Michael Bauer", + "author_inst": "University of Zurich" + }, + { + "author_name": "Reka Hollandi", + "author_inst": "Biological Research Centre, Hungarian Academy of Sciences" + }, + { + "author_name": "Urs F Greber", + "author_inst": "University of Zurich" + }, + { + "author_name": "Peter Horvath", + "author_inst": "Biological Research Centre," + }, + { + "author_name": "Richard B Sessions", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ari Helenius", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Julian A Hiscox", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Tambet Teesalu", + "author_inst": "University of Tartu" + }, + { + "author_name": "David A Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew D Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Peter J Cullen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Yohei Yamauchi", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.06.03.20121301", "rel_title": "Class I HLA allele restricted antigenic coverage for Spike and N proteins is associated with divergent outcomes for COVID-19", @@ -1381831,45 +1378622,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.02.20120360", - "rel_title": "Multi-parametric disease dynamics study and analysis of the COVID-19 epidemic and implementation of population-wide intrusions: The Indian perspective", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120360", - "rel_abs": "The outbreak of COVID-19 had spread at a deadly rate since its onset at Wuhan, China and is now spread across 216 countries and has affected more than 6 million people all over the world. The global response throughout the world has been primarily the implementation of lockdown measures, testing and contact tracing to minimise the spread of the disease. The aim of the present study was to predict the COVID-19 prevalence and disease progression rate in Indian scenario in order to provide an analysis that can shed light on comprehending the trends of the outbreak and outline an impression of the epidemiological stage for each state of a diverse country like India. In addition, the forecast of COVID-19 incidence trends of these states can help take safety measures and policy design for this epidemic in the days to come. In order to achieve the same, we have utilized an approach where we test modelling choices of the spatially unambiguous kind, proposed by the wave of infections spreading from the initial slow progression to a higher curve. We have estimated the parameters of an individual state using factors like population density and mobility. The findings can also be used to strategize the testing and quarantine processes to manipulate the spread of the disease in the future. This is especially important for a country like India that has several limitations about healthcare infrastructure, diversity in socioeconomic status, high population density, housing conditions, health care coverage that can be important determinants for the overall impact of the pandemic. The results of our 5-phase model depict a projection of the state wise infections/disease over time. The model can generate live graphs as per the change in the data values as the values are automatically being fetched from the crowd-sourced database.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Samuel Bharti", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - }, - { - "author_name": "Priyanka Narad", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - }, - { - "author_name": "Parul Chugh", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - }, - { - "author_name": "Alakto Choudhury", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - }, - { - "author_name": "Seema Bhatnagar", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - }, - { - "author_name": "Abhishek Sengupta", - "author_inst": "Amity Institute of Biotechnology, Amity University, Uttar Pradesh, INDIA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.02.20120808", "rel_title": "The Relationship Between COVID-19 Infection and Risk Perception, Knowledge, Attitude As Well As Four Non-pharmaceutical Interventions (NPIs) During the Late Period Of The COVID-19 Epidemic In China An Online Cross-sectional Survey of 8158 Adults", @@ -1382602,6 +1379354,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.02.20120311", + "rel_title": "Are adversities and worries during the COVID-19 pandemic related to sleep quality? Longitudinal analyses of 45,000 UK adults", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120311", + "rel_abs": "There are concerns that both the experience of adversities during the COVID-19 pandemic and worries about experiencing adversities will have substantial and lasting effects on mental health. One pathway through which both experience of and worries about adversity may impact health is through effects on sleep. We used data from 48,723 UK adults in the COVID-19 Social Study assessed weekly from 01/04/2020-12/05/2020 to study the association between adversities and sleep quality. We studied six categories of adversity including both worries and experiences of: illness with COVID-19, financial difficulty, loss of paid work, difficulties acquiring medication, difficulties accessing food, and threats to personal safety. We used random-effect within-between models to account for all time-invariant confounders. Both the total number of adversity experiences and total number of adversity worries were associated with lower quality sleep. Each additional experience was associated with a 1.16 (95% CI = 1.10, 1.22) times higher odds of poor quality sleep while each additional worry was associated with a 1.20 (95% CI = 1.17, 1.22) times higher odds of poor quality sleep. When considering specific experiences and worries, all worries and experiences were significantly related to poorer quality sleep except experiences relating to employment and finances. Having a larger social network offered some buffering effects on associations but there was limited further evidence of moderation by social or psychiatric factors. Poor sleep may be a mechanism by which COVID-19 adversities are affecting mental health. This highlights the importance of interventions that support adaptive coping strategies during the pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Liam Wright", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.02.20120394", "rel_title": "Swab Tests and COVID 19, Italy case studied using Artificial Intelligence, Statistical Analysis and MLR", @@ -1383245,49 +1380024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2020.06.01.20119651", - "rel_title": "Ethnically diverse mutations in PIEZO1 associate with SARS-CoV-2 positivity", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119651", - "rel_abs": "COVID-19, caused by the SARS-CoV-2 virus, carries significant risk of mortality and has spread globally with devastating societal consequences. Endothelial infection has been identified as a feature of the disease and so there is motivation to determine the relevance of endothelial membrane mechanisms affecting viral entry and response. Here, through a study of patient data in UK Biobank released on 16 April 2020, we suggest relevance of PIEZO1, a non-selective cation channel protein that both mediates endothelial responses to mechanical force and unusually indents the cell membrane. PIEZO1 notably has roles that may also be relevant in red blood cell function, pulmonary inflammation, bacterial infection and fibrotic auto-inflammation. We provide evidence that single nucleotide polymorphisms (SNPs) in the gene encoding PIEZO1 are more common in individuals who test positive for SARS-CoV-2 regardless of pre-existing hypertension, myocardial infarction, stroke, diabetes mellitus or arthritis. Some of these SNPs are more common in African and Caribbean populations, which are groups that were recently shown to have greater susceptibility to infection. One of the SNPs is a missense mutation that results in an amino acid change in an evolutionarily conserved and previously unexplored N-terminal region PIEZO1. The data support the notion of genetic factors influencing SARS-CoV-2 infection and suggest a specific role for PIEZO1.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chew W Cheng", - "author_inst": "University of Leeds" - }, - { - "author_name": "Vijayalakshmi Deivasikamani", - "author_inst": "University of Leeds" - }, - { - "author_name": "Melanie J Ludlow", - "author_inst": "University of Leeds" - }, - { - "author_name": "Dario De Vecchis", - "author_inst": "University of Leeds" - }, - { - "author_name": "Antreas C Kalli", - "author_inst": "University of Leeds" - }, - { - "author_name": "David J Beech", - "author_inst": "University of Leeds" - }, - { - "author_name": "Piruthivi Sukumar", - "author_inst": "University of Leeds" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.31.20118760", "rel_title": "Model Based Covid-19 Case Studies in the UK, the USA and India", @@ -1383744,6 +1380480,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.30.20117523", + "rel_title": "Missing clinical trial data: the knowledge gap in the safety of potential COVID-19 drugs", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117523", + "rel_abs": "BackgroundSeveral drugs are being repurposed for the treatment of the coronavirus disease 2019 (COVID-19) pandemic based on in vitro or early clinical findings. As these drugs are being used in varied regimens and dosages, it is important to enable synthesis of existing safety data from clinical trials. However, availability of safety information is limited by a lack of timely reporting of clinical trial results on public registries or through academic publication. We aimed to analyse the evidence gap in safety data by quantifying the number of missing clinical trial results for drugs potentially being repurposed for COVID-19 by conducting a rapid review of results posting on ClinicalTrials.gov and in academic publications.\n\nMethodsClinicalTrials.gov was searched for 19 drugs that have been identified as potential treatments for COVID-19. Relevant clinical trials for any prior indication were listed by identifier (NCT number) and checked for results and for timely result reporting (within 395 days of the primary completion date). Additionally, PubMed and Google Scholar were searched to identify publications of results not listed on the registry. A second, blinded search of 10% of trials was conducted to assess reviewer concordance.\n\nResultsOf 3754 completed trials, 1516 (40.4%) did not post results on ClinicalTrials.gov or in the academic literature. 1172 (31.2%) completed trials had tabular results on ClinicalTrials.gov. A further 1066 (28.4%) completed trials had results from the literature search, but did not report results on ClinicalTrials.gov. Key drugs missing clinical trial results include hydroxychloroquine (37.0% completed trials unreported), favipiravir (77.8%) and lopinavir (40.5%).\n\nConclusionsThere is an important evidence gap for the safety of drugs being repurposed for COVID-19. This uncertainty could cause a large burden of additional morbidity and mortality during the pandemic. We recommend caution in experimental drug use for non-severe disease and urge clinical trial sponsors to report missing results retrospectively.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Florence Rodgers", + "author_inst": "School of Medicine, Imperial College London, London, UK" + }, + { + "author_name": "Toby Pepperrell", + "author_inst": "School of Medicine, Imperial College London, London, UK" + }, + { + "author_name": "Sarai Keestra", + "author_inst": "1.\tSchool of Anthropology & Museum Ethnography, University of Oxford, UK 2.\tDepartment of Global Health & Development, London School of Hygiene and Tropical M" + }, + { + "author_name": "Victoria Pilkington", + "author_inst": "Stoke Mandeville Hospital, Buckinghamshire Healthcare Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.31.20117168", "rel_title": "Using newspapers obituaries to nowcast daily mortality: evidence from the Italian COVID-19 hot-spots", @@ -1384583,29 +1381350,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.31.20118182", - "rel_title": "Forecasting the Peak of Novel Coronavirus Disease in Egypt Using Current Confirmed Cases and Deaths", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118182", - "rel_abs": "The first case of coronavirus disease 2019 (COVID-19) in Egypt was reported on 14 February 2020 and the number of reported cases has increased daily. The purpose of this study is to describe the current situation of Covid-19 in Egypt and to predict the expected timing of the peak of this epidemic using current confirmed cases and deaths. We used one of the online tools; the Epidemic Calculator that utilizes, the well-known SEIR compartmental model. We utilized the daily reports published by the Egyptian Ministry of Health & Population from 14 February to 11 May 2020. Given the highest calculated case fatality rate (7.7%), the number of hospitalized individuals is expected to peak in the middle of June with a peak of hospitalized cases of 20,126 individuals and total expected deaths 12,303. We recommend strengthening of the Egyptian preventive and control measures so as to decrease the CFR and the number of cases to the least possible as we approach the epidemic peak. It is most important that appropriate quarantine measures are retained., the quarantine measures should not be relaxed before the end of June, 2020.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Wagida Abdelrahman Anwar", - "author_inst": "Department of Community Environmental and Occupational Medicine, Faculty of Medicine, Ain Shams University, Egypt --- Research Department, Armed Forces College " - }, - { - "author_name": "Amany Mokhtar AbdelHafez", - "author_inst": "Department of Community Environmental and Occupational Medicine, Faculty of Medicine, Ain Shams University, Egypt & Research Department, Armed Forces College of" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.30.20117283", "rel_title": "Spreading of COVID-19 in Brazil: Impacts and uncertainties in social distancing strategies", @@ -1385062,6 +1381806,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.01.20119198", + "rel_title": "Evaluation of symptomatic patient saliva as a sample type for the Abbott ID NOW COVID-19 assay", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119198", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has presented significant challenges for laboratories including supply chain limitations with restricted access to reagents and sample collection materials (i.e. swabs, viral transport media (VTM)) for patients testing. Therefore, saliva has been evaluated as an alternative specimen for COVID-19 diagnosis. comparable performance between dry nasal swabs (NS) and nasopharyngeal swabs (NPS) collected in VTM has been observed with the ID NOW for SARS-CoV-2; the majority of false-negative results occur with higher cycle number (CN) or cycle threshold (Ct) values suggesting low viral load in these specimens. We performed clinical validation of saliva specimens on the ID NOW molecular platform to detect SARS-CoV-2. Saliva was compared to nasopharyngeal swabs tested on the ID NOW and the Cepheid molecular assay. We also performed stability studies of saliva samples over 5 days. A total of 96 saliva samples and 64 paired NPS were analyzed. We observed 78% (18/23) positive percent agreement (PPA) and 100% (44/44) negative percent agreement (NPA) between matched saliva and nasopharyngeal specimens performed on ID NOW. We found 83% (19/23) PPA and 100% NPA (25/25) between saliva run on the ID NOW and Cepheid assay. Six saliva specimens positive for SARS-CoV-2 were continuously positive for five days when stored at room temperature. Therefore, we propose further investigation of saliva as an alternative sample type for testing symptomatic patients with ID NOW as a promising method to address COVID-19 testing.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jeffrey SoRelle", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Lenin Mahimmainathan", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Clare McCormick-Baw", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Dominick Cavuoti", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Franceca Lee", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Anjali Bararia", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Abey Thomas", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Ravi Sarode", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Andrew E Clark", + "author_inst": "UT Southwestern" + }, + { + "author_name": "Alagarraju Muthukumar", + "author_inst": "UT Southwestern" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.30.20118158", "rel_title": "Development and application of Pandemic Projection Measures (PPM) for forecasting the COVID-19 outbreak", @@ -1385761,41 +1382560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.01.20119073", - "rel_title": "Compliance and containment in social distancing: mathematical modeling of COVID-19 across townships", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119073", - "rel_abs": "In the early development of COVID-19, large-scale preventive measures, such as border control and air travel restrictions, were implemented to slow international and domestic transmissions. When these measures were in full effect, new cases of infection would be primarily induced by community spread, such as the human interaction within and between neighboring cities and towns, which is generally known as the meso-scale. Existing studies of COVID-19 using mathematical models are unable to accommodate the need for meso-scale modeling, because of the unavailability of COVID-19 data at this scale and the different timings of local intervention policies. In this respect, we propose a meso-scale mathematical model of COVID-19 using town-level infection data in the state of Connecticut. We consider the spatial interaction in terms of the inter-town travel in the model. Based on the developed model, we evaluated how different strengths of social distancing policy enforcement may impact future epidemic curves based on two evaluative metrics: compliance and containment. The developed model and the simulation results will establish the foundation for community-level assessment and better preparation for COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xiang Chen", - "author_inst": "Department of Geography, University of Connecticut" - }, - { - "author_name": "Aiyin Zhang", - "author_inst": "Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University" - }, - { - "author_name": "Hui Wang", - "author_inst": "Institute for Modeling Collaboration and Innovation, University of Idaho" - }, - { - "author_name": "Adam Gallaher", - "author_inst": "Department of Geography, University of Connecticut" - }, - { - "author_name": "Xiaolin Zhu", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.01.20119172", "rel_title": "SCALE19: A scalable and cost-efficient method for testing Covid-19 based on hierarchical group testing", @@ -1386368,6 +1383132,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.30.20107888", + "rel_title": "Machine learning in predicting respiratory failure in patients with COVID-19 pneumonia - challenges, strengths, and opportunities in a global health emergency", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20107888", + "rel_abs": "AimsThe aim of this study was to estimate a 48 hour prediction of moderate to severe respiratory failure, requiring mechanical ventilation, in hospitalized patients with COVID-19 pneumonia.\n\nMethodsThis was an observational study that comprised consecutive patients with COVID-19 pneumonia admitted to hospital from 21 February to 6 April 2020. The patients medical history, demographic, epidemiologic and clinical data were collected in an electronic patient chart. The dataset was used to train predictive models using an established machine learning framework leveraging a hybrid approach where clinical expertise is applied alongside a data-driven analysis. The study outcome was the onset of moderate to severe respiratory failure defined as PaO2/FiO2 ratio <150 mmHg in at least one of two consecutive arterial blood gas analyses in the following 48 hours. Shapley Additive exPlanations values were used to quantify the positive or negative impact of each variable included in each model on the predicted outcome.\n\nResultsA total of 198 patients contributed to generate 1068 usable observations which allowed to build 3 predictive models based respectively on 31-variables signs and symptoms, 39-variables laboratory biomarkers and 91-variables as a composition of the two. A fourth \"boosted mixed model\" included 20 variables was selected from the model 3, achieved the best predictive performance (AUC=0.84) without worsening the FN rate. Its clinical performance was applied in a narrative case report as an example.\n\nConclusionThis study developed a machine model with 84% prediction accuracy, which is able to assist clinicians in decision making process and contribute to develop new analytics to improve care at high technology readiness levels.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Davide Ferrari", + "author_inst": "Department of Physical, Computer and Mathematical Sciences, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Jovana Milic", + "author_inst": "Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Roberto Tonelli", + "author_inst": "University of Modena and Reggio Emilia and Azienda Ospedaliero-Universitaria Policlinico of Modena" + }, + { + "author_name": "Francesco Ghinelli", + "author_inst": "University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Marianna Meschiari", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Sara Volpi", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Matteo Faltoni", + "author_inst": "Respiratory Diseases Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Giacomo Franceschi", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Vittorio Iadisernia", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Dina Yaacoub", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Giacomo Ciusa", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Erica Bacca", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Carlotta Rogati", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Marco Tutone", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Giulia Burastero", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Alessandro Raimondi", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Marianna Menozzi", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Erica Franceschini", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Gianluca Cuomo", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Luca Corradi", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Gabriella Orlando", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Antonella Santoro", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Margherita Di Gaetano", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Cinzia Puzzolante", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Federica Carli", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Andrea Bedini", + "author_inst": "Department of Infectious Diseases, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Riccardo Fantini", + "author_inst": "Respiratory Diseases Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Luca Tabb\u00ec", + "author_inst": "Respiratory Diseases Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Ivana Castaniere", + "author_inst": "Respiratory Diseases Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Stefano Busani", + "author_inst": "Department of Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Enrico Clini", + "author_inst": "Respiratory Diseases Unit, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy" + }, + { + "author_name": "Massimo Girardis", + "author_inst": "Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Mario Sarti", + "author_inst": "Clinical Microbiology, Ospedale Civile di Baggiovara, Modena, Italy" + }, + { + "author_name": "Andrea Cossarizza", + "author_inst": "Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Cristina Mussini", + "author_inst": "Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Federica Mandreoli", + "author_inst": "Department of Physical, Computer and Mathematical Sciences, University of Modena and Reggio Emilia, Italy" + }, + { + "author_name": "Paolo Missier", + "author_inst": "Newcastle University" + }, + { + "author_name": "Giovanni Guaraldi", + "author_inst": "Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.05.29.20110098", "rel_title": "Evolutionary trends of the COVID-19 epidemic and effectiveness of government interventions in Nigeria: A data-driven analysis.", @@ -1387311,45 +1384242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20113209", - "rel_title": "Applying Heat and Humidity using Stove Boiled Water for Decontamination of N95 Respirators in Low Resource Settings", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20113209", - "rel_abs": "Global shortages of N95 respirators have led to an urgent need of N95 decontamination and reuse methods that are scientifically validated and available world-wide. Although several large scale decontamination methods have been proposed (hydrogen peroxide vapor, UV-C); many of them are not applicable in remote and low-resource settings. Heat with humidity has been demonstrated as a promising decontamination approach, but care must be taken when implementing this method at a grassroots level. Here we present a simple, scalable method to provide controlled humidity and temperature for individual N95 respirators which is easily applicable in low-resource settings. N95 respirators were subjected to moist heat (>50% relative humidity, 65-80{degrees}C temperature) for over 30 minutes by placing them in a sealed container immersed in water that had been brought to a rolling boil and removed from heat, and then allowing the containers to sit for over 45 minutes. Filtration efficiency of 0.3-4.99um incense particles remained above 97% after 5 treatment cycles across all particle size sub-ranges. This method was then repeated at a higher ambient temperature and humidity in Mumbai, using standard utensils commonly found in South Asia. Similar temperatures and humidities were achieved and filtration efficiencies consistently remained above 94%. Higher temperatures (>70{degrees}C) and longer treatment times (>40 minutes) were obtained by insulating the outer vessel. This simple yet reliable method can be performed even without electricity access using any heat source to boil water, from open-flame stoves to solar heating, and provides a low-cost route for N95 decontamination globally applicable in resource-constrained settings.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Siddharth Doshi", - "author_inst": "Department of Materials Science and Engineering, Stanford University" - }, - { - "author_name": "Samhita P. Banavar", - "author_inst": "Department of Bioengineering, Stanford University" - }, - { - "author_name": "Eliott Flaum", - "author_inst": "Biophysics Graduate Program, Department of Bioengineering, Stanford University" - }, - { - "author_name": "Shailabh Kumar", - "author_inst": "Department of Bioengineering, Stanford University" - }, - { - "author_name": "Tyler Chen", - "author_inst": "Department of Bioengineering, Stanford University" - }, - { - "author_name": "Manu Prakash", - "author_inst": "Department of Bioengineering, Stanford University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.26.20113399", "rel_title": "COVID-19 Trend and Forecast in India: A Joinpoint Regression Analysis", @@ -1387942,6 +1384834,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.29.20113571", + "rel_title": "A Time-Dependent SEIRD Model for Forecasting the COVID-19 Transmission Dynamics", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20113571", + "rel_abs": "The spread of a disease caused by a virus can happen through human to human contact or could be from the environment. A mathematical model could be used to capture the dynamics of the disease spread to estimate the infections, recoveries, and fatalities that may result from the disease. An estimation is crucial to make policy decisions and for the alerts for the medical emergencies that may arise. Many epidemiological models are being used to make such an estimation. One major factor that is important in the forecasts using the models is the dynamic nature of the disease spread. Unless we can come up with a way of estimating the parameters that guide this dynamic spread, the models may not give accurate forecasts. The main principle is to keep the model generic while making minimal assumptions. In this work, we have derived a data-driven model from SEIRD, where we attempt to forecast Infected, Recovered and Deceased rates of COVID-19 up to a week. A method of estimating the parameters of the model is also discussed thoroughly in this work. The model is tested for India at a district level along with the most affected foreign cities like Lombardia from Italy and Moscow from Russia.\n\nThe forecasts can help the governments in planning for emergencies such as ICU requirements, PPEs, hospitalizations, and so on as the infection is going to be prevalent for some time until a vaccine or cure is invented.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taarak Rapolu", + "author_inst": "University of Hyderabad" + }, + { + "author_name": "Brahmani Nutakki", + "author_inst": "University of Hyderabad" + }, + { + "author_name": "T. Sobha Rani", + "author_inst": "University of Hyderabad" + }, + { + "author_name": "S. Durga Bhavani", + "author_inst": "University of Hyderabad" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20114546", "rel_title": "SARS-CoV-2 genetic variations associated with COVID-19 severity", @@ -1389461,37 +1386384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.02.20120089", - "rel_title": "How efficient are the lockdown measures taken for mitigating the Covid-19 epidemic?", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120089", - "rel_abs": "Various lockdown measures have been taken in different countries to mitigate the Covid-19 pandemic. But, for citizens, it is not always simple to understand how these measures have been taken. Should they have been more (or less) restrictive? Should the lockdown period have been longer (or shorter)? What would have been the benefits of starting to confine the population earlier? To provide some elements of response to these questions, we propose a simple behavior model for the government decision-making operation. Although simple and obviously improvable, the proposed model has the merit to implement in a pragmatic and insightful way the tradeoff between health and macroeconomic aspects. For a given tradeoff between the assumed cost functions for the economic and health impacts, it is then possible to determine the best lockdown starting date, the best lockdown duration, and the optimal severity levels during and after lockdown. The numerical analysis is based on a standard SEIR model and performed for the case of France but the adopted approach can be applied to any country. Our analysis, based on the proposed model, shows that for France it would have been possible to have just a quarter of the actual number of people infected (over [March 1, August 31]), while simultaneously having a Gross Domestic Product loss about 30% smaller than the one expected with the current policy", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Samson Lasaulce", - "author_inst": "CRAN, CNRS" - }, - { - "author_name": "VINEETH SATHEESKUMAR VARMA", - "author_inst": "CRAN, CNRS" - }, - { - "author_name": "Constantin Morarescu", - "author_inst": "CRAN, CNRS" - }, - { - "author_name": "Lin Siying", - "author_inst": "CRAN, University of Lorraine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20115063", "rel_title": "The Risk of Lifting COVID-19 Confinement in Mexico", @@ -1390088,6 +1386980,25 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.06.02.129312", + "rel_title": "System Dynamics Modeling Of Within-Host Viral Kinetics Of Coronavirus (SARS CoV-2)", + "rel_date": "2020-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.02.129312", + "rel_abs": "Mathematical models are being used extensively in the study of SARS-CoV-2 transmission dynamics, becoming an essential tool for decision making concerning disease control. It is now required to understand the mechanisms involved in the interaction between the virus and the immune response effector cells, both innate and adaptive, in order to support lines of research related to the use of drugs, production of protective antibodies and of course, vaccines against SARS-CoV-2. The present study, using a system dynamic approach, hypothesizes over the conditions that characterize the fraction of the population which get infected by SARS-CoV-2 as the asymptomatic patients, the mild symptomatic, acute symptomatic, and also super-spreaders, in terms of innate immune response, the initial virus load, the virus burden with shedding events, and the cytokine levels.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Javier Burgos", + "author_inst": "Ciinas Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.06.02.129098", "rel_title": "Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody", @@ -1391099,73 +1388010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.31.20118679", - "rel_title": "Delirium Incidence, Duration and Severity in Critically Ill Patients with COVID-19", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118679", - "rel_abs": "BackgroundDelirium incidence, duration and severity in patients admitted to the intensive care unit (ICU) due to COVID-19 is not known.\n\nMethodsWe conducted an observational study at two large urban academic Level 1 trauma centers. Consecutive patients admitted to the ICU with a positive SARS-CoV-2 nasopharyngeal swab polymerase chain reaction test from March 1st, 2020 to April 27, 2020 were included. Individuals younger than 18 years of age, without any documented delirium assessments (CAM-ICU), or without a discharge disposition were excluded. The primary outcomes were delirium rates and delirium duration and the secondary outcome was delirium severity. Outcomes were assessed for up to the first 14 days of ICU stay.\n\nResultsOf 243 consecutive patients with confirmed COVID-19 admitted to the ICU, 144 met eligibility criteria and were included in the analysis. Delirium occurred in 73.6% (106/144) and delirium or coma occurred in 76.4% (110/144). Sixty-three percent of patients were positive for delirium on the first CAM-ICU assessment. The median duration of delirium and coma was 7 days (IQR: 3-10), and the median delirium duration was 5 days (IQR: 2-7). The median CAM-ICU-7 score was 6 (IQR: 4-7) representing severe delirium. Mechanical ventilation was associated with greater odds of developing delirium (OR: 42.1, 95%CI: 13.0-137.1). Mortality was 26.4% in patients with delirium compared to 15.8% in patients without delirium.\n\nConclusions73.6% of patients admitted to the ICU with COVID-19 experience delirium that persists for approximately 1 week. Invasive mechanical ventilation is significantly associated with odds of delirium. Clinical attention to prevent and manage delirium and reduce delirium duration and severity is urgently needed for patients with COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sikandar H Khan", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Heidi Lindroth", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Anthony J Perkins", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Yasser Jamil", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Sophia Wang", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Scott Roberts", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Mark O Farber", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Omar Rahman", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Sujuan Gao", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Edward R Marcantonio", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Malaz Boustani", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Roberto Machado", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Babar A Khan", - "author_inst": "Indiana University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.31.20118802", "rel_title": "The Association Between Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers and the Number of Covid-19 Confirmed Cases and Deaths in the United States: Geospatial Study", @@ -1391578,6 +1388422,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.31.126524", + "rel_title": "A Scalable Topical Vectored Vaccine Candidate Against SARS-CoV-2", + "rel_date": "2020-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.126524", + "rel_abs": "The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) caused an ongoing unprecedented global public health crises of coronavirus disease in 2019 (CoVID-19). The precipitously increased death rates, its impact on livelihood and trembling economies warrant the urgent development of SARS-CoV-2 vaccine which would be safe, efficacious and scalable. Owing to unavailability of the vaccine, we propose a de novo synthesised avian orthoavulavirus 1 (AOaV-1)-based topical respiratory vaccine candidate against CoVID-19. Avirulent strain of Newcastle disease virus, proto-type virus of AOaV-1, was engineered to express full length spike (S) glycoprotein which is highly neutralizing and major protective antigen of the SARS-CoV-2. Broad-scale in vitro characterization of recombinant vaccine candidate demonstrated efficient co-expression of the hemagglutinin-neuraminidase (HN) of AOaV-1 and S protein of SARS-CoV-2, and comparable replication kinetics were observed in cell culture model. The recombinant vaccine candidate virus actively replicated and spread within cells independently of exogenous trypsin. Interestingly, incorporation of S protein of SARS-CoV-2 into the recombinant AOaV-1 particles attributed the sensitivity to anti-SARS-CoV-2 antiserum and more prominently to anti-AOaV-1 antiserum. Finally, our results demonstrated that the recombinant vaccine vector stably expressed S protein after multiple propagation in chicken embryonated eggs, and this expression did not significantly impact the in vitro growth characteristics of the recombinant. Taken together, the presented respiratory vaccine candidate is highly attenuated in primates per se, safe and lacking pre-existing immunity in human, and carries the potential for accelerated vaccine development against CoVID-19 for clinical studies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohammed A Rohaim", + "author_inst": "Lancaster University" + }, + { + "author_name": "Muhammad Munir", + "author_inst": "Lancaster University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.31.126342", "rel_title": "Improved and Simplified Diagnosis of Covid-19 using TE Extraction from Dry Swabs", @@ -1392468,33 +1389335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115790", - "rel_title": "CoViD-19 in Italy: a mathematical model to analyze the epidemic containment strategy and the economic impacts", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115790", - "rel_abs": "The objective of this paper is to evaluate the potential costs deriving from the adoption of the CoViD-19 epidemic management strategy. For this purpose, we developed a specific methodology that combines an epidemiological model, known in the literature as \"SIR\" (Susceptible - Infected - Recovered), and a probabilistic state model, also known as \"multi-state\". The model thus conceived was then parameterized using the dataset published by the Italian Government through the Civil Protection and the Istituto Superiore di Sanita. We therefore estimated the duration of the disease and the related costs, with reference to the strategy currently under discussion between government institutions and social organizations involved. Given the flexibility of the adopted approach, the tool will also be able to provide useful indications in relation to any alternative strategies that the Government could adopt in the near future, as well as being the starting point of an analysis of the epidemic indirect costs such as losses of GDP fractions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fabio Verachi", - "author_inst": "Intesa Sanpaolo" - }, - { - "author_name": "Luca G Trussoni", - "author_inst": "LTLOGICS" - }, - { - "author_name": "Luciano Lanzi", - "author_inst": "Freelance" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20115527", "rel_title": "Analyzing Covid-19 Data using SIRD Models", @@ -1393163,6 +1390003,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.28.20115667", + "rel_title": "Targeted Immunosuppression Distinguishes COVID-19 from Influenza in Moderate and Severe Disease", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115667", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is characterized by a high incidence of acute respiratory failure. The underlying immunopathology of that failure and how it compares to other causes of severe respiratory distress, such as influenza virus infection, are not fully understood. Here we addressed this by developing a prospective observational cohort of COVID-19 and influenza subjects with varying degrees of disease severity and assessing the quality and magnitude of their immune responses at the cellular and protein level. Additionally, we performed single-cell RNA transcriptional profiling of peripheral blood mononuclear cells from select subjects. The cohort consists of 79 COVID-19 subjects, 26 influenza subjects, and 15 control subjects, including 35 COVID-19 and 7 influenza subjects with acute respiratory failure. While COVID-19 subjects exhibited largely equivalent or greater activated lymphocyte counts compared to influenza subjects, they had fewer monocytes and lower surface HLA-class II expression on monocytes compared to influenza subjects and controls. At least two distinct immune profiles were observed by cytokine levels in severe COVID-19 patients: 3 of 71 patients were characterized by extreme inflammation, with greater than or equal to [~]50% of the 35 cytokines measured greater than 2 standard deviations from the mean level of other severe patients (both influenza and COVID-19); the other immune profile, which characterized 68 of 71 subjects, had a mixed inflammatory signature, where 28 of 35 cytokines in COVID-19 patients had lower mean cytokine levels, though not all were statistically significant. Only 2 cytokines were higher in COVID-19 subjects compared to influenza subjects (IL-6 and IL-8). Influenza and COVID-19 patients could be distinguished statistically based on cytokine module expression, particularly after controlling for the significant effects of age on cytokine expression, but again with lower levels of most cytokines in COVID-19 subjects. Further, high circulating levels of IL-1RA and IL-6 were associated with increased odds of intubation in the combined influenza and COVID-19 cohort [OR = 3.93 and 4.30, respectively] as well as among only COVID-19 patients. Single cell transcriptional profiling of COVID-19 and influenza subjects with respiratory failure identified profound suppression in type I and type II interferon signaling in COVID-19 patients across multiple clusters. In contrast, COVID-19 cell clusters were enriched for alterations in metabolic, stress, and apoptotic pathways. These alterations were consistent with an increased glucocorticoid response in COVID-19 patients compared to influenza. When considered across the spectrum of innate and adaptive immune profiles, the immune pathologies underlying severe influenza and COVID-19 are substantially distinct. The majority of COVID-19 patients with acute respiratory failure do not have a cytokine storm phenotype but instead exhibit profound type I and type II IFN immunosuppression when compared to patients with acute influenza. Upregulation of a small number of inflammatory mediators, including IL-6, predicts acute respiratory failure in both COVID-19 and influenza patients.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Philip A Mudd", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jeremy Chase Crawford", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Jackson S Turner", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Aisha Souquette", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Daniel Reynolds", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Diane Bender", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "James P. Bosanquet", + "author_inst": "Missouri Baptist Medical Center" + }, + { + "author_name": "Nitin J. Anand", + "author_inst": "Missouri Baptist Medical Center" + }, + { + "author_name": "David A. Striker", + "author_inst": "Missouri Baptist Medical Center" + }, + { + "author_name": "R. Scott Martin", + "author_inst": "Missouri Baptist Medical Center" + }, + { + "author_name": "Adrianus C. M. Boon", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Stacey L. House", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Kenneth E. Remy", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Richard S. Hotchkiss", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Rachel M. Presti", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Jane A. OHalloran", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "William G. Powderly", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Paul G. Thomas", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Ali H. Ellebedy", + "author_inst": "Washington University in Saint Louis School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.29.20117184", "rel_title": "How Efficacious Must a COVID-19 Coronavirus Vaccine be to Prevent or Stop an Epidemic by Itself", @@ -1394258,25 +1391189,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.24.20112292", - "rel_title": "A Simple Method of Finding an Approximate Pattern of the COVID-19 Spread", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112292", - "rel_abs": "We are going to show that the pattern of spread of COVID-19 outside China is not monotonic. We have considered the data outside China because we are going to study the data starting from March 21, and by that time the spread had almost come to a stop in China. We have used for our analysis data on total cases outside China till April 25, 2020, and data from April 26 to April 30 for comparison of forecasts and observed values. Right from the beginning the spread pattern was nonlinear, and by the end of the third week of March the nonlinearity became nearly exponential. The exponential pattern thereafter has changed by around March 28, April 5, April 11 and April 18. Since March 21, the spread is following a nearly exponential pattern of growth changing observably at almost regular intervals of seven days. It is but natural that at some point of time the countries that had been contributing in observably large numbers to the total cases would start to show diminishing growth patterns. Therefore long term forecasts using our method would give us slightly overestimated results. However, for short term forecasting our simple method does work very well when we consider the total number of cases in the world and not in any particular country.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Hemanta Kumar Baruah", - "author_inst": "The Assam Royal Global University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.28.20115964", "rel_title": "Measuring COVID-19 and Influenza in the Real World via Person-Generated Health Data", @@ -1394793,6 +1391705,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20117176", + "rel_title": "Investigation of subsequent and co-infections associated with SARS-CoV-2 (COVID-19) in hospitalized patients", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117176", + "rel_abs": "BackgroundSARS-CoV-2 has drastically affected healthcare globally and causes COVID-19, a disease that is associated with substantial morbidity and mortality. We aim to describe rates and pathogens involved in co-infection or subsequent infections and their impact on clinical outcomes among hospitalized patients with COVID-19.\n\nMethodsIncidence of and pathogens associated with co-infections, or subsequent infections, were analyzed in a multicenter observational cohort. Clinical outcomes were compared between patients with a bacterial respiratory co-infection (BRC) and those without. A multivariable Cox regression analysis was performed evaluating survival.\n\nResultsA total of 289 patients were included, 48 (16.6%) had any co-infection and 25 (8.7%) had a BRC. No significant differences in comorbidities were observed between patients with co-infection and those without. Compared to those without, patients with a BRC had significantly higher white blood cell counts, lactate dehydrogenase, C-reactive protein, procalcitonin and interleukin-6 levels. ICU admission (84.0 vs 31.8%), mechanical ventilation (72.0 vs 23.9%) and in-hospital mortality (45.0 vs 9.8%) were more common in patients with BRC compared to those without a co-infection. In Cox proportional hazards regression, following adjustment for age, ICU admission, mechanical ventilation, corticosteroid administration, and pre-existing comorbidities, patients with BRC had an increased risk for in-hospital mortality (adjusted HR, 3.37; 95% CI, 1.39 to 8.16; P = 0.007). Subsequent infections were uncommon, with 21 infections occurring in 16 (5.5%) patients.\n\nConclusionsCo-infections are uncommon among hospitalized patients with COVID-19, however, when BRC occurs it is associated with worse clinical outcomes including higher mortality.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Matthew P Crotty", + "author_inst": "Methodist Dallas Medical Center" + }, + { + "author_name": "Ronda L Akins", + "author_inst": "Methodist Charlton Medical Center" + }, + { + "author_name": "An T Nguyen", + "author_inst": "Methodist Charlton Medical Center" + }, + { + "author_name": "Rania Slika", + "author_inst": "Methodist Mansfield Medical Center" + }, + { + "author_name": "Kristen Rahmanzadeh", + "author_inst": "Methodist Dallas Medical Center" + }, + { + "author_name": "Marie H Wilson", + "author_inst": "Methodist Dallas Medical Center" + }, + { + "author_name": "Edward A Dominguez", + "author_inst": "Methodist Transplant Specialists, Methodist Dallas Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.29.20117309", "rel_title": "Mendelian randomization analysis to characterize causal association between coronary artery disease and COVID-19", @@ -1395524,69 +1392479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.05.28.20115378", - "rel_title": "Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115378", - "rel_abs": "PCR testing of nasopharyngeal swab samples is used for the diagnosis of coronavirus disease 2019 (COVID-19) and for determining timing of discharge. The viral load usually declines at convalescent phase, but sometimes remained positive for a long time even after relief of symptoms. In this study, we identified older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Takeshi Hattori", - "author_inst": "Department of Respiratory Medicine, National Hospital Organization Hokkaido Medical Center" - }, - { - "author_name": "Masaru Amishima", - "author_inst": "Department of Respiratory Medicine, National Hospital Organization Hokkaido Medical Center" - }, - { - "author_name": "Daisuke Morinaga", - "author_inst": "Department of Respiratory Medicine, National Hospital Organization Hokkaido Medical Center" - }, - { - "author_name": "Keisuke Kamada", - "author_inst": "Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University" - }, - { - "author_name": "Sho Nakakubo", - "author_inst": "Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University" - }, - { - "author_name": "Yu Yamashita", - "author_inst": "Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University" - }, - { - "author_name": "Yasuo Shichinohe", - "author_inst": "Department of Emergency and Critical Care Medicine, National Hospital Organization Hokkaido Medical Center" - }, - { - "author_name": "Shinichi Fujisawa", - "author_inst": "Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital" - }, - { - "author_name": "Mutsumi Nishida", - "author_inst": "Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital" - }, - { - "author_name": "Yasuyuki Nasuhara", - "author_inst": "Division of Hospital Safety Management, Hokkaido University Hospital" - }, - { - "author_name": "Takanori Teshima", - "author_inst": "Department of Hematology, Hokkaido University Faculty of medicine" - }, - { - "author_name": "Satoshi Konno", - "author_inst": "Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.27.20114868", "rel_title": "A reductive analysis of a compartmental model for COVID-19: data assimilation andforecasting for the United Kingdom", @@ -1396083,6 +1392975,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.27.20114272", + "rel_title": "How did governmental interventions affect the spread of COVID-19 in European countries?", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114272", + "rel_abs": "BackgroundTo reduce transmission of Coronavirus Disease 2019, European governments have implemented successive measures to encourage social distancing. However, it remained unclear how effectively measures reduced the spread of the virus, due to data complications. We examined how the effective-contact rate (ECR) among European citizens evolved over the period with implemented measures using a new data-oriented approach that is based on an extended Susceptible-Exposed-Infectious-Removed (SEIR) model.\n\nMethodsUsing the available data on the confirmed numbers of infections and hospitalizations, we first estimated the daily number of infectious-, exposed- and susceptible individuals and subsequently estimated the ECR with an iterative Poisson regression model, disregarding information on governmental measures. We then studied change points in the daily ECRs to the moments of the governmental measures.\n\nFindingsThe change points in the daily ECRs were found to align with the implementation of governmental interventions. At the end of the considered time-window, we found similar ECRs for Italy (0{middle dot}29), Spain (0{middle dot}24), and Germany (0{middle dot}27), while the ECR in the Netherlands (0{middle dot}34), Belgium (0{middle dot}35) and the UK (0{middle dot}37) were somewhat higher. The highest ECR was found for Sweden (0{middle dot}45).\n\nInterpretationThere seemed to be an immediate effect of banning events and closing schools, typically among the first measures taken by the governments. The effect of additionally closing bars and restaurants seemed limited. For most countries a somewhat delayed effect of the full lockdown was observed, and the ECR after a full lockdown was not necessarily lower than an ECR after (only) a gathering ban.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Richard Andries Jacobus Post", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Marta Regis", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Zhuozhao Zhan", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Edwin R van den Heuvel", + "author_inst": "Eindhoven Unversity of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20113019", "rel_title": "Modelling Capacity on London Underground Carriages in Light of UK Government Mandated Social Distancing Rules in Response to the Covid-19 Pandemic.", @@ -1396754,65 +1393677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.26.20114025", - "rel_title": "Modelling the thermal inactivation of viruses from the Coronaviridae family in suspensions or on surfaces with various relative humidities.", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20114025", - "rel_abs": "Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-values (time to obtain a log10 reduction of virus infectivity), including values for SARS-CoV-2, were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global dataset of D-values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points or new coronavirus strains.\n\nImportanceThe prediction of the persistence of SARS-CoV-2 on fomites is essential to investigate the importance of contact transmission. This study collects available information on inactivation kinetics of coronaviruses in both solid and liquid fomites and creates a mathematical model for the impact of temperature and relative humidity on virus persistence. The predictions of the model can support more robust decision-making and could be useful in various public health contexts. Having a calculator for the natural clearance of SARS-CoV-2 depending on temperature and relative humidity could be a valuable operational tool for public authorities.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Laurent Guillier", - "author_inst": "ANSES" - }, - { - "author_name": "Sandra Martin-Latil", - "author_inst": "ANSES" - }, - { - "author_name": "Estelle Chaix", - "author_inst": "ANSES" - }, - { - "author_name": "Anne Thebault", - "author_inst": "ANSES" - }, - { - "author_name": "Nicole Pavio", - "author_inst": "ANSES" - }, - { - "author_name": "Sophie Le Poder", - "author_inst": "ENVA" - }, - { - "author_name": "Christophe Batejat", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fabrice Biot", - "author_inst": "IRBA" - }, - { - "author_name": "Lionel Koch", - "author_inst": "IRBA" - }, - { - "author_name": "Don Schaffner", - "author_inst": "Rutgers University" - }, - { - "author_name": "Moez Sanaa", - "author_inst": "ANSES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.25.20112797", "rel_title": "Variation in Covid-19 Cases Across New York City", @@ -1397277,6 +1394141,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.29.20116723", + "rel_title": "A simple Stochastic model for the SARS-CoV-2 Epidemic curve", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116723", + "rel_abs": "An epidemic curve is a graphic depiction of the number of outbreak cases by date of illness onset, ordinarily constructed after the disease outbreak is over. However, a good estimate of the epidemic curve early in an outbreak would be invaluable to health care officials. On the other hand, from the end of February, the SARS-CoV-2 epidemic in Brazil seems to not following the Europe, or in particular, Italy or Spain. Even if less tests have been applied, there are less deaths occurring in Brazil than in both cited countries. However, due to the few applied tests, there is no certain planning on the real number of active cases. To estimate the number of future cases, epidemiologists make an educated guess as to how many people might become affected. We have proposed a simple fitting model using a simulated annealing technique, testing it with the South Korea data. We have tested and discussed the uncertainties of the model. We also have analyzed the trends in the confirmed cases using this model for the five most affected countries plus Brazil along several epidemic weeks.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alysson Nunes Diogenes", + "author_inst": "Universidade Positivo" + }, + { + "author_name": "Daniel Guimaraes Tedesco", + "author_inst": "Universidade Positivo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.28.122648", "rel_title": "Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding", @@ -1398084,49 +1394971,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.26.20114033", - "rel_title": "Continuous Electroencephalography (cEEG) Characteristics and Acute Symptomatic Seizures in COVID-19 Patients", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20114033", - "rel_abs": "BackgroundNeurological manifestations of COVID-19 have only recently been described, with a paucity of literature reporting the potential relationship between COVID-19 and acute symptomatic seizures. Two prior studies found no clinical or electrographic seizures in their cohorts of COVID-19 patients with altered mental status (AMS) and clinical seizure-like events (SLEs).\n\nMethodsIn this retrospective cohort study, 22 critically-ill COVID-19 patients above the age of 18 years who underwent EEG (electroencephalography) monitoring between April 20th, 2020 and May 20th, 2020 were studied. 19 patients underwent continuous EEG (cEEG) for at least 24 hours, and 3 patients underwent routine EEGs (<1 hour). Demographics including age, gender, comorbid medical, and neurological conditions were collected. Clinical variables included EEG findings, anti-seizure medications, discharge disposition, and survival.\n\nFindings17 patients underwent EEG monitoring for unexplained altered mental status changes and 5 patients underwent monitoring for a seizure-like event. 5 patients had epileptiform abnormalities on EEG (4 patients on cEEG, 1 on routine EEG); and only 2 of 5 epileptic EEG patients had a prior history of epilepsy. 2 patients in our cohort had electrographic seizures in the absence of prior epilepsy history. No patients with epileptiform abnormalities or electrographic seizures had acutely abnormal neuroimaging on CT or MRI.\n\nInterpretationEncephalopathic COVID-19 positive patients had a range of EEG abnormalities, and a higher proportion of patients in this series had electrographic seizures than previous literature suggests. This may be influenced by the duration of monitoring with cEEG and the use of a 21 channel electrode system. cEEG findings may help to guide antiseizure medical therapy, as well as the workup of altered mental status in the setting of unremarkable neuroimaging.\n\nFundingNo funding was used for this study.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Shreya Louis", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Andrew Dhawan", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Christopher Newey", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Dileep Nair", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Lara Jehi", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Stephen Hantus", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Vineet Punia", - "author_inst": "Cleveland Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.05.27.20111542", "rel_title": "Ambient air pollutants, meteorological factors and their interactions affect confirmed cases of COVID-19 in 120 Chinese cities", @@ -1398643,6 +1395487,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.28.122143", + "rel_title": "Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states", + "rel_date": "2020-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.122143", + "rel_abs": "The first Indian cases of COVID-19 caused by SARS-Cov-2 were reported in February 29, 2020 with a history of travel from Wuhan, China and so far above 4500 deaths have been attributed to this pandemic. The objectives of this study were to characterize Indian SARS-CoV-2 genome-wide nucleotide variations, trace ancestries using phylogenetic networks and correlate state-wise distribution of viral haplotypes with differences in mortality rates. A total of 305 whole genome sequences from 19 Indian states were downloaded from GISAID. Sequences were aligned using the ancestral Wuhan-Hu genome sequence (NC_045512.2). A total of 633 variants resulting in 388 amino acid substitutions were identified. Allele frequency spectrum, and nucleotide diversity ({pi}) values revealed the presence of higher proportions of low frequency variants and negative Tajimas D values across ORFs indicated the presence of population expansion. Network analysis highlighted the presence of two major clusters of viral haplotypes, namely, clade G with the S:D614G, RdRp: P323L variants and a variant of clade L [Lv] having the RdRp:A97V variant. Clade G genomes were found to be evolving more rapidly into multiple sub-clusters including clade GH and GR and were also found in higher proportions in three states with highest mortality rates namely, Gujarat, Madhya Pradesh and West Bengal.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Bornali Bhattacharjee", + "author_inst": "National Institute of Biomedical Genomics" + }, + { + "author_name": "Bhaswati Pandit", + "author_inst": "National Institute of Biomedical Genomics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.28.118992", "rel_title": "SARS-CoV-2 genomics beyond the consensus sequence: evidence for circulating mixed viral populations", @@ -1399574,37 +1396441,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.26.20113456", - "rel_title": "Burden of COVID-19 pandemic in India: Perspectives from Health Infrastructure", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113456", - "rel_abs": "The coronavirus (COVID-19) is spreading rapidly across the country but Indias testing regime is far from the global standards. It is important to identify the states where testing needs expansion and the magnitudes of active COVID cases are higher focusing on current health infrastructure to meet the pandemic. The data on COVID-19 was extracted from the Application Programming Interface. Test positive rate, test per confirmed case, recovery rate, case fatality rate, and percent distribution of active cases were computed. Availability of hospitals, hospital beds, intensive care unit and ventilators per lakh population was also computed by public and private sector. The result revealed that, Maharashtra constitutes more than one-third positive cases in the country. More than a quarter of the active cases in India belonged to the Mumbai district of Maharashtra, followed by the Chennai district (9.4%) and Ahmedabad district (9.1%). Further, about 40 percent of the active cases in India belonged to the 11 districts of Maharashtra. The increased test positive rate in Maharashtra and Gujarat to almost double in last one month is a concern. In order to bring the states and the country in right track, the test positive rate need to be brought down to below 2 percent. The procurement of higher number of high throughput machine, the Cobas 6800 testing machine, is need of the hour. Only few states have adequate health infrastructure. The priority should be the laid on expansion of more laboratories and hospitals, storage of PPE kit, testing kit, and indigenously developed vaccines.\n\nHighlightsO_LIMaharashtra is having the highest number of positive cases followed by Gujarat and Tamil Nadu. Maharashtra constitutes more than one-third positive cases in the country, but the test per confirmed cases (8) is much lower than the other states.\nC_LIO_LIMore than a quarter of the active cases in India belonged to the Mumbai district (26.1%) of Maharashtra, followed by the Chennai district (9.4%) and Ahmedabad district (9.1%). Further, about 40 percent of the active cases in India belonged to the 11 districts of Maharashtra.\nC_LIO_LIThe test positive rate is higher in Maharashtra, Gujarat and Delhi is a concern.\nC_LIO_LIThe recovery rate in India increased substantially by 26.5 percent point from 11.9 percent on April 14 to 38.4 percent on May 17, 2020.\nC_LIO_LIThe case fatality rate of Covid-19 in India declined by 0.2 percent from 3.4 percent on April 14 to 3.2 percent on May 17 in India.\nC_LIO_LIThe number of Dedicated Covid Hospitals is not sufficient in India.\nC_LIO_LIThe available ventilators in the country will deficit in near future to cater to a growing number of active Covid-19 patients and the burden of other communicable and non-communicable diseases.\nC_LIO_LIIndia has only 569 testing laboratories (396 govt. and 173 private) against its 1.35 billion population. The procurement of higher number of high throughput machine, the Cobas 6800 testing machine, is need of the hour.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Harihar Sahoo", - "author_inst": "International Institute for Population Sciences" - }, - { - "author_name": "Chaitali Mandal", - "author_inst": "International Institute for the Population Sciences" - }, - { - "author_name": "Suyash Mishra", - "author_inst": "International Institute for the Population Sciences" - }, - { - "author_name": "Snigdha Banerjee", - "author_inst": "International Institute for the Population Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20112805", "rel_title": "The association of UV with rates of COVID-19 transmission and deaths in Mexico: the possible mediating role of vitamin D.", @@ -1400129,6 +1396965,129 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.26.117549", + "rel_title": "Development and validation of IMMUNO-COV: a high-throughput clinical assay for detecting antibodies that neutralize SARS-CoV-2", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.26.117549", + "rel_abs": "We here describe the development and validation of IMMUNO-COV, a high-throughput clinical test to quantitatively measure SARS-CoV-2-neutralizing antibodies, the specific subset of anti-SARS-CoV-2 antibodies that block viral infection. The test measures the capacity of serum or purified antibodies to neutralize a recombinant Vesicular Stomatitis Virus (VSV) encoding the SARS-CoV-2 spike glycoprotein. This recombinant virus (VSV-SARS-CoV-2-S-{Delta}19CT) induces fusion in Vero cell monolayers, which is detected as luciferase signal using a dual split protein (DSP) reporter system. VSV-SARS-CoV-2-S-{Delta}19CT infection was blocked by monoclonal -SARS-CoV-2-spike antibodies and by plasma or serum from SARS-CoV-2 convalescing individuals. The assay exhibited 100% specificity in validation tests, and across all tests zero false positives were detected. In blinded analyses of 230 serum samples, only two unexpected results were observed based on available clinical data. We observed a perfect correlation between results from our assay and 80 samples that were also assayed using a commercially available ELISA. To quantify the magnitude of the anti-viral response, we generated a calibration curve by adding stepped concentrations of -SARS-CoV-2-spike monoclonal antibody to pooled SARS-CoV-2 seronegative serum. Using the calibration curve and a single optimal 1:100 serum test dilution, we reliably measured neutralizing antibody levels in each test sample. Virus neutralization units (VNUs) calculated from the assay correlated closely (p < 0.0001) with PRNTEC50 values determined by plaque reduction neutralization test against a clinical isolate of SARS-CoV-2. Taken together, these results demonstrate that the IMMUNO-COV assay accurately quantitates SARS-CoV-2 neutralizing antibodies in human sera and therefore is a potentially valuable addition to the currently available serological tests. The assay can provide vital information for comparing immune responses to the various SARS-CoV-2 vaccines that are currently in development, or for evaluating donor eligibility in convalescent plasma therapy studies.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Rianna Vandergaast", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Timothy Carey", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Samantha Reiter", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Patrycja Lech", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Clement Gnanadurai", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Mulu Tesfay", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Jason Buehler", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Lukkana Suksanpaisan", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Shruthi Naik", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Bethany Brunton", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Jordan Recker", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Michelle Haselton", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Christopher Ziegler", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Anne Roesler", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "John R. Mills", + "author_inst": "Mayo Clinic Department of Laboratory Medicine and Pathology" + }, + { + "author_name": "Elitza Theel", + "author_inst": "Mayo Clinic Department of Laboratory Medicine and Pathology" + }, + { + "author_name": "Scott C. Weaver", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch" + }, + { + "author_name": "Grace Rafael", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch" + }, + { + "author_name": "Matthew M. Roforth", + "author_inst": "Mayo Clinic Advanced Diagnostic Laboratory" + }, + { + "author_name": "Clavin Jerde", + "author_inst": "Mayo Clinic Advanced Diagnostic Laboratory" + }, + { + "author_name": "Sheryl Tran", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Rosa Maria Diaz", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Alice Bexon", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Alina Baum", + "author_inst": "Regeneron Pharmaceuticals Inc." + }, + { + "author_name": "Christos A. Kyratsous", + "author_inst": "Regeneron Pharmaceuticals Inc." + }, + { + "author_name": "Kah-Whye Peng", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Stephen J. Russell", + "author_inst": "Vyriad, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.27.118414", "rel_title": "Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method", @@ -1401016,213 +1397975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.05.26.20112649", - "rel_title": "Seek COVER: Development and validation of a personalized risk calculator for COVID-19 outcomes in an international network", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20112649", - "rel_abs": "ObjectiveTo develop and externally validate COVID-19 Estimated Risk (COVER) scores that quantify a patients risk of hospital admission (COVER-H), requiring intensive services (COVER-I), or fatality (COVER-F) in the 30-days following COVID-19 diagnosis.\n\nMethodsWe analyzed a federated network of electronic medical records and administrative claims data from 14 data sources and 6 countries. We developed and validated 3 scores using 6,869,127 patients with a general practice, emergency room, or outpatient visit with diagnosed influenza or flu-like symptoms any time prior to 2020. The scores were validated on patients with confirmed or suspected COVID-19 diagnosis across five databases from South Korea, Spain and the United States. Outcomes included i) hospitalization with pneumonia, ii) hospitalization with pneumonia requiring intensive services or death iii) death in the 30 days after index date.\n\nResultsOverall, 44,507 COVID-19 patients were included for model validation. We identified 7 predictors (history of cancer, chronic obstructive pulmonary disease, diabetes, heart disease, hypertension, hyperlipidemia, kidney disease) which combined with age and sex discriminated which patients would experience any of our three outcomes. The models achieved high performance in influenza. When transported to COVID-19 cohorts, the AUC ranges were, COVER-H: 0.69-0.81, COVER-I: 0.73-0.91, and COVER-F: 0.72-0.90. Calibration was overall acceptable.\n\nConclusionsA 9-predictor model performs well for COVID-19 patients for predicting hospitalization, intensive services and fatality. The models could aid in providing reassurance for low risk patients and shield high risk patients from COVID-19 during de-confinement to reduce the virus impact on morbidity and mortality.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Ross D. Williams", - "author_inst": "Erasmus University Medical Center" - }, - { - "author_name": "Aniek F. Markus", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Cynthia Yang", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Talita Duarte Salles", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Scott L Duvall", - "author_inst": "Department of Veterans Affairs, USA; University of Utah, USA" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Jitendra Jonnagaddala", - "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" - }, - { - "author_name": "Chungsoo Kim", - "author_inst": "Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Yeunsook Rho", - "author_inst": "Department of Bigdata, Health Insurance Review & Assessment Service, Republic of Korea" - }, - { - "author_name": "Andrew Williams", - "author_inst": "Tufts Institute for Clinical Research and Health Policy Studies, Boston, MA, 02111, USA" - }, - { - "author_name": "Amanda Alberga", - "author_inst": "Independent Epidemiologist, OHDSI" - }, - { - "author_name": "Min Ho An", - "author_inst": "Wando county health center and hospital" - }, - { - "author_name": "Mar\u00eda Arag\u00f3n", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Carlos Areia", - "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford" - }, - { - "author_name": "Edward Burn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Young Choi", - "author_inst": "Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Iannis Drakos", - "author_inst": "Center for Surgical Science, Koege, Denmark" - }, - { - "author_name": "Maria Fernandes Abrah\u00e3o", - "author_inst": "Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Sergio Fern\u00e1ndez-Bertol\u00edn", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "George Hripcsak", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Benjamin Kaas-Hansen", - "author_inst": "Clinical Pharmacology Unit, Zealand University Hospital, Roskilde, Denmark NNF Centre for Protein Research, University of Copenhagen, Denmark" - }, - { - "author_name": "Prasanna Kandukuri", - "author_inst": "Abbvie, Chicago, United States" - }, - { - "author_name": "Jan A. Kors", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, United States" - }, - { - "author_name": "Siaw-Teng Liaw", - "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" - }, - { - "author_name": "Kristine E Lynch", - "author_inst": "Department of Veterans Affairs, USA; University of Utah, USA" - }, - { - "author_name": "Michael E Matheny", - "author_inst": "Department of Veterans Affairs, USA; Vanderbilt University, USA" - }, - { - "author_name": "Gerardo Machnicki", - "author_inst": "Janssen Latin America, Buenos Aires, Argentina" - }, - { - "author_name": "Daniel Morales", - "author_inst": "Division of Population Health and Genomics, University of Dundee, UK" - }, - { - "author_name": "Fredrik Nyberg", - "author_inst": "School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden" - }, - { - "author_name": "Rae Woong Park", - "author_inst": "Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Albert Prats-Uribe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole Pratt", - "author_inst": "Quality Use of Medicines and Pharmacy Research Centre, University of South Australia, Adelaide, Australia" - }, - { - "author_name": "Gowtham Rao", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Christian G. Reich", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, United States" - }, - { - "author_name": "Marcela Rivera", - "author_inst": "Bayer Pharmaceuticals, Bayer Hispania, S.L., Barcelona, Spain" - }, - { - "author_name": "Tom Seinen", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Azza Shoaibi", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Matthew E. Spotnitz", - "author_inst": "mes2165@cumc.columbia.edu" - }, - { - "author_name": "Ewout W. Steyerberg", - "author_inst": "Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands, Department of Biomedical Data Sciences, Leiden University Medical Ce" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA" - }, - { - "author_name": "Seng Chan You", - "author_inst": "Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Lin Zhang", - "author_inst": "School of Population and Global Health, The University of Melbourne & WHO Collaborating Centre on Im" - }, - { - "author_name": "Lili Zhou", - "author_inst": "Abbvie, Chicago, United States" - }, - { - "author_name": "Patrick B. Ryan", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jenna M. Reps", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Peter R. Rijnbeek", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.26.20113316", "rel_title": "Scrutinising the COVID-19 data on 590.000 cases. A retrospective, population-based descriptive study for data quality surveillance and a review at 4.540.000 cases.", @@ -1401831,6 +1398583,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.24.20103648", + "rel_title": "Ataxia as a presenting manifestation of COVID -19: Report of a single case", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20103648", + "rel_abs": "Even though various neurological presentations of COVID-19 have surfaced up, ataxia as a presenting feature has rarely been reported so far. We hereby describe a confirmed case of SARS-CoV-2 infection which not only presented with ataxia but also had delayed onset of typical respiratory features. This case represents an atypical manifestation of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Debaleena Mukherjee", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata, India" + }, + { + "author_name": "Peyalee Sarkar", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata, India" + }, + { + "author_name": "Souvik Dubey", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata, India" + }, + { + "author_name": "Biman Kanti Ray", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata" + }, + { + "author_name": "Alak Pandit", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata" + }, + { + "author_name": "Durjoy Lahiri", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.20.20103762", "rel_title": "Cancer and risk of COVID-19 through a general community survey", @@ -1402610,69 +1399401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.21.20105858", - "rel_title": "Paradigms about the COVID-2 pandemic: knowledge, attitudes and practices from medical students", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20105858", - "rel_abs": "BackgroundAs the disease caused by the new coronavirus has spread globally, economic instability in healthcare systems has been significant, and the lack of knowledge, positive attitudes and appropriate practices among people has led to the magnification of this disease. This reality is especially accentuated in Ecuador where, although many healthcare workers have been called to help in the regions most affected, the shortage of them combined with cultural and macroeconomic factors have led Ecuador to face the most aggressive outbreak in Latin America. In this context, the participation on the front line of final year medical students is indispensable. For that reason, appropriate training on COVID-19 for final year medical students is an urgent need that universities and health systems must guarantee. We aimed to describe the knowledge, attitudes and practices in Ecuadorian final year medical students in order to identify the knowledge gaps, perceptions and behavior patterns which could guide the design of better medical education curricula regarding COVID-19.\n\nMethodsThis was a cross-sectional 33-item online survey conducted between April 6 to April 20 assessing the knowledge, attitudes, and practices toward the diagnosis, treatment, prevention, and prognosis toward COVID-19 in Ecuadorian final year medical students. It was sent by email and by Facebook and WhatsApp.\n\nResultsA total of 309 students responded to the survey. 88% of students scored high ([≥] 70% correct) for knowledge of the disease. The majority of students were pessimistic about possible government actions, which is reflected in the negative attitude towards the control of COVID-19 in Ecuador and volunteering during the outbreak (77%, and 58% of the students, respectively). Moreover, 91% of students said they did not have adequate protective equipment or training in their health facilities.\n\nConclusionsThe high level of students knowledge, with coexisting negative attitudes, suggests Ecuador has a capable upcoming workforce that could benefit from an opportunity to strengthen, improve and advance their training in preparation for COVID-19. Creating a national curriculum may be one of the most effective ways for all students to be trained, while simultaneously focusing on the students most pressing concerns. Hopefully with this, negative attitudes will improve and students will be better qualified.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Eddy Lincango-Naranjo", - "author_inst": "Knowledge and Evaluation Research Unit, Mayo Clinic, Universidad Central del Ecuador" - }, - { - "author_name": "Paola Solis-Pazmino", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, California, USA." - }, - { - "author_name": "Santiago Rodriguez-Villafuerte", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre, Facultad de Medicina, Programa de Pos-graduacao em Hepatologia, Porto Alegre, RS, Brasil, Hospital Vo" - }, - { - "author_name": "Jose Lincango-Naranjo", - "author_inst": "Universidad de las Fuerzas Armadas, Quito, Ecuador." - }, - { - "author_name": "Paul Vinueza-Moreano", - "author_inst": "Universidad Central del Ecuador" - }, - { - "author_name": "Giuseppe Barberis-Barcia", - "author_inst": "Universidad Central del Ecuador" - }, - { - "author_name": "Carlos Ruiz-Sosa", - "author_inst": "Universidad Central del Ecuador" - }, - { - "author_name": "Giovanni Rojas-Velasco", - "author_inst": "Universidad Central del Ecuador, Universidad de Sao Paulo" - }, - { - "author_name": "Derek Gravholt", - "author_inst": "Knowledge and Evaluation Research Unit, Mayo Clinic" - }, - { - "author_name": "Nataly Espinoza-Suarez", - "author_inst": "Knowledge and Evaluation Research Unit, Mayo Clinic" - }, - { - "author_name": "Elizabeth Golembiewski", - "author_inst": "Knowledge and Evaluation Research Unit, Mayo Clinic" - }, - { - "author_name": "Percy Soto-Becerra", - "author_inst": "Facultad de Administracion y Salud Publica, Universidad Peruana Cayetano Heredia, Lima, Peru" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.05.20.20106633", "rel_title": "Clinical and Radiological Evaluations of COVID-19 Patients with Anosmia: Preliminary Report.", @@ -1403377,6 +1400105,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.19.20107045", + "rel_title": "Strict Physical Distancing May Be More Efficient: A Mathematical Argument for Making Lockdowns Count", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107045", + "rel_abs": "COVID-19 created a global public health and economic emergency. Policymakers acted quickly and decisively to contain the spread of disease through physical distancing measures. However, these measures also impact physical, mental and economic well-being, creating difficult trade-offs. Here we use a simple mathematical model to explore the balance between public health measures and their associated social and economic costs. Across a range of cost-functions and model structures, commitment to intermittent and strict social distancing measures leads to better overall outcomes than temporally consistent implementation of moderate physical distancing measures. With regard to the trade-offs that policymakers may soon face, our results emphasize that economic and health outcomes do not exist in full competition. Compared to consistent moderation, intermittently strict policies can better mitigate the impact of the pandemic on both of these priorities for a range of plausible utility functions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Scott R Sheffield", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Anna York", + "author_inst": "Yale University" + }, + { + "author_name": "Nicole A Swartwood", + "author_inst": "Harvard University" + }, + { + "author_name": "Alyssa Bilinski", + "author_inst": "Harvard University" + }, + { + "author_name": "Anne Williamson", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Meagan C Fitzpatrick", + "author_inst": "University of Maryland" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.19.20107144", "rel_title": "A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways", @@ -1404172,73 +1400939,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.22.20107292", - "rel_title": "Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia.", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20107292", - "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main inhouse methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3 end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.\n\nHIGHLIGHTSO_LIColombian SARS-CoV-2 sequences displayed genetic variability in some target regions used for COVID-19 diagnosis.\nC_LIO_LIMismatches in critical primer regions could impact their performance and the rate of false negative results.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Diego Alejandro Alvarez-Diaz", - "author_inst": "Grupo de Salud Materna y Perinatal. Direccion de Investigacion en Salud Publica, Instituto Nacional de Salud." - }, - { - "author_name": "Carlos Franco-Munoz", - "author_inst": "Grupo de Parasitologia. Direccion de Investigacion en Salud Publica, Instituto Nacional de Salud." - }, - { - "author_name": "Katherine Laiton-Donato", - "author_inst": "Unidad de Secuenciacion y Genomica. Direccion de Investigacion en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Jose A Usme-Ciro", - "author_inst": "Centro de Investigacion en Salud para el Tropico - CIST, Universidad Cooperativa de Colombia" - }, - { - "author_name": "Nicolas D Franco-Sierra", - "author_inst": "Instituto de Investigacion de Recursos Biologicos Alexander von Humboldt" - }, - { - "author_name": "Astrid C Florez", - "author_inst": "Direccion de Redes en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Sergio Gomez Rangel", - "author_inst": "Direccion de Vigilancia en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Luz Dary Rodriguez", - "author_inst": "Grupo de Virologia, Direccion de Redes en Salud Publica, Instituto Nacional de Salud." - }, - { - "author_name": "Juliana Barbosa-Ramirez", - "author_inst": "Grupo de Virologia, Direccion de Redes en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Erika X Ospitia-Baez", - "author_inst": "Grupo de Virologia, Direccion de Redes en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Diana M Walteros", - "author_inst": "Direccion de Vigilancia en Salud Publica, Instituto Nacional de Salud" - }, - { - "author_name": "Martha L Ospina Martinez", - "author_inst": "Direccion General, Instituto Nacional de Salud" - }, - { - "author_name": "Marcela Mercado-Reyes", - "author_inst": "Direccion de Investigacion en Salud Publica, Instituto Nacional de Salud" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.19.20107201", "rel_title": "Computational Simulation to Assess Patient Safety of Uncompensated COVID-19 Two-patient Ventilator Sharing Using the Pulse Physiology Engine", @@ -1404759,6 +1401459,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.24.20111633", + "rel_title": "Pitting the Gumbel and logistic growth models against one another to model COVID-19 spread", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111633", + "rel_abs": "In this paper, we investigate briefly the appropriateness of the widely used logistic growth curve modeling with focus on COVID-19 spread, from a data-driven perspective. Specifically, we suggest the Gumbel growth model for behaviour of COVID-19 cases in European countries in addition to the United States of America (US), for better detecting the growth and prediction. We provide a suitable fit and predict the growth of cases for some selected countries as illustration. Our contribution will stimulate the correct growth spread modeling for this pandemic outbreak.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andriette Bekker", + "author_inst": "University of Pretoria" + }, + { + "author_name": "Keunyoung Yoo", + "author_inst": "University of Pretoria" + }, + { + "author_name": "Mohammad Arashi", + "author_inst": "Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.25.20108852", "rel_title": "Impaired T cell functions along with elevated activated Tregs at the early stage of asymptomatic SARS-CoV-2 infection", @@ -1405698,81 +1402425,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20110890", - "rel_title": "SARS-CoV-2 entry related genes are comparably expressed in children's lung as adults", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20110890", - "rel_abs": "To explore whether the expression levels of viral-entry associated genes might contribute to the milder symptoms in children, we analyzed the expression of these genes in both children and adults lung tissues by single cell RNA sequencing (scRNA-seq) and immunohistochemistry (IHC). Both scRNA-seq and IHC analyses showed comparable levels of the key genes for SARS-CoV-2 entry in children and adults, including ACE2, TMPRSS2 and FURIN, suggesting that instead of lower virus intrusion rate, other factors are more likely to be the key reasons for the milder symptoms of SARS-CoV-2 infected children.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yue Tao", - "author_inst": "The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University S" - }, - { - "author_name": "Ruwen Yang", - "author_inst": "The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University S" - }, - { - "author_name": "Chen Wen", - "author_inst": "Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Jue Fan", - "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu Province, China" - }, - { - "author_name": "Jing Ma", - "author_inst": "Department of Pathology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Qiao He", - "author_inst": "Department of Pathology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Zhiguang Zhao", - "author_inst": "Department of Pathology, the Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China" - }, - { - "author_name": "Xinyu Song", - "author_inst": "Department of Cardiothoracic Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China" - }, - { - "author_name": "Hao Chen", - "author_inst": "Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Guocheng Shi", - "author_inst": "Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Minzhi Yin", - "author_inst": "Department of Pathology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Nan Fang", - "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu Province, China" - }, - { - "author_name": "Hao Zhang", - "author_inst": "Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Huiwen Chen", - "author_inst": "Department of Cardiothoracic Surgery, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Xi Mo", - "author_inst": "The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University S" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.05.24.20111625", "rel_title": "Comparison of epidemic control strategies using agent-based simulations", @@ -1406421,6 +1403073,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20112300", + "rel_title": "COVID-19 serology at population scale: SARS-CoV-2-specific antibody responses in saliva", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112300", + "rel_abs": "Non-invasive SARS-CoV-2 antibody testing is urgently needed to estimate the incidence and prevalence of SARS-CoV-2 infection at the general population level. Precise knowledge of population immunity could allow government bodies to make informed decisions about how and when to relax stay-at-home directives and to reopen the economy. We hypothesized that salivary antibodies to SARS-CoV-2 could serve as a non-invasive alternative to serological testing for widespread monitoring of SARS-CoV-2 infection throughout the population. We developed a multiplex SARS-CoV-2 antibody immunoassay based on Luminex technology and tested 167 saliva and 324 serum samples, including 134 and 118 negative saliva and serum samples, respectively, collected before the COVID-19 pandemic, and 33 saliva and 206 serum samples from participants with RT-PCR-confirmed SARS-CoV-2 infection. We evaluated the correlation of results obtained in saliva vs. serum and determined the sensitivity and specificity for each diagnostic media, stratified by antibody isotype, for detection of SARS-CoV-2 infection based on COVID-19 case designation for all specimens. Matched serum and saliva SARS-CoV-2 antigen-specific IgG responses were significantly correlated. Within the 10-plex SARS-CoV-2 panel, the salivary anti-nucleocapsid (N) protein IgG response resulted in the highest sensitivity for detecting prior SARS-CoV-2 infection (100% sensitivity at [≥]10 days post-SARS-CoV-2 symptom onset). The salivary anti-receptor binding domain (RBD) IgG response resulted in 100% specificity. Among individuals with SARS-CoV-2 infection confirmed with RT-PCR, the temporal kinetics of IgG, IgA, and IgM in saliva were consistent with those observed in serum. SARS-CoV-2 appears to trigger a humoral immune response resulting in the almost simultaneous rise of IgG, IgM and IgA levels both in serum and in saliva, mirroring responses consistent with the stimulation of existing, cross-reactive B cells. SARS-CoV-2 antibody testing in saliva can play a critically important role in large-scale \"sero\"-surveillance to address key public health priorities and guide policy and decision-making for COVID-19.\n\n40-word summaryA multiplex immunoassay to detect SARS-CoV-2-specific antibodies in saliva performs with high diagnostic accuracy as early as ten days post-COVID-19 symptom onset. Highly sensitive and specific salivary COVID-19 antibody assays could advance broad immuno-surveillance goals in the USA and globally.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Pranay R Randad", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Nora Pisanic", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Kate Kruczynski", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "David Thomas", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Sabra Klein", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Michael J Betenbaugh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "William A Clarke", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Patrizio P Caturegli", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "H Benjamin Larman", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Barbara Detrick", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Jessica K Fairley", + "author_inst": "Hubert Department of Global Health, Emory University Rollins School of Public Health" + }, + { + "author_name": "Amy C Sherman", + "author_inst": "The Hope Clinic of the Emory Vaccine Center, Emory University School of Medicine" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine" + }, + { + "author_name": "Douglas A Granger", + "author_inst": "Institute for Interdisciplinary Salivary Bioscience Research, University of California Irvine" + }, + { + "author_name": "Steve W Granger", + "author_inst": "Salimetrics, LLC" + }, + { + "author_name": "Matthew Collins", + "author_inst": "The Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine" + }, + { + "author_name": "Christopher D Heaney", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.25.20112912", "rel_title": "Prevalence and risk factors for mortality related to COVID-19 in a severely affected area of Madrid, Spain", @@ -1407224,29 +1403975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20110684", - "rel_title": "Survival in adult inpatients with COVID-19", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20110684", - "rel_abs": "We conducted a nationwide and retrospective cohort study to assess the survival experience and determining factors in adult inpatients with laboratory-confirmed COVID-19. Data from 5,393 individuals were analyzed using the Kaplan-Meier method and a multivariate Cox proportional hazard regression model was fitted. The 7-day survival was 0.822 and went to 0.482, 0.280, and 0.145 on days 15, 21, and 30 of hospital stay, respectively. In the multiple analysis, factors associated with an increased risk of dying were: male gender, age, longer disease evolution before hospital entry, exposure to mechanical ventilator support, and personal history of chronic noncommunicable diseases (namely obesity, type-2 diabetes mellitus, and chronic kidney disease). To the best of our knowledge, this is the first study analyzing the survival probability in a large subset of Latin-American adults with COVID-19 and our results contribute to achieving a better understanding of disease evolution.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Efren Murillo-Zamora", - "author_inst": "Mexican Institute of Social Security" - }, - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.24.20112128", "rel_title": "Estimation and monitoring of COVID-19 transmissibility from publicly available data", @@ -1407695,6 +1404423,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.19.20107326", + "rel_title": "The effect of multiple interventions to balance healthcare demand for controlling COVID-19 outbreaks: a modelling study", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107326", + "rel_abs": "BackgroundRecent outbreak of a novel coronavirus disease 2019 (COVID-19) has led a rapid global spread around the world. For controlling COVID-19 outbreaks, many countries have implemented two non-pharmaceutical interventions: suppression like immediate lock-downs in cities at epicentre of outbreak; or mitigation that slows down but not stopping epidemic for reducing peak healthcare demand. Both interventions have apparent pros and cons; the effectiveness of any one intervention in isolation is limited. It is crucial but hard to know how and when to take which level of interventions tailored to the specific situation in each country. We aimed to conduct a feasibility study for robustly accessing the effect of multiple interventions to control the number and distribution of infections, growth of deaths, peaks and lengths of COVID-19 breakouts in the UK and other European countries, accounting for balance of healthcare demand.\n\nMethodsWe developed a model to attempt to infer the impact of mitigation, suppression and multiple rolling interventions for controlling COVID-19 outbreaks in the UK. Our model assumed that each intervention has equivalent effect on the reproduction number R across countries and over time; where its intensity was presented by average-number contacts with susceptible individuals as infectious individuals; early immediate intensive intervention led to increased health need and social anxiety. We considered two important features: direct link between Exposed and Recovered population, and practical healthcare demand by separation of infections into mild, moderate and critical cases. Our model was fitted and calibrated with date on cases of COVID-19 in Wuhan to estimate how suppression intervention impacted on the number and distribution of infections, growth of deaths over time during January 2020, and April 2020. We combined the calibrated model with data on the cases of COVID-19 in London and non-London regions in the UK during February 2020 and April 2020 to estimate the number and distribution of infections, growth of deaths, and healthcare demand by using multiple interventions. We applied the calibrated model to the prediction of infection and healthcare resource changes in other 6 European countries based on actual measures they have implemented during this period.\n\nFindingsWe estimated given that 1) By the date (5th March 2020) of the first report death in the UK, around 7499 people would have already been infected with the virus. After taking suppression on 23rd March, the peak of infection in the UK would have occurred between 28th March and 4th April 2020; the peak of death would have occurred between 18th April and 24th April 2020. 2) By 29th April, no significant collapse of health system in the UK have occurred, where there have been sufficient hospital beds for severe and critical cases. But in the Europe, Italy, Spain and France have experienced a 3 weeks period of shortage of hospital beds for severe and critical cases, leading to many deaths outside hospitals. 3) One optimal strategy to control COVID-19 outbreaks in the UK is to take region-level specific intervention. If taking suppression with very high intensity in London from 23rd March 2020 for 100 days, and 3 weeks rolling intervention between very high intensity and high intensity in non-London regions. The total infections and deaths in the UK were limited to 9.3 million and 143 thousand; the peak time of healthcare demand was due to the 96th day (12th May, 2020), where it needs hospital beds for 68.9 thousand severe and critical cases. 4) If taking a simultaneous 3 weeks rolling intervention between very high intensity and high intensity in all regions of the UK, the total infections and deaths increased slightly to 10 million and 154 thousand; the peak time of healthcare occurs at the 97th day (13th May, 2020), where it needs equivalent hospital beds for severe and critical cases of 73.5 thousand. 5) If too early releasing intervention intensity above moderate level and simultaneously implemented them in all regions of the UK, there would be a risk of second wave, where the total infections and deaths in the UK possibly reached to 23.4 million and 897 thousand.\n\nInterpretationConsidering social and economic costs in controlling COVID-19 outbreaks, long-term suppression is not economically viable. Our finding suggests that rolling intervention is an optimal strategy to effectively and efficiently control COVID-19 outbreaks in the UK and potential other countries for balancing healthcare demand and morality ratio. As for huge difference of population density and social distancing between different regions in the UK, it is more appropriate to implement regional level specific intervention with varied intensities and maintenance periods. We suggest an intervention strategy to the UK that take a consistent suppression in London for 100 days and 3 weeks rolling intervention in other regions. This strategy would reduce the overall infections and deaths of COVID-19 outbreaks, and balance healthcare demand in the UK.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Po Yang", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "Jun Qi", + "author_inst": "Oxford University" + }, + { + "author_name": "Shuhao Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "gaoshan Bi", + "author_inst": "Yunnan University" + }, + { + "author_name": "Xulong Wang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Yun Yang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Bin Sheng", + "author_inst": "Shanghai Jiaotong University" + }, + { + "author_name": "Xuxin Mao", + "author_inst": "National Institute of Economic and Social Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.23.20110932", "rel_title": "Remdesivir use in patients with coronavirus COVID-19 disease: a systematic review and meta-analysis", @@ -1408406,77 +1405181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.25.115618", - "rel_title": "Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2", - "rel_date": "2020-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.25.115618", - "rel_abs": "The outbreak of COVID-19 has so far inflicted millions of people all around the world and will have a long lasting effect on every aspect of everyones life. Yet there is no effective approved treatment for the disease. In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dehui Yao", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Fang Lao", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Zeyi Zhang", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Yan Liu", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Jianwei Cheng", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Fengjiao Ding", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Xiaofei Wang", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Lun Xi", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Chuang Wang", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Xichong Yan", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Rongkun Zhang", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Fangxing Ouyang", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Hui Ding", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - }, - { - "author_name": "Tianyi Ke", - "author_inst": "Kunshan Xinyunda Biotech Co., Ltd." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.05.23.20111039", "rel_title": "Worldwide and Regional Forecasting of Coronavirus (Covid-19) Spread using a Deep Learning Model", @@ -1409085,6 +1405789,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.05.26.117069", + "rel_title": "SARS-CoV-2 genome evolution exposes early human adaptations", + "rel_date": "2020-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.26.117069", + "rel_abs": "The set of mutations observed at the outset of the SARS-CoV-2 pandemic may illuminate how the virus will adapt to humans as it continues to spread. Viruses are expected to quickly acquire beneficial mutations upon jumping to a new host species. Advantageous nucleotide substitutions can be identified by their parallel occurrence in multiple independent lineages and are likely to result in changes to protein sequences. Here we show that SARS-CoV-2 is acquiring mutations more slowly than expected for neutral evolution, suggesting purifying selection is the dominant mode of evolution during the initial phase of the pandemic. However, several parallel mutations arose in multiple independent lineages and may provide a fitness advantage over the ancestral genome. We propose plausible reasons for several of the most frequent mutations. The absence of mutations in other genome regions suggests essential components of SARS-CoV-2 that could be the target of drug development. Overall this study provides genomic insights into how SARS-CoV-2 has adapted and will continue to adapt to humans.\n\nSUMMARYIn this study we sought signals of evolution to identify how the SARS-CoV-2 genome has adapted at the outset of the COVID-19 pandemic. We find that the genome is largely undergoing purifying selection that maintains its ancestral sequence. However, we identified multiple positions on the genome that appear to confer an adaptive advantage based on their repeated evolution in independent lineages. This information indicates how SARS-CoV-2 will evolve as it diversifies in an increasing number of hosts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erik Scott Wright", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Seema S Lakdawala", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Vaughn S Cooper", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.23.20111104", "rel_title": "Lifestyle acquired immunity, decentralized intelligent infrastructures and revised healthcare expenditures may limit pandemic catastrophe: a lesson from COVID-19", @@ -1409912,57 +1406643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.05.21.20108738", - "rel_title": "Antihypertensive medication uses and serum ACE2 levels", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108738", - "rel_abs": "ImportanceRecent reports have shown that hypertension is the most common comorbidity associated with mortality in the current coronavirus disease 2019 (COVID-19). This has been related to the use of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) as animal studies indicate that these medications increase levels of ACE2, the cellular entry point for the coronavirus SARS-CoV-2. This has prompted clinicians to recommend discontinuing ACEIs and ARBs.\n\nObjectiveTo examine the effect of ACEIs or ARBs treatment on serum levels of ACE2 and other key enzymes in the renin-angiotensin system (RAS).\n\nDesign, Setting, and ParticipantsA single center population-based study of 5457 Icelanders from the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS) of the elderly (mean age 75{+/-}6 years) stratified by ACEIs (N = 699) or ARBs (N = 753) treatment.\n\nMain Outcomes and MeasuresThe AGES-RS study population was stratified by ACEIs and ARBs medication use and compared for age, body mass index (BMI) (kg/m2), hypertension and type 2 diabetes (T2D) as well as serum levels of renin, ACE and ACE2.\n\nResultsWhile renin and ACE levels were significantly raised in serum of individuals on ACEIs or ARBs treatments, the ACE2 levels remained unaffected.\n\nConclusions and RelevanceTreatment with ACEIs or ARBs does not raise ACE2 levels in serum. Therefore, the present study does not support the proposed discontinuation of these medications among patients affected with COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes treatment with the antihypertensive medications angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) result in elevated levels of the cellular receptor for the coronavirus SARS-CoV-2, ACE2?\n\nFindingsIn a single center population-based cohort (AGES-RS), 699 and 753 individuals were either on ACEIs or ARBs treatment, respectively. The serum levels of the key enzymes in the renin-angiotensin system (RAS), renin, ACE and ACE2 were measured in 5457 subjects of the AGES-RS and their serum levels in individuals on ACEIs or ARBs treatment compared to those not using these medications. While renin and ACE were significantly raised in serum of ACEIs and ARBs users, the levels of ACE2 remained unaffected.\n\nMeaningThese results do not support the proposed routine discontinuation of ACEIs or ARBs among patients affected with COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Valur Emilsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Elias F Gudmundsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Thor Aspelund", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Brynjolfur G Jonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Alexander Gudjonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Lenore J Launer", - "author_inst": "Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, MD 20892-9205, USA" - }, - { - "author_name": "Lori L Jennings", - "author_inst": "Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA" - }, - { - "author_name": "Valborg Gudmundsdottir", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Vilmundur Gudnason", - "author_inst": "Icelandic Heart Association" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.22.20110163", "rel_title": "Low Covid-19 hospitalisation in Dumfries and Galloway: comparison with other Scottish health boards", @@ -1410359,6 +1407039,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20107581", + "rel_title": "Prevalence of SARS-CoV-2 infection among asymptomatic healthcare workers in greater Houston: a cross-sectional analysis of surveillance data from a large healthcare system", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20107581", + "rel_abs": "ObjectiveTo determine the prevalence of SARS-CoV-2 infection among asymptomatic COVID-19 facing and non-COVID-19 facing Healthcare Workers (HCWs), with varying job categories across different hospitals.\n\nDesignCross-sectional analysis of a healthcare system surveillance program that included asymptomatic clinical (COVID-19 facing and non-COVID-19 facing), and non-clinical HCWs. A convenience sample of asymptomatic community residents (CR) was also tested. Proportions and 95% confidence Intervals (CI) of SARS-CoV-2 positive HCWs are reported. Proportional trend across HCW categories was tested using Chi Square trend test. Logistic regression model-based likelihood estimates of SARS-CoV-2 prevalence among HCWs with varying job functions and across different hospitals are reported as adjusted odds ratios (aOR) and CI.\n\nSettingHealthcare system comprising one tertiary care academic medical center and six large community hospitals across Greater Houston and a community sample.\n\nParticipants2,872 self-reported asymptomatic adult (> 18 years) HCWs and CRs.\n\nExposureClinical HCWs in COVID-19 and non-COVID-19 units, non-Clinical HCWs, and CRs. Job categories of Nursing, Providers, Allied Health, Support, and Administration / Research. Seven hospitals in the healthcare system.\n\nMain OutcomesPositive reverse transcriptase polymerized chain reaction (RT-PCR) test for SARS-CoV-2\n\nResultsAmong 2,872 asymptomatic HCWs and CRs, 3.9% (CI: 3.2 - 4.7) tested positive for SARS-CoV-2. Mean (SD) age was 40.9 (11.7) years and 73% were females. Among COVID-19 facing HCWs 5.4% (CI: 4.5 - 6.5) were positive, whereas 0.6% (CI: 0.2 - 1.7%) of non COVID-19 facing HCWs and none of the non-clinical HCWs or CRs were positive (Ptrend < 0.001). Among COVID-19 facing HCWs, SARS-CoV-2 positivity was similar for all job categories (p = 0.74). However, significant differences in positivity were observed across hospitals.\n\nConclusions and RelevanceAsymptomatic HCWs with COVID-19 patient exposure had a higher rate of SARS-CoV-2 positive testing than those not routinely exposed to COVID-19 patients and those not engaged in patient care. Among HCWs with routine COVID-19 exposure, all job types had relatively similar infection rates. These data can inform hospital surveillance and infection control practices for patient-facing job classifications and suggest that general environmental exposure within hospitals is not a significant source of asymptomatic SARS-CoV-2 infection.\n\nWhat is already known on this topicO_LIA sizeable proportion of individuals who contract the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can remain largely asymptomatic.\nC_LIO_LIThough such individuals may not develop symptoms, they continue to shed enough viral particles to trigger positive reverse transcriptase polymerized chain reaction (RT PCR) test for SARS-CoV-2\nC_LIO_LIPrior reports on proportion of asymptomatic SARS-CoV-2 individuals are highly variable with positivity ranging across < 1% to 36%\nC_LIO_LIAsymptomatic SARS-CoV-2 infection among healthcare workers is specifically critical to understand\nC_LI\n\nWhat this study addsO_LIThis study demonstrates that overall rate of SARS-CoV-2 infection among asymptomatic healthcare workers in a large healthcare system of a metropolitan city in the United States was 3.9%\nC_LIO_LIThe rate of SARS-CoV-2 infection among healthcare workers who provided direct care to COVID-19 patients was 5.4% whereas it was 0.6% among those healthcare workers who did not provide direct care to COVID-19 patients\nC_LIO_LIThere was no difference in SARS-CoV-2 positivity rate for different job categories of healthcare workers who provided direct care to COVID-19 patients\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Farhaan Vahidy", + "author_inst": "Houston Methodist Research Institute" + }, + { + "author_name": "H Dirk Sostman", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "David Bernard", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Marc L Boom", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Ashley L Drews", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Paul A Christensen", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Jeremy Finkelstein", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Bita A Kash", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Robert A Phillips", + "author_inst": "Houston Methodist Academic Institute" + }, + { + "author_name": "Roberta L Schwartz", + "author_inst": "Houston Methodist Academic Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.20.20107730", "rel_title": "Epidemiological study to detect active SARS-CoV-2 infections and seropositive persons in a selected cohort of employees in the Frankfurt am Main metropolitan area", @@ -1411426,45 +1408161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.24.096164", - "rel_title": "COVIEdb: A database for potential immune epitopes of coronaviruses", - "rel_date": "2020-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.24.096164", - "rel_abs": "2019 novel coronavirus (2019-nCoV) has caused large-scale pandemic COVID-19 all over the world. Its essential to find out which parts of the 2019-nCoV sequence are recognized by human immune system for vaccine development. And for the prevention of the potential outbreak of similar coronaviruses in the future, vaccines against immunogenic epitopes shared by different human coronaviruses are essential. Here we predict all the potential B/T-cell epitopes for SARS-CoV, MERS-CoV, 2019-nCoV and RaTG13-CoV based on the protein sequences. We found YFKYWDQTY in ORF1ab protein, VYDPLQPEL and TVYDPLQPEL in spike (S) protein might be pan-coronavirus targets for vaccine development. All the predicted results are stored in a database COVIEdb (http://biopharm.zju.edu.cn/coviedb/).", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jingcheng Wu", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Wenfan Chen", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Jingjing Zhou", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Wenyi Zhao", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Shuqing Chen", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Zhan Zhou", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.24.113423", "rel_title": "A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point of care", @@ -1411981,6 +1408677,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20111914", + "rel_title": "The spectrum of COVID-19-associated dermatologic manifestations: an international registry of 716 patients from 31 countries", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111914", + "rel_abs": "Key PointsO_ST_ABSQuestionC_ST_ABSWhat are the cutaneous manifestations associated with COVID-19 and do they provide insight into the pathophysiology or prognosis?\n\nFindingsIn this international registry-based case series of 716 patients representing 31 countries, the most common dermatologic morphologies encountered in the 171 COVID-19 confirmed case included morbilliform, pernio-like, urticarial, macular erythema, vesicular, papulosquamous, and retiform purpura. Retiform purpura was seen exclusively in critically ill, hospitalized patients.\n\nMeaningCOVID-19 is associated with a spectrum of skin findings in affected patients. These cutaneous manifestations may vary depending on the severity of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Esther E Freeman", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Devon E McMahon", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jules B Lipoff", + "author_inst": "Department of Dermatology, University of Pennsylvania" + }, + { + "author_name": "Misha Rosenbach", + "author_inst": "Department of Dermatology, University of Pennsylvania" + }, + { + "author_name": "Carrie Kovarik", + "author_inst": "Department of Dermatology, University of Pennsylvania" + }, + { + "author_name": "Seemal R Desai", + "author_inst": "The University of Texas Southwestern Medical Center" + }, + { + "author_name": "Joanna Harp", + "author_inst": "Department of Dermatology, Weill Cornell Medicine" + }, + { + "author_name": "Junko Takeshita", + "author_inst": "Department of Dermatology, University of Pennsylvania" + }, + { + "author_name": "Lars E French", + "author_inst": "Department of Dermatology, University Hospital, Munich University of Ludwig Maximilian" + }, + { + "author_name": "Henry W Lim", + "author_inst": "Department of Dermatology, Henry Ford Health System" + }, + { + "author_name": "Bruce H Thiers", + "author_inst": "Department of Dermatology and Dermatologic Surgery, Medical University of SC" + }, + { + "author_name": "George J Hruza", + "author_inst": "Department of Dermatology, St. Louis University" + }, + { + "author_name": "Lindy P Fox", + "author_inst": "Department of Dermatology, University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "dermatology" + }, { "rel_doi": "10.1101/2020.05.24.20111989", "rel_title": "Epidemic Model Guided Machine Learning for COVID-19 Forecasts in the United States", @@ -1412824,41 +1409587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.23.20110973", - "rel_title": "Modelling the impact of Plasma Therapy and Immunotherapy for Recovery of COVID-19 Infected Individuals", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110973", - "rel_abs": "Since the first case of COVID-19 was detected in Wuhan, China in December 2019, COVID-19 has become a pandemic causing a global economic and public health emergency. There is no known treatment or vaccine available for COVID-19 to date. Immunotherapy and plasma therapy has been used with satisfactory efficacy over the past two decades in many viral infections like SARS (Systemic Acute Respiratory Syndrome), MERS (Middle East Respiratory Syndrome), and H1N1. Limited data from China show clinical benefit, radiological resolution, reduction in viral loads, and improved survival. Our aim is to create a mathematical model for COVID-19 transmission and then apply various control parameters to see their effects on recovery from COVID-19 disease. We have formulated a system of non-linear ordinary differential equations, calculated basic reproduction R0, and applied five different controls (self-isolation, quarantine, herd immunity, immunotherapy, plasma therapy) to test the effectiveness of control strategy. Control optimality was checked by Lagrangian functions. Numerical simulations and bifurcation analyses were carried out. The study concludes that the COVID-19 outbreak can be controlled up to a significant level three weeks after applying all the control strategies together. These strategies lead to a reduction in hospitalization and a rise in recovery from infection. Immunotherapy is highly effective initially in hospitalized infected individuals however better results were seen in the long term with plasma therapy.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nita H Shah", - "author_inst": "Gujarat University" - }, - { - "author_name": "Ankush H Suthar", - "author_inst": "Gujarat University" - }, - { - "author_name": "Ekta N Jayswal", - "author_inst": "Gujarat University" - }, - { - "author_name": "Nehal Shukla", - "author_inst": "Columbus State University" - }, - { - "author_name": "Jagdish Shukla", - "author_inst": "Piedmont Columbus Regional" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.23.20110916", "rel_title": "A systems approach to inflammation identifies therapeutic targets in SARS-CoV-2 infection", @@ -1413491,6 +1410219,89 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.24.111823", + "rel_title": "The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I", + "rel_date": "2020-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.24.111823", + "rel_abs": "SARS-CoV-2 infection have caused global pandemic and claimed over 5,000,000 tolls1-4. Although the genetic sequences of their etiologic viruses are of high homology, the clinical and pathological characteristics of COVID-19 significantly differ from SARS5,6. Especially, it seems that SARS-CoV-2 undergoes vast replication in vivo without being effectively monitored by anti-viral immunity7. Here, we show that the viral protein encoded from open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all the viral proteins, can directly interact with MHC-I molecules and significantly down-regulates their surface expression on various cell types. In contrast, ORF8a and ORF8b of SARS-CoV do not exert this function. In the ORF8-expressing cells, MHC-I molecules are selectively target for lysosomal degradation by an autophagy-dependent mechanism. As a result, CTLs inefficiently eliminate the ORF8-expressing cells. Our results demonstrate that ORF8 protein disrupts antigen presentation and reduces the recognition and the elimination of virus-infected cells by CTLs8. Therefore, we suggest that the inhibition of ORF8 function could be a strategy to improve the special immune surveillance and accelerate the eradication of SARS-CoV-2 in vivo.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yiwen Zhang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Yingshi Chen", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Baohong Luo", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Yaochang Yuan", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Feng Huang", + "author_inst": "Department of Respiratory Diseases, Guangzhou Women and Children Hospital" + }, + { + "author_name": "Tao Yang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Fei Yu", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Jun Liu", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Bingfeng Liu", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Zheng Song", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Jingliang Chen", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Ting Pan", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xu Zhang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Yuzhuang Li", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Rong Li", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Fei Xiao", + "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag" + }, + { + "author_name": "Hui Zhang", + "author_inst": "Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.24.113175", "rel_title": "Structural basis of SARS-CoV-2 spike protein induced by ACE2", @@ -1414194,61 +1411005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20109082", - "rel_title": "Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109082", - "rel_abs": "AimsThis retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs).\n\nMethods and ResultsAll adults with SARS-CoV-2 infection in two Italian provinces were followed for a median of 24 days. ARBs and/or ACEi treatments, and hypertension, diabetes, cancer, COPD, renal and major cardiovascular diseases (CVD) were extracted from clinical charts and electronic health records, up to two years before infection. The sample consisted of 1603 subjects (mean age 58.0y; 47.3% males): 454 (28.3%) had severe symptoms, 192 (12.0%) very severe or lethal disease (154 deaths; mean age 79.3 years; 70.8% hypertensive, 42.2% with CVD). The youngest deceased person aged 44 years. Among hypertensive subjects (n=543), the proportion of those treated with ARBs or ACEi were 88.4%, 78.7% and 80.6% among patients with mild, severe and very severe/lethal disease, respectively. At multivariate analysis, no association was observed between therapy and disease severity (Adjusted OR for very severe/lethal COVID-19: 0.87; 95% CI: 0.50-1.49). Significant predictors of severe disease were older age (with AORs largely increasing after 70 years of age), male gender (AOR: 1.76; 1.40-2.23), diabetes (AOR: 1.52; 1.05-2.18), CVD (AOR: 1.88; 1.32-2.70) and COPD (1.88; 1.11-3.20). Only gender, age and diabetes also predicted very severe/lethal disease.\n\nConclusionNo association was found between COVID-19 severity and treatment with ARBs and/or ACEi, supporting the recommendation to continue medication for all patients unless otherwise advised by their physicians.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Francesca Bravi", - "author_inst": "\"Sant'Anna\" University Hospital of Ferrara, Italy" - }, - { - "author_name": "Maria Elena Flacco", - "author_inst": "Department of Medical Sciences, University of Ferrara, Italy" - }, - { - "author_name": "Tiziano Carradori", - "author_inst": "\"Sant'Anna\" University Hospital of Ferrara, Italy" - }, - { - "author_name": "Carlo Alberto Volta", - "author_inst": "University of Ferrara" - }, - { - "author_name": "Giuseppe Cosenza", - "author_inst": "Local Health Authority of Ferrara, Italy" - }, - { - "author_name": "Aldo De Togni", - "author_inst": "Local Health Authority of Ferrara, Italy" - }, - { - "author_name": "Cecilia Acuti Martellucci", - "author_inst": "Department of Biomedical Sciences and Public Health, University of the Marche Region, Ancona, Italy" - }, - { - "author_name": "Giustino Parruti", - "author_inst": "Local Health Authority of Pescara, Italy" - }, - { - "author_name": "Lorenzo Mantovani", - "author_inst": "School of Medicine and Surgery, University Bicocca, Milan, Italy" - }, - { - "author_name": "Lamberto Manzoli", - "author_inst": "University of Ferrara" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20108860", "rel_title": "Immunity after COVID-19: protection or sensitization ?", @@ -1414645,6 +1411401,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20108753", + "rel_title": "Forecasting trajectories of an emerging epidemic with mathematical modeling in an online dashboard: The case of COVID-19", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108753", + "rel_abs": "We offer an efficient mathematical model for forecasting the course of an emerging epidemic, with COVID-19 as a use case. We predict the future course of confirmed cases in a number of countries, and present the results in a modern online dashboard, updated daily and accessible to the public.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Wojciech M\u0142ocek", + "author_inst": "University of Agriculture in Krakow" + }, + { + "author_name": "Robert Lew", + "author_inst": "Adam Mickiewicz University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20108803", "rel_title": "The Challenge of Using Epidemiological Case Count Data: The Example of Confirmed COVID-19 Cases and the Weather", @@ -1415888,49 +1412667,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.05.21.20109652", - "rel_title": "COVID-19 receptor ACE2 is expressed in human conjunctival tissue, expecially in diseased conjunctival tissue", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109652", - "rel_abs": "COVID-19 virus has currently caused major outbreaks worldwide. ACE2 is a major cellular-entry receptor for the COVID-19 virus. Although ACE2 is known to be expressed in many organs, whether it is expressed by the conjunctival tissue is largely unknown. Human conjunctival tissues from 68 subjects were obtained, which included 10 subjects with conjunctival nevi, 20 subjects with conjunctivitis, 9 subjects with conjunctival papilloma, 16 subjects with conjunctival cyst, 7 subjects with conjunctival polyps, and 6 ocular traumas as normal subjects. Expression of ACE2 was evaluated by immunohistochemistry, immunofluorescence, reverse transcriptase-quantitative polymerase chain reaction, and western blot assay. We observed the expression of ACE2 by conjunctival tissues, expecially in conjunctival epithelial cells. ACE2 was significantly (p<0.001) overexpressed in conjunctival cells obtained from subjects with conjunctivitis, conjunctival nevi, conjunctival papilloma, conjunctival cyst, and conjunctival polyps epithelial cells when compared to that in conjunctival epithelial cells obtained from control subjects. Collectively, clinical features of reported COVID-19 patients combined with our results indicate that COVID-19 is likely to be transmitted through the conjunctiva.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "shengjie li Sr.", - "author_inst": "Fudan University" - }, - { - "author_name": "danhui li", - "author_inst": "Renji Hospital, School of Medicine, Shanghai Jiao Tong University" - }, - { - "author_name": "jianchen fang", - "author_inst": "Renji Hospital, School of Medicine, Shanghai Jiao Tong University" - }, - { - "author_name": "qiang liu", - "author_inst": "Renji Hospital, School of Medicine, Shanghai Jiao Tong University" - }, - { - "author_name": "xinghuai sun", - "author_inst": "Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University" - }, - { - "author_name": "gezhi xu", - "author_inst": "Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College" - }, - { - "author_name": "wenjun cao", - "author_inst": "Department of Clinical Laboratory, Eye & ENT Hospital, Shanghai Medical College, Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2020.05.20.20108183", "rel_title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", @@ -1416455,6 +1413191,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.22.20109942", + "rel_title": "Clustering method for spread pattern analysis of corona-virus (COVID-19) infection in Iran", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109942", + "rel_abs": "The COVID-19 is outbreak from China and infected more than 131,652 people and caused 7,300 deaths in Iran. Unfortunately, the infection numbers and deaths are still increasing rapidly which has put the world on the catastrophic abyss edge. Application of data mining to perform pattern recognition of infection is mainly used for peparing the spread mapping which considred in this work for spatiotemporal distribution assessment and spread pattern analysis of corona-virus (COVID-19) infection in Iran.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mehdi Azarafza", + "author_inst": "University of Tabriz" + }, + { + "author_name": "Mohammd Azarafza", + "author_inst": "University of Isfahan" + }, + { + "author_name": "Haluk Akgun", + "author_inst": "Middle East Technical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20109405", "rel_title": "Time Dynamics of COVID-19", @@ -1417146,73 +1413909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.20.20105312", - "rel_title": "Amplification of human \u03b2-glucoronidase gene for appraising the accuracy of negative SARS-CoV-2 RT-PCR results in upper respiratory tract specimens", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20105312", - "rel_abs": "Real-time reverse transcription polymerase-chain reaction (RT-PCR) is the mainstay of Covid-19 diagnosis. False-negative RT-PCR results may hamper clinical management of patients and hinder the adoption of epidemiological measures to control the pandemic. The current study was aimed at assessing whether amplification of {beta}-glucoronidase (GUSB) gene would help estimate the accuracy of SARS-CoV-2 RT-PCR negative results in upper respiratory tract (URT) specimens. URT specimens that tested negative by SARS-CoV-2 RT-PCR displayed higher GUSB RT-PCR cycle thresholds (CT) (P=0.070) than those testing positive (median, 30.7; range, 27.0-40.0, and median 29.7; range 25.5-36.8, respectively), this reflecting poorer cellularity. Receiver operating characteristic (roc) curve analysis indicated that a CT threshold of 31.2 discriminated best between positive and negative SARS CoV-2 RT-PCRs (area under a curve, 0.66; 95% CI, 0.50-0.81; P=0.08). This cut-off yielded a true negative ratio of 89% and accuracy of 70%. The data suggested that amplification of the GUSB gene by RT-PCR may help to appraise the accuracy of negative SARS-CoV-2 RT-PCR results in patients in whom Covid-19 is eventually diagnosed.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "Blanca Ferrer", - "author_inst": "Hematology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "Ignacio Torres", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." - }, - { - "author_name": "Alicia Serrano", - "author_inst": "Hematology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." - }, - { - "author_name": "Maria Jesus Alcaraz", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain." - }, - { - "author_name": "Javier Buesa", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain. Department of Microbiology, School of Medicine, University o" - }, - { - "author_name": "Carlos Solnao", - "author_inst": "Hematology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain. Department of Microbiology, School of Medicine, University of V" - }, - { - "author_name": "Javier Colomina", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "Felipe Bueno", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "Dixie Huntley", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "beatriz olea", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "Arantxa valdivia", - "author_inst": "Microbiology Service, Hospital Clinico Universitario, INCLIVA Research Institute, Valencia, Spain" - }, - { - "author_name": "David Navarro", - "author_inst": "Microbiology Service, Hospital Clnico Universitario, INCLIVA Research Institute, Valencia, Spain. Department of Microbiology, School of Medicine, University of" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105841", "rel_title": "An Interpretable Machine Learning Framework for Accurate Severe vs Non-severe COVID-19 Clinical Type Classification", @@ -1417853,6 +1414549,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20105999", + "rel_title": "SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20105999", + "rel_abs": "We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples, and when adjusted for the time lag, the virus RNA concentrations tracked the COVID-19 epidemiological curve. SARS-CoV-2 RNA concentrations were a leading indicator of community infection ahead of compiled COVID-19 testing data and local hospital admissions. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jordan Peccia", + "author_inst": "Yale University" + }, + { + "author_name": "Alessandro Zulli", + "author_inst": "Yale University" + }, + { + "author_name": "Doug E. Brackney", + "author_inst": "Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Nathan D. Grubaugh", + "author_inst": "Yale University" + }, + { + "author_name": "Edward H. Kaplan", + "author_inst": "Yale University" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Yale University" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Yale University" + }, + { + "author_name": "Amyn A. Malik", + "author_inst": "Yale University" + }, + { + "author_name": "Dennis Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Mike Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Joshua L. Warren", + "author_inst": "Yale University" + }, + { + "author_name": "Daniel M. Weinberger", + "author_inst": "Yale University" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.111005", "rel_title": "Potently neutralizing human antibodies that block SARS-CoV-2 receptor binding and protect animals", @@ -1418816,97 +1415579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20086488", - "rel_title": "Early risk assessment for COVID-19 patients from emergency department data using machine learning", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20086488", - "rel_abs": "BackgroundSince its emergence in late 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, with more than 4.8 million reported cases and 310 000 deaths worldwide. While epidemiological and clinical characteristics of COVID-19 have been reported, risk factors underlying the transition from mild to severe disease among patients remain poorly understood.\n\nMethodsIn this retrospective study, we analysed data of 820 confirmed COVID-19 positive patients admitted to a two-site NHS Trust hospital in London, England, between January 1st and April 23rd, 2020, with a majority of cases occurring in March and April. We extracted anonymised demographic data, physiological clinical variables and laboratory results from electronic healthcare records (EHR) and applied multivariate logistic regression, random forest and extreme gradient boosted trees. To evaluate the potential for early risk assessment, we used data available during patients initial presentation at the emergency department (ED) to predict deterioration to one of three clinical endpoints in the remainder of the hospital stay: A) admission to intensive care, B) need for mechanical ventilation and C) mortality. Based on the trained models, we extracted the most informative clinical features in determining these patient trajectories.\n\nResultsConsidering our inclusion criteria, we have identified 126 of 820 (15%) patients that required intensive care, 62 of 808 (8%) patients needing mechanical ventilation, and 170 of 630 (27%) cases of in-hospital mortality. Our models learned successfully from early clinical data and predicted clinical endpoints with high accuracy, the best model achieving AUC-ROC scores of 0.75 to 0.83 (F1 scores of 0.41 to 0.56). Younger patient age was associated with an increased risk of receiving intensive care and ventilation, but lower risk of mortality. Clinical indicators of a patients oxygen supply and selected laboratory results were most predictive of COVID-19 patient trajectories.\n\nConclusionAmong COVID-19 patients machine learning can aid in the early identification of those with a poor prognosis, using EHR data collected during a patients first presentation at ED. Patient age and measures of oxygenation status during ED stay are primary indicators of poor patient outcomes.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Frank Stefan Heldt", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Marcela P Vizcaychipi", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK" - }, - { - "author_name": "Sophie Peacock", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Mattia Cinelli", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Lachlan McLachlan", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Fernando Andreotti", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Stojan Jovanovic", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Robert Durichen", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Nadezda Lipunova", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Robert A Fletcher", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Anne Hancock", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Alex McCarthy", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK" - }, - { - "author_name": "Richard A Pointon", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK" - }, - { - "author_name": "Alexander Brown", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK" - }, - { - "author_name": "James Eaton", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK" - }, - { - "author_name": "Roberto Liddi", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Lucy Mackillop", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Lionel Tarassenko", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - }, - { - "author_name": "Rabia Tahir Khan", - "author_inst": "Sensyne Health plc, Schrodinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.19.20099317", "rel_title": "Early antibody response to SARS-CoV-2", @@ -1419523,6 +1416195,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.17.20101063", + "rel_title": "Hospital-acquired infective endocarditis during Covid-19 pandemic", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20101063", + "rel_abs": "BackgroundThe COVID pandemic has had a major impact on healthcare in hospitals, including the diagnosis and treatment of infections. Hospital-acquired infective endocarditis (HAIE) is a severe complication of medical procedures that has shown a progressive increase in recent years.\n\nObjectivesto determine whether the incidence of HAIE during the first two months of the epidemic (March-April 2020) was higher than previously observed and to describe the clinical characteristics of these cases. The probability of studied event (HAIE) during the studied period was calculate by Poisson distribution.\n\nResultsFour cases of HAIE were diagnosed in our institution during the study period. The incidence of HAIE during the study period was 2/patient-month and 0.25/patient-month during the previous 5 years (p=0.024). Two cases appeared during admission for COVID-19 with pulmonary involvement treated with methylprednisolone and tocilizumab. The other two cases were admitted to the hospital during the epidemic. All cases underwent central venous and urinary catheterization during admission. The etiology of HAIE was Enterococcus faecalis (2 cases), Staphylococcus aureus and Candida albicans (one case each). A source of infection was identified in three cases (central venous catheter, peripheral venous catheter, sternal wound infection, respectively). One patient was operated on. There were no fatalities during the first 30 days of follow-up.\n\nConclusionsThe incidence of HAIE during COVID-19 pandemic in our institution was higher than usual. In order to reduce the risk of this serious infection, optimal catheter care, appropriate use of corticosteroids and interleukin antagonists and early treatment of every local infection should be prioritized during coronavirus outbreaks.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio Ramos-Martinez", + "author_inst": "HU Puerta de Hierro-Majadahonda" + }, + { + "author_name": "Ana Fernndez-Cruz", + "author_inst": "HU Puerta de Hierro-Majadahonda" + }, + { + "author_name": "Fernando Dominguez", + "author_inst": "HU Puerta de Hierro-Majadahonda" + }, + { + "author_name": "Alberto Forteza", + "author_inst": "HUY Puerta de Hierro-Majadahinda" + }, + { + "author_name": "Marta Cobo", + "author_inst": "HU Puerta de Hierrro-Majadahonda" + }, + { + "author_name": "Isabel Sanchez-Romero", + "author_inst": "HU Puerta de Hierro-Majadahonda" + }, + { + "author_name": "Angel asensio", + "author_inst": "HU Puerta deHierro-Majadahonda" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.19.20104596", "rel_title": "Susceptibility-adjusted herd immunity threshold model and potential R0 distribution fitting the observed Covid-19 data in Stockholm", @@ -1420430,65 +1417145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.21.20051300", - "rel_title": "Higher serum levels of Chemokine CCL19 are associated with poor SARS-CoV-2 acute respiratory distress syndrome (ARDS) outcomes.", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20051300", - "rel_abs": "The COVID19 pandemic is likely to cause more than a million of deaths worldwide, primarily due to complications from COVID19-associated acute respiratory distress syndrome (ARDS). Controversy surrounds the circulating cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to non-COVID19 ARDS patients and others observing substantial differences. Moreover, while a hyperinflammatory phenotype associates with higher mortality in non-COVID19 ARDS, there is little information on the inflammatory landscapes association with mortality in COVID19 ARDS patients. Even though the circulating leukocytes transcriptomic signature has been associated with distinct phenotypes and outcomes in critical illness including ARDS, it is unclear whether the mortality-associated inflammatory mediators from COVID19 patients are transcriptionally regulated in the leukocyte compartment. Here, we conducted a prospective cohort study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines and their gene expressions in circulating leukocytes. Plasma IL1RA and IL8 were found positively associated with mortality while RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no statistically significant correlation with mortality. These data suggest a unique inflammatory signature associated with severe COVID19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Joseph Balnis", - "author_inst": "Albany Medical Center" - }, - { - "author_name": "Alejandro P Adam", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Amit Chopra", - "author_inst": "Albany Medical Center" - }, - { - "author_name": "Hau C Chieng", - "author_inst": "Albany Medical Center" - }, - { - "author_name": "Paul J Feustel", - "author_inst": "Albany Medical Center" - }, - { - "author_name": "Katherine A Overmyer", - "author_inst": "Morgridge Institute for Research, Madison, WI" - }, - { - "author_name": "Evgenia Shishkova", - "author_inst": "Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI" - }, - { - "author_name": "Joshua J Coon", - "author_inst": "Department of Biomolecular Chemistry, University of Wisconsin-Madison, Morgridge Institute for Research; Madison, WI" - }, - { - "author_name": "Harold A Singer", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Marc A Judson", - "author_inst": "Albany Medical Center" - }, - { - "author_name": "Ariel Jaitovich", - "author_inst": "Albany Medical College" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.17.20104927", "rel_title": "Prevalence Threshold and Temporal Interpretation of Screening Tests: The Example of the SARS-CoV-2 (COVID-19) Pandemic", @@ -1421149,6 +1417805,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.17.20104810", + "rel_title": "Prediction of the coronavirus epidemic prevalence inquarantine conditions based on an approximate calculation model", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104810", + "rel_abs": "A calculation model for predicting the spread of the COVID-19 epidemic under quarantine conditions is proposed. The obtained simple analytical ratios allow estimating the factors determining the intensity of the infection spread, including changing requirements for quarantine severity. The presented method of forecasting allows to calculate both the total number of infected persons and the number of active infections. Comparison of the results of calculations according to the proposed model with the statistics for a number of cities shows their satisfactory qualitative and quantitative compliance. The proposed simple model can be useful in preliminary assessment of possible consequences of changing quarantine conditions.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Denis Below", + "author_inst": "University Potsdam" + }, + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.18.20105445", "rel_title": "Understanding the spreading patterns of COVID-19 in UK and its impact on exit strategies", @@ -1421956,101 +1418635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.16.091520", - "rel_title": "The SARS-CoV-2 cytopathic effect is blocked with autophagy modulators", - "rel_date": "2020-05-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.091520", - "rel_abs": "SARS-CoV-2 is a new type of coronavirus capable of rapid transmission and causing severe clinical symptoms; much of which has unknown biological etiology. It has prompted researchers to rapidly mobilize their efforts towards identifying and developing anti-viral therapeutics and vaccines. Discovering and understanding the virus\u2019 pathways of infection, host-protein interactions, and cytopathic effects will greatly aid in the design of new therapeutics to treat COVID-19. While it is known that chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including inhibiting autophagy, there are also dose-limiting toxicities in patients that make clearly establishing their potential mechanisms-of-action problematic. Therefore, we evaluated a range of other autophagy modulators to identify an alternative autophagy-based drug repurposing opportunity. In this work, we found that 6 of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero-E6 cells with EC50 values ranging from 2.0 to 13 \u00b5M and selectivity indices ranging from 1.5 to >10-fold. Immunofluorescence staining for LC3B and LysoTracker dye staining assays in several cell lines indicated their potency and efficacy for inhibiting autophagy correlated with the measurements in the SARS-CoV-2 cytopathic effect assay. Our data suggest that autophagy pathways could be targeted to combat SARS-CoV-2 infections and become an important component of drug combination therapies to improve the treatment outcomes for COVID-19.One Sentence Summary Blocking SARS-CoV-2 cytopathic effects with selective autophagy inhibitors underlying the clinical benefits of chloroquine and hydroxychloroquine.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Kirill Gorshkov", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Catherine Z. Chen", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Robert Bostwick", - "author_inst": "Southern Research" - }, - { - "author_name": "Lynn Rasmussen", - "author_inst": "Southern Research" - }, - { - "author_name": "Miao Xu", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Manisha Pradhan", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Bruce Nguyen Tran", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Wei Zhu", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Khalida Shamim", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Wenwei Huang", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Xin Hu", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Min Shen", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Carleen Klumpp-Thomas", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Zina Itkin", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Paul Shinn", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Anton Simeonov", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Sam Michael", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Matthew D. Hall", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Donald C. Lo", - "author_inst": "National Center for Advancing Translational Sciences" - }, - { - "author_name": "Wei Zheng", - "author_inst": "National Center for Advancing Translational Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.05.17.20104901", "rel_title": "Development of an interactive, agent-based local stochastic model of COVID-19 transmission and evaluation of mitigation strategies illustrated for the state of Massachusetts, USA", @@ -1422671,6 +1419255,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.19.20106971", + "rel_title": "Cancer immunotherapy does not increase the risk of death by COVID-19 in melanoma patients", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106971", + "rel_abs": "BackgroundCovid-19 pandemic by the new coronavirus SARS-Cov-2 has produced devastating effects on the health care system, affecting also cancer patient care. Data about COVID-19 infection in cancer patients are scarce, and they point out a higher risk of complications due to the viral infection in this population. Moreover, cancer treatments could increase viral complications, specially those treatments based on the use of immunotherapy with checkpoints antibodies. There are no clinical data about the safety of immune check point antibodies in cancer patients when they become infected by SARS-CoV-2. As checkpoint inhibitors, mainly anti PD-1 and anti CTLA-4 antibodies, are an effective treatment for most melanoma patients, avoiding their use during the pandemic could lead to a decrease in the chances of curing melanoma.\n\nMethodsIn Spain we have started a national registry of melanoma patients infected by SARS-Cov-2 since April 1st, 2020. A retrospective analysis of patients included in the Spanish registery has been performed weekly since the activation of the study. Interim analysis shows unexpected findings about cancer treatment safety in SARS-Cov-2 infected melanoma patients, so a rapid communication to the scientific community is mandatory\n\nResultsFifty patients have been included as of May 17th, 2020. Median age is 69 years (range 6 to 94 years), 27 (54%) patients are males and 36 (70%) patients have stage IV melanoma. Twenty-two (44%) patients were on active anticancer treatment with anti PD-1 antibodies, 16 (32%) patients were on treatment with BRAF plus MEK inhibitors and 12 (24%) patients were not on active cancer treatment. COVID-19 episode has been resolved in 43 cases, including 30 (70%) patients cured, four (9%) patients that have died due to melanoma progression, and nine (21%) patients that have died from COVID-19. Mortality rates from COVID-19 according to melanoma treatment type were 16%, 15% and 36% for patients on immunotherapy, targeted drugs, and for those that were not undergoing active cancer treatment, respectively.\n\nConclusionThese preliminary findings show that the risk of death in those patients under going treatment with anti PD-1 antibodies does not exceed the global risk of death in this population. These results could be relevant in order to select melanoma therapy during the COVID-19 pandemic", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Maria Gonzalez-Cao", + "author_inst": "Translational Cancer Research Unit, Instituto Onco" + }, + { + "author_name": "Monica Antonazas-Basa", + "author_inst": "Hospital Clinico San Carlos, Madrid, Spain" + }, + { + "author_name": "Teresa Puertolas", + "author_inst": "Hospital Universitario Miguel Servet, Zaragoza, Spain" + }, + { + "author_name": "Eva Munoz-Couselo", + "author_inst": "Hospital Universitari Vall Hebron, Barcelona, Spain" + }, + { + "author_name": "Jose Luis Manzano", + "author_inst": "Catalonian Institute of Oncology (ICO-Badalona), Medical Oncology Department, Germans Trias i Pujol Research Institute and Hospital (IGTP), Badalona, Barcelona," + }, + { + "author_name": "Cristina Carrera", + "author_inst": "Melanoma Group IDIBAPS, Hospital Clinic, University of Barcelona, (CIBERER) Spain" + }, + { + "author_name": "Ivan Marquez-Rodas", + "author_inst": "Hospital General Universitario Gregorio Maranon and CIBERONC, Madrid, Spain" + }, + { + "author_name": "Pilar Lopez-Criado", + "author_inst": "Hospital MD Anderson, Madrid, Spain" + }, + { + "author_name": "Juan Francisco Rodriguez-Moreno", + "author_inst": "Centro Integral Oncologico HM Clara Campal, Madrid, Spain" + }, + { + "author_name": "Almudena Garcia-Castano", + "author_inst": "Hospital Marques de Valdecilla, Santander, Spain" + }, + { + "author_name": "Juan Martin-Liberal", + "author_inst": "Catalan Institute Of Oncology (ICO) Hospitalet, Barcelona, Spain" + }, + { + "author_name": "Pedro Rodriguez-Jimenez", + "author_inst": "Hospital Universitario La Princesa, Madrid, Spain" + }, + { + "author_name": "Susana Puig", + "author_inst": "Melanoma Group IDIBAPS, Hospital Clinic, University of Barcelona (CIBERER) Spain" + }, + { + "author_name": "Pablo Cerezuela", + "author_inst": "H.U. Virgen de la Arrixaca, Murcia, Spain" + }, + { + "author_name": "Marta Feito-Rodriguez", + "author_inst": "Hospital Universitario La Paz, Madrid, Spain" + }, + { + "author_name": "Belen Rubio-Viqueira", + "author_inst": "Hospital Universitario Quironsalud, Madrid, Spain" + }, + { + "author_name": "Guillermo Crespo", + "author_inst": "Hospital Universitario de Burgos, Burgos, Spain" + }, + { + "author_name": "Pablo Luna-Fra", + "author_inst": "Hospital Son Espases, Mallorca, Spain" + }, + { + "author_name": "Cristina Aguayo", + "author_inst": "Hospital Universitario Infanta Sofia, Madrid, Spain" + }, + { + "author_name": "Pablo Ayala de Miguel", + "author_inst": "Hospital San Pedro de Alcantara, Caceres, Spain" + }, + { + "author_name": "Rosa Feltes", + "author_inst": "Hospital Universitario La Paz, Madrid, Spain" + }, + { + "author_name": "Lara Valles", + "author_inst": "Hospital General de Villalba, Madrid, Spain" + }, + { + "author_name": "Ana Drozdowskyj", + "author_inst": "Translational Cancer Research Unit, Instituto Oncologico Dr Rosell, Dexeus University Hospital, Barcelona, Spain" + }, + { + "author_name": "Ainara Soria", + "author_inst": "Hospital Ramon y Cajal, Madrid, Spain" + }, + { + "author_name": "Cayetana Maldonado", + "author_inst": "Hospital Universitario Central de Asturias, Oviedo, Spain" + }, + { + "author_name": "Luis Fernandez-Morales", + "author_inst": "Parc Tauli Hospital Universitario,Barcelona, Spain" + }, + { + "author_name": "Rafael Rosell", + "author_inst": "Germans Trias i Pujol Research Institute and Hospital (IGTP), Badalona, Spain" + }, + { + "author_name": "Mariano Provencio", + "author_inst": "Hospital Puerta de Hierro, Madrid, Spain" + }, + { + "author_name": "Alfonso Berrocal", + "author_inst": "Hospital Universitario General de Valencia, Valencia, Spain" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.05.15.20103374", "rel_title": "A data-driven method to detect the flattening of the COVID-19 pandemic curve and estimating its ending life-cycle using only the time-series of new cases per day.", @@ -1423302,33 +1420017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.15.20103630", - "rel_title": "Global Analysis of an SEIRS Model for COVID-19 Capturing Saturated Incidence with Treatment Response", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103630", - "rel_abs": "Sequel to [10], who studied the dynamics of COVID-19 using an SEIRUS model. We consider an SEIRS model capturing saturated incidence with treatment response. In this theoretical model, we assumed that the treatment response is proportional to the number of infected as long as the incidence cases are within the capacity of the healthcare system, after which the value becomes constant, when the number of confirmed cases exceed the carrying capacity of the available medical facilities. Thus, we obtain the reproduction number stating that when R0 < 1, the disease free equilibrium is globally asymptotically stable. Also, we studied the existence of the local and global stability of the disease free and endemic equilibria and found that the kind of treatment response and inhibitory measures deployed in tackling the COVID-19 pandemic determines whether the disease will die out or become endemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "David Adeyemi Oluyori", - "author_inst": "Department of Mathematics, Ahmadu Bello University, Zaria, Kaduna State, Nigeria" - }, - { - "author_name": "Helen O. Adebayo", - "author_inst": "Department of Mathematics, Ahmadu Bello University, Kaduna State, Nigeria" - }, - { - "author_name": "\u00c1ngel G. C. P\u00e9rez", - "author_inst": "Universidad Aut\u00f3noma de Yucat\u00e1n" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20104133", "rel_title": "Predicting the COVID-19 positive cases in India with concern to Lockdown by using Mathematical and Machine Learning based Models", @@ -1423709,6 +1420397,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.16.20103796", + "rel_title": "Asymptomatic COVID-19 Have Longer Treatment Cycle Than Moderate Type of Confirmed Patients", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103796", + "rel_abs": "ObjectivesA kind of pneumonia caused by unknown causes that occurred in Wuhan, Hubei, China in December 2019, was reported as a result of novel coronavirus infection on January 7, 2020, and then WHO named it COVID-19. To compare the difference of epidemiology and clinical characteristics between asymptomatic COVID-19 infections and moderate type of confirmed cases.\n\nMethodsRetrospective, single-center cohort study of COVID-19 involving 52 infections of both 26 asymptomatic and 26 moderate type of confirmed cases in the recovery stage at Guizhou Provincial Staff Hospital in Guiyang, China, from January 29, to March 31, 2020; final date of follow-up was April 22. This study was registered in Chinese Clinical Trial Registry Center. Documented the asymptomatic COVID-19 infections and moderate type of confirmed cases. Epidemiological, demographic, clinical, laboratory, radiological, and treatment data were collected and analyzed. Epidemiological and clinical characteristics of asymptomatic COVID-19 infections and moderate type of confirmed cases were compared.\n\nResultsThe median treatment cycle of asymptomatic COVID-19 infections was 16 days (interquartile range, 11-20 days) and longer than 13 days (interquartile range, 10-15 days) of moderate type of confirmed cases (p=0.049). The median incubation period of asymptomatic COVID-19 infections was 10 days (interquartile range, 0-21 days), while the control group was 7 days (interquartile range, 1-15 days) (p=0.27). On the initial chest computerized tomography (CT) check, 18 (69.2%, 18/26) asymptomatic COVID-19 infections were no imaging changes, which was of no significance compared with 12 (46.2%, 12/26) patients with moderate type of confirmed patients (p=0.092).\n\nConclusionsIn this single-center study, we found that asymptomatic COVID-19 infections have longer treatment cycle than those moderate type of confirmed cases.\n\nKey PointsIn this single-center case series involving 52 infections with asymptomatic and moderate type of COVID-19 cases, asymptomatic COVID-19 infections have longer treatment cycle than those moderate type of confirmed patients.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Wei Zhang", + "author_inst": "Affiliated Hospital of Zunyi Medical University" + }, + { + "author_name": "Qinying Long", + "author_inst": "Guizhou University School of Medicine" + }, + { + "author_name": "Yanbiao Huang", + "author_inst": "Guizhou University School of Medicine" + }, + { + "author_name": "Changju Chen", + "author_inst": "Affiliated Hospital of Zunyi Medical University" + }, + { + "author_name": "Jinhua Wu", + "author_inst": "Guizhou Provincial Staff Hospital" + }, + { + "author_name": "Yang Hong", + "author_inst": "Guizhou maternal and Child Health Hospital" + }, + { + "author_name": "Hourong Zhou", + "author_inst": "Guizhou Provincial People's Hospital" + }, + { + "author_name": "Weidong Wu", + "author_inst": "Guizhou Normal College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.106625", "rel_title": "CONTAIN: An open-source shipping container laboratory optimisedfor automated COVID-19 diagnostics", @@ -1424848,29 +1421583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20102392", - "rel_title": "Ostavimir is ineffective against COVID-19: in silico assessment, in vitro and retrospective study", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102392", - "rel_abs": "As a neuraminidase inhibitor, oseltamivir has effectively combated the pandemic influenza A and B, so it is a first-line commonly used antiviral drug, especially in primary hospitals. At the same time, oseltamivir, as an over-the-counter drug, is also a popular antiviral drug. As healthcare workers fighting against coronavirus disease 2019 (COVID-19), we have found that many patients experiencing discomfort or considered to be infected with a virus take oseltamivir. From severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 to middle east respiratory syndrome coronavirus (MERS-CoV) in 2012, and now the current COVID-19 epidemic, there is not plenty of evidence showing that oseltamivir is effective against coronavirus. Still, there is also no sufficient evidence to refute its ineffectiveness. We cannot predict whether there will be a pandemic of respiratory coronavirus in the future, so we hope to initiate such research and preliminarily explore whether oseltamivir is effective for COVID-19, which can better guide healthcare workers in the selection of appropriate antiviral drugs in the face of coronavirus epidemics. If oseltamivir is effective, then a wide promotion of its application often can achieve a double effect with half the effort. If it is not effective, then considering the side effects of oseltamivir, it is not necessary to use unreasonable drugs that will not slow the progression of the disease but can cause adverse reactions. We found that oseltamivir isnt suitable for fighting against COVID-19 through the method of computer aided drug design and in vitro study and retrospective case study. Meanwhile it was high-occurrence seasons for the influenza, COVID-19 should be highly suspected in patients who didnt benefit from oseltamivir. We hope that the result of our study could be shared with the frontline physicians in fighting against COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Qi Tan", - "author_inst": "Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Disease" - }, - { - "author_name": "Yang Jin", - "author_inst": "Wuhan Union Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.16.20102095", "rel_title": "Systematic and Statistical Review of COVID19 Treatment Trials", @@ -1425379,6 +1422091,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.16.20102947", + "rel_title": "Performance of progressive and adaptive COVID-19 exit strategies: a stress test analysis for managing intensive care unit rates", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20102947", + "rel_abs": "BackgroundIn May 2020, many European countries have begun to introduce an exit strategy for the coronavirus disease 2019 (COVID-19) pandemic which involves relaxing social distancing measures. Predictive epidemiological modeling indicates that chances for resurgence are high. However, parametrization of the epidemiological nature of COVID-19 and the effect of relaxing social distancing is not well constrained, resulting in highly uncertain outcomes in view of managing future intensive care unit (ICU) needs.\n\nMethods and findingsFor performance analysis of exit strategies we developed an open-source ensemble-based Susceptible-Exposed-Infectious-Removed (SEIR) model. It takes into account uncertainties for the COVID-19 parametrization and social distancing measures. The model is calibrated to data of the outbreak and lockdown phase. For the exit phase, the model includes the capability to activate an emergency brake, reinstating lockdown conditions. Alternatively, the model uses an adaptive COVID-19 cruise control (ACCC) capable to retain a targeted ICU level. The model is demonstrated for the Netherlands and we analyzed progressive and adaptive exit strategies through a stress test of managing ICU rates. The progressive strategy reflects the outcome of social and economic pressure to use one-way steering toward progressively relaxing measures at an early stage. It is marked by a high probability for the activation of the emergency brake due to an unsolicited growth of ICU needs in the following months. Alternatively, the two-way steering ACCC can flatten ICU needs in a more gradual way and avoids activation of the emergency brake. It also performs well for seasonal variation in the reproduction number of severe acute respiratory syndrome-coronavirus.\n\nConclusionsThe adaptive strategy (ACCC) is favored, as it avoids the use of the emergency brake at the expense of small steps of restrictive measures and allows the exploration of riskier and potentially rewarding measures in the future pathways of the exit strategy.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jan-Diederik van Wees", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Martijn van der Kuip", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Emma Childrens Hos" + }, + { + "author_name": "Sander Osinga", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "David van Westerloo", + "author_inst": "Department of Intensive Care Medicine, Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Michael Tanck", + "author_inst": "Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Amsterdam University Medical Centers, University of Amsterdam, A" + }, + { + "author_name": "Maurice Hanegraaf", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Maarten Pluymaekers", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Olwijn Leeuwenburgh", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Lonneke van Bijsterveldt", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Pien Verreijdt", + "author_inst": "Faculty of Medicine, VUmc School of Medical Sciences, VU Amsterdam, Amsterdam, the Netherlands" + }, + { + "author_name": "Logan Brunner", + "author_inst": "TNO, Netherlands Organization for Applied Scientific Research, The Hague, the Netherlands" + }, + { + "author_name": "Marceline Tutu van Furth", + "author_inst": "Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Emma Childrens Hos" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.18.20102434", "rel_title": "Changing trends of excess self-protective behavior, and association with belief in prevention myths during the COVID-19 epidemic in China: A panel study", @@ -1425922,37 +1422697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.15.20103424", - "rel_title": "Comparative Analysis of the Application of Behavioural Insights of 33 Worldwide Governments on the Landing Pages of their COVID-19 Official Websites and their Impact on the Growth Scale of the Pandemic", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103424", - "rel_abs": "I.The COVID-19 crisis has seen over a third of the world population locked down and this article has sought to understand human behaviour in response to a historical and unprecedented global pandemic. Through the analysis 18 behavioural mechanisms present on the landing pages of the websites of 33 institutional governments from March 1st til May 1st 2020 compared to the WHO data on the number of COVID-19 cases and deaths per million for each country, the authors show that a behavioural consensus was observed across all 33 countries and that Individual and Social nudges had no impact. Whilst the decisions in essentially every country on Earth, were taken with the same aim: to limit population movements and social life, two aggravating factors of the spread of the virus, only the environmental nudges effectively helped slow the virus growth scale. The authors explain the rationale behind these results and suggest that people seek information beyond governmental websites that they generally mistrust. They further suggest using Scientists as role models to encourage governmental websites traffic and designing recursive nudges to increase the impact of individual and social interventions. Together with the new phases of the spread of the virus will come new rules and guidance. Public health policies need to address behavioural change of the population on a global scale in a more targeted manner and it is hoped that this paper will provide some insight on how to do so.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paola Cecchi-Dimeglio", - "author_inst": "Harvard University, Law School & Kennedy School" - }, - { - "author_name": "Raphaela Kitson-Pantano", - "author_inst": "Absolutys" - }, - { - "author_name": "David Luu", - "author_inst": "Absolutys" - }, - { - "author_name": "Yann Cabon", - "author_inst": "People Culture Drive Consulting Group" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.15.20103051", "rel_title": "Data-driven analysis on the simulations of the spread of COVID-19 under different interventions of China", @@ -1426637,6 +1423381,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.13.20100222", + "rel_title": "Silent Disease and Loss of Taste and Smell are Common Manifestations of SARS-COV-2 Infection in a Quarantine Facility: First report from Saudi Arabia", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100222", + "rel_abs": "BACKGROUNDThe Coronavirus disease 2019 (COVID-19) outbreak in Saudi Arabia was first identified in a traveler from Al Qatif city, on March 2nd, 2020. The disease has quickly spread and reached multiple cities within a few weeks. In an attempt to limit the spread of COVID-19 in Saudi Arabia, the government has implemented strict regulations. Starting March 15th, all travelers coming back to the kingdom were tested for COVID-19 and were quarantined in a government-designated facility. The same rule was applied to all positive cases identified by contact tracing. In this study, we aimed to assess the prevalence of asymptomatic carriers, epidemiological characteristics, clinical presentations, and viral clearance of SARS-COV-2 positive quarantined individuals in a quarantine facility in the eastern province.\n\nMETHODSWe conducted a cross-sectional study on 128 laboratory-confirmed COVID-19 subjects who were quarantined in a government-designated facility. The study period was from March 16th - till April 18th, 2020. We collected data on demographics and on clinical symptoms. Also, samples for PCR tests were collected upon admission and were repeated every 72 hours if they were still positive. All negative samples were repeated within 24 hours for confirmation.\n\nRESULTSSixty-nine of the 128 residents (54%) were completely asymptomatic until the end of the study. The remaining 59 residents (46%) had only mild symptoms. The most common symptom was a sudden loss of smell and taste, accounting for 47.5%. The median time to virus clearance was significantly different between the two groups. Symptomatic residents cleared the virus at a median of 17 days (95% CI,12.4-21.6) from the first positive PCR vs. 11days (95% CI, 8.7-13.3) in the asymptomatic group (P=0.011). False-negative test results occurred in 18.8% of the total residents and false positive results in 3%.\n\nCONCLUSIONThe prevalence of asymptomatic carriers is high in our study. Testing, and isolating travelers and contacts of laboratory-confirmed cases, regardless of symptoms, were very effective measures for early disease identification and containment. Loss of taste and smell was the most common presentation in our mild symptomatic residents, and it might be predictive of mild disease. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alanoud A Alshami", + "author_inst": "King Fahad Specialist Hospital Dammam" + }, + { + "author_name": "Rabab A Alattas", + "author_inst": "King Fahad Specialist Dammam" + }, + { + "author_name": "Hadeel F Anan", + "author_inst": "king Fahad Specialist Hospital" + }, + { + "author_name": "Hadi S Al Qahtani", + "author_inst": "King Fahad Specialist Hospital Dammam" + }, + { + "author_name": "Mobarak A Al Mulhim", + "author_inst": "King Fahad Specialist Hospital Dammam" + }, + { + "author_name": "Abdulbari A Alahilmi", + "author_inst": "King Faisal University in Al Ahsa" + }, + { + "author_name": "Ahmed H Alfaraj", + "author_inst": "King Fahad Specialist Hospital Dammam" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20100255", "rel_title": "Manifestations of mortality based global data of COVID-19; unifying global model through single parameter", @@ -1427480,37 +1424267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.14.20100909", - "rel_title": "Rapid estimation of excess mortality in times of COVID-19 in Portugal - Beyond reported deaths", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20100909", - "rel_abs": "BackgroundOne month after the first COVID-19 infection was recorded, Portugal counted 18 051 cases and 599 deaths from COVID-19. To understand the overall impact on mortality of the pandemic of COVID-19, we estimated the excess mortality registered in Portugal during the first month of the epidemic, from March 16 until April 14 using two different methods.\n\nMethodsWe compared the observed and expected daily deaths (historical average number from daily death registrations in the past 10 years) and used 2 standard deviations confidence limit for all-cause mortality by age and specific mortality cause, considering the last 6 years. An adapted ARIMA model was also tested to validate the estimated number of all-cause deaths during the study period.\n\nResultsBetween March 16 and April 14, there was an excess of 1,255 all-cause deaths, 14% more than expected. The number of daily deaths often surpassed the 2 standard deviations confidence limit. The excess mortality occurred mostly in people aged 75+. Forty-nine percent (49%) of the estimated excess deaths were registered as due to COVID-19, The other 51% registered as other natural causes.\n\nConclusionEven though Portugal took early containment measures against COVID-19, and the population complied massively with those measures, there was significant excess mortality during the first month of the pandemic, mostly among people aged 75+. Only half of the excess mortality was registered as directly due do COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Andre Vieira Sr.", - "author_inst": "National School of Public Health" - }, - { - "author_name": "Vasco Ricoca Peixoto Sr.", - "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal" - }, - { - "author_name": "Pedro Aguiar Sr.", - "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal" - }, - { - "author_name": "Alexandre Abrantes", - "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.13.20100651", "rel_title": "Efficacy of moist heat decontamination against various pathogens for the reuse of N95 respirators in the COVID-19 emergency", @@ -1427983,6 +1424739,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20101691", + "rel_title": "Blacks/African Americans are 5 Times More Likely to Develop COVID-19: Spatial Modeling of New York City ZIP Code-level Testing Results", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101691", + "rel_abs": "IntroductionThe population and spatial characteristics of COVID-19 infections are poorly understood, but there is increasing evidence that in addition to individual clinical factors, demographic, socioeconomic and racial characteristics play an important role.\n\nMethodsWe analyzed positive COVID-19 testing results counts within New York City ZIP Code Tabulation Areas (ZCTA) with Bayesian hierarchical Poisson spatial models using integrated nested Laplace approximations.\n\nResultsSpatial clustering accounted for approximately 32% of the variation in the data. For every one unit increase in a scaled standardized measure of Chronic Obstructive Pulmonary Disease (COPD) in a community, there was an approximate 8-fold increase in the risk of a positive COVID-19 test in a ZCTA (Incidence Density Ratio = 8.2, 95% Credible Interval 3.7, 18.3). There was a nearly five-fold increase in the risk of a positive COVID-19 test. (IDR = 4.8, 95% Cr I 2.4, 9.7) associated with the proportion of Black / African American residents. Increases in the proportion of residents older than 65, housing density and the proportion of residents with heart disease were each associated with an approximate doubling of risk. In a multivariable model including estimates for age, COPD, heart disease, housing density and Black/African American race, the only variables that remained associated with positive COVID-19 testing with a probability greater than chance were the proportion of Black/African American residents and proportion of older persons.\n\nConclusionsAreas with large proportions of Black/African American residents are at markedly higher risk that is not fully explained by characteristics of the environment and pre-existing conditions in the population.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Charles DiMaggio", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Michael Klein", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Cherisse Berry", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Spiros Frangos", + "author_inst": "New York University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.14.20101667", "rel_title": "Flatten the Curve! Modeling SARS-CoV-2/COVID-19 Growth in Germany on the County Level", @@ -1428614,69 +1425401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.17.20104943", - "rel_title": "Association of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers with the Risk of Hospitalization and Death in Hypertensive Patients with Coronavirus Disease-19", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104943", - "rel_abs": "BackgroundWhether angiotensin-converting enzyme (ACE) Inhibitors and angiotensin receptor blockers (ARBs) mitigate or exacerbate SARS-CoV-2 infection remains uncertain. In a national study, we evaluated the association of ACE inhibitors and ARB with coronavirus disease-19 (COVID-19) hospitalization and mortality among individuals with hypertension.\n\nMethodsAmong Medicare Advantage and commercially insured individuals, we identified 2,263 people with hypertension, receiving [≥]1 antihypertensive agents, and who had a positive outpatient SARS-CoV-2 test (outpatient cohort). In a propensity score-matched analysis, we determined the association of ACE inhibitors and ARBs with the risk of hospitalization for COVID-19. In a second study of 7,933 individuals with hypertension who were hospitalized with COVID-19 (inpatient cohort), we tested the association of these medications with in-hospital mortality. We stratified all our assessments by insurance groups.\n\nResultsAmong individuals in the outpatient and inpatient cohorts, 31.9% and 29.8%, respectively, used ACE inhibitors and 32.3% and 28.1% used ARBs. In the outpatient study, over a median 30.0 (19.0 - 40.0) days after testing positive, 12.7% were hospitalized for COVID-19. In propensity score-matched analyses, neither ACE inhibitors (HR, 0.77 [0.53, 1.13], P = 0.18), nor ARBs (HR, 0.88 [0.61, 1.26], P = 0.48), were significantly associated with risk of hospitalization. In analyses stratified by insurance group, ACE inhibitors, but not ARBs, were associated with a significant lower risk of hospitalization in the Medicare group (HR, 0.61 [0.41, 0.93], P = 0.02), but not the commercially insured group (HR: 2.14 [0.82, 5.60], P = 0.12; P-interaction 0.09). In the inpatient study, 14.2% died, 59.5% survived to discharge, and 26.3% had an ongoing hospitalization. In propensity score-matched analyses, neither use of ACE inhibitor (0.97 [0.81, 1.16]; P = 0.74) nor ARB (1.15 [0.95, 1.38]; P = 0.15) was associated with risk of in-hospital mortality, in total or in the stratified analyses.\n\nConclusionsThe use of ACE inhibitors and ARBs was not associated with the risk of hospitalization or mortality among those infected with SARS-CoV-2. However, there was a nearly 40% lower risk of hospitalization with the use of ACE inhibitors in the Medicare population. This finding merits a clinical trial to evaluate the potential role of ACE inhibitors in reducing the risk of hospitalization among older individuals, who are at an elevated risk of adverse outcomes with the infection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Rohan Khera", - "author_inst": "UT Southwestern Medical Center" - }, - { - "author_name": "Callahan Clark", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Yuan Lu", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Yinglong Guo", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Sheng Ren", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Brandon Truax", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Erica S Spatz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Karthik Murugiah", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Saad B Omer", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Deneen Vojta", - "author_inst": "UnitedHealth Group" - }, - { - "author_name": "Harlan M Krumholz", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.06.20076687", "rel_title": "COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases", @@ -1429341,6 +1426065,89 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.19.104117", + "rel_title": "Human IgG cell neutralizing monoclonal antibodies block SARS-CoV-2 infection", + "rel_date": "2020-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.104117", + "rel_abs": "The coronavirus induced disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide threat to human lives, and neutralizing antibodies present a great therapeutic potential in curing affected patients. We purified more than one thousand memory B cells specific to SARS-CoV-2 S1 or RBD (receptor binding domain) antigens from 11 convalescent COVID-19 patients, and a total of 729 naturally paired heavy and light chain fragments were obtained by single B cell cloning technology. Among these, 178 recombinant monoclonal antibodies were tested positive for antigen binding, and the top 13 binders with Kd below 0.5 nM are all RBD binders. Importantly, all these 13 antibodies could block pseudoviral entry into HEK293T cells overexpressing ACE2, with the best ones showing IC50s around 2-3 nM. We further identified 8 neutralizing antibodies against authentic virus with IC50s within 10 nM. Among these, 414-1 blocked authentic viral entry at IC50 of 1.75 nM and in combination with 105-38 could achieve IC50 as low as 0.45 nM. Meanwhile, we also found that 3 antibodies could cross-react with the SARS-CoV spike protein. Altogether, our study provided a panel of potent human neutralizing antibodies for COVID19 as therapeutics candidates for further development.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jinkai Wan", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Shenghui Xing", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Longfei Ding", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China" + }, + { + "author_name": "Yongheng Wang", + "author_inst": "Active Motif China Inc., Shanghai, 201315, China" + }, + { + "author_name": "Dandan Zhu", + "author_inst": "National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China" + }, + { + "author_name": "Bowen Rong", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Siqing Wang", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Kun Chen", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Chenxi He", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + }, + { + "author_name": "Songhua Yuan", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China" + }, + { + "author_name": "Chengli Qiu", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China" + }, + { + "author_name": "Chen Zhao", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China" + }, + { + "author_name": "Xiaoyan Zhang", + "author_inst": "Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, 201508, China" + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China" + }, + { + "author_name": "Yanan Lu", + "author_inst": "Active Motif China Inc., Shanghai, 201315, China" + }, + { + "author_name": "Jianqing Xu", + "author_inst": "Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, 201508, China" + }, + { + "author_name": "Fei Lan", + "author_inst": "Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, L" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.14.20090100", "rel_title": "Reciprocal association between participation to a national election and the epidemic spread of COVID-19 in France: nationwide observational and dynamic modeling study.", @@ -1430464,77 +1427271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.06.20092841", - "rel_title": "Modeling the impact of social distancing, testing, contact tracing and household quarantine on second-wave scenarios of the COVID-19 epidemic", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092841", - "rel_abs": "The new coronavirus disease 2019 (COVID-19) has required the implementation of severe mobility restrictions and social distancing measures worldwide. While these measures have been proven effective in abating the epidemic in several countries, it is important to estimate the effectiveness of testing and tracing strategies to avoid a potential second wave of the COVID-19 epidemic. We integrate highly detailed (anonymized, privacy-enhanced) mobility data from mobile devices, with census and demographic data to build a detailed agent-based model to describe the transmission dynamics of SARS-CoV-2 in the Boston metropolitan area. We find that enforcing strict social distancing followed by a policy based on a robust level of testing, contact-tracing and household quarantine, could keep the disease at a level that does not exceed the capacity of the health care system. Assuming the identification of 50% of the symptomatic infections, and the tracing of 40% of their contacts and households, which corresponds to about 9% of individuals quarantined, the ensuing reduction in transmission allows the reopening of economic activities while attaining a manageable impact on the health care system. Our results show that a response system based on enhanced testing and contact tracing can play a major role in relaxing social distancing interventions in the absence of herd immunity against SARS-CoV-2.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Alberto Aleta", - "author_inst": "ISI Foundation" - }, - { - "author_name": "David Martin-Corral", - "author_inst": "Universidad Carlos III de Madrid" - }, - { - "author_name": "Ana Pastore y Piontti", - "author_inst": "Northeastern University" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "FBK" - }, - { - "author_name": "Maria Litvinova", - "author_inst": "ISI Foundation" - }, - { - "author_name": "Matteo Chinazzi", - "author_inst": "Northeastern University" - }, - { - "author_name": "Natalie E Dean", - "author_inst": "University of Florida" - }, - { - "author_name": "M. Elizabeth Halloran", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Ira M Longini", - "author_inst": "University of Florida" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Alex Pentland", - "author_inst": "MIT Media Lab" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Northeastern University" - }, - { - "author_name": "Esteban Moro", - "author_inst": "Universidad Carlos III de Madrid" - }, - { - "author_name": "Yamir Moreno", - "author_inst": "University of Zaragoza" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.12.20099366", "rel_title": "A pitfall in estimating the effective reproductivenumber Rt for COVID-19", @@ -1431183,6 +1427919,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.14.20094144", + "rel_title": "Sarilumab use in severe SARS-CoV-2 pneumonia", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20094144", + "rel_abs": "ImportanceInterleukin-6 signal blockade has shown preliminary beneficial effects in treating aberrant host inflammatory response against SARS-CoV-2 leading to severe respiratory distress.\n\nObjectiveto describe the effect of off-label intravenous use of Sarilumab in patients with severe SARS-CoV-2-related pneumonia.\n\nDesignObservational clinical cohort study.\n\nSettingFondazione Policlinico Universitario A. Gemelli IRCCS as Italian Covid reference center.\n\nParticipantsPatients with laboratory-confirmed SARS-CoV-2 infection and respiratory distress with PaO2/FiO2 ratio<300 treated with Sarilumab between March 23rd - April 4th, 2020. Date of final follow-up was April 18, 2020.\n\nMain outcomes and measuresWe describe the clinical outcomes of 53 patients with SARS-CoV-2 severe pneumonia treated with intravenous Sarilumab in terms of pulmonary function improvement or Intensive Care Unit (ICU) admission rate in medical wards setting and of live discharge rate in ICU treated patients as well as in terms of safety. Each patient received Sarilumab 400 mg administered intravenously on day 1, with eventual additional infusion based on clinical judgement, and was followed for at least 14 days, unless previously discharged or dead. No gluco-corticosteroids were used at baseline.\n\nResultsOf the 53 SARS-CoV-2pos patients receiving Sarilumab, 39 (73.6%) were treated in medical wards (66.7% with a single infusion) while 14 (26.4%) in ICU (92.6% with a second infusion). The median PaO2/FiO2 of patients in the Medical Ward was 146(IQR:120-212) while the median PaO2/FiO2 of patients in ICU was 112(IQR:100-141.5), respectively.\n\nWithin the medical wards, 7(17.9%) required ICU admission, 4 of whom were re-admitted to the ward within 5-8 days. At 19 days median follow-up, 89.7% of medical inpatients significantly improved (46.1% after 24 hours, 61.5% after 3 days), 70.6% were discharged from the hospital and 85.7% no longer needed oxygen therapy. Within patients receiving Sarilumab in ICU, 64.2% were discharged from ICU to the ward and 35.8% were still alive at the last follow-up. Overall mortality rate was 5.7% after Sarilumab administration: 1(2.5%) patient died in the Medical Ward whilst 2(14.2%) patients died in ICU, respectively.\n\nConclusions and relevanceIL-6R inhibition appears to be a potential treatment strategy for severe SARS-CoV-2 pneumonia and intravenous Sarilumab seems a promising treatment approach showing, in the short term, an important clinical benefit and good safety.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSSARS-CoV-2 infection remains a disease with many unknown aspects for which there are no therapies with proven efficacy. To date, it is recognized that COVID-19 disease may lead to the development of a cytokine storm for which drugs as IL-6R inhibitors may have beneficial effect.\n\nFindingsIn this observational clinical study, we reported the efficacy and safety of intravenous Sarilumab use in SARS-CoV-2 severe pneumonia with a global resolution rate of 83.0% (89.7% in medical wards and 64.3% in ICU) and an overall mortality rate of 5.7%.\n\nMeaningIL-6R-inhibition is an effective approach for severe SARS-CoV-2 pneumonia and intravenous Sarilumab is a promising treatment approach leading to an important clinical benefit and good safety in the short term.", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Elisa Gremese", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Antonella Cingolani", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Silvia Laura Bosello", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Stefano Alivernini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Barbara Tolusso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Simone Perniola", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Francesco Landi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Maurizio Pompili", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Rita Murri", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Angelo Santoliquido", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Matteo Garcovich", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Michela Sali", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Gennaro De Pascale", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Maurizio Gabrielli", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Federico Biscetti", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Massimo Montalto", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Alberto Tosoni", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Giovanni Gambassi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Gian Ludovico Rapaccini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Amerigo Iaconelli", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Lorenzo Zileri Dal Verme", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Luca Petricca", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Anna Laura Fedele", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Marco Maria Lizzio", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Enrica Tamburrini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Gerlando Natalello", + "author_inst": "Universita' Cattolica del Sacro Cuore" + }, + { + "author_name": "Laura Gigante", + "author_inst": "Universita' Cattolica del Sacro Cuore" + }, + { + "author_name": "Dario Bruno", + "author_inst": "Universita' Cattolica del Sacro Cuore" + }, + { + "author_name": "Lucrezia Verardi", + "author_inst": "Universita' Cattolica del Sacro Cuore" + }, + { + "author_name": "Manuela Taddeo", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Angelo Calabrese", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Francesco Lombardi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Roberto Bernabei", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Roberto Cauda", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Francesco Franceschi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Raffaele Landolfi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Luca Richeldi", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Maurizio Sanguinetti", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Massimo Fantoni", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Massimo Antonelli", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + }, + { + "author_name": "Antonio Gasbarrini", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.20093997", "rel_title": "Current Evidence of the Pharmacological Treatments for Novel Coronavirus Disease 2019 (COVID-19) A Scoping Review", @@ -1432202,57 +1429117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20095638", - "rel_title": "Clinical assessment and validation of a rapid and sensitive SARS-CoV-2 test using reverse-transcription loop-mediated isothermal amplification", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20095638", - "rel_abs": "Amid the enduring COVID-19 pandemic, there is an urgent need for expanded access to rapid and sensitive SARS-CoV-2 testing worldwide. Here we present a simple clinical workflow that uses a sensitive and highly specific colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) to detect SARS-CoV-2 and takes forty minutes from sample collection to result. This test requires no specialized equipment and costs a few dollars per sample. Nasopharyngeal samples collected in saline were added either directly (unprocessed) to RT-LAMP reactions or first inactivated by a combined chemical and heat treatment step to inhibit RNases and lyse virions and human cells. The specimens were then amplified with two SARS-CoV-2-specific primer sets and an internal specimen control; the resulting color change was visually interpreted. While direct addition of unprocessed specimens to RT-LAMP reactions could reliably detect samples with abundant SARS-CoV-2, the assay sensitivity markedly increased after the addition of an inactivation step. In 62 clinical samples with a wide range of SARS-CoV-2 nucleic acid concentrations, the assay had 87.5% sensitivity and 100% specificity with a limit of detection at least 25 copies/L, making it an ideal test to rule in infection. To increase sensitivity, samples that tested negative for SARS-CoV-2 by direct sample addition could be reflexed to a purification step, to increase the effective per-reaction sample input volume. In 40 purified samples, the assay yielded a 90% sensitivity and 100% specificity, with a limit of detection comparable to commercially available real-time PCR-based diagnostics that have received Emergency Use Authorization (EUA) from the FDA. This test for SARS-CoV-2 can be performed in a range of settings for a fraction of the price of other available tests, with limited equipment, and without relying on over-burdened supply chains to increase overall testing capacity.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Melis N Anahtar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Graham EG McGrath", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Brian A Rabe", - "author_inst": "Harvard University Medical School" - }, - { - "author_name": "Nathan A Tanner", - "author_inst": "New England Biolabs" - }, - { - "author_name": "Benjamin A White", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jochen K.M. Lennerz", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "John A. Branda", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Constance L. Cepko", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Eric S Rosenberg", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.12.20073577", "rel_title": "Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs", @@ -1432701,6 +1429565,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20102210", + "rel_title": "Mental wellbeing in the Bangladeshi healthy population during nationwide lockdown over COVID-19: an online cross-sectional survey", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102210", + "rel_abs": "BackgroundWe aim to profile and contextualize the level of positive mental health among the healthy population during the beginning of nationwide lockdown over COVID-19 in Bangladesh.\n\nDesign and settingAn online sample of 1404 healthy individuals was collected through the authors networks with residents and popular media in Bangladesh. The survey was conducted between March 27, 2020, and April 7, 2020, following the Bangladesh governments lockdown announcement.\n\nMethodA questionnaire comprising the Warwick Edinburgh Mental Wellbeing Scale (WEMWBS) and sociodemographic information was posted to an online survey.\n\nResultsThe mean wellbeing value was 38.4 (standard deviation, 11.2), indicating a lower mental health level exist in adults. Also, the mean wellbeing score for males was 39.0 (10.8) units compared to females with scores 37.0 (11.2), and the highest scores for government workers was 41.2 (11.8). Unemployment (35.6) or business employees (35.5) have a lower level of mental health. In the lockout days, the elderly population of age 50 years and above had high day-to-day variation of wellbeing scores. After confounding adjustment in multivariable linear regression models, there found a better wellbeing scores for males (estimate = 1.79, 95% CI = 0.5, 3.1), and government-workers (estimate = 5.86, 95% CI = 2.2, 9.5). Moreover, the never-married female had significantly higher well-being score compared to married women (estimate = 3.31, 95% CI = 1.0, 5.7).\n\nConclusionThe COVID-19 pandemic has been associated with low mental wellbeing that indicates depression in our study. Suggestions for improvement will be implemented to promote the mental health to women, unemployed and business communities. Older people 50 years of age and over reported a greater day-to-day variation in their mental health. The married women with their decreased mental wellbeing should be given special consideration. The research will help let clinicians and policymakers decide where the measures can be implemented to improve their mental health during and after this pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ahmed Hossain", + "author_inst": "North South University" + }, + { + "author_name": "Mohammad Ali", + "author_inst": "Bangladesh University of Professionals" + }, + { + "author_name": "Hasinur Rahaman Khan", + "author_inst": "University of Dhaka, Bangladesh" + }, + { + "author_name": "Gias Ahsan", + "author_inst": "North South University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.11.20098228", "rel_title": "COVID-19 pandemic: every day feels like a weekday to most", @@ -1433436,29 +1430331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.11.20098475", - "rel_title": "When Second Best Might be the Best: Using Hospitalization Data to Monitor the Novel Coronavirus Pandemic", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098475", - "rel_abs": "The novel coronavirus high rate of asymptomatic transmission combined with a lack of testing kits call for a different approach to monitor its spread and severity. We proposed the use of hospitalizations and hospital utilization data to monitor the spread and severity. A proposed threshold of a declining 7-day moving average over a 14-day period, \"7&14\" was set to communicate when a wave of the novel coronavirus may have passed. The state of Ohio was chosen to illustrate this threshold. While not the ideal solution for monitoring the spread of the epidemic, the proposed approach is an easy to implement framework accounting for limitations of the data inherent in the current epidemic. Hospital administrators and policy makers may benefit from incorporating this approach into their decision making.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Peter J Mallow", - "author_inst": "Xavier University" - }, - { - "author_name": "Michael Jones", - "author_inst": "University of Cincinnati" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.15.20102608", "rel_title": "Fusing a Bayesian case velocity model with random forest for predicting COVID-19 in the U.S.", @@ -1433947,6 +1430819,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.14.20102327", + "rel_title": "Is the Current N95 Respirator Filtration Efficiency Test Sufficient for Evaluating Protection Against Submicrometer Particles Containing SARS-CoV-2?", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102327", + "rel_abs": "The National Institute of Occupational Safety and Health procedure No. TEB-APR-STP-0059 recommend of measuring the respirator filtration efficiency using sodium chloride aerosol with count median diameter of 75 nm {+/-} 20 nm and geometric standard deviation [≤]1.86. This study showed that this method would overestimate the respirators ability to protect against submicrometer particles. In this study, we converted both mobility diameter and equivalent volume diameter to aerodynamic diameter for comparison. The results showed that one unqualified KN95 respirator (with the filtration efficiency of 72%{+/-}3% for [≥]300 nm sodium chloride aerosol) still passed the test with a measured overall filtration efficiency of 98%{+/-}3%, due to its larger most penetrating particle size compared to the typical N95 respirator. In addition, after three cycle H2O2 plasma vaporous sterilizations, the most penetrating particle size for the N95 grade respirators also shifted to 250 nm - 500 nm, in which size the particles carried the peak concentration of the SARS-CoV-2 in hospitals. This size shift caused the significant difference between the size specific (250 nm - 500 nm) filtration efficiency and overall filtration efficiency using the same NaCl test aerosol. For example, after three cycle H2O2 plasma vaporous sterilizations, the size specific filtration efficiency of the N95 was 55%{+/-}2%, however, the measured overall filtration efficiency was still 86%{+/-}5%. The size Specific filtration efficiency of the KN95 was 69%{+/-}2%, but, the measured overall filtration efficiency was still 90%{+/-}3%. In order to protect health care personnel adequately, we recommend increasing the test aerosol size, and measuring the size specific filtration efficiency to evaluate the N95 alternatives (e.g. KN95), and the reuse of N95 level respirators. In addition, multi-cycle sterilization with ultraviolet germicidal irradiation appears to have fewer negative effects than H2O2.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Changjie Cai", + "author_inst": "University of Oklahoma Health Sciences Center" + }, + { + "author_name": "Evan L. Floyd", + "author_inst": "University of Oklahoma Health Sciences Center" + }, + { + "author_name": "Kathleen A. Aithinne", + "author_inst": "University of Oklahoma Health Sciences Center" + }, + { + "author_name": "Toluwanimi Oni", + "author_inst": "University of Oklahoma Health Sciences Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.05.14.20102301", "rel_title": "Reducing visible aerosol generation during phacoemulsification in the era of Covid-19", @@ -1434766,37 +1431669,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.16.099788", - "rel_title": "Nrf2 Activator PB125 as a Potential TherapeuticAgent Against COVID-19", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.099788", - "rel_abs": "Nrf2 is a transcription factor that regulates cellular redox balance and the expression of a wide array of genes involved in immunity and inflammation, including antiviral actions. Nrf2 activity declines with age, making the elderly more susceptible to oxidative stress-mediated diseases, which include type 2 diabetes, chronic inflammation, and viral infections. Published evidence suggests that Nrf2 activity may regulate important mechanisms affecting viral susceptibility and replication. We examined gene expression levels by GeneChip microarray and by RNA-seq assays. We found that the potent Nrf2 activating composition PB125(R) downregulates ACE2 and TMPRSS2 mRNA expression in human liver-derived HepG2 cells. ACE2 is a surface receptor and TMPRSS2 activates the spike protein for SARS-Cov-2 entry into host cells. Furthermore, in endotoxin-stimulated primary human pulmonary artery endothelial cells we report the marked downregulation by PB125 of 36 genes encoding cytokines. These include IL1-beta, IL6, TNF-, the cell adhesion molecules ICAM1, VCAM1, and E-selectin, and a group of IFN-{gamma}-induced genes. Many of these cytokines have been specifically identified in the \"cytokine storm\" observed in fatal cases of COVID-19, suggesting that Nrf2 activation may significantly decrease the intensity of the storm.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Joe M McCord", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Brooks M. Hybertson", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Adela Cota-Gomez", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Bifeng Gao", - "author_inst": "University of Colorado Anschutz Medical Campus" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.05.17.100289", "rel_title": "Establishment of an African green monkey model for COVID-19", @@ -1435325,6 +1432197,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.12.20099473", + "rel_title": "Country differences in hospitalisation, length of stay and admission to Intensive Care Units due to SARS-CoV-2 infection: a rapid review of available literature", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099473", + "rel_abs": "ObjectivesCoronavirus disease (COVID-19) caused by the SARS-CoV-2 virus is spreading rapidly worldwide and threatening the collapse of national health care systems. The development of effective resource models are critical for long term health planning. The aim was to evaluate the available literature, to consider parameters affecting hospital resources, to effectively guide health policy and planning for future waves of infection.\n\nDesignA detailed search of the literature, using Google Scholar, PubMED, MedRxiv and BioRxiv, was conducted for the time period 1st Dec 2019 to 31st May 2020; using appropriate keywords: resultant articles were scrutinised in detail, and appraised for reported data pertaining to hospitalization and hospital length of stay (LOS).\n\nResultsDisease presentation was described in China; 81 % mild, 14 % moderate and 5 % severe. The experience, thus far, in Europe and the USA are suggestive of a higher degree of severity. Initial reports suggest high hospitalisation and ICU admittance rates. More recent reports from the European Centre for Disease Prevention and Control (ECDC) lower this estimation. Perhaps the relative age, the level of pre-existing conditions, and other health factors may be contributors to differences. Data from Irish cases suggest hospitalisation rate may be lower in parts of Europe and time dependent. Hospital LOS is described in 55 articles, with median lengths of stay between 3 and 52 days. The evidence regarding the LOS in ICU is reported in 31 studies, 26 deemed relevant. The majority of studies report ICU LOS between 7 to 11 days. Many of these studies are likely skewed towards shorter stay due to study cut-off dates. Indications based on ICU LOS reported for patients continuing care suggest median ICU stay will progressively increase.\n\nConclusionsThese parameter estimates are key to the development of an effective health care resource model. Based on our appraisal of the literature, is it essential that Europe manages mitigation measures to ensure that hospital and ICU capacity does not become overwhelmed to manage COVID-19 in subsequent infection waves.\n\nStrengths and limitations of this studyO_LIThe study provides timely information on the differences in hospitalisation, length of stay and ICU length of stay due to COVID-19 in a number of countries worldwide at the end of wave one in Europe;\nC_LIO_LIThis rapid review builds on a previously available review paper that reported length of stay in the early phase of the pandemic; many more studies outlining length of stay, and in particular, ICU length of stay, are now available;\nC_LIO_LIThis rapid review reports on study mortality rate giving an interesting insight into differences across countries and continents;\nC_LIO_LILimitations associated with any rapid review are pertinent to this study; a narrow aim was set, and the sources of the literature may be limited by the time-limited constraint of gathering relevant literature; and a number of articles available were in pre-print form and only undergoing peer review; and\nC_LIO_LIThis rapid review provides evidence-based estimates of Hospital and ICU length of stay due to COVID-19 infection across a number of countries to steer policy and provide parameter estimates for utilisation within a hospital resource model as preparations are made for subsequent waves of infection.\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Elizabeth A Lane", + "author_inst": "Department of Agriculture, Food and the Marine" + }, + { + "author_name": "Damien J Barrett", + "author_inst": "Department of Agriculture, Food and the Marine, Ireland" + }, + { + "author_name": "Miriam Casey", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin" + }, + { + "author_name": "Conor G McAloon", + "author_inst": "University College Dublin" + }, + { + "author_name": "Aine B Collins", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin" + }, + { + "author_name": "Kevin Hunt", + "author_inst": "School of Biosystems and Food Engineering, University College Dublin" + }, + { + "author_name": "Andrew W Byrne", + "author_inst": "DAFM" + }, + { + "author_name": "David McEvoy", + "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin" + }, + { + "author_name": "Ann Barber", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin," + }, + { + "author_name": "John M Griffin", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis" + }, + { + "author_name": "Patrick Wall", + "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin" + }, + { + "author_name": "Simon J More", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.12.20099291", "rel_title": "Multilevel Integrated Model with a Novel Systems Approach (MIMANSA) for Simulating the Spread of COVID-19", @@ -1435992,37 +1432927,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.13.20100313", - "rel_title": "Understanding the psychological impact of the COVID-19 pandemic and containment measures: an empirical model of stress.", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100313", - "rel_abs": "Research suggests that epidemics and corresponding containment measures have negative consequences to the individual and cause stress. The psychological mechanisms that determine stress, caused by the COVID-19 pandemic and containment measures, are not yet clear. In a survey during the lockdown in Switzerland (n=1565), we found substantially increased levels of stress in the population. In particular, individuals who did not agree with the containment measures, as well as those who saw nothing positive in the crisis, experienced even higher levels of stress. In contrast, individuals who are part of a risk group or who are working in healthcare or in essential shops experienced similar stress levels as the general public. We conducted a path analysis to gain a deeper understanding of the psychological mechanisms during lockdown. Experiencing fear of the disease is a key driver for being worried. Our model further shows that worries about the individual, social, and economic consequences of the crisis, strongly boost stress. The infection rate in the canton (i.e. state) of residence also contributes to stress. Positive thinking and perceived social, organizational, and governmental support mitigate worries and stress. To prevent stress, authorities should explain containment measures well, highlight positive aspects of the crisis, address worries, and facilitate support.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Bartholom\u00e4us Wissmath", - "author_inst": "University of Bern" - }, - { - "author_name": "Fred W Mast", - "author_inst": "University of Bern" - }, - { - "author_name": "Fabian Kraus", - "author_inst": "w hoch 2 GmbH" - }, - { - "author_name": "David Weibel", - "author_inst": "University of Bern" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.12.20099267", "rel_title": "The impact of containment measures and air temperature on mitigating the transmission of COVID-19: a novel data-based comprehensive modeling analysis", @@ -1436495,6 +1433399,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.05.13.20100131", + "rel_title": "Fast and accurate diagnostics from highly multiplexed sequencing assays", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100131", + "rel_abs": "Scalable, inexpensive, accurate, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays that rely on high-throughput sequencing (HMSAs) can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, the analysis and interpretation of HMSAs requires overcoming several computational and statistical challenges. Using recently acquired experimental data, we present and validate an accurate and fast computational testing workflow based on kallisto and bustools, that utilize robust statistical methods and fast, memory efficient algorithms for processing high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSAs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "A. Sina Booeshaghi", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Nathan B. Lubock", + "author_inst": "Octant Inc." + }, + { + "author_name": "Aaron R. Cooper", + "author_inst": "Octant Inc." + }, + { + "author_name": "Scott W. Simpkins", + "author_inst": "Octant Inc." + }, + { + "author_name": "Joshua S. Bloom", + "author_inst": "Octant Inc.; University of California, Los Angeles" + }, + { + "author_name": "Jase Gehring", + "author_inst": "University of Washington" + }, + { + "author_name": "Laura Luebbert", + "author_inst": "California Institution of Technology" + }, + { + "author_name": "Sriram Kosuri", + "author_inst": "Octant Inc.; University of California, Los Angeles" + }, + { + "author_name": "Lior Pachter", + "author_inst": "California Institution of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.13.20100289", "rel_title": "National age and co-residence patterns shape covid-19 vulnerability", @@ -1437558,37 +1434513,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.14.095133", - "rel_title": "Identification of conserved epitopes in SARS-CoV-2 spike and nucleocapsid protein.", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095133", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first occurred in Wuhan (China) in December 2019, is a novel virus that causes a severe acute respiratory disease. The virus spike glycoproteins and nucleocapsid proteins are the main targets for the development of vaccines and antiviral drugs, to control the disease spread. We herein study the structural order-disorder propensity and the rates of evolution of these two proteins to characterize their B cell and T cell epitopes, previously suggested to contribute to immune response caused by SARS-CoV-2 infections. We first analyzed the rates of evolution along the sequences of spike and nucleocapsid proteins in relation to the spatial locations of their epitopes. For this purpose, we compared orthologs from seven human coronaviruses: SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. We then focus on the local, structural order-disorder propensities of the protein regions where the SARS-CoV-2 epitopes are located. We show that the vast majority of nucleocapsid protein epitopes overlap the RNA-binding and dimerization domains and some of them are characterized by low rates of evolutions. Similarly, spike protein epitopes are preferentially located in regions that are predicted to be ordered and well-conserved, in correspondence of the heptad repeats 1 and 2. Interestingly, both the receptor-binding motif to ACE2 and the fusion peptide of spike protein are characterized by high rates of evolution, probably to overcome host immunity. In conclusion, our results provide evidence for conserved epitopes that may help to develop long-lasting, broad-spectrum SARS-CoV-2 vaccines.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sergio Forcelloni", - "author_inst": "University of Rome \"La Sapienza\"" - }, - { - "author_name": "Anna Benedetti", - "author_inst": "University of Rome \"La Sapienza\"" - }, - { - "author_name": "Maddalena Dilucca", - "author_inst": "Universita degli Studi di Roma La Sapienza" - }, - { - "author_name": "Andrea Giansanti", - "author_inst": "Sapienza Universita di Roma" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.14.095885", "rel_title": "Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2", @@ -1438205,6 +1435129,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.11.20089714", + "rel_title": "Pre-existing Cardiovascular Disease in United States Population at High Risk for Severe COVID-19 Infection", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20089714", + "rel_abs": "Article abstractO_ST_ABSBackground and PurposeC_ST_ABSThere is increasing recognition of a relatively high burden of pre-existing cardiovascular disease in Corona Virus Disease 2019 (COVID-19) infected patients. We determined the burden of pre-existing cardiovascular disease in persons residing in United States (US) who are at risk for severe COVID-19 infection.\n\nMethodsAge ([≥]60 years), presence of chronic obstructive pulmonary disease, diabetes, mellitus, hypertension, and/or malignancy were used to identify persons at risk for admission to intensive care unit, or invasive ventilation, or death with COVID-19 infection. Persons were classified as low risk (no risk factors), moderate risk (1 risk factor), and high risk (two or more risk factors present) using nationally representative sample of US adults from National Health and Nutrition Examination Survey 2017-2018 survey.\n\nResultsAmong a total of 5856 participants, 2386 (40.7%) were considered low risk, 1325 (22.6%) moderate risk, and 2145 persons (36.6%) as high risk for severe COVID-19 infection. The proportion of patients who had pre-existing stroke increased from 0.6% to 10.5% in low risk patients to high risk patients (odds ratio [OR]19.9, 95% confidence interval [CI]11.6-34.3). The proportion of who had pre-existing myocardial infection (MI) increased from 0.4% to 10.4% in low risk patients to high risk patients (OR 30.6, 95% CI 15.7-59.8).\n\nConclusionsA large proportion of persons in US who are at risk for developing severe COVID-19 infection are expected to have pre-existing cardiovascular disease. Further studies need to identify whether targeted strategies towards cardiovascular diseases can reduce the mortality in COVID-19 infected patients.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Adnan I Qureshi", + "author_inst": "Zeenat Qureshi Stroke Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.05.10.20086504", "rel_title": "Modeling COVID 19 in the Basque Country: from introduction to control measure response", @@ -1439143,45 +1436086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.097352", - "rel_title": "Background mechanisms of olfactory dysfunction in COVID-19: expression of ACE2, TMPRSS2, and Furin in the nose and olfactory bulb in human and mice", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.097352", - "rel_abs": "Background Anosmia is a frequent symptom in patients with the coronavirus disease 2019 (COVID-19) driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mostly recovers within weeks. This clinical figure is significantly different from that of anosmia after upper respiratory infection, which occurs in only a small proportion of patients and does not recover or requires months to recover. The background mechanisms of COVID-19 induced olfactory dysfunction have not been elucidated.Methods To address the unique pathophysiology of olfactory dysfunction associated with COVID-19, we examined the existence and distribution of ACE2 (virus binding receptor), TMPRSS2 and Furin (proteases to facilitate virus entry) in the nasal mucosa, composed of the respiratory mucosa (RM) and olfactory mucosa (OM), and the olfactory bulb (OB) in mouse and human tissues by immunohistochemistry and gene analyses.Results Ace2, Tmprss2, and Furin gene expressions were confirmed in the nasal mucosa and OB. ACE2 was widely expressed all in the RM, OM and OB. Co-expression of ACE2, TMPRSS2, and Furin was observed in the RM including the RE and subepithelial glands and in the OM, especially in the supporting cells on the olfactory epithelium and the Bowman\u2019s glands. Notably, the olfactory receptor neurons (ORNs) in the OM were positive for ACE2 but almost negative for TMPRSS2 and Furin. The cells in the OB expressed ACE2 strongly and Furin weakly and did not express TMPRSS2.Conclusions ACE2 was widely expressed in the RM, OM and OB, but TMPRSS2 and Furin were expressed in certain types of cells and were absent in the ORNs. These findings, together with clinically reported ones, suggest that COVID-19 related anosmia can occur due to mainly sensorineural and central dysfunction and, to some extent, conductive olfactory dysfunction. That the ORNs express ACE2 but not TMPRSS2 or Furin may explain the early recovery of anosmia.Short Summary Protein expression patterns of ACE2, TMPRSS, and Furin suggest that COVID-19 related anosmia can occur due to mainly sensorineural dysfunction without olfactory neuronal damage.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Rumi Ueha", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Kenji Kondo", - "author_inst": "Department of Otolaryngology and Head and Neck Surgery, The University of Tokyo" - }, - { - "author_name": "Ryoji Kagoya", - "author_inst": "Department of Otolaryngology and Head and Neck Surgery, The University of Tokyo" - }, - { - "author_name": "Shigeyuki Shichino", - "author_inst": "Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science" - }, - { - "author_name": "Satoshi Ueha", - "author_inst": "Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science" - }, - { - "author_name": "Tatsuya Yamasoba", - "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.05.10.20096925", "rel_title": "NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK", @@ -1439830,6 +1436734,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.09.20096842", + "rel_title": "Impact of COVID-19 infection on maternal and neonatal outcomes: a review of 287 pregnancies", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096842", + "rel_abs": "Pregnant women are vulnerable group in viral outbreaks especially in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The aim of this review was to identify maternal and neonatal outcomes in available articles on pregnancies affected by COVID-19. The articles that had assessed outcomes of pregnancy and perinatal of women with COVID-19 between Oct 2019 and Apr 30, 2020 without language limitation were considered. All kinds of studies such as case report, case series, retrospective cohort, case control were included. We searched databases, selected relevant studies and extracted data regarding maternal and neonatal outcomes from each article. Data of 287 pregnant women with COVID-19 of 6 countries were assessed from 28 articles between December 8, 2019 and April 6, 2020. Most pregnant women reported in their third trimester, 102 (35.5%) cases were symptomatic at the time of admission. Common onset symptoms, abnormal laboratory findings, and chest computed tomography pattern were fever (51.5%), lymphocytopenia (67.9%), and multiple ground-glass opacities (78.5%) respectively. 93% of all deliveries were done through cesarean section. No maternal mortality and 3 % ICU admission were reported. Vertical transmission was not reported but its possibility was suggested in three neonates. One neonatal death, one stillbirth, and one abortion were reported. All newborns were not breastfed. This review showed fewer adverse maternal and neonatal outcomes in pregnant women with COVID-19 in comparison with previous coronavirus outbreak infection in pregnancy. Limited data are available regarding possibility of virus transmission in utero, during vaginal childbirth and breastfeeding. Effect of COVID-19 on first and second trimester and ongoing pregnancy outcomes in infected mothers is still questionable.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Fatemeh Azarkish", + "author_inst": "Department of Midwifery, School of Nursing and Midwifery, Iranshahr University of Medical Sciences, Iranshahr, Iran" + }, + { + "author_name": "Roksana Janghorban", + "author_inst": "Department of Midwifery, School of Nursing and Midwifery, Maternal-Fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2020.05.11.20096347", "rel_title": "The effects of ARBs, ACEIs and statins on clinical outcomes of COVID-19 infection among nursing home residents", @@ -1440957,53 +1437884,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.15.097493", - "rel_title": "Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.097493", - "rel_abs": "The SARS-CoV-2 main protease (Mpro) is essential to viral replication and cleaves highly specific substrate sequences, making it an obvious target for inhibitor design. However, as for any virus, SARS-CoV-2 is subject to constant selection pressure, with new Mpro mutations arising over time. Identification and structural characterization of Mpro variants is thus critical for robust inhibitor design. Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Residue substitution is widely distributed, with some tendency toward larger and more hydrophobic residues. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thomas J Cross", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Gemma R Takahashi", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Elizabeth M Diessner", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Marquise G Crosby", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Vesta Farahmand", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Shannon Zhuang", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Carter Tribley Butts", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Rachel W Martin", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.14.096016", "rel_title": "Transcriptional profiling reveals TRPM5-expressing cells involved in viral infection in the olfactory epithelium", @@ -1441880,6 +1438760,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.11.20098145", + "rel_title": "Early estimation of the risk factors for hospitalisation and mortality by COVID-19 in Mexico", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098145", + "rel_abs": "BackgroundWith its high prevalence of chronic non-degenerative diseases, it is suspected that in Mexico there is a high risk of fatal complications from COVID-19. The present study aims to estimate the risk factors for hospitalisation and death in the Mexican population infected by SARS-CoV-2.\n\nMethods and FindingsWe used the publicly available data released by the Epidemiological Surveillance System for Viral Respiratory Diseases of the Mexican Ministry of Health (Secretaria de Salud, SS). All records of positive SARS-CoV-2 cases were included. Two multiple logistic regression models were fitted to estimate the association between the hospitalisation and mortality, with other covariables. Data on 10,544 individuals (57.68% men), with mean age 46.47{+/-}15.62, were analysed. Men were about 1.54 times as likely to be hospitalized than women (p<0.001, 95% C.I. 1.37-1.74); individuals aged 50-74 and [≥]74 years were more likely to be hospitalized than people from 25-49 years (OR 2.05, p<0.001, 95% C.I. 1.81-2.32, and OR 23.84, p<0.001, 95% C.I. 2.90-5.15, respectively). People with hypertension, obesity, and diabetes were more likely to be hospitalised than people without these morbidities (p<0.01). Men had more risk of death in comparison to women (OR=1.53, p<0.001, 95% C.I. 1.30-1.81) and individuals aged 50-74 and [≥]75 years were more likely to die than people from 25-49 years (OR 1.96, p<0.001, 95% C.I. 1.63-2.34, and OR 3.74, p<0.001, 95% C.I. 2.80-4.98, respectively). Hypertension, obesity, and diabetes presented in combination, provided a higher risk of dying in comparison to not having these diseases (OR=2.10; p<0.001, 95% C.I. 1.50-2.93). Hospitalisation, intubation and pneumonia conferred a higher risk of dying (OR 5.02, p<0.001, 95% C.I. 3.88-6.50; OR 4.27, p<0.001, 95% C.I. 3.26-5.59, and OR=2.57; p<0.001, 95% C.I. 2.11-3.13, respectively). The main limitation of our study is the lack of information on mild (asymptomatic) or moderate cases of COVID-19.\n\nConclusionsThe present study points out that in Mexico, where an important proportion of the population develops two or more chronic conditions simultaneously, high mortality is a sever outcome for those infected by SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Maria Fernanda Carrillo-Vega", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Guillermo Salinas-Escudero", + "author_inst": "Hospital Infantil de Mexico Federico Gomez" + }, + { + "author_name": "Carmen Garcia-Pe\u00f1a", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Luis Miguel Gutierrez-Robledo", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Lorena Parra-Rodriguez", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.092478", "rel_title": "Novel ACE2-Independent Carbohydrate-Binding of SARS-CoV-2 Spike Protein to Host Lectins and Lung Microbiota", @@ -1442715,41 +1439630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.11.20097972", - "rel_title": "Estimating and forecasting COVID-19 attack rates and mortality", - "rel_date": "2020-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097972", - "rel_abs": "We describe a model for estimating past and current infections as well as future deaths due to the ongoing COVID-19 pandemic. The model does not use confirmed case numbers and is based instead on recorded numbers of deaths and on the age-specific population distribution. A regularized deconvolution technique is used to infer past infections from recorded deaths. Forecasting is based on a compartmental SIR-type model, combined with a probability distribution for the time from infection to death. The effect of non-pharmaceutical interventions (NPIs) is modelled empirically, based on recent trends in the death rate. The model can also be used to study counterfactual scenarios based on hypothetical NPI policies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David I. Ketcheson", - "author_inst": "King Abdullah University of Science & Technology" - }, - { - "author_name": "Hernando C. Ombao", - "author_inst": "King Abdullah University of Science & Technology" - }, - { - "author_name": "Paula Moraga", - "author_inst": "University of Bath" - }, - { - "author_name": "Tarig Ballal", - "author_inst": "King Abdullah University of Science & Technology" - }, - { - "author_name": "Carlos M. Duarte", - "author_inst": "King Abdullah University of Science & Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.14.093757", "rel_title": "Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome", @@ -1443254,6 +1440134,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.11.20097709", + "rel_title": "Systemic corticosteroids show no benefit in severe and critical COVID-19 patients in Wuhan, China: A retrospective cohort study", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097709", + "rel_abs": "BackgroundSystemic corticosteroids are recommended by some treatment guidelines and used in severe and critical COVID-19 patients, though evidence supporting such use is limited.\n\nMethodsFrom December 26, 2019 to March 15, 2020, 1514 severe and 249 critical hospitalized COVID-19 patients were collected from two medical centers in Wuhan, China. We performed multivariable Cox models, Cox model with time-varying exposure and propensity score analysis (both inverse-probability-of-treatment-weighting (IPTW) and propensity score matching (PSM)) to estimate the association of corticosteroid use with the risk of in-hospital mortality among severe and critical cases.\n\nResultsCorticosteroids were administered in 531 (35.1%) severe and 159 (63.9%) critical patients. Compared to no corticosteroid use group, systemic corticosteroid use showed no benefit in reducing in-hospital mortality in both severe cases (HR=1.77, 95% CI: 1.08-2.89, p=0.023), and critical cases (HR=2.07, 95% CI: 1.08-3.98, p=0.028). In the time-varying Cox analysis that with time varying exposure, systemic corticosteroid use still showed no benefit in either population (for severe patients, HR=2.83, 95% CI: 1.72-4.64, p<0.001; for critical patients, HR=3.02, 95% CI: 1.59-5.73, p=0.001). Baseline characteristics were matched after IPTW and PSM analysis. For severe COVID-19 patients at admission, corticosteroid use was not associated with improved outcome in either the IPTW analysis. For critical COVID-19 patients at admission, results were consistent with former analysis that corticosteroid use did not reduce in-hospital mortality.\n\nConclusionsCorticosteroid use showed no benefit in reducing in-hospital mortality for severe or critical cases. The routine use of systemic corticosteroids among severe and critical COVID-19 patients was not recommended.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Jianfeng Wu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Jianqiang Huang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Guochao Zhu", + "author_inst": "The Affiliated Hospital of Jianghan University (No. Six Hospital of Wuhan)" + }, + { + "author_name": "Yihao Liu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Han Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Qian Zhou", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Xiang Si", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Hui Yi", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Cuiping Wang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Daya Yang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Shuling Chen", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Xin Liu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Zelong Liu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Qiongya Wang", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Qingquan Lv", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Ying Huang", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Yang Yu", + "author_inst": "The Affiliated Hospital of Jianghan University (No. Six Hospital of Wuhan)" + }, + { + "author_name": "Xiangdong Guan", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yanbing Li", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Krishnarajah Nirantharakumar", + "author_inst": "University of Birmingham, Health Data Research UK" + }, + { + "author_name": "KarKeung Cheng", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sui Peng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Haipeng Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.11.20097741", "rel_title": "Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study", @@ -1444149,97 +1441136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.09.20084202", - "rel_title": "Evolving Epidemiology and Effect of Non-pharmaceutical Interventions on the Epidemic of Coronavirus Disease 2019 in Shenzhen, China", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20084202", - "rel_abs": "Previous studies have demonstrated the characteristics of patients with 2019 novel coronavirus disease (COVID-19). However, the effect of non-pharmaceutical interventions on the epidemic in Shenzhen, China remains unknown. Individual data of 417 cases were extracted from the epidemiological investigations and the National Infectious Disease Information System between January 1, 2020 and February 29, 2020. On the basis of important interventions, the epidemic was divided into four periods (January 1-15, January 16-22, January 23-February 5 and after February 6). We used a susceptible-exposed-infectious-asymptomatic-recovered model to evaluate the effect of interventions. Results suggested that about 53.7% were imported from Wuhan. The median age was 47 years and 52.8% were women. Severity risk increased with age and associated with male and co-existing disorders. The attack rate peaked in the third period and drastically decreased afterwards across sex, age groups and geographic regions. Children younger than 5 years showed a higher attack rate than those aged of 6~19. The effective reproductive number decreased from 1.44 to 0.05 after the highest level emergency response since January 23. Overall, the non-pharmaceutical interventions have effectively mitigated the COVID-19 outbreak in Shenzhen, China. These findings may facilitate the introduction of public health policies in other countries and regions.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Suli Huang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Yongsheng Wu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Shujiang Mei", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Yuan Li", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Xu Xie", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Xiaojian Liu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Xiujuan Tang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Dongfeng Kong", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Xiaoliang Wu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Yu Wu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Lan Wei", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Ziquan Lv", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Shuyuan Yu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Ying Wen", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Guohong Zhou", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Tianmu Chen", - "author_inst": "Xiamen University" - }, - { - "author_name": "Tiejian Feng", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Xuan Zou", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20091454", "rel_title": "Early Awake Prone and Lateral Position in Non-intubated Severe and Critical Patients with COVID-19 in Wuhan: A Respective Cohort Study", @@ -1444788,6 +1441684,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.09.20096032", + "rel_title": "A Novel Box for Aerosol and Droplet Guarding and Evacuation in Respiratory Infection (BADGER): A Potential Mitigating Strategy for the COVID-19 Pandemic and Future Outbreaks", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096032", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected millions and killed hundreds of thousands of people worldwide as of May 2020. Healthcare providers are at increased risks of infection when caring for patients with COVID-19. The mechanism of transmission of SARS-CoV-2 is still not fully understood. However, there is growing evidence for airborne spread, in addition to direct droplet and indirect contact. Here, we report on the design, construction, and testing of the BADGER (Box for Aerosol and Droplet Guarding and Evacuation in Respiratory Infection), an affordable, scalable device that contains droplets and aerosol particles. A semi-sealed environment is created inside the BADGER, which maintains at least twelve-air changes per hour using in-wall vacuum suction, and multiple hand-ports enable healthcare providers to perform essential tasks on a patients airway and head. Overall, the BADGER has the potential to contain large droplets and small airborne particles as demonstrated by simulated qualitative and quantitative assessments to provide an additional layer of protection for healthcare providers treating COVID-19 patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hau D. Le", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Gordon A Novak", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Kevin C Janek", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Jesse Wang", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Khang N Huynh", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Chris Meyer", + "author_inst": "Sector 67" + }, + { + "author_name": "Adam Weinstein", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Erick Oberstar", + "author_inst": "University of Wisconsin - Madison" + }, + { + "author_name": "Jim Rasmussen", + "author_inst": "Sector 67" + }, + { + "author_name": "Timothy Bertram", + "author_inst": "University of Wisconsin - Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.08.20095836", "rel_title": "Serum protein profiling reveals a landscape of inflammation and immune signaling in early-stage COVID-19 infection", @@ -1445431,45 +1442382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.05.09.20096412", - "rel_title": "The Early Food Insecurity Impacts of COVID-19", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096412", - "rel_abs": "BackgroundCOVID-19 has disrupted food access and impacted food insecurity, which is associated with numerous adverse individual and public health outcomes.\n\nMethodsWe conducted a statewide population-level survey in Vermont from March 29-April 12, 2020, during the beginning of a statewide stay-at-home order. We utilized the USDA six-item validated food security module to measure food insecurity before COVID-19 and since COVID-19. We assessed food insecurity prevalence and reported food access challenges, coping strategies, and perceived helpful interventions among food secure, consistently food insecure (pre-and post COVID-19), and newly food insecure (post COVID-19) respondents.\n\nResultsAmong 3,219 respondents, there was a 33% increase in household food insecurity since COVID-19 (p<0.001), with 35.6% of food insecure households classified as newly food insecure. Respondents experiencing a job loss were more likely to experience food insecurity (OR 3.43; 95% CI, 2.45-4.80). Multiple physical and economic barriers, as well as concerns related to food access during COVID-19, are reported, with respondents experiencing household food insecurity more likely to face access challenges (p<0.001). Significant differences in coping strategies were documented between respondents in newly food insecure vs. consistently insecure households.\n\nConclusionsSince the declaration of the COVID-19 pandemic, there has been a significant increase in food insecurity in Vermont, accompanied by major food access barriers. These findings have important potential impacts on individual health, including mental health and malnutrition, as well as on future healthcare costs. We suggest proactive strategies to address food insecurity during this crisis.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Meredith T. Niles", - "author_inst": "University of Vermont" - }, - { - "author_name": "Farryl Bertmann", - "author_inst": "University of Vermont" - }, - { - "author_name": "Emily H. Belarmino", - "author_inst": "University of Vermont" - }, - { - "author_name": "Thomas Wentworth", - "author_inst": "University of Vermont" - }, - { - "author_name": "Erin Biehl", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Roni A. Neff", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2020.05.11.20092528", "rel_title": "ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens", @@ -1446038,6 +1442950,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.05.11.089862", + "rel_title": "Evaluation of the EUROIMMUN Anti-SARS-CoV-2 ELISA Assay for detection of IgA and IgG antibodies", + "rel_date": "2020-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.089862", + "rel_abs": "As the Coronavirus 2019 (COVID-19) pandemic evolves, the development of immunoassays to help determine exposure and potentially predict immunity has become a pressing priority. In this report we present the performance of the EUROIMMUN enzyme-linked immunosorbent assay (ELISA) for semi-quantitative detection of IgA and IgG antibodies in serum and plasma samples using recombinant S1 domain of the SARS-CoV-2 spike protein as antigen. Specimens from patients, with and without COVID-19 infection, were tested at the University of Chicago Clinical Microbiology and Immunology Laboratory. Of 57 samples from COVID-19 PCR-negative patients, including 28 samples positive for common human coronavirus strains, 53 tested negative and 4 tested positive for IgA (93.0% agreement) while 56 tested negative and 1 tested positive for IgG (98.2% agreement). For COVID-19 PCR-positive patients, 29 of 30 (96.7%) samples collected [≥]3 days after positive PCR were positive for IgA, and 28 of 28 samples collected [≥]4 days after positive PCR were positive for IgG.\n\nThe EUROIMMUN Anti-SARS-CoV-2 ELISA Assay demonstrates excellent sensitivity for detection of IgA and IgG antibodies from samples collected [≥]3 days and [≥]4 days, respectively, after COVID-19 diagnosis by PCR. This assay did not demonstrate cross reaction in any of the 28 samples from patients with common human coronaviruses, including types HKU1, NL63, CV229E, and OC43.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Scott Matushek", + "author_inst": "University of Chicago Medicine" + }, + { + "author_name": "Kathleen G. Beavis", + "author_inst": "University of Chicago" + }, + { + "author_name": "Ana Abeleda", + "author_inst": "UNIVERSITY OF CHICAGO MEDICINE" + }, + { + "author_name": "Cindy Bethel", + "author_inst": "University of Chicago" + }, + { + "author_name": "Carlissa Hunt", + "author_inst": "UNIVERSITY OF CHICAGO MEDICINE" + }, + { + "author_name": "Stephanie Gillen", + "author_inst": "UNIVERSITY OF CHICAGO MEDICINE" + }, + { + "author_name": "Angelica Moran", + "author_inst": "University of Chicago Medical Center" + }, + { + "author_name": "Vera Tesic", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.13.093781", "rel_title": "In Vitro Inhibition of SARS-CoV-2 Infection by Bovine Lactoferrin", @@ -1447025,53 +1443984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.05.07.20094573", - "rel_title": "Development and validation of the COVID-19 severity index (CSI): a prognostic tool for early respiratory decompensation", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094573", - "rel_abs": "ObjectiveThe goal of this study was to create a predictive model of early hospital respiratory decompensation among patients with COVID-19.\n\nDesignObservational, retrospective cohort study.\n\nSettingNine-hospital health system within the Northeastern United States.\n\nPopulationsAdult patients ([≥] 18 years) admitted from the emergency department who tested positive for SARS-CoV-2 (COVID-19) up to 24 hours after initial presentation. Patients meeting criteria for respiratory critical illness within 4 hours of arrival were excluded.\n\nMain outcome and performance measuresWe used a composite endpoint of critical illness as defined by oxygen requirement (greater than 10 L/min by low-flow device, high-flow device, non-invasive, or invasive ventilation) or death within the first 24 hours of hospitalization. We developed models predicting our composite endpoint using patient demographic and clinical data available within the first four hours of arrival. Eight hospitals (n = 932) were used for model development and one hospital (n = 240) was held out for external validation. Area under receiver operating characteristic (AU-ROC), precision-recall curves (AU-PRC), and calibration metrics were used to compare predictive models to three illness scoring systems: Elixhauser comorbidity index, qSOFA, and CURB-65.\n\nResultsDuring the study period from March 1, 2020 to April 27,2020, 1,792 patients were admitted with COVID-19. Six-hundred and twenty patients were excluded based on age or critical illness within the first 4 hours, yielding 1,172 patients in the final cohort. Of these patients, 144 (12.3%) met the composite endpoint within the first 24 hours. We first developed a bedside quick COVID-19 severity index (qCSI), a twelve-point scale using nasal cannula flow rate, respiratory rate, and minimum documented pulse oximetry. We then created a machine-learning gradient boosting model, the COVID-19 severity index (CSI), using twelve additional variables including inflammatory markers and liver chemistries. Both the qCSI (AU-ROC mean [95% CI]: 0.90 [0.85-0.96]) and CSI (AU-ROC: 0.91 [0.86-0.97]) outperformed the comparator models (qSOFA: 0.76 [0.69-0.85]; Elixhauser: 0.70 [0.62-0.80]; CURB-65: AU-ROC 0.66 [0.58-0.77]) on cross-validation and performed well on external validation (qCSI: 0.82, CSI: 0.76, CURB-65: 0.50, qSOFA: 0.59, Elixhauser: 0.61). We find that a qCSI score of 0-3 is associated with a less than 5% risk of critical respiratory illness, while a score of 9-12 is associated with a 57% risk of progression to critical illness.\n\nConclusionsA significant proportion of admitted COVID-19 patients decompensate within 24 hours of hospital presentation and these events are accurately predicted using bedside respiratory exam findings within a simple scoring system.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Adrian Haimovich", - "author_inst": "Yale University" - }, - { - "author_name": "Neal G Ravindra", - "author_inst": "Yale University" - }, - { - "author_name": "Stoytcho Stoytchev", - "author_inst": "Yale University" - }, - { - "author_name": "H Patrick Young", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Francis P Wilson", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "David van Dijk", - "author_inst": "Yale University" - }, - { - "author_name": "Wade L Schulz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Richard Andrew Taylor", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.08.20092080", "rel_title": "SELF-POLICING COVID-19 AND CIVIC RESPONSIBILITIES IN LAGOS METROPOLIS, NIGERIA", @@ -1447604,6 +1444516,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.08.20095505", + "rel_title": "Significant Relaxation of SARS-CoV-2-Targeted Non-Pharmaceutical Interventions Will Result in Profound Mortality: A New York State Modelling Study", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095505", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the most significant global health crisis of the 21st century. The aim of this study was to develop a model to estimate the effect of undocumented infections, seasonal infectivity, immunity, and non-pharmaceutical interventions (NPIs), such as social distancing, on the transmission, morbidity, and mortality of SARS-CoV-2 in New York State (NYS). Simulations revealed dramatic infectivity driven by undocumented infections, and a peak basic reproductive number in NYS of 5.7. NPIs have been effective, and relaxation >50% will result in tens-of-thousands more deaths. Endemic infection is likely to occur in the absence of profound sustained immunity. As a result, until an effective vaccine or other effective pharmaceutical intervention is developed, it will be critical to not reduce NPIs >50% below current levels. This study establishes fundamental characteristics of SARS-CoV-2 transmission, which can help policymakers navigate combating this virus in the coming years.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Benjamin U. Hoffman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20095380", "rel_title": "Two alternative scenarios for easing COVID-19 lockdown measures: one reasonable and one catastrophic", @@ -1448475,93 +1445406,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.12.091165", - "rel_title": "Antiviral options against SARS-CoV-2 infection", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091165", - "rel_abs": "As of June 2020, the number of people infected with severe acute respiratory coronavirus 2 (SARS-CoV-2) continues to skyrocket, with more than 6,5 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. However, developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent sera and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here we developed a neutralization assay using SARS-CoV-2 strain and Vero-E6 cells. We identified most potent sera from recovered patients for treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that combinations of virus-directed nelfinavir along with host-directed amodiaquine exhibited the highest synergy. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Aleksandr Ianevski", - "author_inst": "NTNU" - }, - { - "author_name": "Rouan Yao", - "author_inst": "NTNU" - }, - { - "author_name": "Mona H. Fenstad", - "author_inst": "NTNU" - }, - { - "author_name": "Svetlana Biza", - "author_inst": "NTNU" - }, - { - "author_name": "Eva Zusinaite", - "author_inst": "TUIT" - }, - { - "author_name": "Hilde Lysvand", - "author_inst": "NTNU" - }, - { - "author_name": "Kirsti Loeseth", - "author_inst": "NTNU" - }, - { - "author_name": "Veslemoy M. Lamndsem", - "author_inst": "NTNU" - }, - { - "author_name": "Janne F. Malmring", - "author_inst": "St. Olavs Hospital" - }, - { - "author_name": "Valentyn Oksenych", - "author_inst": "NTNU" - }, - { - "author_name": "Sten E Erlandsen", - "author_inst": "NTNU" - }, - { - "author_name": "Per Arne Aas", - "author_inst": "NTNU" - }, - { - "author_name": "Lars Hagen", - "author_inst": "NTNU" - }, - { - "author_name": "Caroline H. Pettersen", - "author_inst": "NTNU" - }, - { - "author_name": "Jan Egil Afset", - "author_inst": "NTNU" - }, - { - "author_name": "Svein Arne Nordbo", - "author_inst": "NTNU" - }, - { - "author_name": "Magnar Bjoras", - "author_inst": "NTNU" - }, - { - "author_name": "Denis E Kainov", - "author_inst": "NTNU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.12.088716", "rel_title": "Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability", @@ -1449161,6 +1446005,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.05.07.20093831", + "rel_title": "Systematic Review and Meta-analysis of the Effectiveness and Safety of Hydroxychloroquine in COVID-19.", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20093831", + "rel_abs": "BackgroundsSince COVID-19 outbreak, various agents have been tested but no proven effective therapies have been identified. This has led to a lot of controversies among associated researches. Hence, in order to address the issue of using hydroxychloroquine (HCQ) in treating COVID-19 patients, we conducted a systematic review and meta-analysis.\n\nMethodsA thorough search was carried out to find relevant studies in MEDLINE, medRxiv, PubMed, Cochrane Database, China Academic Journals Full-text Database and Web of Science. Two investigators independently reviewed 274 abstracts and 23 articles. The trials which evaluated HCQ for treatment of COVID-19 were included for this systematic review. Two investigators assessed quality of the studies and data extraction was done by one reviewer and cross checked by the other.\n\nResultsFive trials involving 677 patients were included while conducting the meta-analysis. Compared with the control group, HCQ with or without azithromycin (AZI) showed benefits in viral clearance of SARS-CoV-2 (odds ratio (OR) 1.95, 95% CI 0.19-19.73) and a reduction in progression rate (OR 0.89, 95% CI 0.58-1.37), but without demonstrating any statistical significance. This systematic review has also suggested a possible synergistic effect of the combination therapy which included HCQ and AZI. However, the use of HCQ was associated with increased mortality in COVID-19 patients.\n\nConclusionsThe use of HCQ with or without AZI for treatment of COVID-19 patients, seems to be effective. The combination of HCQ and AZI has shown synergistic effects. However, mortality rate was increased when the treatment was conducted with HCQ.\n\nSummary of the articles main pointThis study demonstrates that the use of hydroxychloroquine with or without azithromycin might have benefits in viral clearance of SARS-CoV-2 and reduction of progression rate, but was associated with increased mortality in COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Tzu-Han Yang", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Chian-Ying Chou", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Yi-Fan Yang", + "author_inst": "National Taiwan University Hospital" + }, + { + "author_name": "Yi-Ping Yang", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Chian-Shiu Chien", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Aliaksandr A. Yarmishyn", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Tzu-Ying Yang", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Shih-Hwa Chiou", + "author_inst": "Taipei Veterans General Hospital" + }, + { + "author_name": "Yuh-Lih Chang", + "author_inst": "Taipei Veterans General Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20090621", "rel_title": "Prolonged viral RNA shedding after COVID-19 symptom resolution in older convalescent plasma donors", @@ -1449884,153 +1446779,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.07.20073981", - "rel_title": "Treatments administered to the first 9,152 reported cases of COVID19: a systematic review", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20073981", - "rel_abs": "The emergence of SARS-CoV-2/2019 novel coronavirus (COVID19) has created a global pandemic with no approved treatments or vaccines. Many treatments have already been administered to COVID19 patients but have not been systematically evaluated. We performed a systematic literature review to identify all treatments reported to be administered to COVID19 patients and assess time to clinically meaningful response for treatments with sufficient data. We searched PubMed, BioRxiv, MedRxiv, and ChinaXiv for articles reporting treatments for COVID19 patients published between 12/1/2019-3/27/2020. Data were analyzed descriptively. Of the 2,706 articles identified, 155 studies met inclusion criteria, comprising 9,152 patients from 14 different countries. The cohort was 45.4% female and 98.3% hospitalized and mean (SD) age was 44.4 years (SD 21.0). The most frequently administered drug classes were antivirals, antibiotics, and corticosteroids, and of the 115 reported drugs, the most frequently administered was combination lopinavir/ritonavir, which was associated with a time to clinically-meaningful response (complete symptom resolution or hospital discharge) of 11.7 (1.09) days. There was insufficient data to compare across treatments. A large number of treatments have been administered to the first 9,152 reported cases of COVID19. These data serve as the basis for an open-source registry of all reported treatments given to COVID19 patients. Further work is needed to prioritize drugs for investigation in well-controlled clinical trials and treatment protocols.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "David C Fajgenbaum", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Johnson S Khor", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Alek Gorzewski", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Mark-Avery Tamakloe", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Victoria Powers", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Joseph Kakkis", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Mileva Repasky", - "author_inst": "Castleman Disease Collaborative Network" - }, - { - "author_name": "Anne Taylor", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Alexander Beschloss", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Laura Hernandez-Miyares", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Beatrice Go", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Vivek Nimgaonkar", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Madison McCarthy", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Casey J Kim", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Anna Wing", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Michael Mayer", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ruth-Anne Pai", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sarah Frankl", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Megan Fisher", - "author_inst": "Georgetown University" - }, - { - "author_name": "James Germi", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Cornelia Keyser", - "author_inst": "Brown University" - }, - { - "author_name": "Philip Angelides", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ashwin Amurthur", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Joanna Jiang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Rozena Rasheed", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Eric Rodriguez-Lopez", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Erin Napier", - "author_inst": "University of Hawaii Medical School" - }, - { - "author_name": "Bruna Martins", - "author_inst": "Medidata Solutions" - }, - { - "author_name": "Stephen Bambury", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Karen Gunderson", - "author_inst": "CAAcure" - }, - { - "author_name": "Nick Goodyear", - "author_inst": "Castleman Disease Collaborative Network" - }, - { - "author_name": "Duncan Mackay", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sheila K Pierson", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.07.20073817", "rel_title": "The majority of male patients with COVID-19 present low testosterone levels on admission to Intensive Care in Hamburg, Germany: a retrospective cohort study.", @@ -1450683,6 +1447431,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.07.20092775", + "rel_title": "Monitoring the Covid-19 epidemics in Italy from mortality data", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20092775", + "rel_abs": "The mortality data can be used as an alternative source to monitor the status of Covid-19. We have studied a dataset including deaths up to the fourth week of April. There is a large excess, more pronounced at the beginning of the pandemic, showing a difference in age and gender compared to the Covid-19-confirmed cases. The study indicates that mortality information can be used to provide a less biased time profile of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Daniele del Re", + "author_inst": "Universita' Sapienza & INFN" + }, + { + "author_name": "Paolo Meridiani", + "author_inst": "Istituto Nazionale Fisica Nucleare (INFN)" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091934", "rel_title": "Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020.", @@ -1451606,73 +1448377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.06.20093179", - "rel_title": "The first 6 weeks: setting up a UK urgent dental care centre during the COVID-19 pandemic.", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093179", - "rel_abs": "IntroductionThe COVID-19 pandemic has posed many challenges, including provision of urgent dental care. This paper presents a prospective service evaluation during establishment of urgent dental care in the North-East of England over a six-week period.\n\nAimTo monitor patient volumes, demographics and outcomes at the North-East urgent dental care service and confirm appropriate care pathways.\n\nMain Outcome MethodsData were collected on key characteristics of patients accessing urgent care from 23rd March to 3rd May 2020. Analysis was with descriptive statistics.\n\nResultsThere were 1746 patient triages, (1595 telephone and 151 face-to-face) resulting in 1322 clinical consultations. The most common diagnoses were: symptomatic irreversible pulpitis or apical periodontitis. 65% of clinical consultations resulted in extractions, 0.5% an aerosol generating procedure. Patients travelled 25km on average to access care, however this reduced as more urgent care centres were established. The majority of patients were asymptomatic of COVID-19 and to our knowledge no staff acquired infection due to occupational exposure.\n\nConclusionThe urgent dental care centre effectively managed urgent and emergency dental care, with appropriate patient pathways established over the 6-week period. Dental preparedness for future pandemic crisis could be improved and informed by this data.\n\nThree In Brief PointsO_LIA summary is given of how urgent dental care was established in the North East of England during the COVID-19 pandemic which may help with future preparedness for pandemics.\nC_LIO_LIAerosol generating procedures were almost always avoided in the delivery of urgent dental care\nC_LIO_LIA telephone triage system was effectively used to determine who needed clinical care, and to separate symptomatic, asymptomatic and shielding patients, with very few failures in triage noted.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Emily Carter", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Charlotte Currie", - "author_inst": "Newcastle University" - }, - { - "author_name": "Abisola Asuni", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Rachel Goldsmith", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Grace Toon", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Catherine Horridge", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Sarah Simpson", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Christopher Donnell", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Mark Greenwood", - "author_inst": "Newcastle University" - }, - { - "author_name": "Graham Walton", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Ben Cole", - "author_inst": "Newcastle Dental Hospital" - }, - { - "author_name": "Justin Durham", - "author_inst": "Newcastle University" - }, - { - "author_name": "Richard Holliday", - "author_inst": "Newcastle University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2020.05.06.20093724", "rel_title": "Variations in Personal Protective Equipment Preparedness in Intensive Care Units during the COVID-19 Pandemic: A Survey of Asia-Pacific Countries", @@ -1452417,6 +1449121,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.07.20094326", + "rel_title": "Chloroquine and hydroxychloroquine effectiveness in human subjects during coronavirus: a systematic review", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094326", + "rel_abs": "In a search to find effective treatments for COVID-19, chloroquine and hydroxychloroquine have gained attention. We aim to provide evidence to support clinical decision-making regarding medication for the treatment of COVID-19 by carrying out a systematic review of the literature. The electronic databases MEDLINE, EMBASE, Global Health, and HMIC were searched up to April 2020. Eligible study outcomes included: extubation or patient recovery. Relevant data were extracted and analysed by narrative synthesis. Our results included six studies in the review of which four studies were of good or fair quality. All eligible studies included were for coronavirus involving the use of either chloroquine or hydroxychloroquine to treat common symptoms such as fever, cough, shortness of breath and fatigue. Outcomes most commonly reported were improved lung function, viral clearance, and hospital discharge. Strong evidence to support the use of chloroquine and hydroxychloroquine in the treatment of COVID-19 is lacking. Fast track trials are riddled with bias and may not conform to rigorous guidelines which may lead to inadequate data being reported. The use of these drugs in combination with other medications may be useful but without knowing which groups they are suited for and when they may cause more harm than good.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Salman Rawaf", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mohammed Al-Saffar", + "author_inst": "Imperial College London" + }, + { + "author_name": "Harumi Quezada-Yamamoto", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mashael Alshaikh", + "author_inst": "King Saud University" + }, + { + "author_name": "Michael Pelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "David Rawaf", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elizabeth Dubois", + "author_inst": "Imperial College London" + }, + { + "author_name": "Azeem Majeed", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.06.20093468", "rel_title": "YouTube as an information source during the Coronavirus disease (COVID-19) pandemic", @@ -1453244,61 +1449995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.07.20094987", - "rel_title": "Low albumin levels are associated with poorer outcomes in a case series of COVID-19 patients in Spain: a retrospective cohort study", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094987", - "rel_abs": "OBJECTIVETo describe the clinical characteristics and epidemiological features of severe (non-ICU) and critically patients (ICU) with COVID-19 at triage, prior hospitalization, in one of the main hospitals in The Balearic Islands health care system.\n\nDESIGNRetrospective observational study\n\nSETTINGSon Llatzer University Hospital in Palma de Mallorca (Spain)\n\nPARTICIPANTSAmong a cohort of 52 hospitalized patients as of 31 March 2020, 48 with complete demographic information and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive test, were analyzed. Data were collected between March 15th, 2020, and March 31th 2020, inclusive of these dates.\n\nMAIN OUTCOMESClinical, vital signs and routine laboratory outcomes at the time of hospitalization, including symptoms reported prior to hospitalization. Demographics and baseline comorbidities were also collected. Mortality was reported at the end of the study.\n\nRESULTS48 patients (27 non-ICU and 21 ICU) resident in Mallorca, Spain (mean age, 66 years, [range, 33-88 years]; 67% males) with positive SARS-CoV-2 infection were analyzed. There were no differences in age or sex among groups (p >.05). Initial symptoms included fever (100%), coughing (85%), dyspnea (76%), diarrhea (42%) and asthenia (21%). The majority of patients in this case series were hospitalized because of low SpO2 (SpO2 below 90%) and presentation of bilateral pneumonia (94%) at triage. ICU patients had a higher prevalence of dyspnea compared to non-ICU patients (95% vs 61%, p = .022). Acute respiratory syndrome (ARDS) was presented in 100% of the ICU-patients. All the patients included in the study required oxygen therapy. ICU-patients had lymphopenia as well as hypoalbuminemia. Inflammatory markers such as lactate dehydrogenase (LDH), C-reactive protein (CRP), and procalcitonin were significantly higher in ICU patients compared to non-ICU (p < .001).Lower albumin levels were associated with poor prognosis measured as longer hospital length (r= -0.472, p <.001) and mortality (r= -0.424, p=.003). Interestingly we also found, that MCV was lower among of those patients who died (p=.0002). As of April 28, 2020, 10 patients (8 ICU and 2 non-ICU) had died (21% mortality) and while 100% of the non-ICU patients had been discharged, 33% of ICU patients still remained hospitalized (5 in ICU and 2 had been transferred to ward).\n\nCONCLUSIONCritically ill patients with COVID-19 present lymphopenia, hypoalbuminemia as well high levels of inflammation. Lower levels of albumin were associated with poorer outcomes in COVID-19 patients. Albumin might be of importance because of its association with disease severity in patients infected with SARS-CoV-2.\n\nWHAT IS ALREADY KNOWN IN THIS TOPICSpain has been hit particularly hard by the pandemic. By the time that this manuscript was written more than 25.000 deaths related to COVID-19 have been confirmed. There is limited information available describing the clinical and epidemiological features of Spanish patients requiring hospitalization for COVID-19. Also, it is important to know the characteristics of the hospitalized patients who become critically ill\n\nWHAT THIS STUDY ADDSThis small case series provides the first steps towards a comprehensive clinical characterization of severe and critical COVID-19 adult patients in Spain. The overall mortality in our patients was 21%. To our knowledge this is the first report with reporting these features in Spain. At triage the majority of patients had lower SpO2 (<90%) and bilateral pneumonia. The most common comorbidities were hypertension (70%), dyslipidemia (62%) and cardiovascular disease (30%). Critically ill patients present hypoalbuminemia and lymphopenia, as well as higher levels of inflammation. Albumin might be of importance because of its association with disease severity and mortality in patients infected with SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Roberto de la Rica", - "author_inst": "Health Research Institute of the Balearic Islands (IdISBa), Multidisciplinary Sepsis Group" - }, - { - "author_name": "Marcio Borges", - "author_inst": "Hospital Universitario Son LLatzer, Intensive Care Unit" - }, - { - "author_name": "Maria Aranda", - "author_inst": "Hospital Universitario Son Llatzer, Intensive Care Unit" - }, - { - "author_name": "Alberto del Castillo", - "author_inst": "Hospital Universitario Son LLatzer, Intensive Care Unit" - }, - { - "author_name": "Antonia Socias", - "author_inst": "Hospital Universitario Son LLatzer, Intensive Care Unit" - }, - { - "author_name": "Antoni Payeras", - "author_inst": "Hospital Universitario Son LLatzer, Internal Medicine Unit" - }, - { - "author_name": "Gemma Rialp", - "author_inst": "Hospital Universitario Son LLatzer, Intensive Care Unit" - }, - { - "author_name": "Lorenzo Socias", - "author_inst": "Hospital Universitario Son LLatzer, Intensive Care Unit" - }, - { - "author_name": "Lluis Masmiquel", - "author_inst": "Hospital Universitario Son LLatzer, Health Research Institute of the Balearic Islands (IdISBa)" - }, - { - "author_name": "Marta Gonzalez-Freire", - "author_inst": "Health Research Institute of the Balearic Islands, IdISBa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.08.20095075", "rel_title": "A rapid review of available evidence on the serial interval and generation time of COVID-19", @@ -1453951,6 +1450647,29 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.05.11.088781", + "rel_title": "Structural insight into the putative role of Novel Coronavirus-2 E protein in viral infection via in silico approach: a potential target for LAV development and other therapeutic strategies", + "rel_date": "2020-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.088781", + "rel_abs": "The outbreak of COVID-19 across the world has posed unprecedented and global challenges on multiple fronts. Most of the vaccine and drug development has focused on the spike proteins and viral RNA-polymerases. Using bioinformatics and structural modeling approach, we modeled the structure of the envelope (E)-protein of novel SARS-CoV-2. The E-protein of this virus shares sequence similarity with that of SARS-CoV-1, and is highly conserved in the N-terminal regions. Incidentally, compared to spike proteins, E proteins demonstrate lower disparity and mutability among the isolated sequences. Using homology modeling, we found that the most favorable structure could function as a gated proton channel. Combining pocket estimation and docking with water, we determined that GLU 8 and ASN 15 in the N-terminal region were in close proximity to form H-bonds. Additionally, two distinct \u201ccore\u201d structures were visible, the hydrophobic core and the central core, which may regulate the opening/closing of the channel. We propose this as a mechanism of viral proton channeling activity which may play a critical role in viral infection. In addition, it provides a structural basis and additional avenues for generating therapeutic interventions against the virus.One Sentence Summary Structural modeling of the novel coronavirus envelope proteins (E-proteins) demonstrating its possible proton channeling activity.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Manish Sarkar", + "author_inst": "Bose Institute" + }, + { + "author_name": "Soham Saha", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.08.20078386", "rel_title": "Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland", @@ -1454578,53 +1451297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.10.087288", - "rel_title": "SARS-CoV-2 spike protein binds heparan sulfate in a length- and sequence-dependent manner", - "rel_date": "2020-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.10.087288", - "rel_abs": "Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) is causing an unprecedented global pandemic demanding the urgent development of therapeutic strategies. Microarray binding experiments using an extensive heparan sulfate (HS) oligosaccharide library showed that the receptor binding domain (RBD) of the spike of SARS-CoV-2 can bind HS in a length-and sequence-dependent manner. Hexa- and octa-saccharides composed of IdoA2S-GlcNS6S repeating units were identified as optimal ligands. Surface plasma resonance (SPR) showed the SARS-CoV-2 spike protein binds with much higher affinity to heparin (KD = 55 nM) compared to the RBD (KD = 1 M) alone. We also found that heparin does not interfere in angiotensin-converting enzyme 2 (ACE2) binding or proteolytic processing of the spike. Our data supports a model in which HS functions as the point of initial attachment for SARS-CoV-2 infection. Tissue staining studies using biologically relevant tissues indicate that heparan sulfate proteoglycan (HSPG) is a critical attachment factor for the virus. Collectively, our results highlight the potential of using HS oligosaccharides as a therapeutic agent by inhibiting SARS-CoV-2 binding to target cells.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Lin Liu", - "author_inst": "University of Georgia" - }, - { - "author_name": "Pradeep Chopra", - "author_inst": "University of Georgia" - }, - { - "author_name": "Xiuru Li", - "author_inst": "University of Georgia" - }, - { - "author_name": "Kim M Bouwman", - "author_inst": "Utrecht University" - }, - { - "author_name": "Stephen Mark Tompkins", - "author_inst": "University of Georgia" - }, - { - "author_name": "Margreet A Wolfert", - "author_inst": "University of Georgia" - }, - { - "author_name": "Robert P de Vries", - "author_inst": "Utrecht Institute for Pharmaceutical Sciences, Utrecht University" - }, - { - "author_name": "Geert-Jan Boons", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.09.085613", "rel_title": "Potential modes of COVID-19 transmission from human eye revealed by single-cell atlas", @@ -1455369,6 +1452041,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.06.20093351", + "rel_title": "Age-adjusted associations between comorbidity and outcomes of COVID-19: a review of the evidence", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093351", + "rel_abs": "BackgroundCurrent evidence suggests that older people and people with underlying comorbidities are at increased risk of severe disease and death following hospitalisation with COVID-19. As comorbidity increases with age, it is necessary to understand the age-adjusted relationship between comorbidity and COVID-19 outcomes, in order to enhance planning capabilities and our understanding of COVID-19.\n\nMethodsWe conducted a rapid, comprehensive review of the literature up to 10 April 2020, to assess the international empirical evidence on the association between comorbidities and severe or critical care outcomes of COVID-19, after accounting for age, among hospitalised patients with COVID-19.\n\nResultsAfter screening 579 studies, we identified seven studies eligible for inclusion and these were synthesised narratively. All were from China. The emerging evidence base mostly indicates that after adjustment for age (and in some cases other potential confounders), obesity, hypertension, diabetes mellitus, chronic obstructive airways disease (COPD), and cancer are all associated with worse outcomes. The largest study, using a large nationwide sample of COVID-19 patients in China, found that those with multiple comorbidities had more than twice the risk of a severe outcome or death compared with patients with no comorbidities, after adjusting for age and smoking (HR=2.59, 95% CI 1.61, 4.17).\n\nConclusionsThis review summarises for clinicians, policymakers, and academics the most robust evidence to date on this topic, to inform the management of patients and control measures for tackling the pandemic. Given the intersection of comorbidity with ethnicity and social disadvantage, these findings also have important implications for health inequalities. As the pandemic develops, further research should confirm these trends in other settings outside China and explore mechanisms by which various underlying health conditions increase risk of severe COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kate E Mason", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Philip McHale", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andy Pennington", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Gillian Maudsley", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jennifer Day", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Ben Barr", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.06.20093260", "rel_title": "Angiotensin Converting Enzyme Inhibitors and Angiotensin Receptor Blockers and Outcome of COVID-19 : A Systematic Review and Meta-analysis", @@ -1456376,77 +1453087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.06.20087692", - "rel_title": "PROGNOSTIC FACTORS FOR CLINICAL COURSE OF PATIENTS WITH COVID-19: PROTOCOL FOR A RAPID LIVING SYSTEMATIC REVIEW", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20087692", - "rel_abs": "CONTEXT AND OBJECTIVEDetermining prognostic factors in a context of health crises such as the COVID-19 scenario may provide the best possible care for patients and optimize the management and the resource utilization of the health system. Thus, we aim to systematically review the prognostic factors for different outcomes of patients with COVID-19. DESIGN AND SETTING: Protocol for a rapid living systematic review methodology following the recommendations proposed by the Cochrane Handbook. METHODS: We will include cohorts and case-control studies. We will search Medline via PubMed, Embase via Elsevier, Cochrane Library - Cochrane Central Register of Controlled Trials (CENTRAL), Portal Regional BVS-LILACS, Scopus and WebofScience to identify studies. No language restrictions will be applied. We will perform the critical appraisal of included studies with the Quality in Prognosis Studies (QUIPS) tool and the certainty of evidence will be evaluated using the Grading of Recommendations Assessment, Development and Evaluation (GRADE).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Cesar Ramos Rocha Filho", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Ana Carolina Pereira Nunes Pinto", - "author_inst": "Universidade Federal do Amapa/Universidade Federal de Sao Paulo/Cochrane Brazil" - }, - { - "author_name": "Aline Pereira Rocha", - "author_inst": "Universidade Federal de Sao Paulo/Cochrane Brazil" - }, - { - "author_name": "Keilla Machado Martins Milby", - "author_inst": "Universidade Federal de Sao Paulo/Cochrane Brazil" - }, - { - "author_name": "Felipe Sebastiao de Assis Reis", - "author_inst": "Beneficencia Portuguesa - SP" - }, - { - "author_name": "Vinicius Tassoni Civile", - "author_inst": "Universidade Federal de Sao Paulo/Universidade Paulista/Cochrane Brazil" - }, - { - "author_name": "Nelson Carvas Junior", - "author_inst": "Universidade Ibirapuera" - }, - { - "author_name": "Rodolfo Rodrigo Pereira Santos", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Gabriel Sodre Ramalho", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Giulia Fernandes Moca Trevisani", - "author_inst": "Universidade Santo Amaro" - }, - { - "author_name": "Laura Jantsch Ferla", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Maria Eduarda Santos Puga", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Virginia Fernandes Moca Trevisani", - "author_inst": "Universidade Federal de Sao Paulo/Universidade Santo Amaro" - }, - { - "author_name": "Alvaro Nagib Atallah", - "author_inst": "Universidade Federal de Sao Paulo/Cochrane Brazil" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20088906", "rel_title": "Predicting Disease Progression in COVID19: A Score Based On Lab Tests At Time Of Diagnosis", @@ -1457063,6 +1453703,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20092130", + "rel_title": "Phasic containment of COVID-19 in substantially affected states of India", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092130", + "rel_abs": "The spread of COVID-19 epidemic in some highly-impacted Indian states displayed a characteristic sub-exponential growth projected up to 3 May 2020, as a consequence of lockdown strategies, in addition to improvement of reproduction number (R), serial interval, and daily growth rate, but not case fatality rate (CFR). The effect of COVID-19 containment was more prominent in second phase of lockdown with declining R, which was still >1, suggesting the requirement of sustained interventions for effective containment of COVID-19 pandemic in Indian context.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Manisha Mandal", + "author_inst": "Department of Physiology, MGM Medical College, Kishanganj-855107, India" + }, + { + "author_name": "Shyamapada Mandal", + "author_inst": "University of Gour Banga" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20092098", "rel_title": "Using viral genomics to estimate undetected infections and extent of superspreading events for COVID-19", @@ -1457834,29 +1454497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20088567", - "rel_title": "Environmental sampling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a coronavirus disease (COVID-19) outbreak aboard a commercial cruise ship", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088567", - "rel_abs": "BackgroundA COVID-19 outbreak occurred in a cruise ship with 3711 passengers and crew in 2020. This study is to test the hypothesis that environmental surfaces played important roles in transmission for SARS-CoV-2 during this outbreak.\n\nMethodsWe sampled environmental surfaces including air from common areas in the cruise ship and cabins in which confirmed COVID-19 cases and non-cases had stayed after they left the cabins. We tested the samples for SARS-CoV-2 by rt-PCR and conducted viral isolation.\n\nFindingsOf 601 samples tested, SARS-CoV-2 RNA was detected from 58 samples (10%) from case-cabins from which they left 1-17 days before sampling, but not from non-case-cabins. Except for one sample from an air hood in a corridor, SARS-CoV-2 RNA was not detected from samples in common areas. SARS-CoV-2 RNA was not detected from all 14 air samples. RNA was most often detected on the floor around toilet in the bathroom (39%, 13/33, cycle quantification (Cq): 26.21-37.62) and bed pillow (34%, 11/32, Cq: 34.61-38.99). There was no difference in the detection proportion between cabins for symptomatic (15%, 28/189, Cq: 29.79-38.86) and asymptomatic cases (21%, 28/131, Cq: 26.21-38.99). No SARS-CoV-2 virus was isolated from any of the samples.\n\nInterpretationThe environment around the COVID-19 cases was extensively contaminated from SARS-CoV-2 during COVID-19 outbreak in the cruise ship. Transmission risk of SARS-CoV-2 from symptomatic and asymptomatic patients seems to be similar and the environmental surface could involve viral transmission through direct contact.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Taskforce for the COVID-19 Cruise Ship Outbreak", - "author_inst": "" - }, - { - "author_name": "Takuya Yamagishi", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.02.20088013", "rel_title": "Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil", @@ -1458497,6 +1455137,249 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.04.20091017", + "rel_title": "Effects of home confinement on mental health and lifestyle behaviours during the COVID-19 outbreak: Insight from the \"ECLB-COVID19\" multi countries survey", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091017", + "rel_abs": "BackgroundAlthough recognised as effective measures to curb the spread of the COVID-19 outbreak, social distancing and self-isolation, have been suggested to generate burden throughout the population. To provide scientific data to help identify risk-factors for the psychosocial strain during the COVID-19 outbreak, an international cross-disciplinary online survey was circulated in April 2020. This report outlines the mental, emotional and behavioural consequences of COVID-19 home confinement.\n\nMethodThirty-five research organisations from four continents promoted the survey through their networks to the general society, in Ten different languages. Questions were presented in a differential format with questions related to responses \"before\" and \"during\" confinement period.\n\nResults1047 replies (54% women) from Western-Asia (36%), North-Africa (40%), Europe (21%) and other countries (3%) were analysed. The COVID-19 home confinement evoked a negative effect on mental wellbeing and emotional status (P < 0.001; 0.43 [≤] d [≤] 0.65) with a greater proportion of individuals experiencing psychosocial and emotional disorders (10% to 16.5%). These psychosocial tolls were associated with unhealthy lifestyle behaviours with a greater proportion of individuals experiencing (i) physical (+15.2%) and social (71.2%) inactivity, (ii) poor sleep quality (12.8%), (iii) unhealthy diet behaviours (10%), and (iv) unemployment (6%). Conversely, participants demonstrated a greater use (15%) of technology solutions during the confinement period.\n\nConclusionThese findings elucidate the risk of psychosocial strain during the current home confinement period and provide a clear remit for the urgent implementation of technology-based intervention to foster an Active and Healthy Confinement Lifestyle (AHCL).", + "rel_num_authors": 57, + "rel_authors": [ + { + "author_name": "ACHRAF AMMAR", + "author_inst": "Otto-Von-Guericke University" + }, + { + "author_name": "Khaled Trabelsi", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Michael Brach", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany Michael Brach" + }, + { + "author_name": "Hamdi Chtourou", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Omar Boukhris", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Liwa Masmoudi", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Bassem Bouaziz", + "author_inst": "Higher Institute of Computer Science and Multimedia of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Ellen Bentlage", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany Michael Brach" + }, + { + "author_name": "Daniella How", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany Michael Brach" + }, + { + "author_name": "Mona Ahmed", + "author_inst": "Institute of Sport and Exercise Sciences, Munster, Germany Michael Brach" + }, + { + "author_name": "Patrick Mueller", + "author_inst": "Research Group Neuroprotection, German Center for Neurodegenerative Diseases (DZNE), Leipziger Str. 44, Magdeburg, 39120, Germany" + }, + { + "author_name": "Notger Mueller", + "author_inst": "Research Group Neuroprotection, German Center for Neurodegenerative Diseases (DZNE), Leipziger Str. 44, Magdeburg, 39120, Germany" + }, + { + "author_name": "Asma Aloui", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Omar Hammouda", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Laisa Liane Paineiras-Domingos", + "author_inst": "Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Annemarie Braakman-jansen", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Christian Wrede", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Sophia Bastoni", + "author_inst": "Catholic University of the Sacred Heart I UNICATT, Milano, Italy" + }, + { + "author_name": "Carlos Soares Pernambuco", + "author_inst": "Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil" + }, + { + "author_name": "Leonardo Mataruna", + "author_inst": "College of Business Administration, American University in the Emirates, Dubai, UAE" + }, + { + "author_name": "Morteza Taheri", + "author_inst": "Imam Khomeini International University, Qazvin, Iran" + }, + { + "author_name": "Khadijeh Irandoust", + "author_inst": "Imam Khomeini International University, Qazvin, Iran" + }, + { + "author_name": "Aimen Khacharem", + "author_inst": "UVHC, DeVisu, Valenciennes, France; LIRTES - EA 7313.Paris-East Creteil University, Creteil, France" + }, + { + "author_name": "Nicola L Bragazzi", + "author_inst": "Department of Health Sciences (DISSAL), Postgraduate School of Public Health, University of Genoa, Genoa 16132, Italy" + }, + { + "author_name": "Karim Chamari", + "author_inst": "Department of Research and Education / Aspetar, Qatar" + }, + { + "author_name": "Jordan M Glenn", + "author_inst": "Exercise Science Research Center, Department of Health, Human Performance and Recreation, University of Arkansas, AR 72701, Fayetteville, USA" + }, + { + "author_name": "Nicholas T Bott", + "author_inst": "Clinical Excellence Research Center, Department of Medicine, Stanford University School of Medicine, CA 94305, Stanford, USA" + }, + { + "author_name": "Faiez Gargouri", + "author_inst": "Higher Institute of Computer Science and Multimedia of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Lotfi Chaari", + "author_inst": "University of Toulouse, IRIT - INP-ENSEEIHT, France" + }, + { + "author_name": "Hadj Batatia", + "author_inst": "University of Toulouse, IRIT - INP-ENSEEIHT, France" + }, + { + "author_name": "Gamal Mohamed Ali", + "author_inst": "Faculty of Physical Education, Assiut University, Assiut 71515, Egypt" + }, + { + "author_name": "Osama Abdelkarim", + "author_inst": "Karlsruher Institut fur Technologie, Karlsruher, Germany" + }, + { + "author_name": "Mohamed Jarraya", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Kais El Abed", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Nizar Souissi", + "author_inst": "UR18JS01, Observatoire National du Sport, Tunis, Tunisie" + }, + { + "author_name": "Lisette Van Gemert-Pijnen", + "author_inst": "University of Twente, the Netherlands Region de Enschede, Netherland" + }, + { + "author_name": "Bryan L Riemann", + "author_inst": "Georgia Southern University, Statesboro, GA 30458, USA" + }, + { + "author_name": "Laurel Riemann", + "author_inst": "PharmD, BCBS; PharmIAD, Inc,Savannah, GA, USA" + }, + { + "author_name": "Wassim Moalla", + "author_inst": "High Institute of Sport and Physical Education of Sfax, 3000, Sfax, Tunisia" + }, + { + "author_name": "Jonathan Gomez-Raja", + "author_inst": "Health and Social Services, Fundesalud, 06800, Merida, Spain" + }, + { + "author_name": "Monique Epstein", + "author_inst": "The E-senior association, 75020 Paris, France" + }, + { + "author_name": "Robbert Sanderman", + "author_inst": "Department of Health Psychology, University Medical Center Groningen,University of Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Sebastian Schulz", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Achim Jerg", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Ramzi Al-Horani", + "author_inst": "Department of Exercise Science, Yarmouk University, Irbid, Jordan" + }, + { + "author_name": "Taysir Mansi", + "author_inst": "Department of Instruction and Supervision, The University of Jordan, Jordan" + }, + { + "author_name": "Mohamed Jmail", + "author_inst": "Digital Research Centre of Sfax, Sfax, Tunisia" + }, + { + "author_name": "Fernando Barbosa", + "author_inst": "Faculty of Psychology and Education Sciences, University of Porto, Porto Portugal" + }, + { + "author_name": "Fernando Santos", + "author_inst": "ISCTE-Instituto Universitario de Lisboa, Av. das Forcas Armadas, 1649-026 Lisboa, Portugal" + }, + { + "author_name": "Bostjan Simunic", + "author_inst": "Institute for Kinesiology Research, Science and ResearchCentre, Koper, Slovenia" + }, + { + "author_name": "Rado Pisot", + "author_inst": "Institute for Kinesiology Research, Science and ResearchCentre, Koper, Slovenia" + }, + { + "author_name": "Donald Cowan", + "author_inst": "Centre for Bioengineering and Biotechnology University of Waterloo, Waterloo, Canda" + }, + { + "author_name": "Andrea Gaggioli", + "author_inst": "Catholic University of the Sacred Heart I UNICATT, Milano, Italy" + }, + { + "author_name": "Stephen J Bailey", + "author_inst": "School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK" + }, + { + "author_name": "Jurgen Steinacker", + "author_inst": "Department of Medicine, Ulm University, Leimgrubenweg 14, 89075 Ulm, Germany" + }, + { + "author_name": "Tarak Driss", + "author_inst": "Interdisciplinary Laboratory in Neurosciences, Physiology and Psychology: Physical Activity, Health and Learning (LINP2-2APS), UFR STAPS, UPL, Paris Nanterre Un" + }, + { + "author_name": "Anita Hoekelmann", + "author_inst": "Otto-Von-Guericke University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.03.20089771", "rel_title": "Real-time tracking and forecasting of the of COVID-19 outbreak in Kuwait: a mathematical modeling study", @@ -1459500,33 +1456383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20091280", - "rel_title": "Contact tracing strategies for COVID-19 containment with attenuated physical distancing", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091280", - "rel_abs": "Contact tracing has been recommended as a critical component of containment strategies for COVID-19. We used a simple epidemic model to evaluate how contact tracing might enable modification of current physical distancing restrictions. Testing and tracing coverage need to exceed 50% to see substantial gains; if both are below 50%, contact tracing does not reduce transmission by more than 10%. With 90% testing and tracing as well as high isolation and quarantine efficacy, contact tracing could reduce overall transmission by >45%, which would allow for partial loosening of physical distancing measures. Benefits of contact tracing could be enhanced by testing all contacts rather than only those with symptoms and by policies to support high adherence to voluntary isolation and quarantine.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alyssa Bilinski", - "author_inst": "Harvard Graduate School of Arts and Sciences" - }, - { - "author_name": "Farzad Mostashari", - "author_inst": "Aledade, Inc" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20091231", "rel_title": "Point-of-care testing for COVID-19 using SHERLOCK diagnostics", @@ -1460411,6 +1457267,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091389", + "rel_title": "Evolution of COVID-19 pandemic: Power law growth and saturation", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091389", + "rel_abs": "In this paper, we analyze the real-time infection data of COVID-19 epidemic for 21 nations up to June 30, 2020. For most of these nations, the total number of infected individuals exhibits a succession of exponential growth and power-law growth before the flattening of the curve. In particular, we find a universal [Formula] growth before they reach saturation. However, at present, India, which has I(t) ~ t2, and Russia and Brazil, which have I(t) ~ t, are yet to flatten their curves. Thus, the polynomials of the I(t) curves provide valuable information on the stage of the epidemic evolution, thus on the life cycle of COVID-19 pandemic. Besides these detailed analyses, we compare the predictions of an extended SEIR model and a delay differential equation-based model with the reported infection data and observed good agreement among them, including the [Formula] behaviour. We argue that the power laws in the epidemic curves may be due to lockdowns.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Soumyadeep Chatterjee", + "author_inst": "Indian Institute of Technology Kanpur, Kanpur 208016, India" + }, + { + "author_name": "Ali Asad", + "author_inst": "Indian Institute of Technology Kanpur, Kanpur 208016, India" + }, + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Shashwat Bhattacharya", + "author_inst": "Indian Institute of Technology Kanpur, Kanpur 208016, India" + }, + { + "author_name": "Shadab Alam", + "author_inst": "Indian Institute of Technology Kanpur, Kanpur 208016, India" + }, + { + "author_name": "Mahendra K. Verma", + "author_inst": "Indian Institute of Technology Kanpur, Kanpur 208016, India" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091751", "rel_title": "COVID- 19 Infection in Children: Estimating Pediatric Morbidity and Mortality", @@ -1461362,29 +1458257,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.05.07.083147", - "rel_title": "Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.083147", - "rel_abs": "The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sudeep Bhattacharyya", - "author_inst": "University of Wisconsin at Eau Claire" - }, - { - "author_name": "Sanchita Hati", - "author_inst": "University of Wisconsin - Eau Claire" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.05.079400", "rel_title": "Massive Multiplexing Can Deliver a $1 Test for COVID-19", @@ -1462021,6 +1458893,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2020.05.03.20077206", + "rel_title": "Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20077206", + "rel_abs": "ObjectiveTo describe the ischemic stroke subtypes related to COVID-19 in a cohort of NYC hospitals and explore their etiopathogenesis.\n\nBackgroundExtra-pulmonary involvement of COVID-19 has been reported in the hepatic, renal and hematological systems. Most neurological manifestations are non-focal, but few have reported the characteristics of ischemic strokes or investigated its pathophysiology.\n\nMethodsData were collected prospectively from March 15 to April 15, 2020 from four centers in New York City to review possible ischemic stroke types seen in COVID-19 positive patients. Patient presentation, demographics, other related vascular risk factors, associated laboratory and coagulation markers, as well as imaging and outcomes for consecutive stroke patients positive for SARS-COV2 infection over the period studied were collected.\n\nResultsIn our study, the age range of patients was 25-75 with no significant male preponderance. The median age of LVO patients was 48. Stroke was the presenting and hospitalizing event in 70%. One fifth of patients did not have common risk factors for ischemic stroke and none had atrial fibrillation, coronary or cerebrovascular disease, or were smokers. Half had a poor outcome with 40% ending in mortality (60% in LVO group) and one in a critical condition due ARDS. All had high neutrophil/lymphocyte ratio except one who demonstrated some neurological recovery. D-dimer levels showed mild to severe elevation when collected. None of the LVO cases had known cardiac risk factors but two out of five were found to have cardiac abnormalities during their hospitalization. All LVOs had hypercoagulable lab markers especially elevated D-dimer and/or fibrinogen. The LVO patients were younger and sicker with a median age of 46 and mean NIHSS of 24 as opposed to non-LVOs with a median age of 62 and mean NIHSS of 6 respectively.\n\nConclusionCOVID-19 related ischemic events can be small vessel, branch emboli or large vessel occlusions. The latter is often associated with either a hypercoagulable state or cardio-embolism. Patient outcomes were worse when multi-organ or pulmonary system failure prevailed.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ketevan Berekashvili", + "author_inst": "Interventional Neuro Associates, New York University Langone health, Jamaical Hospital Medical Center, Brookdale University Hospital Medical Center, RIchmond Un" + }, + { + "author_name": "Adam A Dmytriw", + "author_inst": "Department of Medical Imaging, University of Toronto" + }, + { + "author_name": "Volodomyr Vulkanov", + "author_inst": "Brookdale University Hospital Medical Center" + }, + { + "author_name": "Shashank Agarwal", + "author_inst": "NYU langone health" + }, + { + "author_name": "Amit Khaneja", + "author_inst": "Jamaica Hospital Medical Center" + }, + { + "author_name": "David Turkel-Parella", + "author_inst": "Interventional Neuro Associates, NYU Langone health, Jamaical Hospital Medical Center, Brookdale University Hospital Medical Center, Richmond University Medical" + }, + { + "author_name": "Jeremy Liff", + "author_inst": "Interventional Neuro Assocates, NYU Langone health, Jamaical Hospital Medical Center, Brookdale University Hospital Medical Center, Richmond University Medical " + }, + { + "author_name": "Jeffrey Farkas", + "author_inst": "Interventional Neuro Associates, NYU Langone health, Jamaical Hospital Medical Center, Brookdale Unviersity Hospital Medical Center, Richmond University Medical" + }, + { + "author_name": "Thambirajah Nandakumar", + "author_inst": "Jamaica Hospital Medical Center" + }, + { + "author_name": "Ting Zhou", + "author_inst": "NYU Langone health" + }, + { + "author_name": "Jennnifer Frontera", + "author_inst": "Nyu Langone health" + }, + { + "author_name": "David E Kahn", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Sun Kim", + "author_inst": "NYU Langone health" + }, + { + "author_name": "Kelly A Humbert", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Matthew D Sanger", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Shadi Yaghi", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Aaron Lord", + "author_inst": "NYU Langone health" + }, + { + "author_name": "Karthikeyan Arcot", + "author_inst": "Interventional Neuro Associates, NYU Langone health, Jamaical Hospital Medical Center, Brookdaly University Hospital Medical Center, Richmond University Medical" + }, + { + "author_name": "Ambooj Tiwari", + "author_inst": "Interventional Neuro Associates, NYU Langone health, Jamaica Hospital Medical Center, Brookdale University Hospital Medical Center, Richmond University Medical" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.04.28.20083360", "rel_title": "Vitamin C for the treatment of COVID-19: A living systematic review", @@ -1462868,33 +1459831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.03.20089649", - "rel_title": "Impact of complete lock-down on total infection and death rates: A hierarchical cluster analysis", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089649", - "rel_abs": "Introduction and AimsRetarding the spread of SARS-CoV-2 infection by preventive strategies is the first line of management. Several countries have declared a stringent lock-down in order to enforce social distancing and prevent the spread of infection. This analysis was conducted in an attempt to understand the impact of lock-down on infection and death rates over a period of time.\n\nMaterial and MethodsA validated database was used to generate data related to countries with declared lock-down. Simple regression analysis was conducted to assess the rate of change in infection and death rates. Subsequently, a k-means and hierarchical cluster analysis was done to identify the countries that performed similarly. Sweden and South Korea were included as counties without lock-down in a second-phase cluster analysis.\n\nResultsThere was a significant 61% and 43% reduction in infection rates 1-week post lock-down in the overall and India cohorts, respectively, supporting its effectiveness. Countries with higher baseline infections and deaths fared poorly compared to those who declared lock-down early on. Sweden and South Korea fared equally well, as most lock-down countries stemmed the growth of infection and death.\n\nConclusionLock-down has proven to be an effective strategy is slowing down the SARS-CoV-2 disease progression exponentially. However, lessons need to be learned from Sweden and South Korea on arresting the disease progression without imposing such stringent measures.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "SAMIT GHOSAL", - "author_inst": "Nightingale Hospital" - }, - { - "author_name": "Rahul Bhattacharyya", - "author_inst": "Private Practitioner" - }, - { - "author_name": "Milan Majumder", - "author_inst": "Independent Statistician" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.03.20089342", "rel_title": "Temperature and relative humidity are not major contributing factor on the occurrence of COVID-19 pandemic: An observational study in 57 countries", @@ -1463695,6 +1460631,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.03.20084442", + "rel_title": "Rapid generation of neutralizing antibody responses in COVID-19 patients", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20084442", + "rel_abs": "SARS-CoV-2 is currently causing a devastating pandemic and there is a pressing need to understand the dynamics, specificity, and neutralizing potency of the humoral immune response during acute infection. Herein, we report the dynamics of antibody responses to the receptor-binding domain (RBD) of the spike protein and virus neutralization activity in 44 COVID-19 patients. RBD-specific IgG responses were detectable in all patients 6 days after PCR confirmation. Using a clinical isolate of SARS-CoV-2, neutralizing antibody titers were also detectable in all patients 6 days after PCR confirmation. The magnitude of RBD-specific IgG binding titers correlated strongly with viral neutralization. In a clinical setting, the initial analysis of the dynamics of RBD-specific IgG titers was corroborated in a larger cohort of PCR-confirmed patients (n=231). These findings have important implications for our understanding of protective immunity against SARS-CoV-2, the use of immune plasma as a therapy, and the development of much-needed vaccines.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew Zimmerman", + "author_inst": "Emory University" + }, + { + "author_name": "Robert Kauffman", + "author_inst": "Emory University" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Emory University" + }, + { + "author_name": "Susanne Linderman", + "author_inst": "Emory University" + }, + { + "author_name": "Abigail Vanderheiden", + "author_inst": "Emory University" + }, + { + "author_name": "Lindsay Nyhoff", + "author_inst": "Emory University" + }, + { + "author_name": "Carl Davis", + "author_inst": "Emory University" + }, + { + "author_name": "Seyi Adekunle", + "author_inst": "Emory University" + }, + { + "author_name": "Maurizio Affer", + "author_inst": "Emory University" + }, + { + "author_name": "Melanie Sherman", + "author_inst": "Emory University" + }, + { + "author_name": "Stacian Reynolds", + "author_inst": "Emory University" + }, + { + "author_name": "Hans Verkerke", + "author_inst": "Emory University" + }, + { + "author_name": "David N Alter", + "author_inst": "Emory University" + }, + { + "author_name": "Jeannette Guarner", + "author_inst": "Emory University" + }, + { + "author_name": "Janetta Bryksin", + "author_inst": "Emory University" + }, + { + "author_name": "Michael Horwath", + "author_inst": "Emory University" + }, + { + "author_name": "Connie Arthur", + "author_inst": "Emory University" + }, + { + "author_name": "Natia Saakadze", + "author_inst": "Emory University" + }, + { + "author_name": "Geoffrey Hughes Smith", + "author_inst": "Emory University" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "Emory University" + }, + { + "author_name": "Erin M Scherer", + "author_inst": "Emory University" + }, + { + "author_name": "Kieffer Hellmeister", + "author_inst": "Emory University" + }, + { + "author_name": "Andrew Cheng", + "author_inst": "Emory University" + }, + { + "author_name": "Juliet A Morales", + "author_inst": "Emory University" + }, + { + "author_name": "Andrew S Neish", + "author_inst": "Emory University" + }, + { + "author_name": "Sean R Stowell", + "author_inst": "Emory University" + }, + { + "author_name": "Filipp Frank", + "author_inst": "Emory University" + }, + { + "author_name": "Eric Ortlund", + "author_inst": "Emory University" + }, + { + "author_name": "Evan Anderson", + "author_inst": "Emory University" + }, + { + "author_name": "Vineet Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Aneesh Metha", + "author_inst": "Emory University" + }, + { + "author_name": "David S Stephens", + "author_inst": "Emory University" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Emory University" + }, + { + "author_name": "John Roback", + "author_inst": "Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.04.20084657", "rel_title": "SARS-CoV-2 detection in setting of viral swab scarcity: are MRSA swabs and viral swabs equivalent?", @@ -1464426,41 +1461525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20090639", - "rel_title": "Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090639", - "rel_abs": "Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between February 28 and March 20. Estimates of the impact of these interventions on SARS-CoV-2 transmission are critical for decision making in this and future outbreaks. We here aim to assess the impact of these NPIs on disease transmission by estimating changes in the basic reproduction number (R0) at national and cantonal levels in relation to the timing of these NPIs. We estimate the time-varying R0 nationally and in twelve cantons by fitting a stochastic transmission model explicitly simulating within hospital dynamics. We use individual-level data of >1,000 hospitalized patients in Switzerland and public daily reports of hospitalizations and deaths. We estimate the national R0 was 3.15 (95% CI: 2.13-3.76) at the start of the epidemic. Starting from around March 6, we find a strong reduction in R0 with a 85% median decrease (95% quantile range, QR: 83%-90%) to a value of 0.44 (95% QR: 0.27-0.65) in the period of March 29-April 5. At the cantonal-level R0 decreased over the course of the epidemic between 71% and 94%. We found that reductions in R0 were synchronous with changes in mobility patterns as estimated through smartphone activity, which started before the official implementation of NPIs. We found that most of the reduction of transmission is due to behavioural changes as opposed to natural immunity, the latter accounting for only about 3% of the total reduction in effective transmission. As Switzerland considers relaxing some of the restrictions of social mixing, current estimates of R0 well below one are promising. However most of inferred transmission reduction was due to behaviour change (<3% due to natural immunity buildup), with an estimated 97% (95% QR: 96.6%-97.2%) of the Swiss population still susceptible to SARS-CoV-2 as of April 24. These results warrant a cautious relaxation of social distance practices and close monitoring of changes in both the basic and effective reproduction numbers.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Joseph Chadi Lemaitre", - "author_inst": "EPFL" - }, - { - "author_name": "Javier Perez-Saez", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Andrew Azman", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Andrea Rinaldo", - "author_inst": "EPFL" - }, - { - "author_name": "Jacques Fellay", - "author_inst": "EPFL" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20090258", "rel_title": "Safe Blues: A Method for Estimation and Control in the Fight Against COVID-19", @@ -1464813,6 +1461877,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091363", + "rel_title": "COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2", + "rel_date": "2020-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091363", + "rel_abs": "The ongoing SARS-CoV-2 pandemic has caused large outbreaks around the world and every heavily affected community has experienced a substantial strain on the health care system and a high death toll. Communities therefore have to monitor the incidence of COVID-19 carefully and attempt to project the demand for health care. To enable such projections, we have developed an interactive web application that simulates an age-structured SEIR model with separate compartments for severely and critically ill patients. The tool allows the users to modify most parameters of the model, including age specific assumptions on severity. Infection control and mitigation measures that reduce transmission can be specified, as well as age-group specific isolation.\n\nThe simulation of the model runs entirely on the client side in the browser; all parameter settings and results of the simulation can be exported for further downstream analysis. The tool is available at covid19-scenarios.org and the source code at github.com/neherlab/covid19_scenarios.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Nicholas B Noll", + "author_inst": "University of Basel" + }, + { + "author_name": "Ivan Aksamentov", + "author_inst": "University of Basel" + }, + { + "author_name": "Valentin Druelle", + "author_inst": "Biozentrum - University of Basel" + }, + { + "author_name": "Abrie Badenhorst", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Bruno Ronzani", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Gavin Jefferies", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Jan Albert", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Richard Neher", + "author_inst": "University of Basel" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20077743", "rel_title": "A non-competing pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2", @@ -1466027,81 +1463138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.04.20090878", - "rel_title": "The disproportionate rise in COVID-19 cases among Hispanic/Latinx in disadvantaged communities of Orange County, California: A socioeconomic case-series", - "rel_date": "2020-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090878", - "rel_abs": "BackgroundRecent epidemiological evidence has demonstrated a higher rate of COVID-19 hospitalizations and deaths among minorities. This pattern of race-ethnic disparities emerging throughout the United States raises the question of what social factors may influence spread of a highly transmissible novel coronavirus. The purpose of this study is to describe race-ethnic and socioeconomic disparities associated with COVID-19 in patients in our community in Orange County, California and understand the role of individual-level factors, neighborhood-level factors, and access to care on outcomes.\n\nMethodsThis is a case-series of COVID-19 patients from the University of California, Irvine (UCI) across six-weeks between 3/12/2020 and 4/22/2020. Note, Californias shelter-in-place order began on 3/19/2020. Individual-level factors included race-ethnicity status were recorded. Neighborhood-level factors from census tracts included median household income, mean household size, proportion without a college degree, proportion working from home, and proportion without health insurance were also recorded.\n\nResultsA total of 210-patients tested were COVID-19 positive, of which 73.3% (154/210) resided in Orange County. Hispanic/Latinx patients residing in census tracts below the median income demonstrated exponential growth (rate = 55.9%, R2 = 0.9742) during the study period. In addition, there was a significant difference for both race-ethnic (p < 0.001) and income bracket (p = 0.001) distributions prior to and after Californias shelter-in-place. In addition, the percentage of individuals residing in neighborhoods with denser households (p = 0.046), lower levels of college graduation (p < 0.001), health insurance coverage (p = 0.01), and ability to work from home (p < 0.001) significantly increased over the same timeframe.\n\nConclusions and RelevanceOur study examines the race-ethnic disparities in Orange County, CA, and highlights vulnerable populations that are at increased risk for contracting COVID-19. Our descriptive case series illustrates that we also need to consider socioeconomic factors, which ultimately set the stage for biological and social disparities.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Daniel S Chow", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Jennifer Soun", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Justin Gavis-Bloom", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Brent Weinberg", - "author_inst": "Emory University" - }, - { - "author_name": "Peter Chang", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Simukayi Mutasa", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Edwin Monuki", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Jung In Park", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Xiaohui Xie", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Daniela Bota", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Jie Wu", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Leslie Thompson", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Alpesh Amin", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Saahir Khan", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Bernadette Boden-Albala", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.04.20090746", "rel_title": "Urban Air Pollution May Enhance COVID-19 Case-Fatality and Mortality Rates in the United States", @@ -1466554,6 +1463590,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20088237", + "rel_title": "Associations of stay-at-home order and face-masking recommendation with trends in daily new cases and deaths of laboratory-confirmed COVID-19 in the United States", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20088237", + "rel_abs": "Background and objectivesPublic health interventions were associated with reduction in coronavirus disease 2019 (COVID-19) transmission in China, but their impacts on COVID-19 epidemiology in other countries are unclear. We examined the associations of stay-at-home order (SAHO) and face-masking recommendation with epidemiology of laboratory-confirmed COVID-19 in the United States.\n\nMethodsIn this quasi-experimental study, we modeled the temporal trends in daily new cases and deaths of COVID-19, and COVID-19 time-varying reproduction numbers (Rt) in the United States between March 1 and April 20, 2020, and conducted simulation studies.\n\nResultsThe number and proportion of U.S. residents under SAHO increased between March 19 and April 7, and plateaued at 29,0829,980 and 88.6%, respectively. Trends in COVID-19 daily cases and Rt reduced after March 23 (P<0.001) and further reduced on April 3 (P<0.001), which was associated with implementation of SAHO by 10 states on March 23, and face-masking recommendation on April 3, respectively. The estimates of Rt eventually fell below/around 1.0 on April 13. Similar turning points were identified in the trends of daily deaths with a lag time. Early implementation and early-removal of SAHO would be associated with significantly reduced and increased daily new cases and deaths, respectively.\n\nConclusionsThere were 2 turning points of COVID-19 daily new cases or deaths in the U.S., which appeared to associate with implementation of SAHO and the CDCs face-masking recommendation. These findings may inform decision-making of lifting SAHO and face-masking recommendation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jie Xu", + "author_inst": "Shanghai Ninth Hospital, Shanghai, China" + }, + { + "author_name": "Sabiha Hussain", + "author_inst": "Rutgers University" + }, + { + "author_name": "Guanzhu Lu", + "author_inst": "Shanghai Ninth Hospital, Shanghai, China" + }, + { + "author_name": "Kai Zheng", + "author_inst": "Department of Informatics, Donald Bren School of Information and Computer Sciences, University of California, Irvine, CA" + }, + { + "author_name": "Shi Wei", + "author_inst": "University of Alabama at Birmingham, AL" + }, + { + "author_name": "Wei Bao", + "author_inst": "University of Iowa" + }, + { + "author_name": "Lanjing Zhang", + "author_inst": "Princeton Medical Center/Rutgers University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20088591", "rel_title": "Predictive mathematical models for the number of individuals infected with COVID-19", @@ -1467361,29 +1464440,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.05.079087", - "rel_title": "SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage", - "rel_date": "2020-05-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079087", - "rel_abs": "Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andres M Alonso", - "author_inst": "CONICET" - }, - { - "author_name": "Luis Diambra", - "author_inst": "UNLP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.03.20081380", "rel_title": "FACTORS INFLUENCING MENTAL HEALTH DURING COVID-19 OUTBREAK: AN EXPLORATORY SURVEY AMONG INDIAN POPULATION", @@ -1467984,6 +1465040,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.02.20089094", + "rel_title": "Clinical characteristics and fecal-oral transmission potential of patients with COVID-19", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20089094", + "rel_abs": "BackgroundA significant proportion of patients with COVID-19 generate negative pharyngeal swab viral nucleic acid test results but test positive using fecal samples. However, fecal-oral transmission of COVID-19 has not been established to date. The purpose of this study was to evaluate the duration of fecal swab positivity in COVID-19 patients after pharyngeal swab nucleic acid test turned negative and to explore its potential for fecal-oral transmission.\n\nMethodsA retrospective analysis of clinical records, laboratory results, and chest computed tomography (CT) findings of 17 COVID-19 patients confirmed by laboratory tests from January 22 to February 7, 2020 at a tertiary hospital was performed. The potential of fecal-oral transmission was assessed by detecting the presence of SARS-CoV-2 nucleic acid in fecal swab samples.\n\nResultsA total of 16 patients (94.1%) had fever; other symptoms included dry cough, dyspnea, nausea, diarrhea, sore throat, fatigue, and muscle pain. Three patients had decreased white blood cell counts, 7 had decreased lymphocyte numbers, and 7 had increased C-reactive protein levels. Fecal samples of 11 patients tested positive for SARS-CoV-2 nucleic acid, of whom the time for the fecal samples to become SARS-CoV-2 nucleic acid-negative was longer in 10 patients than that for pharyngeal swab samples, and only one case exhibited a shorter time for his fecal sample to become SARS-CoV-2 nucleic acid-negative compared to his pharyngeal swab sample. The remaining 6 patients were negative for SARS-CoV-2 nucleic acid in fecal samples.\n\nConclusionIn COVID-19 patients who tested positive for SARS-CoV-2 nucleic acid in both pharyngeal swab and fecal samples, the time for the fecal samples to become SARS-CoV-2 nucleic acid-negative was generally longer than that in pharyngeal swab samples. However, there is currently no evidence demonstrating that the virus can be transmitted through the fecal-oral route.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Saibin Wang", + "author_inst": "Jinhua Municipal Central Hospital" + }, + { + "author_name": "Junwei Tu", + "author_inst": "Jinhua Municipal Central Hospital" + }, + { + "author_name": "Yijun Sheng", + "author_inst": "Jinhua Municipal Central Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089201", "rel_title": "A note on COVID-19 seroprevalence studies: a meta-analysis using hierarchical modelling", @@ -1468851,49 +1465934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.01.20087031", - "rel_title": "Cancer is associated with the severity and mortality of patients with COVID-19: a systematic review and meta-analysis", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087031", - "rel_abs": "BackgroundCancer patients are considered a highly vulnerable population in the COVID-19 epidemic, but the relationship between cancer and the severity and mortality of patients with COVID-19 remains unclear. This study aimed to explore the prevalence of cancer in patients with COVID-19 and to examine whether cancer patients with COVID-19 may be at an increased risk of severe illness and mortality.\n\nMethodsA comprehensive electronic search in seven databases was performed, to identified studies reporting the prevalence of cancer in COVID-19 patients, or providing data of cancer between patients with severe or non-severe illness or between non-survivors and survivors. Meta-analyses were performed to estimate the pooled prevalence and odds risk (OR) using the inverse variance method with the random-effects model.\n\nResultsThirty-four studies with 8080 patients were included. The pooled prevalence of cancer in patients with COVID-19 was 2.0% (95% CI: 2.0% to 3.0%). The prevalence in Italy (5.0%), France (6.0%), and Korea (4.0%) were higher than that in China (2.0%). Cancer was associated with a 2.84-fold significantly increased risk of severe illness (OR = 2.84, 95%CI: 1.75 to 4.62, P < 0.001) and a 2.60-fold increased risk of death (OR = 2.60, 95%CI: 1.28 to 5.26, P = 0.008) in patients with COVID-19. Sensitivity analyses showed that the results were stable after excluding studies with a sample size of less than 100.\n\nConclusionsCancer patients have an increased risk of COVID-19 and cancer was associated with a significantly increased risk of severity and mortality of patients with COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ya Gao Sr.", - "author_inst": "Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Ming Liu Sr.", - "author_inst": "Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Shuzhen Shi", - "author_inst": "Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Yamin Chen", - "author_inst": "Evidence-Based Nursing Center, School of Nursing, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Yue Sun", - "author_inst": "Evidence-Based Nursing Center, School of Nursing, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Ji Chen", - "author_inst": "Evidence-Based Nursing Center, School of Nursing, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Jinhui Tian Sr.", - "author_inst": "Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.05.01.20087080", "rel_title": "Early phases of COVID-19 are characterized by a reduction of lymphocyte populations and the presence of atypical monocytes", @@ -1469530,6 +1466570,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.05.01.20087684", + "rel_title": "Identification of IgG antibody response to SARS-CoV-2 spike protein and its receptor binding domain does not predict rapid recovery from COVID-19", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087684", + "rel_abs": "Diagnostic testing and evaluation of patient immunity against the novel severe acute respiratory syndrome (SARS) corona virus that emerged last year (SARS-CoV-2) are essential for health and economic crisis recovery of the world. It is suggested that potential acquired immunity against SARS-CoV-2 from prior exposure may be determined by detecting the presence of circulating IgG antibodies against viral antigens, such as the spike glycoprotein and its receptor binding domain (RBD). Testing our asymptomatic population for evidence of COVID-19 immunity would also offer valuable epidemiologic data to aid health care policies and health care management. Currently, there are over 100 antibody tests that are being used around the world without approval from the FDA or similar regulatory bodies, and they are mostly for rapid and qualitative assessment, with different degrees of error rates. ELISA-based testing for sensitive and rigorous quantitative assessment of SARS-CoV-2 antibodies can potentially offer mechanistic insights into the COVID-19 disease and aid communities uniquely challenged by limited financial resources and access to commercial testing products. Employing recombinant SARS-CoV-2 RBD and spike protein generated in the laboratory, we devised a quantitative ELISA for the detection of circulating serum antibodies. Serum from twenty SARS-CoV-2 RT-PCR confirmed COVID-19 hospitalized patients were used to detect circulating IgG titers against SARS-CoV-2 spike protein and RBD. Quantitative detection of IgG antibodies to the spike glycoprotein or the RBD in patient samples was not always associated with faster recovery, compared to patients with borderline antibody response to the RBD. One patient who did not develop antibodies to the RBD completely recovered from COVID-19. In surveying 99 healthy donor samples (procured between 2017-February 2020), we detected RBD antibodies in one donor from February 2020 collection with three others exhibiting antibodies to the spike protein but not the RBD. Collectively, our study suggests that more rigorous and quantitative analysis, employing large scale samples sets, is required to determine whether antibodies to SARS-CoV-2 spike protein or RBD is associated with protection from COVID-19 disease. It is also conceivable that humoral response to SARS-CoV-2 spike protein or RBD works in association with adaptive T cell response to determine clinical sequela and severity of COVID-19 disease.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kathleen M McAndrews", + "author_inst": "MD Anderson Cancer Center" + }, + { + "author_name": "Dara P Dowlatshahi", + "author_inst": "MD Anderson Cancer Center" + }, + { + "author_name": "Janine Hensel", + "author_inst": "MD Anderson Cancer Center" + }, + { + "author_name": "Luis L Ostrosky-Zeichner", + "author_inst": "Memorial Hermann Texas Medical Center" + }, + { + "author_name": "Ramesh Papanna", + "author_inst": "UT Medical School at Houston" + }, + { + "author_name": "Valerie S LeBleu", + "author_inst": "MD Anderson Cancer Center" + }, + { + "author_name": "Raghu Kalluri", + "author_inst": "MD Anderson Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.01.20087650", "rel_title": "Control dynamics of the COVID-19 pandemic in China and South Korea", @@ -1470137,77 +1467220,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.01.20087494", - "rel_title": "COVID-19 AND PATIENTS UNDERGOING PHARMACOLOGICAL TREATMENTS FOR IMMUNE-MEDIATED INFLAMMATORY DISEASES: PROTOCOL FOR A RAPID LIVING SYSTEMATIC REVIEW", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087494", - "rel_abs": "CONTEXT AND OBJECTIVEWe propose to systematically review the available evidence to evaluate if patients with immune mediated inflammatory diseases under pharmacological treatment with immunosuppressants, immunobiologics, Disease-Modifying Anti-Rheumatic Drugs (DMARD) or targeted synthetic DMARDs have better or worse outcomes when infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study is a protocol for our rapid living systematic review. METHODS: Protocol for a rapid living systematic review methodology following the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) guidance. To conduct the rapid systematic review, we will employ abbreviated systematic review methods, including: not performing independent screens of abstracts and not searching grey literature. As this will be a living review, it will be continuously updated.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Aline Pereira Rocha", - "author_inst": "Universidade Federal de Sao Paulo/Cochrane Brazil" - }, - { - "author_name": "Alvaro Nagib Atallah", - "author_inst": "Universidade Federal de Sao Paulo/ Cochrane Brazil" - }, - { - "author_name": "Ana Carolina Pereira Nunes Pinto", - "author_inst": "Universidade Federal do Amapa/Universidade Federal de Sao Paulo/Cochrane Brazil" - }, - { - "author_name": "Cesar Ramos Rocha Filho", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Felipe Sebastiao de Assis Reis", - "author_inst": "Beneficencia Portuguesa-SP" - }, - { - "author_name": "Keilla Machado Martins Milby", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Vinicius Tassoni Civile", - "author_inst": "Universidade Federal de Sao Paulo/Universidade Paulista/Cochrane Brazil" - }, - { - "author_name": "Nelson Carvas Junior", - "author_inst": "Universidade Ibirapuera" - }, - { - "author_name": "Rodolfo Rodrigo Pereira Santos", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Laura Jantsch Ferla", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Giulia Fernandes Moca Trevisani", - "author_inst": "Universidade Santo Amaro" - }, - { - "author_name": "Gabriel Sodre Ramalho", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Maria Eduarda dos Santos Puga", - "author_inst": "Universidade Federal de Sao Paulo" - }, - { - "author_name": "Virginia Fernandes Moca Trevisani", - "author_inst": "Universidade Federal de Sao Paulo/Universidade Santo Amaro" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2020.05.01.20087973", "rel_title": "COVID-19 Utilization and Resource Visualization Engine (CURVE) to Forecast In-Hospital Resources", @@ -1470976,6 +1467988,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.04.29.20085621", + "rel_title": "Is Hydroxychloroquine Safe During Pregnancy? Observations from Penn Medicine", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085621", + "rel_abs": "A novel strain of coronavirus appeared in December 2019. Over the next few months, this novel coronavirus spread throughout the world, being declared a pandemic by the World Health Organization on March 11, 2020. As of this writing (March 28, 2020) over one hundred thousand individuals in the United States of America were confirmed cases. One way of treating the associated disease, COVID-19, is to reuse existing FDA-approved medications. One medication that has shown promise is hydroxychloroquine (HCQ). However, the utility and safety of HCQ among pregnant COVID-19 patients remains a concern.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lena Davidson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Silvia Canelon", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mary Regina Boland", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20088302", "rel_title": "Management and Outcomes of ST-segment Elevation Myocardial Infarction During Coronavirus 2019 Pandemic in a Center with 24/7 Primary Angioplasty Capability: Should We Change Our Practice During Outbreak?", @@ -1471819,33 +1468858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.29.20085761", - "rel_title": "Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: an Exploratory Randomized, Controlled Trial", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085761", - "rel_abs": "BackgroundEffective antiviral drugs for COVID-19 are still lacking. This study aims to evaluate the clinical outcomes and plasma concentrations of baloxavir marboxil and favipiravir in COVID-19 patients.\n\nMethodsFavipiravir and baloxavir acid were evaluated for their antiviral activity against SARS-CoV-2 in vitro before the trial initiation. We conducted an exploratory trial with 3 arms involving hospitalized adult patients with COVID-19. Patients were randomized assigned in a 1:1:1 ratio into baloxavir marboxil group, favipiravir group, and control group. The primary outcome was the percentage of subjects with viral negative by Day 14 and the time from randomization to clinical improvement. Virus load reduction, blood drug concentration and clinical presentation were also observed. The trial was registered with Chinese Clinical Trial Registry (ChiCTR 2000029544).\n\nResultsBaloxavir showed antiviral activity in vitro with the half-maximal effective concentration (EC50) of 5.48 {micro}M comparable to arbidol and lopinavir, but favipiravir didnt demonstrate significant antiviral activity up to 100 {micro}M. Thirty patients were enrolled. The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. One reason for the lack of virological effect and clinical benefits may be due to insufficient concentrations of these drugs relative to their antiviral activities.\n\nConclusionsOur findings do not support that adding either baloxavir or favipiravir under the trial dosages to the existing standard treatment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yan Lou", - "author_inst": "Zhejiang University School of Medicine First Affiliated Hospital" - }, - { - "author_name": "Lin Liu", - "author_inst": "Zhejiang University School of Medicine First Affiliated Hospital" - }, - { - "author_name": "Yunqing Qiu", - "author_inst": "Zhejiang University School of Medicine First Affiliated Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.04.29.20085787", "rel_title": "A systematic review to evaluate the clinical outcomes in COVID -19 patients on angiotensin converting enzyme inhibitors or angiotensin receptor blockers", @@ -1472426,6 +1469438,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.30.20086108", + "rel_title": "A clinical and biological framework on the role of visceral fat tissue and leptin in SARS-CoV-2 infection related respiratory failure", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086108", + "rel_abs": "Obesity is a risk factor for SARS-CoV-2 infected patients to develop respiratory failure. Leptin produced in visceral fat might play a role in the deterioration to mechanical ventilation. A cross sectional study was performed. The mean BMI was 31 kg/m2 (range 24.8 - 48.4) for the 31 SARS-CoV-2 ventilated patients and 26 kg/m2 (range 22.4-33.5) for the 8 controls. SARS-CoV-2 infected patients with a similar BMI as control patients appear to have significantly higher levels of serum leptin. The mean leptin level was 21.2 (6.0-85.2) vs 5.6 (2.4-8.2) ug/L for SARS-CoV-2 and controls respectively (p=0.0007). With these findings we designed a clinical and biological framework that explains clinical observations. The ACE2 utilization by the virus leads to local pulmonary inflammation due to ACE2-ATII disbalance. This is enhanced by an increase in leptin production induced by SARS-CoV-2 infection of visceral fat. Leptin receptors in the lungs are now more activated to enhance local pulmonary inflammation. This adds to the pre-existent chronic inflammation in obese patients. Visceral fat, lung tissue and leptin production play an interconnecting role. This insight can lead the way to further research and treatment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Peter van der Voort", + "author_inst": "UMCG" + }, + { + "author_name": "Jill Moser", + "author_inst": "UMCG" + }, + { + "author_name": "Durk F Zandstra", + "author_inst": "None" + }, + { + "author_name": "Anneke C Muller Kobold", + "author_inst": "UMCG" + }, + { + "author_name": "Marjolein Knoester", + "author_inst": "UMCG" + }, + { + "author_name": "Cornelis F Calkhoven", + "author_inst": "UMCG" + }, + { + "author_name": "Inge Hamming", + "author_inst": "None" + }, + { + "author_name": "Matijs van Meurs", + "author_inst": "UMCG" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.04.29.20085407", "rel_title": "Elevated D-Dimer Levels are Associated with Increased Risk of Mortality in COVID-19: A Systematic Review and Meta-Analysis", @@ -1473177,65 +1470236,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20086736", - "rel_title": "Neutrophil extracellular traps and thrombosis in COVID-19", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086736", - "rel_abs": "BackgroundEarly studies of patients with COVID-19 have demonstrated markedly dysregulated coagulation and a high risk of morbid arterial and venous thrombotic events. While elevated levels of blood neutrophils and neutrophil extracellular traps (NETs) have been described in patients with COVID-19, their potential role in COVID-19-associated thrombosis remains unknown.\n\nObjectivesTo elucidate the potential role of hyperactive neutrophils and NET release in COVID-19-associated thrombosis.\n\nPatients/MethodsThis is a retrospective, case-control study of patients hospitalized with COVID-19 who developed thrombosis (n=11), as compared with gender- and age-matched COVID-19 patients without clinical thrombosis (n=33). In addition to capturing clinical data, we measured remnants of NETs (cell-free DNA, myeloperoxidase-DNA complexes, and citrullinated histone H3) and neutrophil-derived S100A8/A9 (calprotectin) in patient sera.\n\nResultsThe majority of patients (9/11) were receiving at least prophylactic doses of heparinoids at the time thrombosis was diagnosed. As compared with controls, patients with COVID-19-associated thrombosis had significantly higher blood levels of markers of NETs (cell-free DNA, myeloperoxidase-DNA complexes, citrullinated histone H3) and neutrophil activation (calprotectin). The thrombosis group also had higher levels of D-dimer, CRP, ferritin, and platelets, but not troponin or neutrophils. Finally, there were strong associations between markers of hyperactive neutrophils (calprotectin and cell-free DNA) and D-dimer.\n\nConclusionElevated levels of neutrophil activation and NET formation in patients hospitalized with COVID-19 are associated with higher risk of morbid thrombotic complications. These observations underscore the need for urgent investigation into the potential relationship between NETs and unrelenting thrombosis in COVID-19.\n\nESSENTIALSO_LIMechanisms contributing to frequent thrombosis in COVID-19 remain unknown\nC_LIO_LINETs and neutrophil activation were measured in patients with COVID-19 -associated thrombosis\nC_LIO_LIThrombosis in COVID-19 was associated with higher levels of circulating NETs and calprotectin\nC_LIO_LIContributions of neutrophils and NETs to thrombosis in COVID-19 warrant urgent investigation\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yu Zuo", - "author_inst": "University of Michigan" - }, - { - "author_name": "Melanie Zuo", - "author_inst": "University of Michigan" - }, - { - "author_name": "Srilakshmi Yalavarthi", - "author_inst": "University of Michigan" - }, - { - "author_name": "Kelsey Gockman", - "author_inst": "University of Michigan" - }, - { - "author_name": "Jacqueline A. Madison", - "author_inst": "University of Michigan" - }, - { - "author_name": "Hui Shi", - "author_inst": "University of Michigan" - }, - { - "author_name": "Wrenn Woodard", - "author_inst": "University of Michigan" - }, - { - "author_name": "Sean P. Lezak", - "author_inst": "University of Michigan" - }, - { - "author_name": "Njira L. Lugogo", - "author_inst": "University of Michigan" - }, - { - "author_name": "Jason S. Knight", - "author_inst": "University of Michigan" - }, - { - "author_name": "Yogendra Kanthi", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.30.20086181", "rel_title": "A Simple Method for Estimating the Number of Unconfirmed COVID-19 Cases in a Local Area that Includes a Confidence Interval: A Case Study of Whatcom County, Washington", @@ -1473708,6 +1470708,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.05.078238", + "rel_title": "Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses", + "rel_date": "2020-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.078238", + "rel_abs": "Within four months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in the ORF1 of the virus isolated from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of nonsynonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerated sites towards uracil residues is seen in ORF1 of all the studied coronaviruses. A more substantial mutational U pressure is observed in ORF1a than in ORF1b owing to the translation of ORF1ab via programmed ribosomal frameshifting. Unlike other nucleotide mutations, mutational U pressure caused by cytosine deamination, mostly occurring in the RNA-plus strand, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the direction of mutational pressure during translation of viral RNA-plus strands has implications for vaccine and nucleoside analogue development for treating covid-19 and other coronavirus infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Vladislav Victorovich Khrustalev", + "author_inst": "Belarusian State Medical University" + }, + { + "author_name": "Rajanish Giri", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Tatyana Aleksandrovna Khrustaleva", + "author_inst": "Institute of Physiology of the National Academy of Sciences of Belarus" + }, + { + "author_name": "Shivani Krishna Kapuganti", + "author_inst": "Indian Institute of Technology Mandi" + }, + { + "author_name": "Aleksander Nicolaevich Stojarov", + "author_inst": "Belarusian State Medical University" + }, + { + "author_name": "Victor Vitoldovich Poboinev", + "author_inst": "Belarusian State Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.05.078956", "rel_title": "Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV", @@ -1474459,33 +1471498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.28.20083675", - "rel_title": "BRAZIL IS PROJECTED TO BE THE NEXT GLOBAL COVID-19 PANDEMIC EPICENTER", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083675", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a disease triggered by SARS-CoV-2 infection, which is related in the most recent pandemic situation, significantly affecting health and economic systems. In this study we assessed the death rate associated to COVID-19 in Brazil and the United States of America (USA) to estimate the probability of Brazil becoming the next pandemic epicenter. We equated data between Brazil and USA obtained through the Worldometer website (www.worldometer.info). Epidemic curves from Brazil and USA were associated and regression analysis was undertaken to predict the Brazilian death rate regarding COVID-19 in June. In view of data from April 9th 2020, death rates in Brazil follow a similar exponential increase to USA (r=0.999; p<0.001), estimating 64,310 deaths by June 9th 2020. In brief, our results demonstrated that Brazil follows an analogous progression of COVID-19 deaths cases when compared to USA, signifying that Brazil could be the next global epicenter of COVID-19. We highlight public strategies to decrease the COVID-19 outbreak.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pedro de Lemos Menezes", - "author_inst": "University of Health Sciences of Alagoas, AL, Brazil" - }, - { - "author_name": "David M. Garner", - "author_inst": "Cardiorespiratory Research Group, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington Camp" - }, - { - "author_name": "Vitor E Valenti", - "author_inst": "SaoPaulo State University, UNESP, Marilia, SP, Brazil." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.04.28.20083956", "rel_title": "Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative", @@ -1475178,6 +1472190,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.28.20083840", + "rel_title": "Effect of ethanol cleaning on the permeability of FFP2 mask", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083840", + "rel_abs": "In this study we assessed the effect of ethanol on the filtering properties of FFP2 masks. The permeability of parts of a FFP2 mask was measured before and after six cleanings with ethanol. As for any porous medium, the filtering properties of a mask are related to the size and tortuosity of the pores of the filter, and are quantified by its permeability. Any damage to the filter will change its permeability. We show here that after six cleaning cycles, the permeability remains very close to the permeability before cleaning. Amid the COVID-19 pandemic and the shortage of protective masks, this study suggests that ethanol could be used to sanitize a FFP2 mask without significantly altering its filtering properties. Additional measurements on FFP2 and N95 masks from different manufacturers need to be performed to validate this study.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Roland Lenormand", + "author_inst": "CYDAREX" + }, + { + "author_name": "Guillaume Lenormand", + "author_inst": "CYDAREX" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.30.20083907", "rel_title": "First case of placental infection with SARS-CoV-2", @@ -1476077,113 +1473112,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.079194", - "rel_title": "Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention", - "rel_date": "2020-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079194", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health threat with more than two million infected people since its emergence in late 2019. Detailed knowledge of the molecular biology of the infection is indispensable for understanding of the viral replication, host responses, and disease progression. We provide gene expression profiles of SARS-CoV and SARS-CoV-2 infections in three human cell lines (H1299, Caco-2 and Calu-3 cells), using bulk and single-cell transcriptomics. Small RNA profiling showed strong expression of the immunity and inflammation-associated microRNA miRNA-155 upon infection with both viruses. SARS-CoV-2 elicited approximately two-fold higher stimulation of the interferon response compared to SARS-CoV in the permissive human epithelial cell line Calu-3, and induction of cytokines such as CXCL10 or IL6. Single cell RNA sequencing data showed that canonical interferon stimulated genes such as IFIT2 or OAS2 were broadly induced, whereas interferon beta (IFNB1) and lambda (IFNL1-4) were expressed only in a subset of infected cells. In addition, temporal resolution of transcriptional responses suggested interferon regulatory factors (IRFs) activities precede that of nuclear factor-{kappa}B (NF-{kappa}B). Lastly, we identified heat shock protein 90 (HSP90) as a protein relevant for the infection. Inhibition of the HSP90 charperone activity by Tanespimycin/17-N-allylamino-17-demethoxygeldanamycin (17-AAG) resulted in a reduction of viral replication, and of TNF and IL1B mRNA levels. In summary, our study established in vitro cell culture models to study SARS-CoV-2 infection and identified HSP90 protein as potential drug target for therapeutic intervention of SARS-CoV-2 infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Emanuel Wyler", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Kirstin M\u00f6sbauer", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Vedran Franke", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Asija Diag", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Lina Theresa Gottula", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Roberto Arsie", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Filippos Klironomos", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association; Department of Pediatrics, Charite - Unive" - }, - { - "author_name": "David Koppstein", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Salah Ayoub", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Christopher Buccitelli", - "author_inst": "Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Anja Richter", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Ivano Legnini", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Andranik Ivanov", - "author_inst": "Core Unit Bioinformatics, Berlin Institute of Health, Charite - University Hospital Berlin" - }, - { - "author_name": "Tommaso Mari", - "author_inst": "Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Simone Del Giudice", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Jan Patrick Papies", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Marcel Alexander M\u00fcller", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Daniela Niemeyer", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Matthias Selbach", - "author_inst": "Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Altuna Akalin", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Nikolaus Rajewsky", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin and Berlin Institute of Health" - }, - { - "author_name": "Markus Landthaler", - "author_inst": "Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.02.20084673", "rel_title": "Disruption of the CCL5/RANTES-CCR5 Pathway Restores Immune Homeostasis and Reduces Plasma Viral Load in Critical COVID-19", @@ -1476804,6 +1473732,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20064279", + "rel_title": "Population vulnerability to COVID-19 in Europe: a burden of disease analysis", + "rel_date": "2020-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20064279", + "rel_abs": "BackgroundEvidence has emerged showing that elderly people and those with pre-existing chronic health conditions may be at higher risk of developing severe health consequences from COVID-19. In Europe, this is of particular relevance with ageing populations living with non-communicable diseases, multi-morbidity and frailty. Published estimates of Years Lived with Disability (YLD) from the Global Burden of Disease (GBD) study help to characterise the extent of these effects. Our aim was to identify the countries across Europe that have populations at highest risk from COVID-19 by using estimates of population age structure and YLD for health conditions linked to severe illness from COVID-19.\n\nMethodsPopulation and YLD estimates from GBD 2017 were extracted for 45 countries in Europe. YLD was restricted to a list of specific health conditions associated with being at risk of developing severe consequences from COVID-19 based on guidance from the United Kingdom Government. This guidance also identified individuals aged 70 years and above as being at higher risk of developing severe health consequences. Study outcomes were defined as: (i) proportion of population aged 70 years and above; and (ii) rate of YLD for COVID-19 for vulnerable health conditions across all ages. Bivariate groupings were established for each outcome and combined to establish overall population-level vulnerability.\n\nResultsCountries with the highest proportions of elderly residents were Italy, Greece, Germany, Portugal and Finland. When assessments of population-level YLD rates for COVID-19 vulnerable health conditions were made the highest rates were observed for Bulgaria, Czech Republic, Croatia, Hungary and Bosnia and Herzegovina. A bivariate analysis indicated that the countries at high-risk across both measures of vulnerability were: Bulgaria; Portugal; Latvia; Lithuania; Greece; Germany; Estonia; and Sweden.\n\nConclusionRoutine estimates of population structures and non-fatal burden of disease measures can be usefully combined to create composite indicators of vulnerability for rapid assessments, in this case to severe health consequences from COVID-19. Countries with available results for sub-national regions within their country, or national burden of disease studies that also use sub-national levels for burden quantifications, should consider using non-fatal burden of disease estimates to estimate geographical vulnerability to COVID-19.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Grant MA Wyper", + "author_inst": "Public Health Scotland, Scotland, United Kingdom" + }, + { + "author_name": "Ricardo MA Assuncao", + "author_inst": "Food and Nutrition, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal" + }, + { + "author_name": "Sarah Cuschieri", + "author_inst": "Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida, Malta" + }, + { + "author_name": "Brecht Devleeschauwer", + "author_inst": "Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium" + }, + { + "author_name": "Eilidh Fletcher", + "author_inst": "Public Health Scotland, Scotland, United Kingdom" + }, + { + "author_name": "Juanita A Haagsma", + "author_inst": "Department of Public Health, Erasmus MC University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Henk Hilderink", + "author_inst": "Centre for Public Health Forecasting, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" + }, + { + "author_name": "Jane Idavain", + "author_inst": "National Institute for Health Development, Hiiu, Tallinn, Estonia" + }, + { + "author_name": "Tina Lesnik", + "author_inst": "National Institute of Public Health, Ljubljana, Slovenia" + }, + { + "author_name": "Elena Von der Lippe", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Marek Majdan", + "author_inst": "Department of Public Health, Institute for Global Health and Epidemiology, Faculty of Health Sciences and Social Work, Trnava University, Trnava, Slovakia" + }, + { + "author_name": "Milena S Milicevic", + "author_inst": "Faculty of Medicine University of Belgrade, Serbia" + }, + { + "author_name": "Elena Pallari", + "author_inst": "Health Service and Population Research Department, King's College, London, United Kingdom" + }, + { + "author_name": "Jose L Penalvo", + "author_inst": "Unit of Noncommunicable Diseases, Department of Public Health, Institute of Tropical Medicine, Nationalestraat, Antwerp, Belgium" + }, + { + "author_name": "Sara M Pires", + "author_inst": "National Food Institute, Technical University of Denmark, Denmark" + }, + { + "author_name": "Dietrich Plass", + "author_inst": "Exposure Assessment and Environmental Health Indicators, German Environment Agency, Berlin, Germany" + }, + { + "author_name": "Joao V Santos", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Portugal" + }, + { + "author_name": "Sofie T Thomsen", + "author_inst": "National Food Institute, Technical University of Denmark, Denmark" + }, + { + "author_name": "Diane L Stockton", + "author_inst": "Public Health Scotland, Scotland, United Kingdom" + }, + { + "author_name": "Ian Grant", + "author_inst": "Public Health Scotland, Scotland, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.28.20075788", "rel_title": "Analysis of hospitalized COVID-19 patients in the Mount Sinai Health System using electronic medical records (EMR) reveals important prognostic factors for improved clinical outcomes", @@ -1478187,29 +1475210,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.02.071506", - "rel_title": "Computational methods to develop potential neutralizing antibody Fab region against SARS-CoV-2 as therapeutic and diagnostic tool", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.071506", - "rel_abs": "SARS-CoV-2, a global pandemic originated from Wuhan city of China in the month of December 2019. There is an urgency to identify potential antibodies to neutralize the virus and also as a diagnostic tool candidate. At present palliative treatments using existing antiviral drugs are under trails to treat SARS-CoV-2.Whole Genome sequence of Wuhan market sample of SARS-CoV-2 was obtained from NCBI Gene ID MN908947.3.Spike protein sequence PDB ID 6VSB obtained from RCSB database. Spike protein sequence had shown top V gene match with IGLV1-44*01, IGLV1-47*02 and has VL type chain. Whole Genome sequence had shown top V gene match with IGHV1-38-4*01 and has VH type chain. VD chain had shown link to allele HLA-A0206 80%, HLA-A0217 80%, HLA-A2301 75%, HLA-A0203 75%, HLA-A0202 70% and HLA-A0201 55% of binding levels. Some conserved regions of spike protein had shown strong binding affinity with HLA-A-0*201, HLA-A24, HLA-B-5701 and HLA-B-5703 alpha chains. Synthetic Fab construct BCR type antibody IgG (CR5840) had shown Polyspecific binding activity with spike glycoprotein when compared with available Anti-SARS antibody CR3022.Thus we propose CR5840 Fab constructed antibody as potential neutralizing antibody for SARS-CoV-2. Based on germline analysis we also propose cytotoxic T lymphocyte epitope peptide selective system as effective tool for the development of SARS-CoV-2 vaccine.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hemanth K Manikyam", - "author_inst": "Faculty of Science, North East Frontier Technical University, Arunachal Pradesh, India." - }, - { - "author_name": "Sunil K Joshi", - "author_inst": "University of Miami School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.03.075473", "rel_title": "Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2", @@ -1478634,6 +1475634,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.04.27.20081349", + "rel_title": "Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081349", + "rel_abs": "The authors have withdrawn this manuscript (Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route) from medRxiv, because it was found that the statistical and analytical methods used in the manuscript had certain controversies after further discussion, so the authors of the manuscipt disclaimed that this conclusion cannot be used as the basis for the origin and evolution of SARS-COV-2, also as information to guide clinical practice and health-related behaviors, it should not be reported as established facts in the news media and \"We-Media\". No one should do too much extended interpretation of the content of this manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lehai Zhang", + "author_inst": "Qilu Children's Hospital of Shandong University" + }, + { + "author_name": "shifu wang", + "author_inst": "Shandong University" + }, + { + "author_name": "Qian Ren", + "author_inst": "Qilu Children's Hospital of Shandong University" + }, + { + "author_name": "Junjie Yang", + "author_inst": "Qilu Normal University" + }, + { + "author_name": "Yanqin Lu", + "author_inst": "Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences" + }, + { + "author_name": "Lei Zhang", + "author_inst": "Shandong Institute of Industrial Technology for Health Sciences and Precision Medicine" + }, + { + "author_name": "Zhongtao Gai", + "author_inst": "Qilu Children's Hospital of Shandong University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.27.20082032", "rel_title": "Direct observation of repeated infections with endemic coronaviruses", @@ -1479809,25 +1476852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.04.27.20081562", - "rel_title": "Incidence of COVID-19 and Connections with Air Pollution Exposure: Evidence from the Netherlands", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081562", - "rel_abs": "The fast spread of severe acute respiratory syndrome coronavirus 2 has resulted in the emergence of several hot-spots around the world. Several of these are located in areas associated with high levels of air pollution. This study investigates the relationship between exposure to particulate matter and COVID-19 incidence in 355 municipalities in the Netherlands. The results show that atmospheric particulate matter with diameter less than 2.5 is a highly significant predictor of the number of confirmed COVID-19 cases and related hospital admissions. The estimates suggest that expected COVID-19 cases increase by nearly 100 percent when pollution concentrations increase by 20 percent. The association between air pollution and case incidence is robust in the presence of data on health-related preconditions, proxies for symptom severity, and demographic control variables. The results are obtained with ground-measurements and satellite-derived measures of atmospheric particulate matter as well as COVID-19 data from alternative dates. The findings call for further investigation into the association between air pollution and SARS-CoV-2 infection risk. If particulate matter plays a significant role in COVID-19 incidence, it has strong implications for the mitigation strategies required to prevent spreading.\n\nHighlightsO_ST_ABSBackgroundC_ST_ABSResearch on viral respiratory infections has found that infection risks increase following exposure to high concentrations of particulate matter. Several hot-spots of Severe Acute Respiratory Syndrome Coronavirus 2 infections are in areas associated with high levels of air pollution.\n\nApproachThis study investigates the relationship between exposure to particulate matter and COVID-19 incidence in 355 municipalities in the Netherlands using data on confirmed cases and hospital admissions coded by residence, along with local PM2.5, PM10, population density, demographics and health-related pre-conditions. The analysis utilizes different regression specifications that allow for spatial dependence, nonlinearity, alternative error distributions and outlier treatment.\n\nResultsPM2.5 is a highly significant predictor of the number of confirmed COVID-19 cases and related hospital admissions. Taking the WHO guideline of 10mcg/m3 as a baseline, the estimates suggest that expected COVID-19 cases increase by nearly 100% when pollution concentrations increase by 20%.\n\nConclusionThe findings call for further investigation into the association between air pollution on SARS-CoV-2 infection risk. If particulate matter plays a significant role in the incidence of COVID-19 disease, it has strong implications for the mitigation strategies required to prevent spreading, particularly in areas that have high levels of pollution.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Bo Pieter Johannes Andree", - "author_inst": "World Bank" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.27.20081711", "rel_title": "Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study", @@ -1480628,6 +1477652,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20082057", + "rel_title": "Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20082057", + "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan1,2, China, and has subsequently spread worldwide. Knowledge of coronavirus-related risk factors can help countries build more systematic and successful responses to COVID-19 disease outbreak. Here we used Supervised Machine Learning and Empirical Bayesian Kriging (EBK) techniques to reveal correlates and patterns of COVID-19 Disease outbreak in sub-Saharan Africa (SSA).\n\nMethodsWe analyzed time series aggregate data compiled by Johns Hopkins University on the outbreak of COVID-19 disease across SSA. COVID-19 data was merged with additional data on socio-demographic and health indicator survey data for 39 of SSAs 48 countries that reported confirmed cases and deaths from coronavirus between February 28, 2020 through March 26, 2020. We used supervised machine learning algorithm, Lasso for variable selection and statistical inference. EBK was used to also create a raster estimating the spatial distribution of COVID-19 disease outbreak.\n\nResultsThe lasso Cross-fit partialing out predictive model ascertained seven variables significantly associated with the risk of coronavirus infection (i.e. new HIV infections among pediatric, adolescent, and middle-aged adult PLHIV, time (days), pneumococcal conjugate-based vaccine, incidence of malaria and diarrhea treatment). Our study indicates, the doubling time in new coronavirus cases was 3 days. The steady three-day decrease in coronavirus outbreak rate of change (ROC) from 37% on March 23, 2020 to 23% on March 26, 2020 indicates the positive impact of countries steps to stymie the outbreak. The interpolated maps show that coronavirus is rising every day and appears to be severely confined in South Africa. In the West African region (i.e. Burkina Faso, Ghana, Senegal, Cote dIviore, Cameroon, and Nigeria), we predict that new cases and deaths from the virus are most likely to increase.\n\nInterpretationIntegrated and efficiently delivered interventions to reduce HIV, pneumonia, malaria and diarrhea, are essential to accelerating global health efforts. Scaling up screening and increasing COVID-19 testing capacity across SSA countries can help provide better understanding on how the pandemic is progressing and possibly ensure a sustained decline in the ROC of coronavirus outbreak.\n\nFundingAuthors were wholly responsible for the costs of data collation and analysis.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Amobi Andrew Onovo", + "author_inst": "USAID Nigeria; Institute of Global Health, University of Geneva." + }, + { + "author_name": "Akinyemi Atobatele", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Abiye Kalaiwo", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Christopher Obanubi", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Ezekiel James", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Pamela Gado", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Gertrude Odezugo", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Doreen Magaji", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Dolapo Ogundehin", + "author_inst": "USAID Nigeria" + }, + { + "author_name": "Michele Russell", + "author_inst": "USAID Nigeria" + } + ], + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20082107", "rel_title": "Race, Socioeconomic Deprivation, and Hospitalization for COVID-19 in English participants of a National Biobank", @@ -1481555,57 +1478634,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.02.074021", - "rel_title": "An artificial intelligence system reveals liquiritin inhibits SARS-CoV-2 by mimicking type I interferon", - "rel_date": "2020-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.074021", - "rel_abs": "The pandemic COVID-19 has spread to all over the world and greatly threatens safety and health of people. COVID-19 is highly infectious and with high mortality rate. As no effective antiviral treatment is currently available, new drugs are urgently needed. We employed transcriptional analysis to uncover potential antiviral drugs from natural products or FDA approved drugs. We found liquiritin significantly inhibit replication of SARS-CoV-2 in Vero E6 cells with EC50 = 2.39 M. Mechanistically, we found liquiritin exerts anti-viral function by mimicking type I interferon. Upregulated genes induced by liquiritin are enriched in GO categories including type I interferon signaling pathway, negative regulation of viral genome replication and etc. In toxicity experiment, no death was observed when treated at dose of 300 mg/kg for a week in ICR mice. All the organ indexes but liver and serum biochemical indexes were normal after treatment. Liquiritin is abundant in licorice tablet (~0.2% by mass), a traditional Chinese medicine. Together, we recommend liquiritin as a competitive candidate for treating COVID-19. We also expect liquiritin to have a broad and potent antiviral function to other viral pathogens, like HBV, HIV and etc.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jie Zhu", - "author_inst": "Peking University" - }, - { - "author_name": "Yong-Qiang Deng", - "author_inst": "Academy of Military Medical Sciences, Beijing, China" - }, - { - "author_name": "Xin Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Xiao-Feng Li", - "author_inst": "Academy of Military Medical Sciences, Beijing, China" - }, - { - "author_name": "Na-Na Zhang", - "author_inst": "Academy of Military Medical Sciences, Beijing, China" - }, - { - "author_name": "Zurui Liu", - "author_inst": "Gigaceuticals Co., Ltd." - }, - { - "author_name": "Bowen Zhang", - "author_inst": "Peking University" - }, - { - "author_name": "Chengfeng Qin", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Zhengwei Xie", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.02.071811", "rel_title": "Structural and Functional Implications of Non-synonymous Mutations in the Spike protein of 2,954 SARS-CoV-2 Genomes", @@ -1482174,6 +1479202,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.04.28.20083279", + "rel_title": "CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083279", + "rel_abs": "Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Douglas Arneson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew Elliott", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Arman Mosenia", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Boris Oskotsky", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rohit Vashisht", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Travis Zack", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Paul Bleicher", + "author_inst": "Evident Health Strategies, West Newton, MA" + }, + { + "author_name": "Atul J. Butte", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Vivek A. Rudrapatna", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.29.20085183", "rel_title": "How should hospitals manage the backlog of patients awaiting surgery following the COVID-19 pandemic? A demand modelling simulation case study for carotid endarterectomy", @@ -1483173,37 +1480252,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20080531", - "rel_title": "Impact of virus testing on COVID-19 case fatality rate: estimate using a fixed-effects model", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080531", - "rel_abs": "BackgroundIn response to the SARS-CoV2 pandemic, governments have adopted a variety of public health measures. There are variations in how much testing has been done across countries. South Korea, Germany, and Iceland take the bet of massive testing of their population. Whereas tests were not performed widely in southern European countries. As the former undergo a lower case-fatality rate due to the COVID-19 than the latter, the impact of the testing strategy must be investigated. In this study, we aimed to evaluate the impact of testing on the case fatality rate.\n\nMethodsWe use data on inpatients across French geographic areas and propose a novel methodology that exploits policy discontinuities at region borders to estimate the effect of COVID-19 tests on the case-fatality rate. In France, testing policies are determined locally. We compare all contiguous department pairs located on the opposite sides of a region border. The heterogeneity in testing rate between department pairs together with the similarities in other dimensions allow us to mimic the existence of treatment and control groups and to identify the impact of testing on mortality.\n\nResultsThe increase of one percentage point in the test rate is associated with a decrease of 0.001 percentage point in the death rate. In other words, for each additional 1000 tests, one person would have remained alive.\n\nConclusionMassive population testing could have a significant effect on mortality in different ways. Mass testing may help decision-makers to implement healthcare measures to limit the spread of the disease.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Anthony Terriau", - "author_inst": "GAINS -Le Mans University" - }, - { - "author_name": "Julien Albertini", - "author_inst": "GATES - Lyon 2 University" - }, - { - "author_name": "Arthur Poirier", - "author_inst": "GAINS -Le Mans University" - }, - { - "author_name": "Quentin LE BASTARD", - "author_inst": "Nantes University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.26.20075937", "rel_title": "Using the COVID-19 to influenza ratio to estimate the numbers of symptomatic COVID-19 cases in Wuhan prior to the lockdown", @@ -1483960,6 +1481008,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.04.27.20073379", + "rel_title": "Hydroxychloroquine application is associated with a decreased mortality in critically ill patients with COVID-19", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20073379", + "rel_abs": "ImportanceCoronavirus disease 2019 (COVID-19) is a pandemic with no specific drugs and high mortality. The most urgent thing is to find effective treatments.\n\nObjectiveTo determine whether hydroxychloroquine application may be associated with a decreased risk of death in critically ill COVID-19 patients and what is potential mechanism.\n\nDesign, Setting and PatientsThis retrospective study included all 568 critically ill COVID-19 patients who were confirmed by pathogen laboratory tests despite antiviral treatment and had severe acute respiratory distress syndrome, PAO2/FIO2 <300 with need of mechanical ventilation in Tongji Hospital, Wuhan, between February 1 of 2020 to April 8 of 2020. All 568 patients received comparable basic treatments including antiviral drugs and antibiotics, and 48 of them additionally received oral hydroxychloroquine (HCQ) treatment (200 mg twice a day for 7-10 days). Primary endpoint is mortality of patients, and inflammatory cytokines levels were compared between hydroxychloroquine and non-hydroxychloroquine (NHCQ) treatments.\n\nMAIN OUTCOMES AND MEASURESIn-hospital death and hospital stay time (day) were obtained, level of inflammatory cytokine (IL-6) was measured and compared between HCQ and NHCQ treatments.\n\nRESULTSThe median age of 568 critically ill patients is 68 (57, 76) years old with 37.0% being female. Mortalities are 18.8% (9/48) in HCQ group and 45.8% (238/520) in NHCQ group (p<0.001). The time of hospital stay before patient death is 15 (10-21) days and 8 (4 - 14) days for the HCQ and NHCQ groups, respectively (p<0.05). The level of inflammatory cytokine IL-6 was significantly lowered from 22.2 (8.3-118.9) pg/mL at the beginning of the treatment to 5.2 (3.0-23.4) pg/ml (p<0.05) at the end of the treatment in the HCQ group but there is no change in the NHCQ group.\n\nCONCLUSIONS AND RELEVANCEHydroxychloroquine treatment is significantly associated with a decreased mortality in critically ill patients with COVID-19 through attenuation of inflammatory cytokine storm. Therefore, hydroxychloroquine should be prescribed for treatment of critically ill COVID-19 patients to save lives.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSCould hydroxychloroquine administration be beneficial in the treatment of critically ill patients with COVID-19?\n\nFindingsIn this retrospective study, a total of 568 critically ill patients with COVID-19 all received basic therapy and additionally 48 of them received hydroxychloroquine for 7-10 days (200 mg twice per day). Hydroxychloroquine treatment is significantly associated with a decreased mortality in critically ill COVID-19 patients and attenuated inflammatory cytokine IL-6 level.\n\nMeaningOur data suggest that hydroxychloroquine could be used to treat critically ill patients with COVID-19 which may save a lot of lives.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Bo Yu", + "author_inst": "Tongji Hospital, Wuhan" + }, + { + "author_name": "Dao Wen Wang", + "author_inst": "Tongji Hospital, Wuhan" + }, + { + "author_name": "Chenze Li", + "author_inst": "Tongji Hospital, Wuhan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.04.27.20082537", "rel_title": "Mathematical Model to Study Early COVID-19 Transmission Dynamics in Sri Lanka", @@ -1484675,69 +1481750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20080226", - "rel_title": "Review and methodological analysis of trials currently testing treatment and prevention options for the novel coronavirus disease (COVID-19) globally.", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20080226", - "rel_abs": "BackgroundAs COVID-19 cases continue to rise globally within an unprecedented short period of time, solid evidence from large randomised controlled trials is still lacking. Currently, numerous trials testing potential treatment and preventative options are undertaken globally.\n\nObjectivesWe summarised all currently registered clinical trials examining treatment and prevention options for COVID-19. Additionally, we evaluated the quality of the retrieved interventional studies.\n\nData sourcesClinicaltrials.gov, the Chinese Clinical Trial Registry and the European Union Clinical Trials Register were systematically searched.\n\nStudy eligibility criteriaRegistered clinical trials examining treatment and/or prevention options for COVID-19 were included. No language, country or study design restrictions were applied. We excluded withdrawn or cancelled studies and trials not reporting therapeutic or preventative strategies for COVID-19.\n\nParticipants and interventionsNo restrictions in terms of participants age and medical background or type of intervention were enforced.\n\nMethodsThe registries were searched using the term \"coronavirus\" or \"COVID-19\" from their inception until 26th March 2020. Additional manual search of the registries was also performed. Eligible studies were summarised and tabulated. Interventional trials were methodologically analysed, excluding expanded access studies and trials testing Traditional Chinese Medicine.\n\nResultsIn total, 309 trials evaluating therapeutic management options, 23 studies assessing preventive strategies and 3 studies examining both were retrieved. Interventional treatment studies were mostly randomised (n=150, 76%) and open-label (n=73, 37%) with a median number of planned inclusions of 90 (IQR 40-200). Major categories of interventions that are currently being investigated are discussed.\n\nConclusionNumerous clinical trials have been registered since the onset of the COVID-19 pandemic. Summarised data on these trials will assist physicians and researchers to promote patient care and guide future research efforts for COVID-19 pandemic containment. However, up to the end of March, 2020, significant information on reported trials was often lacking.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Paraskevi C. Fragkou", - "author_inst": "4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece" - }, - { - "author_name": "Drifa Belhadi", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "Nathan Peiffer-Smadja", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "Charalampos D. Moschopoulos", - "author_inst": "4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece" - }, - { - "author_name": "Fran\u00e7ois-Xavier Lescure", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "Hannah Janocha", - "author_inst": "Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Centre (UGMLC), Philipps University Marburg, German Centre for Lung Research (DZL) Ma" - }, - { - "author_name": "Emmanouil Karofylakis", - "author_inst": "4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "France Mentr\u00e9", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "Chrysanthi Skevaki", - "author_inst": "Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Centre (UGMLC), Philipps University Marburg, German Centre for Lung Research (DZL) Ma" - }, - { - "author_name": "C\u00e9dric Laou\u00e9nan", - "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France" - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.26.20080648", "rel_title": "Risk assessment via layered mobile contact tracing for epidemiological intervention", @@ -1485210,6 +1482222,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.28.20078071", + "rel_title": "ACE inhibitors, AT1 receptor blockers and COVID-19: clinical epidemiology evidences for a continuation of treatments. The ACER-COVID study", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20078071", + "rel_abs": "AimsThe question of interactions between the renin angiotensin aldosterone system drugs and the incidence and prognosis of COVID-19 infection has been raised by the medical community. We hypothesised that if patients treated with ACE inhibitors (ACEI) or AT1 receptor blockers (ARB) were more prone to SARS-CoV2 infection and had a worse prognosis than untreated patients, the prevalence of consumption of these drugs would be higher in patients with COVID-19 compared to the general population.\n\nMethods and resultsWe used a clinical epidemiology approach based on the estimation of standardised prevalence ratio (SPR) of consumption of ACEI and ARB in four groups of patients (including 187 COVID-19 positive) with increasing severity referred to the University hospital of Lille and in three French reference samples (the exhaustive North population (n=1,569,968), a representative sample of the French population (n=414,046), a random sample of Lille area (n=1,584)).\n\nThe SPRs of ACEI and ARB did not differ as the severity of the COVID-19 patients increased, being similar to the regular consumption of these drugs in the North of France population with the same non-significant increase for both treatment (1.17 [0.83-1.67]). A statistically significant increase in the SPR of ARB (1.56 [1.02-2.39]) was observed in intensive care unit patients only. After stratification on obesity, this increase was limited to the high risk subgroup of obese patients.\n\nConclusionsOur results strongly support the recommendation that ACEI and ARB should be continued in the population and in COVID-19 positive patients, reinforcing the position of several scientific societies.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Luc Dauchet", + "author_inst": "Univ Lille, Inserm, CHU de Lille, Institut Pasteur de Lille U1167 RID-AGE Risk Factors and Molecular Determinants of Aging Related Diseases and CHU Lille Depart" + }, + { + "author_name": "Marc Lambert", + "author_inst": "Univ Lille, Inserm, CHU de Lille, Institut Pasteur de Lille U1167 RID-AGE Risk Factors and Molecular Determinants of Aging Related Diseases and CHU Lille Intern" + }, + { + "author_name": "Victoria Gauthier", + "author_inst": "Univ Lille, Inserm, CHU de Lille, Institut Pasteur de Lille U1167 RID-AGE Risk Factors and Molecular Determinants of Aging Related Diseases" + }, + { + "author_name": "Julien Poissy", + "author_inst": "CHU Lille Department of Intensive Care" + }, + { + "author_name": "Karine Faure", + "author_inst": "CHU Lille Department of Infectious Diseases and Univ Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immun" + }, + { + "author_name": "Alain Facon", + "author_inst": "CHU Lille SAMU59 and Emergency Department" + }, + { + "author_name": "C\u00e9cile Yelnik", + "author_inst": "CHU Lille Internal Medicine Department" + }, + { + "author_name": "Sophie Panaget", + "author_inst": "CHU Lille Department of Infectious Diseases" + }, + { + "author_name": "Thierry Plagnieux", + "author_inst": "DRSM Hauts de France, F-59009 Villeneuve d'Ascq" + }, + { + "author_name": "Florent Verfaillie", + "author_inst": "DRSM Hauts de France, F-59009 Villeneuve d'Ascq" + }, + { + "author_name": "Daniel Mathieu", + "author_inst": "CHU Lille Department of Intensive Care" + }, + { + "author_name": "Patrick Goldstein", + "author_inst": "CHU Lille SAMU59 and Emergency Department" + }, + { + "author_name": "Aline Meirhaeghe", + "author_inst": "Univ Lille, Inserm, CHU de Lille, Institut Pasteur de Lille U1167 RID-AGE Risk Factors and Molecular Determinants of Aging Related Diseases" + }, + { + "author_name": "Philippe Amouyel", + "author_inst": "Univ Lille, Inserm, CHU de Lille, Institut Pasteur de Lille U1167 RID-AGE Risk Factors and Molecular Determinants of Ageing Related Diseases and CHU Lille Depar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.05.01.072652", "rel_title": "Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas", @@ -1486025,85 +1483108,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.01.072371", - "rel_title": "SARS-CoV-2 spike protein predicted to form stable complexes with host receptor protein orthologues from mammals, but not fish, birds or reptiles", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.072371", - "rel_abs": "SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Su Datt Lam", - "author_inst": "Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, 43600, Malaysia" - }, - { - "author_name": "Nicola Bordin", - "author_inst": "University College London" - }, - { - "author_name": "Vaishali P Waman", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Harry M Scholes", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Paul Ashford", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Neeladri Sen", - "author_inst": "Indian Institute of Science Education and Research, Pune, 411008, India" - }, - { - "author_name": "Lucy van Dorp", - "author_inst": "UCL Genetics Institute" - }, - { - "author_name": "Clemens Rauer", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Natalie L Dawson", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Camilla SM Pang", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Mahnaz Abbasian", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Ian Sillitoe", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Sarah JL Edwards", - "author_inst": "Department of Science and Technology Studies, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Jonathan G Lees", - "author_inst": "Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 OBP, UK" - }, - { - "author_name": "Joanne M Santini", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - }, - { - "author_name": "Christine A Orengo", - "author_inst": "Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.01.067769", "rel_title": "Heat inactivation of the Severe Acute Respiratory Syndrome Coronavirus 2", @@ -1486668,6 +1483672,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.29.20085910", + "rel_title": "Validation of an extraction-free RT-PCR protocol for detection of SARS-CoV2 RNA", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085910", + "rel_abs": "In light of supply chain failures for reagents and consumables needed for purification of nucleic acid for detection of SARS-CoV-2 RNA by RT-PCR, we aim to verify the performance and utility of a non-extraction protocol for RT-PCR (\"direct RT-PCR\").\n\nWe report improved sensitivity compared to earlier reports of direct RT-PCR testing of swab samples, in particular at the lower limit of detection (sensitivity 93% overall; 100% for specimens with high to moderate viral titre, Ct <34; 81% for specimens with a low viral titre, Ct [≥]34). Sensitivity is improved (from 90 to 93%) by testing in duplicate. We recommend swabs are re-suspended in water to minimise PCR inhibition. A cellular target is necessary to control for PCR inhibition and specimen quality.\n\nDirect RT-PCR is best suited to population level screening where results are not clinically actionable, however in the event of a critical supply chain failure direct RT-PCR is fit for purpose for the detection of SARS-CoV-2 infection.\n\nThe results from our study offer front-line laboratories additional reagent options for performing extraction-free RT-PCR protocols.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Julianne R Brown", + "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" + }, + { + "author_name": "Laura Atkinson", + "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" + }, + { + "author_name": "Divya Shah", + "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" + }, + { + "author_name": "Kathryn Harris", + "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.29.20085514", "rel_title": "Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic", @@ -1487427,25 +1484462,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.26.20080523", - "rel_title": "Solvable delay model for epidemic spreading: the case of Covid-19 in Italy", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080523", - "rel_abs": "We present a simple but realistic model for describing the diffusion of an infectious disease on a population of individuals. The dynamics is governed by a single functional delay differential equation, which, in the case of a large population, can be solved exactly, even in the presence of a time-dependent infection rate. This delay model has a higher degree of accuracy than the so-called SIR model, commonly used in epidemiology, which, instead, is formulated in terms of a set of three ordinary differential equations. We apply our model to describe the outbreak of the new virus COVID-19 in Italy, taking into account the containment measures implemented by the government in order to mitigate the spreading of the virus and the social costs for the population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Luca Dell'Anna", - "author_inst": "University of Padova" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.25.20079996", "rel_title": "Public perceptions of COVID-19 in Australia: perceived risk, knowledge, health-protective behaviours, and vaccine intentions", @@ -1487950,6 +1484966,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.25.20079343", + "rel_title": "Poolkeh Finds the Optimal Pooling Strategy for a Population-wide COVID-19 Testing (Israel, UK, and US as Test Cases)", + "rel_date": "2020-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079343", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe SARS-CoV-2 pandemic has changed the lifestyle of citizens of the world. In order for decision makers to manage the viral spread of COVID-19 both in the intra-national and the international frontiers, it is essential to operate based on data-driven assessments. Its crucial to do so rapidly and frequently, since the nature of the viral spread grows exponentially and can burst worldwide again. A fast and accurate health status of individuals globally during a pandemic can save many lives and bring life back to a new normal. Herein, we present a data-driven tool to allow decision-makers to assess the spread of the virus among the world population. Our framework allows health agencies to maximize the throughput of COVID-19 tests among the world population by finding the best test pooling that fits the current SIR-D [1] status of the nation.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yossi Eliaz", + "author_inst": "University of Houston" + }, + { + "author_name": "Mark Danovich", + "author_inst": "Amey PLC" + }, + { + "author_name": "Gregory P Gasic", + "author_inst": "University of Houston" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.22.20071498", "rel_title": "A deeper look at COVID-19 CFR: health care impact and roots of discrepancy", @@ -1488789,101 +1485832,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.04.28.20084038", - "rel_title": "Validation of N95 filtering facepiece respirator decontamination methods available at a large university hospital", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20084038", - "rel_abs": "ImportanceFiltering facepiece respirators, including N95 masks, are a critical component of infection prevention in hospitals. Due to unprecedented shortages in N95 respirators, many healthcare systems have explored reprocessing of N95 respirators. Data supporting these approaches are lacking in real hospital settings. In particular, published studies have not yet reported an evaluation of multiple viruses, bacteria, and fungi along with respirator filtration and fit in a single, full-scale study.\n\nObjectiveWe initiated a full-scale study to evaluate different N95 FFR decontamination strategies and their impact on respirator integrity and inactivating multiple microorganisms, with experimental conditions informed by the needs and constraints of the hospital.\n\nMethodsWe explored several reprocessing methods using new 3M 1860 N95 respirators, including dry (<10% relative humidity) and moist (62-66% relative humidity) heat (80-82 {degrees}C) in the drying cycle of industrial instrument washers, ethylene oxide (EtO), pulsed xenon UV (UV-PX), hydrogen peroxide gas plasma (HPGP), and vaporous hydrogen peroxide (VHP). Respirator samples were treated and analyzed for biological indicator inactivation using four viruses (MS2, phi6, influenza A virus, murine hepatitis virus), three bacteria (Escherichia coli, Staphylococcus aureus, Geobacillus stearothermophilus), and the fungus Aspergillus niger. The impact of different application media was also evaluated. In parallel, decontaminated respirators were evaluated for filtration integrity and fit.\n\nResultsVHP resulted in >2 log10 inactivation of all tested biological indicators. The combination of UV-PX + moist heat resulted in >2 log10 inactivation of all biological indicators except G. stearothermohphilus. Greater than 95% filtration efficiency was maintained following 2 (UV-PX + <10% relative humidity heat) or 10 (VHP) cycles of treatment, and proper fit was also preserved. UV-PX + dry heat was insufficient to inactivate all biological indicators. Although very effective at virus decontamination, HPGP resulted in decreased filtration efficiency after 3 cycles, and EtO treatment raised potential toxicity concerns. The observed inactivation of viruses with UV-PX, heat, and hydrogen peroxide treatments varied as a function of which culture media (PBS buffer or DMEM) they were deposited in.\n\nConclusions and RelevanceHigh levels of biological indicator inactivation were achieved following treatment with either moist heat or VHP. These same treatments did not significantly impact mask filtration or fit. Hospitals have a variety of scalable options to safely reprocess N95 masks. Beyond value in the current Covid-19 pandemic, the broad group of microorganisms and conditions tested make these results relevant in potential future pandemic scenarios.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Krista R. Wigginton", - "author_inst": "University of Michigan" - }, - { - "author_name": "Peter J. Arts", - "author_inst": "University of Michigan" - }, - { - "author_name": "Herek Clack", - "author_inst": "University of Michigan" - }, - { - "author_name": "William J Fitzsimmons", - "author_inst": "University of Michigan" - }, - { - "author_name": "Mirko Gamba", - "author_inst": "University of Michigan" - }, - { - "author_name": "Katherine R. Harrison", - "author_inst": "University of Michigan" - }, - { - "author_name": "William LeBar", - "author_inst": "University of Michigan" - }, - { - "author_name": "Adam S. Lauring", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lucinda Li", - "author_inst": "University of Michigan" - }, - { - "author_name": "William W. Roberts", - "author_inst": "University of Michigan" - }, - { - "author_name": "Nicole Rockey", - "author_inst": "University of Michigan" - }, - { - "author_name": "Jania Torreblanca", - "author_inst": "University of Michigan" - }, - { - "author_name": "Carol Young", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lo\u00efc C. Anderegg", - "author_inst": "Harvard University" - }, - { - "author_name": "Amy Cohn", - "author_inst": "University of Michigan" - }, - { - "author_name": "John M. Doyle", - "author_inst": "Harvard University" - }, - { - "author_name": "Cole O. Meisenhelder", - "author_inst": "Harvard University" - }, - { - "author_name": "Lutgarde Raskin", - "author_inst": "University of Michigan" - }, - { - "author_name": "Nancy G Love", - "author_inst": "University of Michigan" - }, - { - "author_name": "Keith S. Kaye", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083998", "rel_title": "Assessment of the outbreak risk, mapping and infestation behavior of COVID-19: Application of the autoregressive and moving average (ARMA) and polynomial models", @@ -1489368,6 +1486316,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20077933", + "rel_title": "Comprehensive Investigation and Isolation have Effectively Suppressed the Spread of COVID-19", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077933", + "rel_abs": "The outbreak of COVID-19 since Dec. 2019 has caused severe life and economic damage worldwide, many countries are trapped by medical resource constraints or absence of targeted therapeutics, and therefore the implement of systemic policies to block this pandemic should be prioritized. Based on the transmission mechanisms and physicochemical properties of betacoron-aviruses, we construct a fine-grained transmission dynamics model (ICRD) to forecast the crucial information of public concern, therein using dynamical coefficients to quantify the impact of the implement time and intensity of containment policies on the spread of epidemic. We find that the comprehensive investigation policy for susceptible population and the quarantine for suspected cases eminently contribute to reduce casualties during the phase of the dramatic increase of diagnosed cases. Statistic evidences strongly suggest that society should take such forceful public health interventions to cut the infection channels in the initial stage until the pandemic is interrupted.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yubo Huang", + "author_inst": "Shanghai Jiao Tong university" + }, + { + "author_name": "Weidong Zhang", + "author_inst": "Shanghai Jiaotong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20077842", "rel_title": "The values of coagulation function in COVID-19 patients", @@ -1489947,33 +1486918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.25.20079749", - "rel_title": "Who is at the highest risk from COVID-19 in India? Analysis of health, healthcare access, and socioeconomic indicators at the district level", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079749", - "rel_abs": "IntroductionDespite measures such as travel restrictions and lockdowns, the novel coronavirus (SARS-COV-2) is projected to spread across India. Considering that a vaccine for COVID-19 is will not be available soon, it is important to identify populations with high risk from COVID-19 and take measures to prevent outbreaks and build healthcare infrastructure at the local level.\n\nMethodsWe used data from two large nationally representative household surveys, administrative sources, and published studies to estimate the risk of COVID-19 at the district level in India. We employed principal component analysis to create an index of the health risk of COVID-19 from demographic and comorbidity indicators such as the proportions of elderly population and rates of diabetes, hypertension, and respiratory illnesses. Another principal component index examined the socioeconomic and healthcare access risk from COVID-19, based on the standard of living, proportion of caste groups, and per capita access to public healthcare in each district.\n\nResultsDistricts in northern, southern and western Indian states such as Punjab, Tamil Nadu, Kerala, and Maharashtra were at the highest health risk from COVID-19. Many of these districts have been designated as COVID-19 hotspots by the Indian government because of emergent outbreaks. Districts in eastern and central states such as Uttar Pradesh, Bihar, and Madhya Pradesh have higher socioeconomic and healthcare access risk as compared with other areas.\n\nConclusionDistricts at high risk of COVID-19 should prioritize policy measures for preventing outbreaks, and improving critical care infrastructure and socioeconomic safety nets.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Arindam Nandi", - "author_inst": "The Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Ruchita Balasubramanian", - "author_inst": "The Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Ramanan Laxminarayan", - "author_inst": "The Center for Disease Dynamics, Economics & Policy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.24.20078923", "rel_title": "Real-time time-series modelling for prediction of COVID-19 spread and intervention assessment", @@ -1490410,6 +1487354,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.25.20079178", + "rel_title": "A COVID-19 epidemic model integrating direct and fomite transmission as well as household structure", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079178", + "rel_abs": "This paper stresses its base contribution on a new SIR-type model for COVID-19 including direct and fomite transmission as well as the effect of distinct household structures. To what extent increasing the physical-distancing-related contact radius and enhancing mass control (public curfew, lockdown, workplace clearance, and school closure) reduce the number of predicted active cases is studied via parameter estimation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Karunia Putra Wijaya", + "author_inst": "University of Koblenz" + }, + { + "author_name": "Naleen Ganegoda", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Yashika Jayatunga", + "author_inst": "University of Koblenz" + }, + { + "author_name": "Thomas Goetz", + "author_inst": "University Koblenz" + }, + { + "author_name": "Wolfgang Bock", + "author_inst": "Technical University of Kaiserslautern" + }, + { + "author_name": "Moritz Schaefer", + "author_inst": "University of Koblenz" + }, + { + "author_name": "Peter Heidrich", + "author_inst": "University of Koblenz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.25.20079103", "rel_title": "The role of asymptomatic SARS-CoV-2 infections: rapid living systematic review and meta-analysis", @@ -1491399,148 +1488386,65 @@ "category": "biochemistry" }, { - "rel_doi": "10.1101/2020.04.29.068890", - "rel_title": "Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068890", - "rel_abs": "In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Wioletta Rut", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Zongyang Lv", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Mikolaj Zmudzinski", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Stephanie Patchett", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Digant Nayak", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Scott J Snipas", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Farid El Oualid", - "author_inst": "UbiQ Bio B.V." - }, - { - "author_name": "Miklos Bekes", - "author_inst": "Arvinas, Inc.," - }, - { - "author_name": "Tony T Huang", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Marcin Drag", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Shaun K Olsen", - "author_inst": "Medical University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, - { - "rel_doi": "10.1101/2020.04.29.068486", - "rel_title": "SARS-CoV-2 Spike S1 Receptor Binding Domain undergoes Conformational Change upon Interaction with Low Molecular Weight Heparins.", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068486", - "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses when added exogenously, including S-associated coronavirus strain HSR1 and inhibits cellular invasion by SARS-CoV-2. We have previously demonstrated that unfractionated heparin binds to the Spike (S1) protein receptor binding domain, induces a conformational change and have reported the structural features of heparin on which this interaction depends. Furthermore, we have demonstrated that enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. Here we expand upon these studies, to a wide range of low molecular weight heparins and demonstrate that they induce a variety of conformational changes in the SARS-CoV-2 RBD. These findings may have further implications for the rapid development of a first-line therapeutic by repurposing low molecular weight heparins, as well as for next-generation, tailor-made, GAG-based antiviral agents, against SARS-CoV-2 and other members of the Coronaviridae.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Courtney Mycroft-West", - "author_inst": "Keele University" - }, - { - "author_name": "Dunhao Su", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yong Li", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Scott Guimond", - "author_inst": "Keele University" - }, - { - "author_name": "Timothy Rudd", - "author_inst": "National Institute for Biological Standards and Control" - }, - { - "author_name": "Stefano Elli", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Gavin Miller", - "author_inst": "Keele University" - }, - { - "author_name": "Quentin Nunes", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Patricia Procter", - "author_inst": "Keele University" - }, - { - "author_name": "Antonella Bisio", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "Nicholas Forsyth", - "author_inst": "Keele University" - }, - { - "author_name": "Jeremy Turnbull", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marco Guerrini", - "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" - }, - { - "author_name": "David Fernig", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Edwin Yates", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Marcelo Lima", - "author_inst": "Keele University" - }, - { - "author_name": "Mark Skidmore", - "author_inst": "Keele University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, - { + "rel_doi": "10.1101/2020.04.29.068890", + "rel_title": "Activity profiling of SARS-CoV-2-PLpro protease provides structural framework for anti-COVID-19 drug design", + "rel_date": "2020-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068890", + "rel_abs": "In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wioletta Rut", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Zongyang Lv", + "author_inst": "Medical University of South Carolina" + }, + { + "author_name": "Mikolaj Zmudzinski", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Stephanie Patchett", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Digant Nayak", + "author_inst": "Medical University of South Carolina" + }, + { + "author_name": "Scott J Snipas", + "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" + }, + { + "author_name": "Farid El Oualid", + "author_inst": "UbiQ Bio B.V." + }, + { + "author_name": "Miklos Bekes", + "author_inst": "Arvinas, Inc.," + }, + { + "author_name": "Tony T Huang", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Marcin Drag", + "author_inst": "Wroclaw University of Science and Technology" + }, + { + "author_name": "Shaun K Olsen", + "author_inst": "Medical University of South Carolina" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, + { "rel_doi": "10.1101/2020.04.29.067728", "rel_title": "An engineered stable mini-protein to plug SARS-Cov2 Spikes", "rel_date": "2020-04-29", @@ -1491928,6 +1488832,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.04.25.20079251", + "rel_title": "Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079251", + "rel_abs": "ObjectivesWe aimed to identify key demographic risk factors for hospital attendance with COVID-19 infection.\n\nDesignCommunity survey\n\nSettingThe COVID Symptom Tracker mobile application co-developed by physicians and scientists at Kings College London, Massachusetts General Hospital, Boston and Zoe Global Limited was launched in the UK and US on 24th and 29th March 2020 respectively. It captured self-reported information related to COVID-19 symptoms and testing.\n\nParticipants2,618,948 users of the COVID Symptom Tracker App. UK (95.7%) and US (4.3%) population. Data cut-off for this analysis was 21st April 2020.\n\nMain outcome measuresVisit to hospital and for those who attended hospital, the need for respiratory support in three subgroups (i) self-reported COVID-19 infection with classical symptoms (SR-COVID-19), (ii) selfreported positive COVID-19 test results (T-COVID-19), and (iii) imputed/predicted COVID-19 infection based on symptomatology (I-COVID-19). Multivariate logistic regressions for each outcome and each subgroup were adjusted for age and gender, with sensitivity analyses adjusted for comorbidities. Classical symptoms were defined as high fever and persistent cough for several days.\n\nResultsOlder age and all comorbidities tested were found to be associated with increased odds of requiring hospital care for COVID-19. Obesity (BMI >30) predicted hospital care in all models, with odds ratios (OR) varying from 1.20 [1.11; 1.31] to 1.40 [1.23; 1.60] across population groups. Pre-existing lung disease and diabetes were consistently found to be associated with hospital visit with a maximum OR of 1.79 [1.64,1.95] and 1.72 [1.27; 2.31]) respectively. Findings were similar when assessing the need for respiratory support, for which age and male gender played an additional role.\n\nConclusionsBeing older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. It is of utmost importance for governments and the scientific and medical communities to work together to find evidence-based means of protecting those deemed most vulnerable from COVID-19.\n\nTrial registrationThe App Ethics have been approved by KCL ethics Committee REMAS ID 18210, review reference LRS-19/20-18210", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mary Ni Lochlainn", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Karla A Lee", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Carole H Sudre", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Thomas Varsavsky", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "M. Jorge Cardoso", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Cristina Menni", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Ruth C. E. Bowyer", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Long H. Nguyen", + "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, MA, USA" + }, + { + "author_name": "David Alden Drew", + "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, MA, USA" + }, + { + "author_name": "Sajaysurya Ganesh", + "author_inst": "Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK" + }, + { + "author_name": "Julien Lavigne du Cadet", + "author_inst": "Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK" + }, + { + "author_name": "Alessia Visconti", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Maxim B Freydin", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Marc Modat", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Mark S Graham", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Joan Capdevila Pujol", + "author_inst": "Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK" + }, + { + "author_name": "Benjamin Murray", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Julia S El-Sayed Moustafa", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Xinyuan Zhang", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Richard Davies", + "author_inst": "Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK" + }, + { + "author_name": "Mario Falchi", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Timothy D Spector", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Andrew T Chan", + "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, MA, USA" + }, + { + "author_name": "Sebastien Ourselin", + "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, Westminster Bridge Road, SE17EH London, UK" + }, + { + "author_name": "Claire J Steves", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, Westminster Bridge Road, SE17EH London, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20079129", "rel_title": "CovidNLP: A Web Application for Distilling Systemic Implications of COVID-19 Pandemic with Natural Language Processing", @@ -1493031,57 +1490050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20077024", - "rel_title": "Effectiveness of isolation, testing, contact tracing and physical distancing on reducing transmission of SARS-CoV-2 in different settings", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077024", - "rel_abs": "BackgroundIsolation of symptomatic cases and tracing of contacts has been used as an early COVID-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. To maintain control of infection while also reducing disruption to populations, there is a need to understand what combination of measures - including novel digital tracing approaches and less intensive physical distancing - may be required to reduce transmission.\n\nMethodsUsing a model of individual-level transmission stratified by setting (household, work, school, other) based on BBC Pandemic data from 40,162 UK participants, we simulated the impact of a range of different testing, isolation, tracing and physical distancing scenarios. As well as estimating reduction in effective reproduction number, we estimated, for a given level of COVID-19 incidence, the number of contacts that would be newly quarantined each day under different strategies.\n\nResultsUnder optimistic but plausible assumptions, we estimated that combined testing and tracing strategies would reduce transmission more than mass testing or self-isolation alone (50-65% compared to 2-30%). If limits are placed on gatherings outside of home/school/work (e.g. maximum of 4 daily contacts in other settings), then manual contact tracing of acquaintances only could have a similar effect on transmission reduction as detailed contact tracing. In a scenario where there were 10,000 new symptomatic cases per day, we estimated in most contact tracing strategies, 140,000 to 390,000 contacts would be newly quarantined each day.\n\nConclusionsConsistent with previous modelling studies and country-specific COVID-19 responses to date, our analysis estimates that a high proportion of cases would need to self-isolate and a high proportion of their contacts to be successfully traced to ensure an effective reproduction number that is below one in the absence of other measures. If combined with moderate physical distancing measures, self-isolation and contact tracing would be more likely to achieve control.\n\nFundingWellcome Trust, EPSRC, European Commission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Petra Klepac", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Andrew Conlan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Stephen M Kissler", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Maria Tang", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Hannah Fry", - "author_inst": "UCL" - }, - { - "author_name": "Julia Gog", - "author_inst": "University of Cambridge" - }, - { - "author_name": "John Edmunds", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077271", "rel_title": "Enacting national social distancing policies corresponds with dramatic reduction in COVID19 infection rates", @@ -1493414,6 +1490382,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.24.20077776", + "rel_title": "Development and potential usefulness of the COVID-19 Ag Respi-Strip diagnostic assay in a pandemic context.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077776", + "rel_abs": "IntroductionCOVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. In this Original Research article, we describe the conception, the analytical and clinical performances as well as the risk management of implementing the COVID-19 Ag Respi-Strip in a diagnostic decision algorithm.\n\nMaterials and MethodsDevelopment of the COVID-19 Ag Respi-Strip resulted in a ready- to-use ICT assay based on a membrane technology with colloidal gold nanoparticles using monoclonal antibodies directed against the SARS-CoV and SARS-CoV-2 highly conserved nucleoprotein antigen. Four hundred observations were recorded for the analytical performance study and thirty tests were analysed for the cross-reactivity study. The clinical performance study was performed in a retrospective multi-centric evaluation on aliquots of 328 nasopharyngeal samples. COVID-19 Ag Respi-Strip results were compared with qRT-PCR as golden standard for COVID-19 diagnostics.\n\nResultsIn the analytical performance study, the reproducibility showed a between-observer disagreement of 1.7%, a robustness of 98%, an overall satisfying user friendliness and no cross-reactivity with other virus-infected nasopharyngeal samples. In the clinical performance study performed in three different clinical laboratories we found an overall sensitivity and specificity of 57.6% and 99.5% respectively with an accuracy of 82.6%. The cut-off of the assay was found at Ct<22. User-friendliness analysis and risk management assessment through Ishikawa diagram demonstrate that COVID-19 Ag Respi-Strip may be implemented in clinical laboratories according to biosafety recommendations.\n\nConclusionThe COVID-19 Ag Respi-Strip represents a promising rapid SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 in 15 minutes. Its role in the proposed diagnostic algorithm is complementary to the currently-used molecular techniques.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Olivier Vandenberg", + "author_inst": "LHUB-ULB," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20077735", "rel_title": "A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19", @@ -1494717,33 +1491704,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.23.20074575", - "rel_title": "Wisconsin April 2020 Election Not Associated with Increase in COVID-19 Infection Rates", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20074575", - "rel_abs": "BackgroundWisconsin (WI) held a primary election in the midst of the COVID-19 pandemic. Live voting at polls was allowed despite concern over increasing the spread of COVID-19. In addition to 1.1 million absentee ballots cast, 453,222 persons voted live. The purpose of our study was to determine if an increase in COVID-19 activity was associated with the election.\n\nMethodsUsing the voting age population for the United States (US), WI, and its 3 largest counties, and daily new COVID-19 case reports from various COVID-19 web-based dashboards, daily new case rates were calculated. With election day April 7, the incubation period included April 12-21. The new case activity in the rest of the US was compared with the Wisconsin activity during the incubation period.\n\nResultsWI daily new case rates were lower than those of the rest of the US for the 10-day period before the election and remained lower during the post exposure incubation period. The ratio of Wisconsin new case rates to US new case rates was 0.34 WI: 1 US for the 10 days leading up to the election and declined to 0.28 WI: 1 US for the 10-day post-incubation period after the election. Similar analysis for Milwaukee county showed a pre-election ratio of 1.02 Milwaukee: 1 US and after the election the ratio was 0.63 Milwaukee: 1 US. Dane county had a pre-election ratio of 0.21 Dane: 1 US case, and it fell to 0.13 Dane: 1 US after the election. Waukesha county had a pre-election ratio of 0.27 Waukesha: 1 US case and that fell to 0.19 Waukesha: 1 US after the election.\n\nConclusionsThere was no increase in COVID-19 new case daily rates observed for Wisconsin or its 3 largest counties following the election on April 7, 2020, as compared to the US, during the post-incubation interval period.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew C Berry", - "author_inst": "Division of Gastroenterology, Larkin Community Hospital, South Miami, FL, USA" - }, - { - "author_name": "Madhuri S Mulekar", - "author_inst": "Department of Mathematics and Statistics, University of South Alabama, Mobile, AL, USA" - }, - { - "author_name": "Bruce B Berry", - "author_inst": "Department of Medicine, Froedtert & The Medical College of Wisconsin, Milwaukee, WI, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20070649", "rel_title": "Performance of temporal artery temperature measurement in ruling out fever: implications for COVID-19 screening.", @@ -1495208,6 +1492168,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20076471", + "rel_title": "Pharmacokinetic bases of the hydroxychloroquine response in COVID-19: implications for therapy and prevention", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076471", + "rel_abs": "Chloroquine/hydroxychloroquine has recently been the subject of intense debate in regard to its potential antiviral activity against SARS-Cov-2, the etiological agent of COVID-19. Some report possible curative effects, others do not. In order to shed some light on this rather controversial topic, we used mathematical modelling to simulate possible scenarios of response to hydroxychloroquine in COVID-19 patients. Our computer-aided simulations show that hydroxychloroquine may have an impact on the amplitude of the viral load peak but that viral clearance is not significantly accelerated if the drug is not administered early enough (i.e. when viral loads range from 1 to 1,000 copies/mL). Although some authors had used the trough plasma concentrations or the theoretical drug distribution in the lung to model the effect of chloroquine/hydroxychloroquine on COVID-19, the theoretical drug response based on the trough whole blood concentrations of the drug agreed well with the results of the clinical trials so far reported. Moreover, the effects of chloroquine/hydroxychloroquine could be fully explained when taking into account also the capacity of this drug to raise cell-mediated responses against the productively SARS-Cov-2-infected cells. On the whole, the present study suggests that chloroquine/hydroxychloroquine has a narrow therapeutic window, which overlaps with the highest tolerated doses. These considerations may have implications for development of anti-COVID-19 combination therapies and prevention strategies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Andrea Savarino", + "author_inst": "Department of Infectious Diseases, Italian Institute of Health, Rome, Italy." + }, + { + "author_name": "Mohammad Tarek", + "author_inst": "Bioinformatics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.23.20076042", "rel_title": "Features of 16,749 hospitalised UK patients with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol", @@ -1496115,25 +1493098,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20076430", - "rel_title": "A poor-man's approach to the effective reproduction number: the COVID-19 case", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076430", - "rel_abs": "It is shown that estimates of the effective reproduction number Rt for COVID-19 using standard packages such as EO_SCPLOWPIC_SCPLOWEO_SCPLOWSTIMC_SCPLOW can be reproduced very accurately using the expression Rt = c(t)/c(t -{tau} ), where c(t) is the incidence at time t and{tau} the mean value of the series interval.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jose Menendez", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20076166", "rel_title": "Early detection of superspreaders by mass group pool testing can mitigate COVID-19 pandemic", @@ -1496806,6 +1493770,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.26.063024", + "rel_title": "Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication", + "rel_date": "2020-04-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.26.063024", + "rel_abs": "1.The open reading frame (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase (RdRp); helicase and 3-5 exonuclease. Sequence analyses of ORF1ab unravelled emergence of mutations especially in the viral RdRp and helicase at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp (at position 4715 in the context of the polyprotein/ at position 323 of RdRp) leads to rigidification of structure and that mutation in the helicase (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp better for therapeutic intervention.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Feroza Begum", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "DEBICA MUKHERJEE", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "SANDEEPAN DAS", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "DLUYA THAGRIKI", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "PREM PRAKASH TRIPATHI", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "ARUP KUMAR BANERJEE", + "author_inst": "North Bengal Medical College and Hospital" + }, + { + "author_name": "UPASANA RAY", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.26.062422", "rel_title": "Quality control of low-frequency variants in SARS-CoV-2 genomes", @@ -1497533,25 +1494540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20076026", - "rel_title": "Strict Lower Bound on the COVID-19 Fatality Rate in Overwhelmed Healthcare Systems", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076026", - "rel_abs": "The Infection Fatality Rate (IFR) for COVID-19 is a poorly known, yet crucial, aspect of the disease. Counting only current deaths in a region and assuming everyone in that region is infected provides an absolute lower bound on the IFR. Using this estimator for New York City, Lombardy and Madrid yields strong bounds on the average IFR in overwhelmed health systems. Their combined 35, 152 deaths implies an IFR [≥] 0.14% averaged over 25.1 million people. This is the best-case scenario and conclusively demonstrates that COVID-19 is more deadly than influenza. The actual value of the average COVID-19 IFR is likely to be higher than this bound.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Bruce A Bassett", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20076075", "rel_title": "How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?", @@ -1497924,6 +1494912,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.21.20072637", + "rel_title": "Research on CNN-based Models Optimized by Genetic Algorithm and Application in the Diagnosis of Pneumonia and COVID-19", + "rel_date": "2020-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20072637", + "rel_abs": "In this research, an optimized deep learning method was proposed to explore the possibility and practicality of neural network applications in medical imaging. The method was used to achieve the goal of judging common pneumonia and even COVID-19 more effectively. Where, the genetic algorithm was taken advantage to optimize the Dropout module, which is essential in neural networks so as to improve the performance of typical neural network models. The experiment results demonstrate that the proposed method shows excellent performance and strong practicability in judging pneumonia, and the application of advanced artificial intelligence technology in the field of medical imaging has broad prospects.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zihan Zeng", + "author_inst": "Beijing Normal University, Zhuhai" + }, + { + "author_name": "Bo Wang", + "author_inst": "Beijing Normal University, Zhuhai" + }, + { + "author_name": "Zhiwen Zhao", + "author_inst": "Beijing Normal University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.21.20074732", "rel_title": "Forecasting the impact of the first wave of the COVID-19 pandemic on hospital demand and deaths for the USA and European Economic Area countries", @@ -1498511,65 +1495526,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.22.055608", - "rel_title": "Self-amplifying RNA SARS-CoV-2 lipid nanoparticle vaccine induces equivalent preclinical antibody titers and viral neutralization to recovered COVID-19 patients", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.055608", - "rel_abs": "The spread of the SARS-CoV-2 into a global pandemic within a few months of onset motivates the development of a rapidly scalable vaccine. Here, we present a self-amplifying RNA encoding the SARS-CoV-2 spike protein encapsulated within a lipid nanoparticle as a vaccine and demonstrate induction of robust neutralization of a pseudo-virus, proportional to quantity of specific IgG and of higher quantities than recovered COVID-19 patients. These data provide insight into the vaccine design and evaluation of immunogenicity to enable rapid translation to the clinic.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Paul F. McKay", - "author_inst": "Imperial College London" - }, - { - "author_name": "Kai Hu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anna K. Blakney", - "author_inst": "Imperial College London" - }, - { - "author_name": "Karnyart Samnuan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Clement R. Bouton", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Rogers", - "author_inst": "Imperial College London" - }, - { - "author_name": "Krunal Polra", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paulo J. C. Lin", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Christopher Barbosa", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Ying Tam", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Robin J. Shattock", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.19.048991", "rel_title": "CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2", @@ -1499218,6 +1496174,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.23.20076455", + "rel_title": "Role of the atmospheric pollution in the Covid-19 outbreak risk in Italy", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076455", + "rel_abs": "After the initial outbreak in China, the diffusion in Italy of SARS-CoV-2 is exhibiting a clear regional trend with Northern areas being the most affected in terms of both frequency and severity of cases. Among multiple factors possibly involved in such geographical differences, a role has been hypothesized for atmospheric pollution. We provide additional evidence on the possible influence of air quality, particularly in terms of chronicity of exposure on the spread viral infection in Italian regions. Actual data on COVID-19 outbreak in Italian provinces and corresponding long-term air quality evaluations, were obtained from Italian and European agencies, elaborated and tested for possible interactions. Our elaborations reveal that, beside concentrations, the chronicity of exposure may influence the anomalous variability of SARS-CoV-2 in Italy. Data on distribution of atmospheric pollutants (NO2, O3, PM2.5 and PM10) in Italian regions during the last 4 years, days exceeding regulatory limits, and years of the last decade (2010-2019) in which the limits have been exceeded for at least 35 days, confirmed that Northern Italy has been constantly exposed to chronic air pollution. Long-term air-quality data significantly correlated with cases of Covid-19 in up to 71 Italian provinces (updated 27 April 2020) providing further evidence that chronic exposure to atmospheric contamination may represent a favourable context for the spread of the virus. Pro-inflammatory responses and high incidence of respiratory and cardiac affections are well known, while the capability of this coronavirus to bind particulate matters remains to be established. Atmospheric and environmental pollution should be considered as part of an integrated approach for sustainable development, human health protection and prevention of epidemic spreads but in a long-term and chronic perspective, since adoption of mitigation actions during a viral outbreak could be of limited utility.\n\nCapsuleChronic exposure to air pollutants might have a role in the spread of COVID-19 in Italian regions. Diffusion of Covid-19 in 71 Italian provinces correlated with long-term air-quality data.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Daniele Fattorini", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Francesco Regoli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.22.20076091", "rel_title": "Gut microbiota may underlie the predisposition of healthy individuals to COVID-19", @@ -1500173,29 +1497152,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.04.21.20074591", - "rel_title": "COVID-19 Fatality and Comorbidity Risk Factors among Confirmed Patients in Mexico", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074591", - "rel_abs": "As of April 18, 2020, 2.16 million patients in the world had been tested positive with Coronavirus (COVID-19) and 146,088 had died, which accounts for a case fatality rate of 6.76%. In Mexico, according to official statistics (April 18), 7,497 cases have been confirmed with 650 deaths, for a case fatality rate of 8.67%. These estimates, however, may not reflect the final fatality risk among COVID-19 confirmed patients, because they are based on cross-sectional counts of diagnosed and deceased patients, and therefore are not adjusted by time of exposure and right-censorship. In this paper we estimate fatality risks based on survival analysis methods, calculated from individual-level data on symptomatic patients confirmed with COVID-19 recently released by the Mexican Ministry of Health. The estimated fatality risk after 35 days of onset of symptoms is 12.38% (95% CI: 11.37-13.47). Fatality risks sharply rise with age, and significantly increase for males (59%) and individuals with comorbidities (38%-168%, depending on the disease). Two reasons may explain the high COVID-19 related fatality risk observed in Mexico, despite its younger age structure: the high selectivity and self-selectivity in testing and the high prevalence of chronic-degenerative diseases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Patricio Sol\u00eds", - "author_inst": "El Colegio de M\u00e9xico" - }, - { - "author_name": "Hiram Carre\u0148o", - "author_inst": "El Colegio de M\u00e9xico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.21.20074435", "rel_title": "The spatio-temporal epidemic dynamics of COVID-19 outbreak in Africa", @@ -1500656,6 +1497612,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.20.20064105", + "rel_title": "Clinical and Imaging Findings in COVID-19 Patients Complicated by Pulmonary Embolism", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20064105", + "rel_abs": "ObjectiveTo describe clinical, and imaging findings including the evolution pattern in COVID-19 pneumonia complicated by pulmonary embolism (PE).\n\nMethodsEleven of 1453 patients with a probable diagnosis of COVID-19 pneumonia were retrospectively selected for the presence of PE. Clinical and laboratory data were recorded. All cross-sectional CT imaging was qualitatively scored for the first 28 days after onset of symptoms.\n\nResultsOf 24 patients underwent CTA-PE, 11 were confirmed with PE. All 11 patients developed acute respiratory distress syndrome (ARDS). The pulmonary emboli were most common in segmental and subsegmental pulmonary arteries. We observed an evolution pattern of predominant findings with ground-glass opacities (GGO) to GGO with crazy paving in 3 patients, then to consolidation with linear densities, or to reticulation in 9 patients. Lung cysts or traction bronchiectasis could be seen from day 5 to 9 after symptoms and reticulation, subpleural curvilinear lines were more common from day 20. The pulmonary opacities were predominantly peripheral in distribution with relative sparing of nondependent lungs. The severity of lung involvement was high with an average score of 9.7 in the first phase, 18 in the second phase plateauing in the next two phases, with a slight decrease to 16.9 in the late phase.\n\nConclusionThe incidence of PE among suspected patients in COVID-19 was high. The pulmonary emboli were most common in segmental and subsegmental pulmonary arteries. Our study suggests PE may occur with increased frequency in the ARDS subgroup. The evolution of radiographic abnormalities showed a general pattern, but are also unique with more extensive lung injury and specific imaging features, which may due to the exist of ARDS in these patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ting Li", + "author_inst": "The Central Hospital of Wuhan, Tongji Medical College, Huzhong University of Science and Technology, Wuhan, Hubei, China" + }, + { + "author_name": "Gregory Kicska", + "author_inst": "University of Washington" + }, + { + "author_name": "Paul E Kinahan", + "author_inst": "University of Washington" + }, + { + "author_name": "Chengcheng Zhu", + "author_inst": "University of Washington" + }, + { + "author_name": "Murat Alp Oztek", + "author_inst": "University of Washington" + }, + { + "author_name": "Wei Wu", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.23.057190", "rel_title": "Genetic analysis of the novel SARS-CoV-2 host receptor TMPRSS2 in different populations.", @@ -1501767,45 +1498762,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.24.050534", - "rel_title": "ACE2 Homo-dimerization, Human Genomic variants and Interaction of Host Proteins Explain High Population Specific Differences in Outcomes of COVID19", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.050534", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive single-stranded RNA virus that causes a highly contagious Corona Virus Disease (COVID19). Entry of SARS-CoV-2 in human cells depends on binding of the viral spike (S) proteins to cellular receptor Angiotensin-converting enzyme 2 (ACE2) and on S-protein priming by host cell serine protease TMPRSS2. Recently, COVID19 has been declared pandemic by World Health Organization (WHO) yet high differences in disease outcomes across countries have been seen. We provide evidences to explain these population-level differences. One of the key factors of entry of the virus in host cells presumably is because of differential interaction of viral proteins with host cell proteins due to different genetic backgrounds. Based on our findings, we conclude that a higher expression of ACE2 is facilitated by natural variations, acting as Expression quantitative trait loci (eQTLs), with different frequencies in different populations. We suggest that high expression of ACE2 results in homo-dimerization, proving disadvantageous for TMPRSS2 mediated cleavage of ACE2; whereas, the monomeric ACE2 has higher preferential binding with SARS-CoV-2 S-Protein vis-a-vis its dimerized counterpart. Further, eQTLs in TMPRSS2 and natural structural variations in the gene may also result in differential outcomes towards priming of viral S-protein, a critical step for entry of the Virus in host cells. In addition, we suggest that several key host genes, like SLC6A19, ADAM17, RPS6, HNRNPA1, SUMO1, NACA, BTF3 and some other proteases as Cathepsins, might have a critical role. To conclude, understanding population specific differences in these genes may help in developing appropriate management strategies for COVID19 with better therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Swarkar Sharma", - "author_inst": "Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India" - }, - { - "author_name": "Inderpal Singh", - "author_inst": "Independent Researcher, Bioinfores Pvt. Ltd., R. S. Pura, Jammu, Jammu and Kashmir, India" - }, - { - "author_name": "Shazia Haider", - "author_inst": "Jaypee Institute of Information Technology, Noida, sector-62, Uttar Pradesh, India" - }, - { - "author_name": "Md. Zubbair Malik", - "author_inst": "Jawaharlal Nehru University, New Delhi, India" - }, - { - "author_name": "Kalaiarasan Ponnusamy", - "author_inst": "School of Biotechnology, Jawaharlal Nehru University, New Delhi, India" - }, - { - "author_name": "Ekta Rai", - "author_inst": "Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.04.20.20065953", "rel_title": "The production of antibodies for SARS-CoV-2 and its clinical implication", @@ -1502426,6 +1499382,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071357", + "rel_title": "Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men?", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071357", + "rel_abs": "The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome events (CME) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (CME and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, CME and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Luis A Perez-Jurado", + "author_inst": "Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM)" + }, + { + "author_name": "Alejandro Caceres", + "author_inst": "ISGlobal" + }, + { + "author_name": "Tonu Esko", + "author_inst": "EGCUT" + }, + { + "author_name": "Miguel Lopez de Heredia", + "author_inst": "Centro de Investigacion Biomodica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain." + }, + { + "author_name": "Ines Quintela", + "author_inst": "Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain." + }, + { + "author_name": "Raquel Cruz", + "author_inst": "Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain." + }, + { + "author_name": "Pablo Lapunzina", + "author_inst": "Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain." + }, + { + "author_name": "Angel Carracedo", + "author_inst": "Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain." + }, + { + "author_name": "- SCOURGE Cohort Group", + "author_inst": "" + }, + { + "author_name": "Juan R Gonzalez", + "author_inst": "Barcelona Institute for Global Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.04.20.20073288", "rel_title": "A follow-up study of children infected with SARS-CoV-2 from Western China", @@ -1503521,45 +1500532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.04.20.20070938", - "rel_title": "Variational-LSTM Autoencoder to forecast the spread of coronavirus across the globe", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20070938", - "rel_abs": "Modelling the spread of coronavirus globally while learning trends at global and country levels remains crucial for tackling the pandemic. We introduce a novel variational LSTM-Autoencoder model to predict the spread of coronavirus for each country across the globe. This deep spatio-temporal model does not only rely on historical data of the virus spread but also includes factors related to urban characteristics represented in locational and demographic data (such as population density, urban population, and fertility rate), an index that represent the governmental measures and response amid toward mitigating the outbreak (includes 13 measures such as: 1) school closing, 2) workplace closing, 3) cancelling public events, 4) close public transport, 5) public information campaigns, 6) restrictions on internal movements, 7) international travel controls, 8) fiscal measures, 9) monetary measures, 10) emergency investment in health care, 11) investment in vaccines, 12) virus testing framework, and 13) contact tracing). In addition, the introduced method learns to generate graph to adjust the spatial dependences among different countries while forecasting the spread. We trained two models for short and long-term forecasts. The first one is trained to output one step in future with three previous timestamps of all features across the globe, whereas the second model is trained to output 10 steps in future. Overall, the trained models show high validation for forecasting the spread for each country for short and long-term forecasts, which makes the introduce method a useful tool to assist decision and policymaking for the different corners of the globe.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohamed R. Ibrahim", - "author_inst": "University College London (UCL)" - }, - { - "author_name": "James Haworth", - "author_inst": "University College London" - }, - { - "author_name": "Aldo Lipani", - "author_inst": "University College London" - }, - { - "author_name": "Nilufer Aslam", - "author_inst": "University College London" - }, - { - "author_name": "Tao Cheng", - "author_inst": "University College London" - }, - { - "author_name": "Nicola Christie", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.19.20071761", "rel_title": "Minimising lockdown periods for regional elimination of covid-19", @@ -1504184,6 +1501156,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.04.21.20073734", + "rel_title": "COVID-19 epidemic in Sri Lanka: A mathematical and computational modelling approach to control", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073734", + "rel_abs": "The ongoing COVID19 outbreak originated in the city of Wuhan, China has caused a significant damage to the world population and the global economy. It has claimed more than 50,000 lives worldwide and more than one million of people have been infected as of 04th April 2020.\n\nIn Sri Lanka, the first case of COVI19 was reported late January 2020 was a Chinese national and the first local case was identified in the second week of March. Since then, the government of Sri Lanka introduced various sequential measures to improve social distancing such as closure of schools and education institutes, introducing work from home model to reduce the public gathering, introducing travel bans to international arrivals and more drastically, imposed island wide curfew expecting to minimize the burden of the disease to the Sri Lankan health system and the entire community. Currently, there are 159 cases with five fatalities and also reported that 24 patients are recovered and discharged from hospitals.\n\nIn this study, we use the SEIR conceptual model and its modified version by decomposing infected patients into two classes; patients who show mild symptoms and patients who tend to face severe respiratory problems and are required to treat in intensive care units. We numerically simulate the models for about five months period considering three critical parameters of COVID transmission mainly in the Sri Lankan context; efficacy of control measures, rate of overseas imported cases and time to introduce social distancing measures by the respective authorities.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Tharindu Wickramaarachchi", + "author_inst": "The Open University of sri Lanka" + }, + { + "author_name": "Sanjeewa Perera", + "author_inst": "Department of Mathematics, University of Colombo, Colombo 03, Sri Lanka" + }, + { + "author_name": "Saroj Jayasinghe", + "author_inst": "University of Colombo Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072223", "rel_title": "Predicting mortality attributable to SARS-CoV-2: A mechanistic score relating obesity and diabetes to COVID-19 outcomes in Mexico", @@ -1505047,101 +1502046,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.23.056853", - "rel_title": "Mapping the Immunodominance Landscape of SARS-CoV-2 Spike Protein for the Design of Vaccines against COVID-19", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.23.056853", - "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic is a serious threat to global public health, and imposes severe burdens on the entire human society. The severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) can cause severe respiratory illness and death. Currently, there are no specific antiviral drugs that can treat COVID-19. Several vaccines against SARS-CoV-2 are being actively developed by research groups around the world. The surface S (spike) protein and the highly expressed internal N (nucleocapsid) protein of SARS-CoV-2 are widely considered as promising candidates for vaccines. In order to guide the design of an effective vaccine, we need experimental data on these potential epitope candidates. In this study, we mapped the immunodominant (ID) sites of S protein using sera samples collected from recently discharged COVID-19 patients. The SARS-CoV-2 S protein-specific antibody levels in the sera of recovered COVID-19 patients were strongly correlated with the neutralising antibody titres. We used epitope mapping to determine the landscape of ID sites of S protein, which identified nine linearized B cell ID sites. Four out of the nine ID sites were found in the receptor-binding domain (RBD). Further analysis showed that these ID sites are potential high-affinity SARS-CoV-2 antibody binding sites. Peptides containing two out of the nine sites were tested as vaccine candidates against SARS-CoV-2 in a mouse model. We detected epitope-specific antibodies and SARS-CoV-2-neutralising activity in the immunised mice. This study for the first time provides human serological data for the design of vaccines against COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Bao-zhong Zhang", - "author_inst": "Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" - }, - { - "author_name": "Ye-fan Hu", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Lin-lei Chen", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Yi-gang Tong", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Jing-chu Hu", - "author_inst": "Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" - }, - { - "author_name": "Jian-piao Cai", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kwok-Hung Chan", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Ying Dou", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Jian Deng", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Hua-rui Gong", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Chaiyaporn Kuwentrai", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Wenjun Li", - "author_inst": "Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" - }, - { - "author_name": "Xiao-lei Wang", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Hin Chu", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Can-hui Su", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Ivan Fan-Ngai Hung", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Thomas Chung Cheung Yau", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kelvin Kai-Wang To", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kwok Yung Yuen", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Jian-Dong Huang", - "author_inst": "University of Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.16.20067744", "rel_title": "Psychiatric Symptoms Related to the COVID-19 Pandemic", @@ -1505610,6 +1502514,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20073130", + "rel_title": "Characteristics of scientific articles on COVID-19 published during the initial three months of the pandemic: a meta-epidemiological study", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20073130", + "rel_abs": "ImportanceThe COVID-19 pandemic has been characterized by an unprecedented amount of published scientific articles.\n\nObjectiveTo assess the characteristics of articles published during the first 3 months of the COVID-19 pandemic and to compare it with articles published during 2009 H1N1 swine influenza pandemic.\n\nData sourcesArticles on COVID-19 and on H1N1 swine influenza indexed in PubMed (Medline) during the first 3 months of these pandemics.\n\nStudy selectionAny article published in the respective study periods that included any terminology related to COVID-19 or H1N1 in the title, abstract or full-text was eligible for inclusion. Articles that did not present an English abstract, as well as correspondence to previous research and erratum were excluded.\n\nData Extraction and SynthesisTwo operators conducted the selection of articles and data extraction procedures independently. The article is reported following STROBE guidelines for observational studies.\n\nMain Outcomes and MeasuresPrevalence of primary and secondary articles. Prevalence of reporting of limitations in the abstracts.\n\nResultsOf the 2482 articles retrieved, 1165 were included. Approximately half of them were secondary articles (575, 49.4%). Common primary articles were: human medical research (340, 59.1%), in silico studies (182, 31.7%) and in vitro studies (26, 4.5%). Of the human medical research, the vast majority were observational studies and cases series, followed by single case reports and one randomized controlled trial. Secondary articles were mainly reviews, viewpoints and editorials (373, 63.2%). The second largest category was guidelines or guidance articles, including 193 articles (32.7%), of which 169 were indications for specific departments, patients or procedures. Limitations were reported in 42 out of 1165 abstracts (3.6%), with 10 abstracts reporting actual methodological limitations.\n\nIn a similar timeframe in 2009 there were 223 articles published on the H1N1 pandemic. As compared to that pandemic, during COVID-19 there were higher chances to publish reviews and guidance articles and lower chances to publish in vitro and animal research studies.\n\nConclusions and RelevanceAs compared to the most recent pandemic, there is an overwhelming amount of information published on COVID-19. However, the majority of the articles published do not add significant information, possibly diluting the original information published. Also, only a negligible number of published articles reports limitations in the abstracts, hindering a rapid interpretation of their shortcomings.\n\nProtocol RegistrationOur protocol was registered in Open Science Framework: https://osf.io/eanzr\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSPatients, health care professionals, policy makers, and the general public want to know what has been published on COVID-19 and what quality of research was available for decision making.\n\nFindingsHalf of the publications with an abstract were original research studies, i.e., for every original research article (primary article) on COVID-19 there was at least one other article that discussed or summarized what was already known (secondary article). Only 3.6% of the abstracts reported a clear statement on the limitations of the article.\n\nMeaningClinicians and policy makers have to filter out a large body of secondary articles, which may slow down decision making during the COVID-19 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Nicola Di Girolamo", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Reint Meursinge Reynders", + "author_inst": "University of Amsterdam" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20073098", "rel_title": "A cell phone data driven time use analysis of the COVID-19 epidemic", @@ -1506665,61 +1503592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.04.18.20071019", - "rel_title": "Distinguish Coronavirus Disease 2019 Patients in General Surgery Emergency by CIAAD Scale: Development and Validation of a Prediction Model Based on 822 Cases in China", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20071019", - "rel_abs": "ABATRACTO_ST_ABSIMPORTANCEC_ST_ABSIn the epidemic, surgeons cannot distinguish infectious acute abdomen patients suspected COVID-19 quickly and effectively.\n\nOBJECTIVETo develop and validate a predication model, presented as nomogram and scale, to distinguish infectious acute abdomen patients suspected coronavirus disease 2019 (COVID-19).\n\nDESIGNDiagnostic model based on retrospective case series.\n\nSETTINGTwo hospitals in Wuhan and Beijing, China.\n\nPTRTICIPANTS584 patients admitted to hospital with laboratory confirmed SARS-CoV-2 from 2 Jan 2020 to15 Feb 2020 and 238 infectious acute abdomen patients receiving emergency operation from 28 Feb 2019 to 3 Apr 2020.\n\nMETHODSLASSO regression and multivariable logistic regression analysis were conducted to develop the prediction model in training cohort. The performance of the nomogram was evaluated by calibration curves, receiver operating characteristic (ROC) curves, decision curve analysis (DCA) and clinical impact curves in training and validation cohort. A simplified screening scale and managing algorithm was generated according to the nomogram.\n\nRESULTSSix potential COVID-19 prediction variables were selected and the variable abdominal pain was excluded for overmuch weight. The five potential predictors, including fever, chest computed tomography (CT), leukocytes (white blood cells, WBC), C-reactive protein (CRP) and procalcitonin (PCT), were all independent predictors in multivariable logistic regression analysis (p [≤]0.001) and the nomogram, named COVID-19 Infectious Acute Abdomen Distinguishment (CIAAD) nomogram, was generated. The CIAAD nomogram showed good discrimination and calibration (C-index of 0.981 (95% CI, 0.963 to 0.999) and AUC of 0.970 (95% CI, 0.961 to 0.982)), which was validated in the validation cohort (C-index of 0.966 (95% CI, 0.960 to 0.972) and AUC of 0.966 (95% CI, 0.957 to 0.975)). Decision curve analysis revealed that the CIAAD nomogram was clinically useful. The nomogram was further simplified into the CIAAD scale.\n\nCONCLUSIONSWe established an easy and effective screening model and scale for surgeons in emergency department to distinguish COVID-19 patients from infectious acute abdomen patients. The algorithm based on CIAAD scale will help surgeons manage infectious acute abdomen patients suspected COVID-19 more efficiently.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Bangbo Zhao", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Yingxin Wei", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Wenwu Sun", - "author_inst": "Department of Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Sciences and Technology" - }, - { - "author_name": "Cheng Qin", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xingtong Zhou", - "author_inst": "Department of Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Zihao Wang", - "author_inst": "Department of Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Tianhao Li", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Hongtao Cao", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Weibin Wang", - "author_inst": "Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Yujun Wang", - "author_inst": "Department of Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Sciences and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2020.04.17.20069930", "rel_title": "A single-cell atlas of the peripheral immune response to severe COVID-19", @@ -1507308,6 +1504180,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.18.20071035", + "rel_title": "Outbreak dynamics of COVID-19 in Europe and the effect of travel restrictions", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20071035", + "rel_abs": "For the first time in history, on March 17,2020, the European Union closed all its external borders to contain the spreading of the coronavirus 2019, COVID-19. Throughout two past months, governments around the world have implemented massive travel restrictions and border control to mitigate the outbreak of this global pandemic. However, the precise effects of travel restrictions on the outbreak dynamics of COVID-19 remain unknown. Here we combine a global network mobility model with a local epidemiology model to simulate and predict the outbreak dynamics and outbreak control of COVID-19 across Europe. We correlate our mobility model to passenger air travel statistics and calibrate our epidemiology model using the number of reported COVID-19 cases for each country. Our simulations show that mobility networks of air travel can predict the emerging global diffusion pattern of a pandemic at the early stages of the outbreak. Our results suggest that an unconstrained mobility would have significantly accelerated the spreading of COVID-19, especially in Central Europe, Spain, and France. Ultimately, our network epidemiology model can inform political decision making and help identify exit strategies from current travel restrictions and total lockdown.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kevin Linka", + "author_inst": "Stanford University" + }, + { + "author_name": "Mathias Peirlinck", + "author_inst": "Stanford University" + }, + { + "author_name": "Francisco Sahli Costabal", + "author_inst": "Pontificia Universidad Catolica de Chile" + }, + { + "author_name": "Ellen Kuhl", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.19.20070995", "rel_title": "Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn's disease", @@ -1508495,77 +1505398,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.17.20061242", - "rel_title": "Distinguishing COVID-19 from influenza pneumonia in the early stage through CT imaging and clinical features", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20061242", - "rel_abs": "PurposeTo identify differences in CT imaging and clinical features between COVID-19 and influenza pneumonia in the early stage, and to identify the most valuable features in the differential diagnosis.\n\nMaterials and MethodA consecutive cohort of 73 COVID-19 and 48 influenza pneumonia patients were retrospectively recruited from five independent institutions. The courses of both diseases were confirmed to be in the early stages (2.66 {+/-} 2.62 days for COVID-19 and 2.19 {+/-} 2.10 days for influenza pneumonia after onset). The chi-square test, students t-test, and Kruskal-Wallis H-test were performed to compare CT imaging and clinical features between the two groups. Spearman or Kendall correlation tests between feature metrics and diagnosis outcomes were also assessed. The diagnostic performance of each feature in differentiating COVID-19 from influenza pneumonia was evaluated with univariate analysis. The corresponding area under the curve (AUC), accuracy, specificity, sensitivity and threshold were reported.\n\nResultsThe ground-glass opacification (GGO) was the most common imaging feature in COVID-19, including pure-GGO (75.3%) and mixed-GGO (78.1%), mainly in peripheral distribution. For clinical features, most COVID-19 patients presented normal white blood cell (WBC) count (89.04%) and neutrophil count (84.93%). Twenty imaging features and 6 clinical features were identified to be significantly different between the two diseases. The diagnosis outcomes correlated significantly with the WBC count (r=-0.526, P<0.001) and neutrophil count (r=-0.500, P<0.001). Four CT imaging features had absolute correlations coefficients higher than 0.300 (P<0.001), including crazy-paving pattern, mixed-GGO in peripheral area, pleural effusions, and consolidation.\n\nConclusionsAmong a total of 1537 lesions and 62 imaging and clinical features, 26 features were demonstrated to be significantly different between COVID-19 and influenza pneumonia. The crazy-paving pattern was recognized as the most powerful imaging feature for the differential diagnosis in the early stage, while WBC count yielded the highest diagnostic efficacy in clinical manifestations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zhiqi Yang", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China." - }, - { - "author_name": "Daiying Lin", - "author_inst": "Department of Radiology, Shantou Central Hospital, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Xiaofeng Chen", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China" - }, - { - "author_name": "Jinming Qiu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Shengkai Li", - "author_inst": "Department of Radiology, Huizhou Municipal Central Hospital, Huizhou, Guangdong 516001, China." - }, - { - "author_name": "Ruibin Huang", - "author_inst": "Department of Radiology, First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Hongfu Sun", - "author_inst": "School of Information Technology and Electrical Engineering, University of Queensland, Queensland, 4072, Australia." - }, - { - "author_name": "Yuting Liao", - "author_inst": "GE Healthcare, Guangzhou 510623, China." - }, - { - "author_name": "Jianning Xiao", - "author_inst": "Department of Radiology, Shantou Central Hospital, Shantou, Guangdong, 515041, P. R. China." - }, - { - "author_name": "Yanyan Tang", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Guorui Liu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Renhua Wu", - "author_inst": "Department of Radiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, 515000, P. R. China" - }, - { - "author_name": "Xiangguang Chen", - "author_inst": "Department of Radiology, Meizhou People`s Hospital, Guangdong, 514031, P. R. China." - }, - { - "author_name": "Zhuozhi Dai", - "author_inst": "Second Affiliated Hospital of Shantou University Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.04.17.20064469", "rel_title": "Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis", @@ -1509294,6 +1506126,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.12.20062687", + "rel_title": "Controlled Avalanche: A Regulated Voluntary Exposure Approach for Addressing Covid19", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062687", + "rel_abs": "BackgroundThe ongoing Covid-19 pandemic has driven many countries to take radical suppression measures. While reducing mortality, these measures result in severe economic repercussions, and inhibit the development of herd immunity. Until an effective vaccine will be available, we propose an alternative approach, akin to avalanche control at ski resorts, a practice which intentionally triggers small avalanches in order to prevent a singular catastrophic one. Its main goal is to approach herd immunity faster than the current alternatives, with lower mortality rates and lower demand for critical health-care resources. According to this approach, individuals whose probability of developing serious health conditions is low (i.e. 20-49 years old with no comorbidities) will be offered the option to be voluntarily exposed to the virus under controlled supervision, and will then be issued immunity certificates if they are confirmed to have developed SARS-CoV-2 antibodies.\n\nMethodsUsing a compartmental model we examine the implications of the controlled avalanche (CA) strategy over the population in Israel. We compare four scenarios: in two scenarios the CA program is applied to the low-risk population (with the rest of the population subject to mitigation measures), followed by mitigation for the entire population or by uncontrolled spread. These are compared to mitigated and uncontrolled scenarios without the CA program. We discuss the economic, ethical and public health implications of the CA strategy.\n\nFindingsWe show that compared to mitigation of the entire population, the CA strategy reduces the overall mortality by 43%, reduces the maximum number of people in need for ICUs by 62% and decreases the time required for release of 50% of the low-risk population by more than 2 months.\n\nInterpretationThis study suggests an ethically acceptable practice, that enables reaching herd immunity faster than the current alternatives, with low mortality and minimal economic damage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Eyal Klement", + "author_inst": "Hebrew University, Jerusalem, Israel" + }, + { + "author_name": "Alon Klement", + "author_inst": "Buchmann Faculty of Law, Tel-Aviv University, Israel" + }, + { + "author_name": "David Chinitz", + "author_inst": "Department of Health Policy and Management, School of Public Health, Hebrew University, Jerusalem, Israel" + }, + { + "author_name": "Alon Harel", + "author_inst": "Phillip and Estelle Mizock Chair in Administrative and Criminal Law, The Faculty of Law, the Hebrew University, Jerusalem, Israel" + }, + { + "author_name": "Eyal Fattal", + "author_inst": "Department of Applied Mathematics, Israel Institute for Biological Research, Ness-Ziona, Israel" + }, + { + "author_name": "Ziv Klausner", + "author_inst": "Department of Applied Mathematics, Israel Institute for Biological Research, Ness-Ziona, Israel" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.18.20064774", "rel_title": "How many are at increased risk of severe COVID-19 disease? Rapid global, regional and national estimates for 2020", @@ -1510021,65 +1506892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.17.20068460", - "rel_title": "CAN-NPI: A Curated Open Dataset of Canadian Non-Pharmaceutical Interventions in Response to the Global COVID-19 Pandemic", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068460", - "rel_abs": "Non-pharmaceutical interventions (NPIs) have been the primary tool used by governments and organizations to mitigate the spread of the ongoing pandemic of COVID-19. Natural experiments are currently being conducted on the impact of these interventions, but most of these occur at the subnational level - data not available in early global datasets. We describe the rapid development of the first comprehensive, labelled dataset of 1640 NPIs implemented at federal, provincial/territorial and municipal levels in Canada to guide COVID-19 research. For each intervention, we provide: a) information on timing to aid in longitudinal evaluation, b) location to allow for robust spatial analyses, and c) classification based on intervention type and target population, including classification aligned with a previously developed measure of government response stringency. This initial dataset release (v1.0) spans January 1st, and March 31st, 2020; bi-weekly data updates to continue for the duration of the pandemic. This novel dataset enables robust, inter-jurisdictional comparisons of pandemic response, can serve as a model for other jurisdictions and can be linked with other information about case counts, transmission dynamics, health care utilization, mobility data and economic indicators to derive important insights regarding NPI impact.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Liam G McCoy", - "author_inst": "Faculty of Medicine, University of Toronto; Institute of Health Policy, Management and Evaluation, University of Toronto" - }, - { - "author_name": "Jonathan Smith", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "Kavya Anchuri", - "author_inst": "Cumming School of Medicine, University of Calgary" - }, - { - "author_name": "Isha Berry", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Joanna Pineda", - "author_inst": "Department of Computer Science, University of Toronto; Ontario Institute for Cancer Research" - }, - { - "author_name": "Vinyas Harish", - "author_inst": "Faculty of Medicine, University of Toronto; Institute of Health Policy, Management and Evaluation, University of Toronto" - }, - { - "author_name": "Andrew T Lam", - "author_inst": "Faculty of Medicine, University of Toronto" - }, - { - "author_name": "Seung Eun Yi", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "Sophie Hu", - "author_inst": "Cumming School of Medicine, University of Calgary" - }, - { - "author_name": "Canadian Open Data Working Group: Non-Pharmaceutical Interventions", - "author_inst": "" - }, - { - "author_name": "Benjamin Fine", - "author_inst": "Institute for Better Health, Trillium Health Partners; Department of Medical Imaging, University of Toronto" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.17.20070052", "rel_title": "Surveying Tenants of Permanent Supportive Housing in Skid Row about COVID-19", @@ -1510632,6 +1507444,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20069435", + "rel_title": "EFFECTS OF COVID-19 INFECTION DURING PREGNANCY AND NEONATAL PROGNOSIS: WHAT IS THE EVIDENCE?", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069435", + "rel_abs": "BackgroundLittle is known about how COVID-19 infection affects pregnant women, as well as about the possibility of vertical transmission or complications in childbirth. This studys aims to assess the current evidence presented in the literature regarding the potential risks of COVID-19 infection among pregnant women and consequent fetal transmission.\n\nMethodsa systematic literature review assessing papers published in the most comprehensive databases in the field of health, intended to answer the question: \"What are the effects of COVID-19 infection during pregnancy and what is the neonatal prognosis?\"\n\nResults42 papers published in 2020 were eligible. Were included 19 case reports (45%), 15 cross-sectional descriptive studies (35%), 6 cross-sectional analytical studies (14%), one case-control study (3%) and one cohort study (3%), presenting low levels of evidence. A total of 650 pregnant women and 511 infants were assessed. More than half of pregnant women having cesarean deliveries (324/64%). Only 410 (80%) infants were tested for SARS-CoV-2, of which 8 (2%) were positive, however, based on what was assessed that there is no evidence of vertical transmission so far, as there are gaps concerning the care taken during and after delivery, and biological sample proper for testing the SARS-CoV-2.\n\nConclusionshealth professionals cannot rule out a possible worsening of the clinical picture of the pregnant woman infected with SARS-CoV-2 because she is asymptomatic or does not have comorbidities related to gestation. Pregnant women and health professionals should be cautious and vigilant, as soon as their pregnancy is confirmed, with or without confirmed infection, as this review checks for infected pregnant women in all trimesters of pregnancy.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alvaro Francisco Lopes de Sousa", + "author_inst": "Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa" + }, + { + "author_name": "Herica Emilia Felix de Carvalho", + "author_inst": "Escola de Enfermagem de Ribeirao Preto da Universidade de Sao Paulo" + }, + { + "author_name": "Layze Braz de Oliveira", + "author_inst": "Escola de Enfermagem de Ribeirao Preto da Universidade de Sao Paulo" + }, + { + "author_name": "Guilherme Schneider", + "author_inst": "Escola de Enfermagem de Ribeirao Preto da Universidade de Sao Paulo" + }, + { + "author_name": "Emerson Lucas Silva Camargo", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Evandro Watanabe", + "author_inst": "Universidade de Sao Paulo" + }, + { + "author_name": "Denise Andrade", + "author_inst": "Escola de Enfermagem de Ribeirao Preto da Universidade de Sao Paulo" + }, + { + "author_name": "Ana Fatima Carvalho", + "author_inst": "Universidade Federal do Ceara" + }, + { + "author_name": "Isabel Amelia Costa Mendes", + "author_inst": "Escola de Enfermagem de Ribeirao Preto da Universidade de Sao Paulo" + }, + { + "author_name": "Ines Fronteira", + "author_inst": "Instituto de Higiene e Medicina Tropical" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069187", "rel_title": "AI-Driven CT-based quantification, staging and short-term outcome prediction of COVID-19 pneumonia", @@ -1511439,117 +1508306,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.19.048751", - "rel_title": "REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING", - "rel_date": "2020-04-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.19.048751", - "rel_abs": "Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Rebecca J Rockett", - "author_inst": "University of Sydney" - }, - { - "author_name": "Alicia Arnott", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Connie Lam", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Rosemarie Sadsad", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Verlaine Timms", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Karen-Ann Gray", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "John-Sebastian Eden", - "author_inst": "University of Sydney" - }, - { - "author_name": "Sheryl Le Chang", - "author_inst": "University of Sydney" - }, - { - "author_name": "Mailie Gall", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Jenny Draper", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Eby Sim", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Nathan L Bachmann", - "author_inst": "Westmead Hospital" - }, - { - "author_name": "Ian Carter", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Kerri Basile", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Roy Byun", - "author_inst": "NSW Ministry of Health" - }, - { - "author_name": "Matthew V O Sullivan", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Sharon C-A Chen", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Susan Maddocks", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Tania C Sorrell", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Dominic E Dwyer", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Jen Kok", - "author_inst": "NSW Health Pathology" - }, - { - "author_name": "Mikhail Prokopenko", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Vitali Sintchenko", - "author_inst": "The University of Sydney" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.16.20067835", "rel_title": "Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs", @@ -1512210,6 +1508966,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.17.20069443", + "rel_title": "A Path to the End of COIVD-19 - a Mathematical Model", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069443", + "rel_abs": "In this work we use mathematical modeling to describe a possible route to the end of COVID-19, which does not feature either vaccination or herd immunity. We call this route self-burnout. We consider a region with (a) no influx of corona cases from the outside, (b) extensive social distancing, though not necessarily a full lockdown, and (c) high testing capacity relative to the actual number of new cases per day. These conditions can make it possible for the region to initiate the endgame phase of epidemic management, wherein the disease is slowly made to burn itself out through a combination of social distancing, sanitization, contact tracing and preventive testing. The dynamics of the case trajectories in this regime are governed by a single-variable first order linear delay differential equation, whose stability criterion can be obtained analytically. Basis this criterion, we conclude that the social mobility restrictions should be such as to ensure that on the average, one person interacts closely (from the transmission viewpoint) with at most one other person over a 4-5 day period. If the endgame can be played out for a long enough time, we claim that the Coronavirus can eventually get completely contained without affecting a significant fraction of the regions population. We present estimates of the duration for which the epidemic is expected to last, finding an interval of approximately 5-15 weeks after the self-burnout phase is initiated. South Korea, Austria, Australia, New Zealand and the states of Goa, Kerala and Odisha in India appear to be well on the way towards containing COVID by this method.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Richard H Rand", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.17.20069021", "rel_title": "America Addresses Two Epidemics: Cannabis and Coronavirus and their Interactions: An Ecological Geospatial Study", @@ -1513013,53 +1509792,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.19.20071597", - "rel_title": "COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling.", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071597", - "rel_abs": "Epidemiological models are widely used to analyse the spread of diseases such as the global COVID-19 pandemic caused by SARS-CoV-2. However, all models are based on simplifying assumptions and on sparse data. This limits the reliability of parameter estimates and predictions.\n\nIn this manuscript, we demonstrate the relevance of these limitations by performing a study of the COVID-19 outbreak in Wuhan, China. We perform parameter estimation, uncertainty analysis and model selection for a range of established epidemiological models. Amongst others, we employ Markov chain Monte Carlo sampling, parameter and prediction profile calculation algorithms.\n\nOur results show that parameter estimates and predictions obtained for several established models on the basis of reported case numbers can be subject to substantial uncertainty. More importantly, estimates were often unrealistic and the confidence / credibility intervals did not cover plausible values of critical parameters obtained using different approaches. These findings suggest, amongst others, that several models are oversimplistic and that the reported case numbers provide often insufficient information.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Elba Raim\u00fandez", - "author_inst": "University of Bonn" - }, - { - "author_name": "Erika Dudkin", - "author_inst": "University of Bonn" - }, - { - "author_name": "Jakob Vanhoefer", - "author_inst": "University of Bonn" - }, - { - "author_name": "Emad Alamoudi", - "author_inst": "University of Bonn" - }, - { - "author_name": "Simon Merkt", - "author_inst": "University of Bonn" - }, - { - "author_name": "Lara Fuhrmann", - "author_inst": "University of Bonn" - }, - { - "author_name": "Fan Bai", - "author_inst": "University of Bonn" - }, - { - "author_name": "Jan Hasenauer", - "author_inst": "University of Bonn, Technische Universitaet Muenchen and Helmholtz Zentrum Muenchen" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071852", "rel_title": "A Bayesian analysis of the total number of cases of the COVID 19 when only a few data is available. A case study in the state of Goias, Brazil", @@ -1513480,6 +1510212,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.20.052159", + "rel_title": "A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material", + "rel_date": "2020-04-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.052159", + "rel_abs": "The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly-trained personnel, and large upfront investment. Here we showcase an orthogonal pipeline we call CREST (Cas13-based, Rugged, Equitable, Scalable Testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows for a binary interpretation of results. CREST may provide a point- of-care solution to increase the distribution of COVID-19 surveillance.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jennifer N Rauch", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Eric Valois", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Sabrina C Solley", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Friederike Braig", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Morgane Audouard", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Ryan S Lach", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Jose Carlos Ponce-Rojas", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Michael S Costello", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Naomi J Baxter", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Kenneth S Kosik", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Carolina Arias", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Diego Acosta-Alvear", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Maxwell Z Wilson", + "author_inst": "University of California Santa Barbara" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.21.051201", "rel_title": "No evidence that androgen regulation of pulmonary TMPRSS2 explains sex-discordant COVID-19 outcomes", @@ -1514447,101 +1511246,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20067231", - "rel_title": "Development and Multicenter Performance Evaluation of The First Fully Automated SARS-CoV-2 IgM and IgG Immunoassays", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067231", - "rel_abs": "BACKGROUNDThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread globally. The laboratory diagnosis of SARS-CoV-2 infection has relied on nucleic acid tests. However, there are many limitations of nucleic acid tests, including low throughput and high rates of false negatives. More sensitive and accurate tests to effectively identify infected patients are needed.\n\nMETHODSThis study has developed fully automated chemiluminescent immunoassays (CLIA) to determine IgM and IgG antibodies to SARS-CoV-2 in human serum. The assay performance has been evaluated at 10 hospitals. Clinical specificity was evaluated by measuring 972 hospitalized patients with diseases other than COVID-19, and 586 donors of a normal population. Clinical sensitivity was assessed on 503 confirmed cases of SARS-CoV-2 by RT-PCR and 52 suspected cases.\n\nRESULTSThe assays demonstrated satisfied assay precision with coefficient of variation (CV) of less than 4.45%. Inactivation of specimen does not affect assay measurement. SARS-CoV-2 IgM shows clinical specificity of 97.33% and 99.49% for hospitalized patients and normal population respectively. SARS-CoV-2 IgG shows clinical specificity of 97.43% and 99.15% for the hospitalized patients and the normal population respectively. SARS-CoV-2 IgM and IgG show clinical sensitivity of 85.88% and 96.62% respectively for confirmed SARS-Cov-2 infection with RT-PCR, of 73.08% and 86.54% respectively for suspected cases.\n\nCONCLUSIONSwe have developed fully automated immunoassays for detecting SARS-CoV-2 IgM and IgG antibodies in human serum. The assays demonstrated high clinical specificity and sensitivity, and add great value to nucleic acid testing in fighting against the global pandemic of the SARS-CoV-2 infection.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Chungen Qian", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Mi Zhou", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Fangming Cheng", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Xiaotao Lin", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Yijun Gong", - "author_inst": "Shenzhen YHLO Biotech Co., Ltd" - }, - { - "author_name": "Xiaobing Xie", - "author_inst": "the First Affiliated Hospital of Hunan University of Chinese Medicine" - }, - { - "author_name": "Ping Li", - "author_inst": "the First Affiliated Hospital of Hunan University of Chinese Medicine" - }, - { - "author_name": "Zhiyong Li", - "author_inst": "the First Affiliated Hospital of Xiamen University" - }, - { - "author_name": "Pingan Zhang", - "author_inst": "Renmin Hospital of Wuhan University" - }, - { - "author_name": "Zejin Liu", - "author_inst": "Wuhan Asia General Hospital" - }, - { - "author_name": "Fang Hu", - "author_inst": "Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University)" - }, - { - "author_name": "Yun Wang", - "author_inst": "TongJi Hospital, TongJi Medical college, HUST" - }, - { - "author_name": "Quan Li", - "author_inst": "Changshou Peoples Hospital" - }, - { - "author_name": "Yan Zhu", - "author_inst": "Shenzhen Maternity & Child Healthcare Hospital" - }, - { - "author_name": "Guikai Duan", - "author_inst": "Shenzhen Maternity & Child Healthcare Hospital" - }, - { - "author_name": "Yinting Xing", - "author_inst": "The First Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "Huanyu Song", - "author_inst": "The First Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "Wenfang Xu", - "author_inst": "Affiliated Hospital of Shaoxing University" - }, - { - "author_name": "Bi-Feng Liu", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Fuzhen Xia", - "author_inst": "Reagent R&D Center, Shenzhen YHLO Biotech Co., Ltd" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20066159", "rel_title": "Susceptibility and Sustainability of India against CoVid19: a multivariate approach", @@ -1515310,6 +1512014,33 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.04.17.042366", + "rel_title": "Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.042366", + "rel_abs": "There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There is an urgent need for rapid, simplified and cost-effective detection methods. We have developed and analytically validated a protocol for direct rapid extraction-free PCR (DIRECT-PCR) detection of SARS-CoV-2 without the need for nucleic acid purification. As few as 6 RNA copies per reaction of viral nucleocapsid (N) gene from respiratory samples such as sputum and nasal exudate can be detected directly using our one-step inhibitor-resistant assay. The performance of this assay was validated on a commercially available portable PCR thermocycler. Viral lysis, reverse transcription, amplification and detection are achieved in a single-tube homogeneous reaction within 36 minutes. This minimized hands-on time, reduces turnaround-time for sample-to-result and obviates the need for RNA purification reagents. It could enable wider use of Covid-19 testing for diagnosis, screening and research in countries and regions where laboratory capabilities are limiting.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Soon Keong Wee", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Suppiah Paramalingam Sivalingam", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Eric Peng Huat Yap", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.046144", "rel_title": "A scientometric overview of CORD-19", @@ -1516557,37 +1513288,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.15.20066894", - "rel_title": "Knowledge and practice of preventive measures against COVID-19 infection among pregnant women in a low-resource African setting", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066894", - "rel_abs": "BackgroundCoronavirus disease pandemic has resulted in death of thousands of people across several countries. Several preventive measures have been recommended to halt the spread of the disease and its associated mortality. However, the level knowledge and practice of these preventive measures against COVID-19 infection among pregnant women, which constitute vulnerable groups, are yet to be evaluated.\n\nAimTo determine the knowledge and practice of preventive measures against COVID-19 infection among pregnant women in Abakaliki.\n\nMaterials and MethodsThis was a self-administered questionnaire-based cross-sectional study conducted from February 1, 2020 to March 31, 2020 among 284 antenatal clinic attendees at Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State. A pretested and validated questionnaire was used to collect the data. Data analysis was done using SPSS version 22.\n\nResultsOf 284 participants, 60.9% (n=173) had adequate knowledge of the preventive measures against COVID-19 infection. However, the overall practice of these preventive measures among the participants were poor as 69.7% of the participants were not practicing the preventive measures against the coronavirus. The determinants of poor practice of the preventive measures among the participants were being in age group 31-40 years (AOR=2.04, 95%CI: 1.26 - 5.37, p=0.022), married (AOR=2.99, 95%CI: 1.40 - 6.33, p=0.035) grandmultiparous (AOR=3.11, 95%CI: 1.32 - 6.56, p=0.021), residing in rural area (AOR=2.08, 95%CI: 1.32 - 4.05, p=0.031), and having no formal education (AOR=6.73, 95%CI: 2.66 - 18.34, p=0.002).\n\nConclusionThe study showed that most of the participants had adequate knowledge of preventive measures against COVID-19 infection but the practice of these preventive measures were poor among the participants.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Johnbosco Ifunanya Nwafor", - "author_inst": "Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria" - }, - { - "author_name": "Joseph Kenechi Aniukwu", - "author_inst": "Emergency Department, Qatif Central Hospital, Kingdom of Saudi Arabia" - }, - { - "author_name": "Bonaventure Okechukwu Anozie", - "author_inst": "Department of Obstetrics and Gynaecology, Alex Ekwueme Federal University Teaching Hospital, Abakaliki" - }, - { - "author_name": "Arinze Chidiebere Ikeotuonye", - "author_inst": "Department of Obstetrics and Gynaecology, Alex Ekwueme Federal University Teaching Hospital, Abakaliki." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.04.15.20067066", "rel_title": "Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys", @@ -1517284,6 +1513984,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.15.20067272", + "rel_title": "Mandatory social distancing associated with increased doubling time: an example using hyperlocal data", + "rel_date": "2020-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20067272", + "rel_abs": "In a hyperlocal analysis of doubling time of COVID-19, we found that a county that implemented mandatory social distancing and other measures to reduce spread of infection saw an earlier increase in doubling time than surrounding counties.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mark Ebell", + "author_inst": "University of Georgia" + }, + { + "author_name": "Grace Bagwell-Adams", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.15.20067025", "rel_title": "Modeling quarantine during epidemics by mass-testing with drones", @@ -1518259,97 +1514982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.16.045302", - "rel_title": "Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates", - "rel_date": "2020-04-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.045302", - "rel_abs": "The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species from very high to very low. Only mammals fell into the medium to very high categories, and only catarrhine primates in the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Joana Damas", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Graham M. Hughes", - "author_inst": "University College Dublin, Ireland" - }, - { - "author_name": "Kathleen C. Keough", - "author_inst": "University of California San Francisco, USA; Gladstone Institute of Data Science and Biotechnology, USA" - }, - { - "author_name": "Corrie A. Painter", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA" - }, - { - "author_name": "Nicole S. Persky", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Marco Corbo", - "author_inst": "University of California Davis, USA" - }, - { - "author_name": "Michael Hiller", - "author_inst": "Max Planck Institute of Molecular Cell Biology and Genetics, Germany; Max Planck Institute for the Physics of Complex Systems, Germany; Center for Systems Biolo" - }, - { - "author_name": "Klaus-Peter Koepfli", - "author_inst": "Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, USA" - }, - { - "author_name": "Andreas R. Pfenning", - "author_inst": "Carnegie Mellon University, USA" - }, - { - "author_name": "Huabin Zhao", - "author_inst": "Wuhan University, China" - }, - { - "author_name": "Diane P. Genereux", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Ross Swofford", - "author_inst": "Broad Institute of MIT and Harvard, USA" - }, - { - "author_name": "Katherine S. Pollard", - "author_inst": "University of California San Francisco, USA; Gladstone Institute of Data Science and Biotechnology, USA; Chan Zuckerberg Biohub, USA" - }, - { - "author_name": "Oliver A. Ryder", - "author_inst": "San Diego Zoo Institute for Conservation Research, USA; University of California San Diego, USA" - }, - { - "author_name": "Martin T. Nweeia", - "author_inst": "Harvard School of Dental Medicine, USA; Case Western Reserve University School of Dental Medicine, USA; Smithsonian Institution, USA" - }, - { - "author_name": "Kerstin Lindblad-Toh", - "author_inst": "Broad Institute of MIT and Harvard, USA; Uppsala University, Sweden" - }, - { - "author_name": "Emma C. Teeling", - "author_inst": "University College Dublin, Ireland" - }, - { - "author_name": "Elinor K. Karlsson", - "author_inst": "Broad Institute of MIT and Harvard, USA; University of Massachusetts Medical School, USA" - }, - { - "author_name": "Harris A. Lewin", - "author_inst": "University of California Davis, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.16.045419", "rel_title": "Synthetic nanobodies targeting the SARS-CoV-2 receptor-binding domain", @@ -1518946,6 +1515578,25 @@ "type": "contradictory results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.04.18.045963", + "rel_title": "Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19", + "rel_date": "2020-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.18.045963", + "rel_abs": "In times of public crises, including the current Covid-19 pandemic, rapid dissemination of relevant scientific knowledge is of paramount importance. The duration of scholarly journals\u2019 publication process is one of the main factors hindering quick delivery of new information. While proper editorial assessment and peer review obviously require some time, turnaround times for medical journals can be up to several months, which is undesirable in the era of a crisis. Following initiatives of medical journals and scholarly publishers to accelerate their publication process, this study assesses whether medical journals have indeed managed to speed up their publication process for Covid-19 related articles. It studies the duration of 14 medical journals\u2019 publication process both during and prior to the current pandemic. Assessing a total of 669 articles, the study concludes that medical journals have indeed drastically accelerated the publication process for Covid-19 related articles since the outbreak of the pandemic. Compared to articles published in the same journals before the pandemic, turnaround times have decreased on average by 49%. The largest decrease in number of days between submission and publication of articles was due to a decrease in the number of days required for peer review. For articles not related to Covid-19, no acceleration of the publication process is found. While the acceleration of journals\u2019 publication process is laudable from the perspective of quick information dissemination, it also raises concerns relating to the quality of the peer review process and the quality of the resulting publications.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Serge P.J.M. Horbach", + "author_inst": "Radboud University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2020.04.18.047951", "rel_title": "Significant expression of FURIN and ACE2 on oral epithelial cells may facilitate the efficiency of 2019-nCov entry", @@ -1520145,53 +1516796,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.15.20065623", - "rel_title": "Neutralizing Antibodies Responses to SARS-CoV-2 in COVID-19 Inpatients and Convalescent Patients", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065623", - "rel_abs": "BackgroundCOVID-19 is a pandemic with no specific antiviral treatments or vaccines. The urgent needs for exploring the neutralizing antibodies from patients with different clinical characteristics are emerging.\n\nMethodsA total of 117 blood samples were collected from 70 COVID-19 inpatients and convalescent patients. The presence of neutralizing antibody was determined with a modified cytopathogenic assay based on live SARS-CoV-2. The dynamics of neutralizing antibody levels at different with different clinical characteristics were analyzed.\n\nResultsThe seropositivity rate reached up to 100.0% within 20 days since onset, and remained 100.0% till day 41-53. The total GMT was 1:163.7 (95% CI, 128.5 to 208.6), and the antibody level was highest during day 31-40 since onset, and then decreased slightly. Individual differences in changes of antibody levels were observed among 8 representative convalescent patients. In multivariate GEE analysis, patients at age of 31-60 and 61-84 had a higher antibody level than those at age of 16-30 ({beta}=1.0518, P=0.0152; {beta}=1.3718, P=0.0020). Patients with a worse clinical classification had a higher antibody titer ({beta}=0.4639, P=0.0227).\n\nConclusionsThe neutralizing antibodies were detected even at the early stage of disease, and a significant response showed in convalescent patients. Moreover, changes on antibody levels ware individual specific.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Xiaoli Wang", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - }, - { - "author_name": "Xianghua Guo", - "author_inst": "Beijing YouAn hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Qianqian Xin", - "author_inst": "Sinovac Biotech Co., Ltd., Beijing, China" - }, - { - "author_name": "Yang Pan", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - }, - { - "author_name": "Jing Li", - "author_inst": "Sinovac Biotech Co., Ltd., Beijing, China" - }, - { - "author_name": "Yanhui Chu", - "author_inst": "Xicheng District Center for Disease Prevention and Control, Beijing, China" - }, - { - "author_name": "Yingmei Feng", - "author_inst": "Beijing YouAn hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Quanyi Wang", - "author_inst": "Beijing Center for Disease Prevention and Control, Beijing, China;School of Public Health, Capital Medical University, Beijing, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20065425", "rel_title": "A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases", @@ -1520672,6 +1517276,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.14.041319", + "rel_title": "A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities", + "rel_date": "2020-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041319", + "rel_abs": "The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 (CL2) laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the methods for a quantitative real-time reverse transcriptase PCR (qRT-PCR) detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sushmita Sridhar", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Sally Forrest", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Iain Kean", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Jamie Young", + "author_inst": "Academic department of Medical genetics" + }, + { + "author_name": "Josefin Bartholdson Scott", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease" + }, + { + "author_name": "Mailis Maes", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Joana Pereira-Dias", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Surendra Parmar", + "author_inst": "Public Health England Diagnostic Laboratory, Addenbrookes Hospital, Cambridge, UK" + }, + { + "author_name": "Matthew Routledge", + "author_inst": "Infectious Diseases, Addenbrookes Hospital, Cambridge, UK" + }, + { + "author_name": "Lucy Rivett", + "author_inst": "Infectious Diseases, Addenbrookes Hospital, Cambridge, UK" + }, + { + "author_name": "Gordon Dougan", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Michael Weekes", + "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)" + }, + { + "author_name": "Martin Curran", + "author_inst": "Public Health England Diagnostic Laboratory, Addenbrookes Hospital, Cambridge, UK" + }, + { + "author_name": "Ian G. Goodfellow", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Stephen Baker", + "author_inst": "Cambridge University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.13.20064139", "rel_title": "Partial unlock caseload management for COVID-19 can save 1-2 million lives worldwide", @@ -1521723,37 +1518402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.14.20064956", - "rel_title": "Multinational modeling of SARS-CoV-2 spreading dynamics: Insights on the heterogeneity of COVID-19 transmission and its potential healthcare burden", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064956", - "rel_abs": "BackgroundModelling and projections of COVID-19 using a single set of transmission parameters can be an elaborated because the application of different levels of containment measures at different stages of the worldwide COVID-19 outbreak.\n\nMethodsWe developed a piecewise fitting SEIR methodology to fit the progress of the COVID-19 that can be applied on any of the 185 countries listed in John Hopkins Coronavirus Resource Center. The contagious contact rate, the rate of removal and the initially exposed population were obtained at three different stages of the pandemic for a set of 18 countries, and globally for the total number of cases worldwide. The active number of infections and the removed populations were fitted simultaneously to validate the SEIR model against the available time series reports on the number of confirmed infections, recoveries and deaths. We evaluate the effect of a reduction of contagious contact rate on the level of burden put on local healthcare infrastructure considering different levels of intervention. As a guideline for future public health interventions, we also estimated the maximum number of future cases and its potential peak date.\n\nFindingsWe project that the peak in the number of infections worldwide will take place after the third quarter of 2020 with a decline rate that might extend beyond 2020. For 12 out of the 18 countries analyzed, we observe that, following the trend at the date of this study, the number of severe infections will surpass their healthcare capacity. For a 90% reduction scenario of the contagious contact rate, four out of the 18 countries analyzed will undergo a significant delay in the peak of infection, extending the course of the epidemic further than our simulation window (365 days).\n\nInterpretationWe identify three stages for the COVID-19 transmission dynamics, which suggest that it is highly heterogeneous between countries and its contagious contact rate, is currently affected by both local responses of the public health interventions and to the populations adherence to the measures.\n\nFundingNo funding received.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Erick R Martinez-Loran", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "J Jesus Naveja", - "author_inst": "UNAM" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "National Institute of Geriatrics" - }, - { - "author_name": "Flavio Fernando Contreras-Torres", - "author_inst": "Tecnologico de Monterrey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.13.20063412", "rel_title": "Analysis of COVID-19 spread in South Korea using the SIR model with time-dependent parameters and deep learning", @@ -1522366,6 +1519014,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.14.20065151", + "rel_title": "Epidemic Landscape and Forecasting of SARS-CoV-2 in India", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065151", + "rel_abs": "BACKGROUNDIndia was one of the countries to institute strict measures for SARS-CoV-2 control in early phase. Since, then, the epidemic growth trajectory was slow before registering an explosion of cases due to local cluster transmissions.\n\nMETHODSWe estimated growth rate and doubling time of SARS-CoV-2 for India and high burden states using crowd sourced time series data. Further, we also estimated Basic Reproductive Number (R0) and time dependent reproductive number (Rt) using serial intervals from the data. We compared the R0 estimated from five different methods and R0 from SB was further used in analysis. We modified standard SIR models to SIRD model to accommodate deaths using R0 with the Sequential Bayesian method (SBM) for simulation in SIRD models.\n\nRESULTSOn an average, 2.8 individuals were infected by an index case. The mean serial interval was 3.9 days. The R0 estimated from different methods ranged from 1.43 to 1.85. The mean time to recovery was 14 {+/-} 5.3 days. Daily epidemic growth rate of India was 0.16 [95%CI; 0.14, 0.17] with a doubling time of 4.30 days [95%CI; 3.96, 4.70]. From the SIRD model, it can be deduced that the peak of SARS-CoV-2 in India will be around mid-July to early August 2020 with around 12.5% of population likely to be infected at the peak time.\n\nCONCLUSIONSThe pattern of spread of SARS-CoV-2 in India is suggestive of community transmission. There is a need to increase fund for infectious disease research and epidemiologic studies. All the current gains may be reversed rapidly if air travel and social mixing resumes rapidly. For the time being, these must be resumed only in a phased manner, and should be back to normal levels only after we are prepared to deal with the disease with efficient tools like vaccine or a medicine.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Aravind Lathika Rajendrakumar", + "author_inst": "University of Dundee, UK" + }, + { + "author_name": "Anand Thakarakkattil Narayanan Nair", + "author_inst": "University of Dundee, UK" + }, + { + "author_name": "Charvi Nangia", + "author_inst": "University of Dundee, UK" + }, + { + "author_name": "Prabal Kumar Chourasia", + "author_inst": "Mary Washington Hospital, Fredericksburg WV, USA" + }, + { + "author_name": "Mehul Kumar Chourasia", + "author_inst": "School of Medicine, University of Dundee" + }, + { + "author_name": "Mohammad Ghouse Syed", + "author_inst": "University of Dundee, UK" + }, + { + "author_name": "Anu Sasidharan Nair", + "author_inst": "Health System Research India Initiative, Kerala, India" + }, + { + "author_name": "Arun B Nair", + "author_inst": "Health System Research India Initiative" + }, + { + "author_name": "Muhammed Shaffi Fazaludeen Koya", + "author_inst": "School of Public Health, Boston University, MA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20065524", "rel_title": "Investigating spatial variability in COVID-19 pandemic severity across 19 geographic areas, Spain, 2020", @@ -1523061,25 +1519760,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20065268", - "rel_title": "Countries should aim to lower the reproduction number R close to 1.0 for the short-term mitigation of COVID-19 outbreaks", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065268", - "rel_abs": "The COVID-19 pandemic is still in its early stages and given the speed and magnitude of local outbreaks it is urgent to understand how mitigation measures translate into changes in key epidemiological and clinical outcomes. Here, we employ a mathematical model to explore the short-term consequences of lowering the reproduction number [R]0 and delaying measures on total infections and fatalities. The positive implications of mitigation generally accrue as these measures are adopted early, with the most striking effects seen when the reproductive number is lowered to a level [R]C{approx}1.0. As the delay in adopting measures exceeds approximately the half-way point to the peak of an outbreak, the effects of lowering [R]0 markedly decrease. Aiming for reproduction numbers close to 1.0 can substantially reduce fatality probabilities over short time scales, particularly for larger populations. We conclude that research is urgently needed on how mitigation measures impact [R]0 and how these can be optimized so as to achieve [R]C{approx}1.0 whilst supporting individual freedoms, society and the economy.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Michael E. Hochberg", - "author_inst": "University of Montpellier, France; Santa Fe Institute, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065300", "rel_title": "The Easter and Passover Blip in New York City", @@ -1523600,6 +1520280,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.16.20060566", + "rel_title": "Delayed clearance of SARS-CoV2 in male compared to female patients: High ACE2 expression in testes suggests possible existence of gender-specific viral reservoirs", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20060566", + "rel_abs": "The novel coronavirus SARS-CoV2 has been observed to cause a higher incidence and greater severity of disease in males, as seen in multiple cohorts across the globe. The reasons for gender disparity in disease severity is unclear and can be due to host factors. To determine whether males have delayed viral clearance after infection, we evaluated the time to clearance in symptomatic patients tested by serial oropharyngeal/nasopharyngeal swabs followed by RT-PCR at a reference lab in Mumbai, India. A total of 68 subjects with median age of 37 years (3-75 range) were examined and included 48 (71%) males and 20 (29%) females. We observed that females were able to achieve viral clearance significantly earlier than males, with a median difference of 2 days in achieving a negative PCR result (P value = 0.038). Furthermore, examination of 3 families with both male and female patients followed serially, demonstrated that female members of the same household cleared the SARS-CoV2 infection earlier in each family. To determine reasons for delayed clearance in males, we examined the expression patterns of the SARS-CoV2 receptor, Angiotensin-converting enzyme 2 (ACE2), in tissue specific repositories. We observed that the testes was one of the highest sites of ACE2 expression in 3 independent RNA expression databases (Human Protein Atlas, FAMTOM5 and GETx). ACE2 was also determined to be highly expressed in testicular cells at the protein levels. Interestingly, very little expression of ACE2 was seen in ovarian tissue. Taken together, these observations demonstrate for the first time that male subjects have delayed viral clearance of SARS-CoV2. High expression of ACE2 in testes raises the possibility that testicular viral reservoirs may play a role in viral persistence in males and should be further investigated.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Aditi Shastri", + "author_inst": "Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY" + }, + { + "author_name": "Justin Wheat", + "author_inst": "Albert Einstein College of Medicine, Bronx, NY" + }, + { + "author_name": "Sachee Agrawal", + "author_inst": "Topiwala National Medical College & BYL Nair Hospital, Kasturba Hospital for Infections Diseases, Mumbai, India" + }, + { + "author_name": "Nirjhar Chaterjee", + "author_inst": "Topiwala National Medical College & BYL Nair Hospital Kasturba Hospital for Infections Diseases, Mumbai, India" + }, + { + "author_name": "Kith Pradhan", + "author_inst": "Albert Einstein College of Medicine, Bronx, NY" + }, + { + "author_name": "Mendel Goldfinger", + "author_inst": "Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY" + }, + { + "author_name": "Noah Kornblum", + "author_inst": "Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY" + }, + { + "author_name": "Ulrich Steidl", + "author_inst": "Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY" + }, + { + "author_name": "Amit Verma", + "author_inst": "Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, NY" + }, + { + "author_name": "Jayanthi Shastri", + "author_inst": "Topiwala National Medical College & BYL Nair Hospital, Kasturba Hospital for Infections Diseases, Mumbai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20060491", "rel_title": "Monitoring and predicting viral dynamics in SARS-CoV-2-infected Patients", @@ -1524175,73 +1520910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20059501", - "rel_title": "A High Through-put Assay for Circulating Antibodies Directed against the S Protein of Severe Acute Respiratory Syndrome Corona virus 2", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20059501", - "rel_abs": "BackgroundMore than one million infections with the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) have been confirmed. While PCR-based assays are used for diagnosis, high through-put serologic methods are needed to detect antibodies for seroserveillance and for identification of seroconversion, potential plasma donors, and the nature of the immune response to this pathogen.\n\nMethodsA Luminex binding assay was used to assess the presence of antibodies in human sera from COVID-19-infected and -uninfected individuals specific for two recombinant proteins of SARS-CoV-2.\n\nFindingsFluorochrome-labeled beads were coated with a recombinant soluble stabilized trimeric SARS-CoV-2 S protein ectodomain or its central portion, the receptor binding domain (RBD). Coated beads were incubated with sera, followed by incubation with biotinylated anti-human total Ig antibodies and phycoerythrin (PE)-labeled streptavidin. Readout using a Luminex analyzer clearly differentiated between sera of the infected and uninfected subjects, delineating a wide range of serum antibody levels in infected subjects.\n\nInterpretationAntibody assays of sera can identify individuals who are infected with SARS-CoV-2 and have seroconverted, as well as subjects who have been infected and recovered. The use of the Luminex binding Ab assay has the advantage that it can be run in approximately 2.5 hours, uses very little antigen, and permits a high through-put of samples/day.\n\nFundingNIAID contracts and grants, Department of Veterans Affairs grants, the Microbiology Laboratory Clinical Services, Translational Science Hub, and Personalized Virology Initiative, and Department of Medicine of Mount Sinai Health System and Icahn School of Medicine at Mount Sinai.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe outbreak of infections with SARS-CoV-2 began in late 2019. Specimens from nasopharyngeal swabs are being used in PCR-based assays to test for the presence of the virus. Until the first week in April, 2020 there were no licensed tests for the presence of serum antibodies against proteins of the virus. The first approved tests are now becoming available, but none use a format that can be scaled up for mass screening which is now needed for implementing various public health measures. As per a recent Pubmed search, less than 10 studies using serologic assays have been published and none are high through-put.\n\nAdded value of this studyHigh through-put antibody tests are needed in order to identify seroconversion, to perform serosurveys, identify potential donors for plasma therapy, assess the prevalence of infection in populations, identify healthcare workers who may be immune to SARS-CoV-2, and to study the nature of the immune response to this pathogen. The method described for detecting antibodies in SARS-CoV-2-infected patients can be applied in hospital and reference labs, allowing the assessment of present and past infection in a much higher number of donors per unit of time than assays described heretofore.\n\nImplications of all the available evidenceThis study shows that a test in which magnetic beads are coated with soluble forms of the spike protein of SARS-CoV-2 can be used to test for the presence of antibodies targeting this pathogen. The platform allows for the efficient testing of multiple specimens simultaneously using as little as 5 nanograms of antigen per test. This test affords the possibility of large scale, economical and efficient antibody testing.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Svenja Weiss", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jeromine Klingler", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Catarina Hioe", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ian Baine", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erna Milunka Kojic", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Mount Sinai West and Moriningside, NY, USA" - }, - { - "author_name": "Jonathan Stoever", - "author_inst": "Pulmonary and Critical Care Medicine, Mount Sinai West, NY, USA" - }, - { - "author_name": "Sean Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Denise Jurczyszak", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Maria Bermudez-Gonzalez", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Susan Zolla-Pazner", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.14.20059733", "rel_title": "Distinct early IgA profile may determine severity of COVID-19 symptoms: an immunological case series", @@ -1524706,6 +1521374,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.04.13.20063560", + "rel_title": "Knowledge and practices towards COVID-19 during its outbreak: a multinational cross-sectional study", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063560", + "rel_abs": "BackgroundThe emergence of COVID-19 globally coupled with its unknown aetiology and its high transmission rate has created an unprecedented state of emergency worldwide. Public knowledge and awareness about COVID-19 are essential in suppressing its pandemic status.\n\nMethodA cross-sectional study using an online survey was conducted between 19th of March and 6th of April 2020 in three Middle Eastern countries (Jordan, Saudi Arabia and Kuwait) to explore the knowledge and practices of Middle Eastern population towards COVID-19. A previously developed questionnaire was used. Multiple linear regression analysis was used to identify predictors of COVID-19 knowledge.\n\nResultsA total of 1,208 participants were involved in this study from the three countries (Jordan = 389, Saudi Arabia = 433, and Kuwait = 386). The majority of participants (n = 810, 67.2%) were females and aged 30 to 49 years (n = 501, 41.5%). Participants had moderate overall COVID-19 knowledge with a mean score of 7.93 ({+/-}1.72) out of 12, 66.1%. Participants had better knowledge about disease prevention and control with 83.0%, whereas the lowest sub-scale scores were for questions about disease transmission routes (43.3%). High education level was an important predictor of greater COVID-19 knowledge scores (p<0.01).\n\nConclusionMiddle Eastern participants are of a relatively low level of knowledge about COVID-19, particularly regarding its transmission routes. Policymakers are recommended to develop informative COVID-19 related campaigns targeted specifically towards university students, unemployed individuals and those with lower levels of education.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Abdallah Y Naser", + "author_inst": "Isra University" + }, + { + "author_name": "Eman Zmaily Dahmash", + "author_inst": "Isra University" + }, + { + "author_name": "Hassan Alwafi", + "author_inst": "Umm Alqura University" + }, + { + "author_name": "Zahra Khalil Alsairafi", + "author_inst": "Kuwait University" + }, + { + "author_name": "Ahmed M. Al Rajeh", + "author_inst": "King Faisal University" + }, + { + "author_name": "Yosra J Alhartani", + "author_inst": "Isra University" + }, + { + "author_name": "Fawaz Mohammad Turkistani", + "author_inst": "Alnoor Hospital - Ministry of Health" + }, + { + "author_name": "Hamad S. Alyami", + "author_inst": "Najran University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.13.20063248", "rel_title": "Time-variant strategies for optimizing the performance of non-pharmaceutical interventions (NPIs) in protecting lives and livelihoods during the COVID-19 pandemic", @@ -1525349,29 +1522064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.15.20062752", - "rel_title": "Analysis of the COVID-19 epidemic in french overseas department Mayotte based on a modified deterministic and stochastic SEIR model", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20062752", - "rel_abs": "In order to anticipate a future trends in the development of the novel coronavirus COVID-19 epidemic started early at march 13, in the french overseas department Mayotte, we consider in this paper a modified deterministic and stochastic epidemic model. The model divides the total population into several possible states or compartment: susceptible (S), exposed (E) infected and being under an incubation period, infected (I) being infectious, simple or mild removed RM, severe removed (including hospitalized) RS and death cases (D). The adding of the two new compartment RM and RS are driven by data which together replace the original R compartment in the classical SEIR model.\n\nWe first fit the constant transmission rate parameter to the epidemic data in Mayotte during an early exponential growth phase using an algorithm with a package of the software R and based on a Maximum Likewood estimator. This allows us to predict the epidemic without any control in order to understand how the control measure and public policies designed are having the desired impact of controlling the epidemic. To do this, we introduce a temporally varying decreasing transmission rate parameter with a control or quarantine parameter q. Then we pointed out some values of q to maintain control which is critical in Mayotte given the fragility of its health infrastructure and the significant fraction of the population without access to water.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Solym MANOU-ABI", - "author_inst": "IMAG-Montpellier" - }, - { - "author_name": "Julien BALICCHI", - "author_inst": "French National Health Agency of Mayotte" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062927", "rel_title": "MARKOVIAN RANDOM WALK MODELING AND VISUALIZATION OF THE EPIDEMIC SPREAD OF COVID-19", @@ -1525856,6 +1522548,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.13.20064022", + "rel_title": "Importance of untested infectious individuals for the suppression of COVID-19 epidemics", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064022", + "rel_abs": "The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 50% to 80% of the infected individuals. Even when unreported cases are taken into account, we estimate that less than 8% of the population would have been exposed to SARS-CoV-2 by 09/04/2020 in the analysed outbreaks. These levels are far below the 70-85% needed to ensure herd immunity and would predict a resurgence of infection if ongoing lockdowns in the outbreaks are fully lifted. We propose that partially lifted lockdowns together with early and thorough testing allowing for quick isolation of both symptomatic and asymptomatic cases could lead to suppression of secondary waves of COVID-19 epidemics.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Francisco J. Perez-Reche", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Ken J. Forbes", + "author_inst": "University Aberdeen" + }, + { + "author_name": "Norval J. C. Strachan", + "author_inst": "University of Aberdeen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20064659", "rel_title": "Lymphocytopaenia is associated with severe SARS-CoV-2 disease: A Systematic Review and Meta-Analysis of Clinical Data", @@ -1526427,29 +1523146,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.10.20061051", - "rel_title": "A Mathematical prediction of the time evolution of the Covid-19 pandemic in some countries of the European Union using Monte Carlo simulations", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061051", - "rel_abs": "In this paper we study the statistical evolution in time of the Covid-19 pandemic in Spain, Italy, Germany, Belgium, The Netherlands, Austria and Portugal, i.e., the countries of the European Union (EU) that have a number of positive cases higher than 12 thousand at April 7, 2020. France is the third country of the EU for number of cases but a jump in the data on April 3, 2020 does not allow, at least for the moment, to have a reliable prediction curve. The analysis is based on the use of a function of the type of a Gauss Error Function, with four parameters, as a Cumulative Distribution Function (CDF). A Monte Carlo analysis is used to estimate the uncertainty. The approach used in this paper is mathematical and statistical and thus does not explicitly consider a number of relevant issues, including number of nasopharyngeal swabs, mitigation measures, social distancing, virologic, epidemiological and models of contamination diffusion.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ignazio Ciufolini", - "author_inst": "University of Salento" - }, - { - "author_name": "Antonio Paolozzi", - "author_inst": "Sapienza University of Rome" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.12.20062943", "rel_title": "Incidence, clinical outcomes, and transmission dynamics of hospitalized 2019 coronavirus disease among 9,596,321 individuals residing in California and Washington, United States: a prospective cohort study", @@ -1527066,6 +1523762,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.11.20062190", + "rel_title": "Estimating the real-time case fatality rate of COVID-19 using Poisson mixtures model", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062190", + "rel_abs": "We proposed using Poisson mixtures model that utilized data of deaths, recoveries, and total confirmed cases in each day since the outbreak. We demonstrated that our CFR estimates for Hubei Province and other parts of China were superior to the simple CFR estimators in the early stage of COVID-19 outbreak.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.11.20056010", "rel_title": "Household Secondary Attack Rate of COVID-19 and Associated Determinants", @@ -1527785,29 +1524495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.10.20060822", - "rel_title": "Estimate of the Maximum Limit of Total Cases of Infected Patients COVID-19", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060822", - "rel_abs": "In this work, we present a method to estimate the maximum limit of total cases COVID-19 cases considering that the time in which the maximum number of new daily cases occurs corresponds to the inflection point of the curve described by the total number of cases that assumed to have a growth according to a logistical function in which the number of total cases at the inflection point will correspond to half of the maximum limit of total cases COVID-19. We estimate this maximum limit for China and South Korea, obtaining results compatible with the observations. And we also estimate for Italy, Germany, United Kingdom, United States and Spain.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Carlos Maximiliano Dutra Sr.", - "author_inst": "Universidade Federal do Pampa - UNIPAMPA" - }, - { - "author_name": "Carlos Augusto Riella de Melo Sr.", - "author_inst": "Universidade Federal do Pampa - UNIPAMPA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.11.20061465", "rel_title": "Hospitalization time and outcome in patients with Coronavirus Disease 2019 (COVID-19): analysis data from China", @@ -1528372,6 +1525059,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.14.041434", + "rel_title": "Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041434", + "rel_abs": "There appears to be large regional variations for susceptibility, severity and mortality for Covid-19 infections. We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARS- CoV-2. By comparing 56,885 Non-Finnish European and 9,197 East Asians (including 1,909 Koreans) four missense mutations were noted in the hACE2 gene. Molecular dynamic demonstrated that two of these variants (K26R and I468V) may affect binding characteristics between S protein of the virus and hACE2 receptor. We also examined hACE2 gene expression in eight global populations from the HapMap3 and noted marginal differences in expression for some populations as compared to the Chinese population. However, for both of our studies, the magnitude of the difference was small and the significance is not clear in the absence of further in vitro and functional studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Quan Li", + "author_inst": "University Health Network" + }, + { + "author_name": "Zanxia Cao", + "author_inst": "Dezhou University" + }, + { + "author_name": "Proton Rahman", + "author_inst": "Memorial University of Newfoundland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "genetics" + }, { "rel_doi": "10.1101/2020.04.15.997254", "rel_title": "Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics", @@ -1529363,33 +1526077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.09.20059550", - "rel_title": "Diminishing Marginal Benefit of Social Distancing in Balancing COVID-19 Medical Demand-to-Supply", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059550", - "rel_abs": "Social distancing has been adopted as a non-pharmaceutical intervention to prevent the COVID-19 pandemic from overwhelming the medical resources across the United States (US). The catastrophic socio-economic impacts of this intervention could outweigh its benefits if the timing and duration of implementation are left uncontrolled and ill-strategized. Here we investigate the dynamics of social distancing on age-stratified US population and benchmark its effectiveness in reducing the burden on hospital and ICU beds. Our findings highlight the diminishing marginal benefit of social distancing, characterized by a linear decrease in medical demands against an exponentially increasing social distancing duration. We determine an optimal intermittent social-to-no-distancing ratio of 5:1 corresponding to [~]80% reduction in healthcare demands - beyond this ratio, benefit of social distancing diminishes to a negligible level.\n\nCOVID-19 Medical Demand Forecasthttps://eece.wustl.edu/chakrabarty-group/covid/", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pai Liu", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Payton Beeler", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Rajan K Chakrabarty", - "author_inst": "Washington University in Saint Louis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20059113", "rel_title": "Transmission routes of Covid-19 virus in the Diamond Princess Cruise ship", @@ -1529810,6 +1526497,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.20059592", + "rel_title": "Between Geography and Demography: Key Interdependencies and Exit Mechanisms for Covid-19", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059592", + "rel_abs": "We develop a minimal compartmental model to analyze policies on mobility restriction in Italy during the Covid-19 outbreak. Our findings show that a premature lockdown barely shifts the epidemic in time: moreover, beyond a critical value of the lockdown strength, an epidemic that seems to be quelled fully recovers after lifting the restrictions. We investigate the effects on lockdown scenarios and exit strategies by introducing heterogeneities in the model. In particular, we consider Italian regions as separate administrative entities in which social interactions through different age classes occur. We find that, due to the sparsity of the mobility matrix, epidemics develop independently in different regions once the outbreak starts. Moreover, after the epidemics ha started, the influence of contacts with other regions becomes soon irrelevant. Sparsity might be responsible for the observed delays among different regions. Analogous arguments apply to the world/countries scenario. We also find that disregarding the structure of social contacts could lead to severe underestimation of the post-lockdown effects. Nevertheless, age class based strategies can help to mitigate rebound effects with milder strategies. Finally, we point out that these results can be generalized beyond this particular model by providing a description of the effects of key parameters on non-medical epidemic mitigation strategies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio Scala", + "author_inst": "Institute of Complex Systems, CNR" + }, + { + "author_name": "Andrea Flori", + "author_inst": "Politecnico di Milano" + }, + { + "author_name": "Alessandro Spelta", + "author_inst": "Univ. di Pavia" + }, + { + "author_name": "Emanuele Brugnoli", + "author_inst": "CNR-ISC" + }, + { + "author_name": "Matteo Cinelli", + "author_inst": "CNR-ISC" + }, + { + "author_name": "Walter Quattrociocchi", + "author_inst": "Univ. di Venezia 'Ca Foscari" + }, + { + "author_name": "Fabio Pammolli", + "author_inst": "Politecnico di Milano" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.09.20059790", "rel_title": "Estimating cost-benefit of quarantine length for Covid-19 mitigation", @@ -1530489,89 +1527219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.07.20054767", - "rel_title": "Pulmonary radiological change of COVID-19 patients with 99mTc-MDP treatment", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20054767", - "rel_abs": "BackgroundAs increasing cases of COVID-19 around world, urgent need for effective COVID-19-specific therapeutic drugs is necessary; therefore, we conducted a pilot randomized-controlled study to evaluate the efficacy of 99mTc-MDP for COVID-19 therapeutic treatment.\n\nMethodsA total of 21 mild patients with COVID-19 were enrolled in this pilot RCT from February 2020 through March 2020, and then were assigned, in a 1:1 ratio, into control (11 patients) and 99mTc-MDP group (10 patients). Patients in the control group received routine treatment and patients assigned to the 99mTc-MDP group received a combination of routine treatment and an administration of 99mTc-MDP injection of 5ml/day. Both of the patients in the control and 99mTc-MDP groups were treated for 7 days with the primary end point of CT-based radiological pulmonary changes during 7-day follow-up.\n\nFindingsFrom baseline to the day 7, 8 (80%) of 10 mild patients in the 99mTc-MDP group had a significant radiological improvement in lung and a decline in inflammatory infiltration, whereas only 1 (9.1%) of 11 patients in the control group had a radiological improvement in lung. None of the patients in the 99mTc-MDP group had disease progression from mild to severe, as well as an inflammatory cytokine storm, and 2 mild patients (18.2%) in the control group developed severe. During days 7 through 14, the number of patients with radiological improvement in the 99mTc-MDP group remained consistent, and only 1 additional case (22%) in the control group were reported.\n\nConclusionIn this randomized pilot study, 99mTc-MDP had an effective inhibitory effect on the inflammatory disease progression for the therapy of COVID-19, and it can accelerate the absorption of pulmonary inflammation in a short period of time during the process of treatment.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Xiaolin Yuan", - "author_inst": "Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Wanrong Yi", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Baoyi Liu", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Simiao Tian", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Fang Cao", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Ruoyu Wang", - "author_inst": "Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Baiwen Qi", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Faqiang Lu", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Meiyun Fang", - "author_inst": "Department of Rheumotology, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Fuyang Pei", - "author_inst": "Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Ming Chen", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lichuan Zhang", - "author_inst": "Department of Respiratory Medicine, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Yong Zhang", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Xiuzhi Zhang", - "author_inst": "Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University" - }, - { - "author_name": "Zhenyu Pan", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Dewei Zhao", - "author_inst": "Affiliated Zhongshan hospital of Dalian University" - }, - { - "author_name": "Aixi Yu", - "author_inst": "Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.10.20059121", "rel_title": "ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study", @@ -1531152,6 +1527799,41 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.04.10.20060301", + "rel_title": "Should contact bans be lifted in Germany? A quantitative prediction of its effects", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060301", + "rel_abs": "Many countries consider the lifting of restrictions of social contacts (RSC). We quantify the effects of RSC for Germany. We initially employ a purely statistical approach to predicting prevalence of COVID19 if RSC were upheld after April 20. We employ these findings and feed them into our theoretical model. We find that the peak of the number of sick individuals would be reached already mid April. The number of sick individuals would fall below 1,000 at the beginning of July. When restrictions are lifted completely on April 20, the number of sick should rise quickly again from around April 27. A balance between economic and individual costs of RSC and public health objectives consists in lifting RSC for activities that have high economic benefits but low health costs. In the absence of large-scale representative testing of CoV-2 infections, these activities can most easily be identified if federal states of Germany adopted exit strategies that differ across states.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jean Roch Donsimoni", + "author_inst": "Johannes Gutenberg-Universit\u00e4t" + }, + { + "author_name": "Ren\u00e9 Glawion", + "author_inst": "Universit\u00e4t Hamburg" + }, + { + "author_name": "Bodo Plachter", + "author_inst": "Johannes Gutenberg-Universit\u00e4t" + }, + { + "author_name": "Constantin Weiser", + "author_inst": "Johannes Gutenberg-Universit\u00e4t" + }, + { + "author_name": "Klaus W\u00e4lde", + "author_inst": "Johannes Gutenberg-Universit\u00e4t" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.04.13.038687", "rel_title": "Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro", @@ -1532043,29 +1528725,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.04.10.20060319", - "rel_title": "Analysing recovery from pandemics by Learning Theory: the case of CoVid-19", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060319", - "rel_abs": "We present a method for predicting the recovery time from infectious diseases outbreaks such as the recent CoVid-19 virus. The approach is based on the theory of learning from errors, specifically adapted to the control of the virus spread by reducing infection rates using countermeasures such as medical treatment, isolation, social distancing etc. When these are effective, the infection rate, after reaching a peak, declines following a given recovery rate curve. We use presently available data from China, South Korea and others to make actual predictions of the time needed for securing minimum infection rates in the future.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Romney B. Duffey", - "author_inst": "Idaho Falls" - }, - { - "author_name": "Enrico Zio", - "author_inst": "Politecnico di Milano" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.13.039263", "rel_title": "Comparative in vitro transcriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes.", @@ -1532670,6 +1529329,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20058594", + "rel_title": "Preliminary study to identify severe from moderate cases of COVID-19 using NLR&RDW-SD combination parameter", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20058594", + "rel_abs": "ObjectivesInvestigate the characteristics and rules of hematology changes in patients with COVID-19, and explore the possibility to identify moderate and severe patients using conventional hematology parameters or combined parameters.\n\nMethodsThe clinical data of 45 moderate and severe type patients with SARS-CoV-2 infections in Jingzhou Central Hospital from January 23 to February 13, 2020 were collected. The epidemiological indexes, clinical symptoms and laboratory test results of the patients were retrospectively analyzed. Those parameters with significant differences between the two groups were analyzed, and the combination parameters with best diagnostic performance were selected using the LDA method.\n\nResultsOf the 45 patients with COVID-19 (35 moderate and 10 severe cases), 23 were male and 22 female, aged 16-62 years. The most common clinical symptoms were fever (89%) and dry cough (60%). As the disease progressed, WBC, Neu#, NLR, PLR, RDW-CV and RDW-SD parameters in the severe group were significantly higher than that in the moderate group (P<0.05); meanwhile, Lym#, Eos#, HFC%, RBC, HGB and HCT parameters in the severe group were significantly lower than that in the moderate group (P<0.05). For NLR, the AUC, the best cut-off value, the sensitivity and the specificity were 0.890, 13.39, 83.3% and 82.4% respectively, and for PLR, the AUC, the best cut-off, the sensitivity and the specificity were 0.842, 267.03, 83.3% and 74.0% respectively. The combined parameter NLR&RDW-SD had the best diagnostic efficiency (AUC was 0.938) and when the cut-off value was 1.046, the sensitivity and the specificity were 90.0% and 84.7% respectively, followed by the fitting parameter NLR&RDW-CV (AUC = 0.923). When the cut-off value was 0.62, the sensitivity and the specificity for distinguishing severe type from moderate cases of COVID-19 were 90.0% and 82.4% respectively.\n\nConclusionsThe combined parameter NLR&RDW-SD is the best hematology index and can help clinicians to predict the severity of COVID-19 patients, and it can be used as a useful indicator to help prevent and control the epidemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "changzheng wang", + "author_inst": "The Second Clinical Medical College ,Yangtze University" + }, + { + "author_name": "Chengbin Li", + "author_inst": "The Second Clinical Medical College ,Yangtze University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.09.20058941", "rel_title": "Associations of clinical characteristics and antiviral drugs with viral RNA clearance in patients with COVID-19 in Guangzhou, China: a retrospective cohort study", @@ -1533505,61 +1530187,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.12.025577", - "rel_title": "Mechanistic modeling of the SARS-CoV-2 disease map", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.12.025577", - "rel_abs": "Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map in which the detailed activity of the human signaling circuits related to the viral infection and the different antiviral responses, including immune and inflammatory activities, can be inferred from gene expression experiments. Moreover, given to the mechanistic properties of the model, the effect of potential interventions, such as knock-downs, over-expression or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied in specific conditions. By providing a holistic, systems biology approach to the understanding of the complexities of the viral infection process, this tool will become an important asset in the search for efficient antiviral treatments.\n\nThe tool is freely available at: http://hipathia.babelomics.org/covid19/", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kinza Rian", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Marina Esteban-Medina", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Marta R Hidalgo", - "author_inst": "Centro de Investigacion Principe Felipe" - }, - { - "author_name": "Cankut Cubuk", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Matias M Falco", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Carlos Loucera", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Devrim Gunyel", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Marek Ostaszewski", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Maria Pena-Chilet", - "author_inst": "Fundacion Progreso y Salud" - }, - { - "author_name": "Joaquin Dopazo", - "author_inst": "Fundacion Progreso y Salud" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.04.10.036335", "rel_title": "A Computational Approach to Design Potential siRNA Molecules as a Prospective Tool for Silencing Nucleocapsid Phosphoprotein and Surface Glycoprotein Gene of SARS-CoV-2", @@ -1534100,6 +1530727,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.06.20055582", + "rel_title": "Estimates of the Undetected Rate among the SARS-CoV-2 Infected using Testing Data from Iceland", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055582", + "rel_abs": "In the early stages of the COVID-19 pandemic, international testing efforts tended to target individuals whose symptoms and/or jobs placed them at a high presumed risk of infection. Testing regimes of this sort potentially result in a high proportion of cases going undetected. Quantifying this parameter, which we refer to as the undetected rate, is an important contribution to the analysis of the spread of the SARS-CoV-2 virus. We show that partial identification techniques can credibly deal with the data problems that common COVID-19 testing programs induce (i.e. excluding quarantined individuals from testing and low participation in random screening programs). We use public data from two Icelandic testing regimes during the first month of the outbreak and estimate an identified interval for the undetected rate. Our main approach estimates that the undetected rate was between 89% and 93% before the medical system broadened its eligibility criteria and between 80% and 90% after.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "James H Stock", + "author_inst": "Harvard University" + }, + { + "author_name": "Karl M Aspelund", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Michael Droste", + "author_inst": "Harvard University" + }, + { + "author_name": "Christopher D Walker", + "author_inst": "Harvard University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20056051", "rel_title": "Exercising caution in correlating COVID-19 incidence and mortality rates with BCG vaccination policies due to variable rates of SARS CoV-2 testing", @@ -1534699,73 +1531357,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.06.20054890", - "rel_title": "Key to successful treatment of COVID-19: accurate identification of severe risks and early intervention of disease progression", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20054890", - "rel_abs": "BackgroundCOVID-19 is a new and highly contagious respiratory disease that has caused global spread, high case fatality rate in severe patients, and a huge medical burden due to invasive mechanical ventilation. The current diagnosis and treatment guidelines are still need to be improved, and more excellent clinical experience is needed to provide reference.\n\nMethodsWe analyzed and summarized clinical data of 97 confirmed COVID-19 adult patients (including 26 severe cases) admitted to the Fifth Affiliated Hospital of Sun Yat-sen University from January 17, 2020 to March 10, 2020, included laboratory examination results, imaging findings, treatment effect, prognosis, etc, in order to put forward prediction index of severe COVID-19 patients, principles of early intervention and methylprednisolone usages in COVID-19 patients.\n\nResultsO_LIHypoxemia, hyperlactic acid, hypoproteinemia, and hypokalemia were prevalent in COVID-19 patients. The significant low lymphocyte count, hypoproteinemia, hypokalemia, the persistent or worsen high CRP, high D-dimer, and high BNP, and the occurrence of hemoptysis and novel coronavirus (SARS-CoV-2) viremia were important indicators for early diagnosis and prediction of severe disease progression.\nC_LIO_LICharacteristic images of lung CT had a clear change in COVID-19, Ground-glass opacity (GGO) and high-density linear combinations may indicate different pathological changes. Rapid lobular progression of GGO suggests the possibility of severe disease.\nC_LIO_LIBasic principles of early intervention treatment of COVID-19: on the premise of no effective antiviral drugs, treatment is based on supportive and symptomatic therapy (albumin supplementation, supplement of potassium, supplement blood plasma, etc.) in order to maintain the stability of the intracellular environment and adequately reactivate body immunity to clean up SARS-CoV-2.\nC_LIO_LIAccording to severity, oxygenation index, body weight, age, underlying diseases, appropriate amount methylprednisolone application on severe/critical COVID-19 patients on demand, improved blood oxygen and reduced the utilization rate of invasive mechanical ventilation, case fatality rate and medical burden significantly. The most common indications for invasive mechanical ventilation should be strictly control in critical COVID-19 patients.\nC_LI\n\nConclusionsO_LIAccurate and timely identification of clinical features in severe risks, and early and appropriate intervention can block disease progression. 2. Appropriate dose of methylprednisolone can effectively avoid invasive mechanical ventilation and reduce case fatality rate in critical COVID-19 patients.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "meizhu chen", - "author_inst": "hospital" - }, - { - "author_name": "changli tu", - "author_inst": "hospital" - }, - { - "author_name": "Cuiyan Tan", - "author_inst": "hospital" - }, - { - "author_name": "Xiaobin Zheng", - "author_inst": "hospital" - }, - { - "author_name": "xiaohua wang", - "author_inst": "hospital" - }, - { - "author_name": "jian wu", - "author_inst": "hospital" - }, - { - "author_name": "Yiying Huang", - "author_inst": "hospital" - }, - { - "author_name": "zhenguo wang", - "author_inst": "hospital" - }, - { - "author_name": "yan yan", - "author_inst": "hospital" - }, - { - "author_name": "zhonghe li", - "author_inst": "hospital" - }, - { - "author_name": "hong shan", - "author_inst": "hospital" - }, - { - "author_name": "Jing Liu", - "author_inst": "Fifth Affiliated Hospital of Sun Yan-sen University" - }, - { - "author_name": "jin huang", - "author_inst": "hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.07.20056390", "rel_title": "Adjuvant corticosteroid therapy for critically ill patients with COVID-19", @@ -1535398,6 +1531989,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.06.20055624", + "rel_title": "To mask or not to mask: Modeling the potential for face mask use by the general public to curtail the COVID-19 pandemic", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055624", + "rel_abs": "Face mask use by the general public for limiting the spread of the COVID-19 pandemic is controversial, though increasingly recommended, and the potential of this intervention is not well understood. We develop a compartmental model for assessing the community-wide impact of mask use by the general, asymptomatic public, a portion of which may be asymptomatically infectious. Model simulations, using data relevant to COVID-19 dynamics in the US states of New York and Washington, suggest that broad adoption of even relatively ineffective face masks may meaningfully reduce community transmission of COVID-19 and decrease peak hospitalizations and deaths. Moreover, mask use decreases the effective transmission rate in nearly linear proportion to the product of mask effectiveness (as a fraction of potentially infectious contacts blocked) and coverage rate (as a fraction of the general population), while the impact on epidemiologic outcomes (death, hospitalizations) is highly nonlinear, indicating masks could synergize with other non-pharmaceutical measures. Notably, masks are found to be useful with respect to both preventing illness in healthy persons and preventing asymptomatic transmission. Hypothetical mask adoption scenarios, for Washington and New York state, suggest that immediate near universal (80%) adoption of moderately (50%) effective masks could prevent on the order of 17-45% of projected deaths over two months in New York, while decreasing the peak daily death rate by 34-58%, absent other changes in epidemic dynamics. Even very weak masks (20% effective) can still be useful if the underlying transmission rate is relatively low or decreasing: In Washington, where baseline transmission is much less intense, 80% adoption of such masks could reduce mortality by 24-65% (and peak deaths 15-69%), compared to 2-9% mortality reduction in New York (peak death reduction 9-18%). Our results suggest use of face masks by the general public is potentially of high value in curtailing community transmission and the burden of the pandemic. The community-wide benefits are likely to be greatest when face masks are used in conjunction with other non-pharmaceutical practices (such as social-distancing), and when adoption is nearly universal (nation-wide) and compliance is high.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Steffen E. Eikenberry", + "author_inst": "Arizona State University" + }, + { + "author_name": "Marina Mancuso", + "author_inst": "Arizona State University" + }, + { + "author_name": "Enahoro Iboi", + "author_inst": "Arizona State University" + }, + { + "author_name": "Tin Phan", + "author_inst": "Arizona State University" + }, + { + "author_name": "Keenan Eikenberry", + "author_inst": "Arizona State University" + }, + { + "author_name": "Yang Kuang", + "author_inst": "Arizona State University" + }, + { + "author_name": "Eric Kostelich", + "author_inst": "Arizona State University" + }, + { + "author_name": "Abba B. Gumel", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.09.20056341", "rel_title": "Population age structure only partially explains the large number of COVID-19 deaths at the oldest ages", @@ -1536009,69 +1532647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.10.032342", - "rel_title": "Potential host range of multiple SARS-like coronaviruses and an improved ACE2-Fc variant that is potent against both SARS-CoV-2 and SARS-CoV-1", - "rel_date": "2020-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.032342", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a currently uncontrolled pandemic and the etiological agent of coronavirus disease 2019 (COVID-19). It is important to study the host range of SARS-CoV-2 because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. Here we show that ACE2 orthologs of a wide range of domestic and wild animals support entry of SARS-CoV-2, as well as that of SARS-CoV-1, bat coronavirus RaTG13, and a coronavirus isolated from pangolins. Some of these species, including camels, cattle, horses, goats, sheep, pigs, cats, and rabbits may serve as potential intermediate hosts for new human transmission, and rabbits in particular may serve as a useful experimental model of COVID-19. We show that SARS-CoV-2 and SARS-CoV-1 entry could be potently blocked by recombinant IgG Fc-fusion proteins of viral spike protein receptor-binding domains (RBD-Fc) and soluble ACE2 (ACE2-Fc). Moreover, an ACE2-Fc variant, which carries a D30E mutation and has ACE2 truncated at its residue 740 but not 615, outperforms all the other ACE2-Fc variants on blocking entry of both viruses. Our data suggest that RBD-Fc and ACE2-Fc could be used to treat and prevent infection of SARS-CoV-2 and any new viral variants that emerge over the course of the pandemic.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yujun Li", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Haimin Wang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Xiaojuan Tang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Danting Ma", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Chengzhi Du", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Yifei Wang", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Hong Pan", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Qing Zou", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Jie Zheng", - "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" - }, - { - "author_name": "Liangde Xu", - "author_inst": "School of Biomedical Engineering and Eye Hospital, Wenzhou Medical University" - }, - { - "author_name": "Michael Farzan", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute" - }, - { - "author_name": "Guocai Zhong", - "author_inst": "Shenzhen Bay Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.08.20057919", "rel_title": "Burden and prevalence of prognostic factors for severe covid-19 disease in Sweden", @@ -1536512,6 +1533087,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.08.20058719", + "rel_title": "Temporal rise in the proportion of both younger adults and older adolescents among COVID-19 cases in Germany: evidence of lesser adherence to social distancing practices?", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058719", + "rel_abs": "BackgroundThere is uncertainty about the role of different age groups in propagating the SARS-CoV-2 epidemics in different countries, particularly under current social distancing practices.\n\nMethodsWe used the Robert Koch Institute data on weekly COVID-19 cases in different age groups in Germany. To minimize the effect of changes in healthcare seeking behavior (e.g. for older adults) and testing practices, we included the following eight 5-year age groups in the analyses: 10-14y through 45-49y. For each age group g, we considered the proportion PL(g) of individuals in age group g among all detected cases aged 10-49y during weeks 13-14, 2020 (later period), as well as corresponding proportion PE(g) for weeks 10-11, 2020 (early period), and defined the relative risk RR(g) for the age group g to be the ratio RR (g) = PL(g)/PE(g). For each pair of age groups g1, g2, a higher value of RR(g1) compared to RR(g2), or, alternatively, a value above 1 for the odds ratio OR (g1, g2) = RR(g1)/RR(g2) for a COVID-19 case to be in group g1 vs. g2 for the later vs. early periods is interpreted as the relative increase in the population incidence of SARS-Cov-2 in the age group g1 compared to g2 for the later vs. early period.\n\nResultsThe relative risk RR(g) was highest for individuals aged 20-24y (RR=1.4(95% CI (1.27,1.55))), followed by individuals aged 15-19y (RR=1.14(0.99,1.32)), aged 30-34y (RR= 1.07(0.99,1.16)), aged 25-29y (RR= 1.06(0.98,1.15)), aged 35-39y (RR=0.95(0.87,1.03)), aged 40-44y (RR=0.9(0.83,0.98)), aged 45-49y (RR=0.83(0.77,0.89)) and aged 10-14y (RR=0.78(0.64,0.95)). For the age group 20-24y, the odds ratio relative to any other age group for a case to be during the later vs. early period was significantly above 1. For the age group 15-19y, the odds ratio relative to any other age group either above 35y or 10-14y for a case to be during the later vs. early period was significantly above 1.\n\nConclusionsThe observed relative increase with time in the prevalence of individuals aged 15-34y (particularly those aged 20-24y) among detected COVID-19 cases in Germany is unlikely to be explained by increases in the likelihood of seeking medical care or the likelihood of being tested for individuals in those age groups compared to individuals aged 35-49y or 10-14y, and should be indicative of the actual increase in the prevalence of individuals aged 15-34y among SARS-CoV-2 infections in the German population. That increase likely reflects elevated mixing among individuals aged 15-34y (particularly those aged 20-24y) compared to other age groups, possibly due to lesser adherence to social distancing practices.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Edward Goldstein", + "author_inst": "Harvard TH Chan School of Public Health" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.10.029454", "rel_title": "Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence", @@ -1537310,61 +1533908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20057901", - "rel_title": "Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20057901", - "rel_abs": "BACKGROUNDSwabs for SARS-CoV-2 are routinely collected by health care workers, putting them at risk of infection and requiring use of personal protective equipment (PPE). Self-collected swabs offer many advantages provided detection rate of SARS-CoV-2 and other respiratory viruses is not compromised.\n\nMETHODSIn a prospective study, patients attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) nasal and throat swabs prior to health worker collection (HC). Two different laboratory services participated, with HC at Site 1 collecting nasal and throat swabs and at Site 2 nasopharyngeal (NP) and throat swabs. Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohens kappa ({kappa}).\n\nRESULTSOf 236 patients sampled by HC and SC, 25 had COVID-19 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 by SC). SC was highly concordant with HC ({kappa} = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method ({kappa} = 0.959 vs 0.933).\n\nCONCLUSIONSSelf-collection of throat and nasal swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other common respiratory viruses. High viral load of SARS-CoV-2 throughout the respiratory tract and sensitive molecular methods may explain these findings. Self-collection also provides patients with easier access to testing, reduces the exposure of the community and health workers to those undergoing testing and reduces the requirement for PPE.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael C Wehrhahn", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Jennifer Robson", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "Suzanne Brown", - "author_inst": "Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital" - }, - { - "author_name": "Evan Bursle", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "Shane Byrne", - "author_inst": "Sullivan Nicolaides Pathology" - }, - { - "author_name": "David New", - "author_inst": "Clinipath Pathology" - }, - { - "author_name": "Smathi Chong", - "author_inst": "Clinipath Pathology" - }, - { - "author_name": "James P Newcombe", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Terri Sivertsen", - "author_inst": "Douglass Hanly Moir Pathology" - }, - { - "author_name": "Narelle Hadlow", - "author_inst": "Clinipath Pathology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.08.20057794", "rel_title": "Factors associated with hospitalization and critical illness among 4,103 patients with COVID-19 disease in New York City", @@ -1537745,6 +1534288,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20058164", + "rel_title": "Is the spread of COVID-19 across countries influenced by environmental, economic and social factors?", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058164", + "rel_abs": "The SARS-CoV-2 virus, emerged from Wuhan, China is spreading all over the world in an unprecedented manner, causing millions of infections and thousands of deaths. However, the spread of the disease across countries and regions are not even. Why some countries and regions are more affected than some other countries and regions? We employ simple statistical methods to investigate any linkage between the severity of the disease and the environmental, economic and social factors of countries. The estimation results indicate that the number of confirmed cases of Coronavirus infection is higher in countries with lower yearly average temperatures, higher economic openness and stronger political democracy. However, findings of this analysis should be interpreted carefully keeping in mind the fact that statistical relations do not necessarily imply causation. Only clinical experiments with medical expertise can confirm how the virus behaves in the environment.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mohammad Alamgir Hossain", + "author_inst": "University of Surrey, Guildford, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20057067", "rel_title": "Experience with Social Distancing Early in the COVID-19 Pandemic in the United States: Implications for Public Health Messaging", @@ -1538448,33 +1535010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.06.20053561", - "rel_title": "Probability of current COVID-19 outbreaks in all US counties", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20053561", - "rel_abs": "For each US county, we calculated the probability of an ongoing COVID-19 epidemic that may not yet be apparent. Based on confirmed cases as of April 15, 2020, COVID-19 is likely spreading in 86% of counties containing 97% of US population. Proactive measures before two cases are confirmed are prudent.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Emily M. Javan", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Spencer J. Fox", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20058974", "rel_title": "Predicting the number of reported and unreported cases for the COVID-19 epidemics in China, South Korea, Italy, France, Germany and United Kingdom", @@ -1539015,6 +1535550,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.07.20051060", + "rel_title": "The respiratory sound features of COVID-19 patients fill gaps between clinical data and screening methods", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20051060", + "rel_abs": "BackgroundThe 2019 novel coronavirus (COVID-19) has continuous outbreaks around the world. Lung is the main organ that be involved. There is a lack of clinical data on the respiratory sounds of COVID-19 infected pneumonia, which includes invaluable information concerning physiology and pathology. The medical resources are insufficient, which are now mainly supplied for the severe patients. The development of a convenient and effective screening method for mild or asymptomatic suspicious patients is highly demanded.\n\nMethodsThis is a retrospective case series study. 10 patients with positive results of nucleic acid were enrolled in this study. Lung auscultation was performed by the same physician on admission using a hand-held portable electronic stethoscope delivered in real time via Bluetooth. The recorded audio was exported, and was analyzed by six physicians. Each physician individually described the abnormal breathing sounds that he heard. The results were analyzed in combination with clinical data. Signal analysis was used to quantitatively describe the most common abnormal respiratory sounds.\n\nResultsAll patients were found abnormal breath sounds at least by 3 physicians, and one patient by all physicians. Cackles, asymmetrical vocal resonance and indistinguishable murmurs are the most common abnormal breath sounds. One asymptomatic patient was found vocal resonance, and the result was correspondence with radiographic computed tomography. Signal analysis verified the credibility of the above abnormal breath sounds.\n\nConclusionsThis study describes respiratory sounds of patients with COVID-19, which fills up for the lack of clinical data and provides a simple screening method for suspected patients.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Ying hui Huang", + "author_inst": "First Hospital of Nanping, Nanping" + }, + { + "author_name": "Si jun Meng", + "author_inst": "The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yi Zhang", + "author_inst": "Pucheng County Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Shui sheng Wu", + "author_inst": "Fujian University of Traditional Chinese Medicine" + }, + { + "author_name": "Yu Zhang", + "author_inst": "Zhejiang provincial people's hospital, People's Hospital of Hangzhou Medical College" + }, + { + "author_name": "Ya wei Zhang", + "author_inst": "The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yi xiang Ye", + "author_inst": "First Hospital of Nanping" + }, + { + "author_name": "Qi feng Wei", + "author_inst": "First Hospital of Nanping" + }, + { + "author_name": "Nian gui Zhao", + "author_inst": "The Second Afficiated Hospital of Xiamen Medical College" + }, + { + "author_name": "Jian ping Jiang", + "author_inst": "Pucheng County Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Xiao ying Ji", + "author_inst": "The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Chun xia Zhou", + "author_inst": "The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Chao Zheng", + "author_inst": "The First Affiliated Hospital of XiaMen University" + }, + { + "author_name": "Wen Zhang", + "author_inst": "Friedman Brain Institute, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Li zhong Xie", + "author_inst": "Pucheng County Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Yong chao Hu", + "author_inst": "Pucheng County Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Jian quan He", + "author_inst": "Zhongshan Hospital Xiamen University" + }, + { + "author_name": "Jian Chen", + "author_inst": "Zhongshan Hospital Xiamen University" + }, + { + "author_name": "Wang yue Wang", + "author_inst": "Zhejiang provincial people's hospital, People's Hospital of Hangzhou Medical College" + }, + { + "author_name": "Chang hua Zhang", + "author_inst": "Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Liming Cao", + "author_inst": "Zhejiang provincial people's hospital, People's Hospital of Hangzhou Medical College" + }, + { + "author_name": "Wen Xu", + "author_inst": "Fujian University of Traditional Chinese Medicine" + }, + { + "author_name": "Yunhong Lei", + "author_inst": "Department of Emergency and Critical Care Medicine, The First College of Clinical Medical Science, T" + }, + { + "author_name": "Zheng hua Jian", + "author_inst": "First Hospital of Nanping" + }, + { + "author_name": "Wei ping Hu", + "author_inst": "The First Affiliated Hospital of XiaMen University" + }, + { + "author_name": "Wen juan Qin", + "author_inst": "Zhongshan Hospital Xiamen University" + }, + { + "author_name": "Wan yu Wang", + "author_inst": "The First Affiliated Hospital of XiaMen University" + }, + { + "author_name": "Yu long He", + "author_inst": "The First College of Clinical Medical Science" + }, + { + "author_name": "Hang Xiao", + "author_inst": "Jiying (XiaMen) Technology Co." + }, + { + "author_name": "Xiao fang Zheng", + "author_inst": "Pucheng County Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Yi Qun Hu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Wen Sheng Pan", + "author_inst": "Zhejiang provincial people's hospital, People's Hospital of Hangzhou Medical College" + }, + { + "author_name": "Jian feng Cai", + "author_inst": "First Hospital of Nanping" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.20053124", "rel_title": "Recent update on COVID-19 in India: Is locking down the country enough?", @@ -1539550,41 +1536232,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.03.024885", - "rel_title": "Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing", - "rel_date": "2020-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.03.024885", - "rel_abs": "Rapidly responding to novel pathogens, such as SARS-CoV-2, represents an extremely challenging and complex endeavor. Numerous promising therapeutic and vaccine research efforts to mitigate the catastrophic effects of COVID-19 pandemic are underway, yet an efficacious countermeasure is still not available. To support these global research efforts, we have used a novel computational pipeline combining machine learning, bioinformatics, and supercomputing to predict antibody structures capable of targeting the SARS-CoV-2 receptor binding domain (RBD). In 22 days, using just the SARS-CoV-2 sequence and previously published neutralizing antibody structures for SARS-CoV-1, we generated 20 initial antibody sequences predicted to target the SARS-CoV-2 RBD. As a first step in this process, we predicted (and publicly released) structures of the SARS-CoV-2 spike protein using homology-based structural modeling. The predicted structures proved to be accurate within the targeted RBD region when compared to experimentally derived structures published weeks later. Next we used our in silico design platform to iteratively propose mutations to SARS-CoV-1 neutralizing antibodies (known not to bind SARS-Cov-2) to enable and optimize binding within the RBD of SARS-CoV-2. Starting from a calculated baseline free energy of -48.1 kcal/mol ({+/-} 8.3), our 20 selected first round antibody structures are predicted to have improved interaction with the SARS-CoV-2 RBD with free energies as low as -82.0 kcal/mole. The baseline SARS-CoV-1 antibody in complex with the SARS-CoV-1 RBD has a calculated interaction energy of -52.2 kcal/mole and neutralizes the virus by preventing it from binding and entering the human ACE2 receptor. These results suggest that our predicted antibody mutants may bind the SARS-CoV-2 RBD and potentially neutralize the virus. Additionally, our selected antibody mutants score well according to multiple antibody developability metrics. These antibody designs are being expressed and experimentally tested for binding to COVID-19 viral proteins, which will provide invaluable feedback to further improve the machine learning-driven designs. This technical report is a high-level description of that effort; the Supplementary Materials includes the homology-based structural models we developed and 178,856 in silico free energy calculations for 89,263 mutant antibodies derived from known SARS-CoV-1 neutralizing antibodies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Desautels", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Adam Zemla", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Edmond Lau", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Magdalena Franco", - "author_inst": "Lawrence Livermore National Laboratory" - }, - { - "author_name": "Daniel Faissol", - "author_inst": "Lawrence Livermore National Laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.07.20057356", "rel_title": "The Immediate Effect of COVID-19 Policies on Social Distancing Behavior in the United States", @@ -1540169,6 +1536816,49 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.04.10.20053207", + "rel_title": "Homologous protein domains in SARS-CoV-2 and measles, mumps and rubella viruses: preliminary evidence that MMR vaccine might provide protection against COVID-19", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20053207", + "rel_abs": "The COVID-19 disease is one of worst pandemics to sweep the globe in recent times. It is noteworthy that the disease has its greatest impact on the elderly. Herein, we investigated the potential of childhood vaccination, specifically against measles, mumps and rubella (MMR), to identify if this could potentially confer acquired protection over SARS-CoV-2. We identified sequence homology between the fusion proteins of SARS-CoV-2 and measles and mumps viruses. Moreover, we also identified a 29% amino acid sequence homology between the Macro (ADP-ribose-1-phosphatase) domains of SARS-CoV-2 and rubella virus. The rubella Macro domain has surface-exposed conserved residues and is present in the attenuated rubella virus in MMR. Hence, we hypothesize that MMR could protect against poor outcome in COVID-19 infection. As an initial test of this hypothesis, we identified that 1) age groups that most likely lack of MMR vaccine-induced immunity had the poorest outcome in COVID-19, and 2) COVID-19 disease burden correlates with rubella antibody titres, potentially induced by SARS-CoV2 homologous sequences. We therefore propose that vaccination of at risk age groups with an MMR vaccination merits further consideration as a time appropriate and safe intervention.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Robin Franklin", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Adam Young", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Bjoern Neumann", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rocio Fernandez", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Alexis Joannides", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Amir Reyahi", + "author_inst": "Luton & Dunstable University Hospital NHS Foundation Trust" + }, + { + "author_name": "Yorgo Modis", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.07.029017", "rel_title": "Currently available intravenous immunoglobulin (Gamunex(C)-C and Flebogamma(C) DIF) contains antibodies reacting against SARS-CoV-2 antigens", @@ -1541376,117 +1538066,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.08.029769", - "rel_title": "Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.029769", - "rel_abs": "ABSTRACTDespite the current devastation of the COVID-19 pandemic, several recent studies have suggested that the immunosuppressive drug Tocilizumab can powerfully treating inflammatory responses that occur in this disease. Here, by employing single-cell analysis of the immune cell composition of severe-stage COVID-19 patients and these same patients in post Tocilizumab-treatment remission, we have identified a monocyte subpopulation specific to severe disease that contributes to inflammatory storms in COVID-19 patients. Although Tocilizumab treatment attenuated the strong inflammatory immune response, we found that immune cells including plasma B cells and CD8+ T cells still exhibited an intense humoral and cell-mediated anti-virus immune response in COVID-19 patients after Tocilizumab treatment. Thus, in addition to providing a rich, very high-resolution data resource about the immune cell distribution at multiple stages of the COVID-19 disease, our work both helps explain Tocilizumab\u2019s powerful therapeutic effects and defines a large number of potential new drug targets related to inflammatory storms.Competing Interest StatementJingwen Fang is the executive officer of HanGen BiotechView Full Text", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Chuang Guo", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Bin Li", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Huan Ma", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Xiaofang Wang", - "author_inst": "Department of Hepatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of Chin" - }, - { - "author_name": "Pengfei Cai", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Qiaoni Yu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Lin Zhu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Liying Jin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Chen Jiang", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Jingwen Fang", - "author_inst": "HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, China" - }, - { - "author_name": "Qian Liu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Dandan Zong", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Wen Zhang", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Yichen Lu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Kun Li", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Xuyuan Gao", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Binqing Fu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Lianxin Liu", - "author_inst": "Department of Hepatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of Chin" - }, - { - "author_name": "Xiaoling Ma", - "author_inst": "Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," - }, - { - "author_name": "Jianping Weng", - "author_inst": "Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences of Medicine, University of Science and Technology o" - }, - { - "author_name": "Haiming Wei", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Tengchuan Jin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Jun Lin", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - }, - { - "author_name": "Kun Qu", - "author_inst": "Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Di" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.07.030742", "rel_title": "Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue", @@ -1542223,6 +1538802,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.06.20055426", + "rel_title": "Understanding the CoVID-19 pandemic Curve through statistical approach", + "rel_date": "2020-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055426", + "rel_abs": "Current research is an attempt to understand the CoVID-19 pandemic curve through statistical approach of probability density function with associated skewness and kurtosis measures, change point detection and polynomial fitting to estimate infected population along with 30 days projection. The pandemic curve has been explored for above average affected countries, six regions and global scale during 64 days of 22nd January to 24th March, 2020. The global cases infection as well as recovery rate curves remained in the ranged of 0 - 9.89 and 0 - 8.89%, respectively. The confirmed cases probability density curve is high positive skewed and leptokurtic with mean global infected daily population of 6620. The recovered cases showed bimodal positive skewed curve of leptokurtic type with daily recovery of 1708. The change point detection helped to understand the CoVID-19 curve in term of sudden change in term of mean or mean with variance. This pointed out disease curve is consist of three phases and last segment that varies in term of day lengths. The mean with variance based change detection is better in differentiating phases and associated segment length as compared to mean. Global infected population might rise in the range of 0.750 to 4.680 million by 24th April 2020, depending upon the pandemic curve progress beyond 24th March, 2020. Expected most affected countries will be USA, Italy, China, Spain, Germany, France, Switzerland, Iran and UK with at least infected population of over 0.100 million. Infected population polynomial projection errors remained in the range of -78.8 to 49.0%.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ibrar ul Hassan Akhtar", + "author_inst": "COMSATS University Islamabad" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.05.20049346", "rel_title": "N95 Mask Decontamination using Standard Hospital Sterilization Technologies", @@ -1542937,33 +1539535,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.03.20052563", - "rel_title": "Interaction between malarial transmission and BCG vaccination with COVID-19 incidence in the world map: A changing landscape human immune system?", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052563", - "rel_abs": "BackgroundCOVID-19 (Corona virus Disease-2019) is a new public health emergency and is a pandemic currently. Incidence and mortality of COVID-19 vary in different geographical areas. In this study we aimed to analyse the relationship between malaria transmission and BCG vaccination with COVID-19 incidence in the world map.\n\nMaterials and methodsWe collected malaria cases data (World Health Organisation (WHO), 2018), worldwide COVID-19 cases and mortality data (European Centre for Disease Prevention and Control) and data on BCG vaccination. COVID-19 incidence and mortality was compared.\n\nFindingsData on 5316978938 persons from 166 countries were analysed. Malaria incidence rate was negatively correlated with COVID-19 incidence rate (correlation coefficient = -0.513, p<0.001). Malaria free countries had significantly higher number of COVID-19 cases compared to malaria endemic countries. In Europe and Americas, countries, which have higher BCG vaccination coverage, had significantly less mortality per thousand population compared to those with low BCG coverage (median 0.0002 (0-0.0005) vs 0.0029 (0.0002-0.0177), p=0.017). The case fatality ratio of COVID-19 was related nonlinearly to the malaria incidence.\n\nConclusionsThe results suggest the changing human immune system as we progress to eliminate parasitic diseases with time. Chloroquine exposure in malaria endemic zones might have a protective effect.\n\nSummary boxO_ST_ABS\"What is already known on this subject?\"C_ST_ABSTo the best of the authors no similar evidence, of the effect of malarial transmission on the COVID-19 global distribution is known. The effect of the Bacille Calmette Guerin (BCG) vaccine on modifying the human immune system has been reported before and is postulated to protective against certain viral infections like Influenza A (H1N1) and herpes virus.\n\n\"What this study adds?\"This study finds that COVID-19 incidence, worldwide is less in countries, which are malaria-endemic. In the European and American countries, increased BCG coverage may have some mortality advantage against COVID-19. The case fatality rate was related to malaria incidence, however, in a complex way. This could be a window into the changing landscape of human immune system as we progress to eliminate parasitic disease with time or this could be due to long-term protective body level of anti-malarials like chloroquine or hydroxychloroquine in countries with higher malaria incidence rate.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rudra Prosad Goswami", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Dheeraj K Mittal", - "author_inst": "AIIMS, New Delhi, India" - }, - { - "author_name": "Rama Prosad Goswami", - "author_inst": "School of Tropical Medicine, Kolkata, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.026765", "rel_title": "Noisy Pooled PCR for Virus Testing", @@ -1543500,6 +1540071,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.07.20056309", + "rel_title": "A Simulated Single Ventilator / Dual Patient Ventilation Strategy for Acute Respiratory Distress Syndrome During the COVID-19 Pandemic", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056309", + "rel_abs": "The potential for acute shortages of ventilators at the peak of the Covid-19 pandemic has raised the possibility of needing to support two patients from a single ventilator. To provide a system for understanding and prototyping designs we have developed a mathematical model of two patients supported by a mechanical ventilator. We propose a standard setup where we simulate the introduction of T-splitters to supply air to two patients and a modified setup where we introduce a variable resistance in each inhalation pathway and one-way valves in each exhalation pathway. Using the standard setup, we demonstrate that ventilating two patients with mismatched lung compliances from a single ventilator will lead to clinically-significant reductions in tidal volume in the patient with the lowest respiratory compliance. Using the modified setup, we demonstrate that it could be possible to achieve the same tidal volumes in two patients with mismatched lung compliances, and we show that the tidal volume of one patient can be manipulated independently of the other. The results indicate that, with appropriate modifications, two patients could be supported from a single ventilator with independent control of tidal volumes.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jose A. Solis-Lemus", + "author_inst": "King's College London" + }, + { + "author_name": "Edward Costar", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Denis Doorly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Eric C. Kerrigan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline H. Kennedy", + "author_inst": "Evelina Childrens Hospital" + }, + { + "author_name": "Frances Tait", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Steven A Niederer", + "author_inst": "king's College London" + }, + { + "author_name": "Peter E. Vincent", + "author_inst": "Imperial College London" + }, + { + "author_name": "Steven E. Williams", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.04.05.20054429", "rel_title": "Feasibility of Controlling COVID-19 Outbreaks in the UK by Rolling Interventions", @@ -1544191,73 +1540813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.05.20046433", - "rel_title": "The phenotypic changes of \u03b3\u03b4 T cells in COVID-19 patients", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20046433", - "rel_abs": "A novel pneumonia-associated respiratory syndrome named coronavirus disease-2019 (COVID-19), which caused by SARS-CoV-2 and broken in Wuhan, China in the end of 2019. Unfortunately, there is no specific antiviral agent or vaccine available to treat SARS-CoV-2 infections. Also, information regarding the immunological characteristics in COVID-19 patients remains limited. Here we collected the blood samples from 18 healthy donors (HD) and 38 COVID-19 patients to analyze changes in {gamma}{delta} T cells. In comparison to HD, the {gamma}{delta} T cells percentage was decreased. {gamma}{delta} T cells are able to immediately respond to SARS-CoV-2 infection and upregulate the activation marker CD25. In addition, the increased expression of CD4 in {gamma}{delta} T cells may serve as a biomarker for the assessment of SARS-CoV-2 infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Lei Lei", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Hongbo Qian", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Xiaofeng Yang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Xiaobo Zhou", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Xingzhe Zhang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Dan Zhang", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Tongxin Dai", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Rui Guo", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - }, - { - "author_name": "Lin Shi", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Yanbin Cheng", - "author_inst": "Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center" - }, - { - "author_name": "Baojun Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jinsong Hu Hu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yaling Guo", - "author_inst": "Department of Clinical Laboratory, The 8th hospital of Xi'an" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.04.03.20051649", "rel_title": "Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis", @@ -1544774,6 +1541329,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.05.20051540", + "rel_title": "SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20051540", + "rel_abs": "Wastewater surveillance may represent a complementary approach to measure the presence and even prevalence of infectious diseases when the capacity for clinical testing is limited. Moreover, aggregate, population-wide data can help inform modeling efforts. We tested wastewater collected at a major urban treatment facility in Massachusetts and found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR. We then confirmed the identity of the PCR product by direct DNA sequencing. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of March 25. The reason for the discrepancy is not yet clear, and until further experiments are complete, these data do not necessarily indicate that clinical estimates are incorrect. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Fuqing Wu", + "author_inst": "Center for Microbiome Informatics and Therapeutics, Departments of Biological Engineering and Civil & Environmental Engineering, Massachusetts Institute of Tech" + }, + { + "author_name": "Amy Xiao", + "author_inst": "Center for Microbiome Informatics and Therapeutics, Departments of Biological Engineering and Civil & Environmental Engineering, Massachusetts Institute of Tech" + }, + { + "author_name": "Jianbo Zhang", + "author_inst": "Center for Microbiome Informatics and Therapeutics, Departments of Biological Engineering and Civil & Environmental Engineering, Massachusetts Institute of Tech" + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology, National University of Singapore" + }, + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology, National University of Singapore" + }, + { + "author_name": "Kathryn Kauffman", + "author_inst": "University of Buffalo, The State University of New York" + }, + { + "author_name": "William Hanage", + "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston" + }, + { + "author_name": "Mariana Matus", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Newsha Ghaeli", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Noriko Endo", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Claire Duvallet", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Katya Moniz", + "author_inst": "Center for Microbiome Informatics and Therapeutics, Departments of Biological Engineering and Civil & Environmental Engineering, Massachusetts Institute of Tech" + }, + { + "author_name": "Timothy Erickson", + "author_inst": "Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital" + }, + { + "author_name": "Peter Chai", + "author_inst": "Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Singapore Center for Environmental Life Sciences Engineering, Asian School of the Environment, Nanyang Technological University, Singapore" + }, + { + "author_name": "Eric Alm", + "author_inst": "Center for Microbiome Informatics and Therapeutics, Department of Biological Engineering and Civil & Environmental Engineering, Massachusetts Institute of Techn" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.05.20054577", "rel_title": "A Bayesian Logistic Growth Model for the Spread of COVID-19 in New York", @@ -1545389,49 +1542023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.05.20053769", - "rel_title": "Validation of reported risk factors for disease classification and prognosis in COVID-19: a descriptive and retrospective study", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20053769", - "rel_abs": "Risk indicators viral load (ORF1ab Ct), lymphocyte percentage (LYM%), C-reactive protein (CRP), interleukin-6 (IL-6), procalcitonin (PCT) and lactic acid (LA) in COVID-19 patients have been proposed in recent studies. However, the predictive effects of those indicators on disease classification and prognosis remains largely unknown. We dynamically measured those reported indicators in 132 cases of COVID-19 patients including the moderate-cured (moderated and cured), severe-cured (severe and cured) and critically ill (died). Our data showed that CRP, PCT, IL-6, LYM%, lactic acid and viral load could predict prognosis and guide classification of COVID-19 patients in different degrees. CRP, IL-6 and LYM% were more effective than other three factors in predicting prognosis. For disease classification, CRP and LYM% were sensitive in identifying the types between critically ill and severe (or moderate). Notably, among the investigated factors, LYM% was the only one that could distinguish between the severe and moderate types. Collectively, we concluded that LYM% was the most sensitive and reliable predictor for disease typing and prognosis. During the COVID-19 pandemic, the precise classification and prognosis prediction are critical for saving the insufficient medical resources, stratified treatment and improving the survival rate of critically ill patients. We recommend that LYM% be used independently or in combination with other indicators in the management of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Li Tan", - "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" - }, - { - "author_name": "Xia Kang", - "author_inst": "Third Military Medical University (Army Medical University)" - }, - { - "author_name": "Xinran Ji", - "author_inst": "Chinese People's Liberation Army General Hospital (301 Hospital)" - }, - { - "author_name": "Qi Wang", - "author_inst": "General hospital of Central Threater Command,PRC" - }, - { - "author_name": "Yongsheng li", - "author_inst": "Third Military Medical University (Army Medical University)" - }, - { - "author_name": "Qiongshu Wang", - "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" - }, - { - "author_name": "Hongming Miao", - "author_inst": "Third Military Medical University (Army Medical University)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.03.20052878", "rel_title": "Search for trends of Covid-19 infection in India, China, Denmark, Brazil, France. Germany and the USA on the basis of power law scaling", @@ -1545856,6 +1542447,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20047365", + "rel_title": "Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047365", + "rel_abs": "BackgroundThe COVID-19 pandemic caused by SARS-CoV-2 coronavirus threatens global public health. Currently, neutralizing antibodies (NAbs) versus this virus are expected to correlate with recovery and protection of this disease. However, the characteristics of these antibodies have not been well studied in association with the clinical manifestations in patients.\n\nMethodsPlasma collected from 175 COVID-19 recovered patients with mild symptoms were screened using a safe and sensitive pseudotyped-lentiviral-vector-based neutralization assay. Spike-binding antibody in plasma were determined by ELISA using RBD, S1, and S2 proteins of SARS-CoV-2. The levels and the time course of SARS-CoV-2-specific NAbs and the spike-binding antibodies were monitored at the same time.\n\nFindingsSARS-CoV-2 NAbs were unable to cross-reactive with SARS-CoV virus. SARS-CoV-2-specific NAbs were detected in patients from day 10-15 after the onset of the disease and remained thereafter. The titers of NAb among these patients correlated with the spike-binding antibodies targeting S1, RBD, and S2 regions. The titers of NAbs were variable in different patients. Elderly and middle-age patients had significantly higher plasma NAb titers (P<0.0001) and spike-binding antibodies (P=0.0003) than young patients. Notably, among these patients, there were ten patients whose NAb titers were under the detectable level of our assay (ID50: < 40); while in contrast, two patients, showed very high titers of NAb, with ID50 :15989 and 21567 respectively. The NAb titers were positive correlated with plasma CRP levels but negative correlated with the lymphocyte counts of patients at the time of admission, indicating an association between humoral response and cellular immune response.\n\nInterpretationThe variations of SARS-CoV-2 specific NAbs in recovered COVID-19 patients may raise the concern about the role of NAbs on disease progression. The correlation of NAb titers with age, lymphocyte counts, and blood CRP levels suggested that the interplay between virus and host immune response in coronavirus infections should be further explored for the development of effective vaccine against SARS-CoV-2 virus. Furthermore, titration of NAb is helpful prior to the use of convalescent plasma for prevention or treatment.\n\nFundingMinistry of Science and Technology of China, National Natural Science Foundation of China, Shanghai Municipal Health Commission, and Chinese Academy of Medical Sciences", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fan Wu", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Aojie Wang", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Mei Liu", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Qimin Wang", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Jun Chen", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Shuai Xia", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Yun Ling", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Yuling Zhang", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Jingna Xun", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Lu Lu", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Shibo Jiang", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Hongzhou Lu", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Yumei Wen", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + }, + { + "author_name": "Jinghe Huang", + "author_inst": "Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.02.20051482", "rel_title": "A novel cohort analysis approach to determining the case fatality rate of COVID-19 and other infectious diseases", @@ -1546799,45 +1543461,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.02.20051441", - "rel_title": "Chaos theory applied to the outbreak of Covid-19: an ancillary approach to decision-making in pandemic context", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051441", - "rel_abs": "Predicting the course of an epidemic is difficult, predicting the course of a pandemic from an emerging virus even more so. The validity of most predictive models relies on numerous parameters, involving biological and social characteristics often unknown or highly uncertain. Data of the COVID-19 epidemics in China, Japan, South Korea and Italy were used to build up deterministic models without strong hypothesis. These models were then applied to other countries to identify the closest scenarios in order to foresee their coming behaviour. The models enabled to predict situations that were confirmed little by little, proving that these tools can be efficient and useful for decision-making in a quickly evolving operational context.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sylvain Mangiarotti", - "author_inst": "Centre d'Etudes Spatiales de la Biosphere" - }, - { - "author_name": "Marisa Peyre", - "author_inst": "ASTRE" - }, - { - "author_name": "Yan Zhang", - "author_inst": "CESBIO" - }, - { - "author_name": "Mireille Huc", - "author_inst": "CESBIO" - }, - { - "author_name": "Francois Roger", - "author_inst": "ASTRE" - }, - { - "author_name": "Yann Kerr", - "author_inst": "CESBIO" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20051466", "rel_title": "Predictions for COVID-19 outbreak in India using Epidemiological models", @@ -1547242,6 +1543865,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.04.03.20048868", + "rel_title": "Classification of Coronavirus Images using Shrunken Features", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20048868", + "rel_abs": "Necessary screenings must be performed to control the spread of the Corona Virus (COVID-19) in daily life and to make a preliminary diagnosis of suspicious cases. The long duration of pathological laboratory tests and the wrong test results led the researchers to focus on different fields. Fast and accurate diagnoses are essential for effective interventions with COVID-19. The information obtained by using X-ray and Computed Tomography (CT) images is vital in making clinical diagnoses. Therefore it was aimed to develop a machine learning method for the detection of viral epidemics by analyzing X-ray images. In this study, images belonging to 6 situations, including coronavirus images, are classified. Since the number of images in the dataset is deficient and unbalanced, it is more convenient to analyze these images with hand-crafted feature extraction methods. For this purpose, firstly, all the images in the dataset are extracted with the help of four feature extraction algorithms. These extracted features are combined in raw form. The unbalanced data problem is eliminated by producing feature vectors with the SMOTE algorithm. Finally, the feature vector is reduced in size by using a stacked auto-encoder and principal component analysis to remove interconnected features in the feature vector. According to the obtained results, it is seen that the proposed method has leveraging performance, especially in order to make the diagnosis of COVID-19 in a short time and effectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Saban Ozturk", + "author_inst": "Amasya University" + }, + { + "author_name": "Umut Ozkaya", + "author_inst": "Konya Technical University" + }, + { + "author_name": "Mucahid Barstugan", + "author_inst": "Konya Technical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.01.20049742", "rel_title": "Perceived vulnerability to COVID-19 infection from event attendance: Results from Louisiana, USA, two weeks preceding the national emergency declaration", @@ -1547993,45 +1544643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.03.20050195", - "rel_title": "Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20050195", - "rel_abs": "ObjectivesTo establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2.\n\nMethodsThe most efficient pool size was determined to be 5 specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 microliter from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 microliter each) for a total volume of 250 microliter l. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12-pools.\n\nResultsAll 25 pools were positive with Cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that two pools were positive followed by identification of two individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions.\n\nConclusionsWhen the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.\n\nKey PointsSARS CoV-2, COVID-19, Group testing", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Baha Abdalhamid", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Christopher R Bilder", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Emily L McCutchen", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Steven H Hinrichs", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Scott A Koepsell", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Peter C Iwen", - "author_inst": "Nebraska Public Health Laboratory, University of Nebraska Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20050997", "rel_title": "Acute liver injury and its association with death risk of patients with COVID-19: a hospital-based prospective case-cohort study", @@ -1548428,6 +1545039,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.01.20049759", + "rel_title": "Flattening the curve before it flattens us: hospital critical care capacity limits and mortality from novel coronavirus (SARS-CoV2) cases in US counties", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049759", + "rel_abs": "BackgroundAs of March 26, 2020, the United States had the highest number of confirmed cases of Novel Coronavirus (COVID-19) of any country in the world. Hospital critical care is perhaps the most important medical system choke point in terms of preventing deaths in a disaster scenario such as the current COVID-19 pandemic. We therefore brought together previously established disease modeling estimates of the growth of the COVID-19 epidemic in the US under various social distancing contact reduction assumptions, with local estimates of the potential critical care surge response across all US counties.\n\nMethodsEstimates of spatio-temporal COVID-19 demand and medical system critical care supply were calculated for all continental US counties. These estimates were statistically summarized and mapped for US counties, regions and urban versus non-urban areas. Estimates of COVID-19 infections and patients needing critical care were calculated from March 24, 2020 to April 24, 2020 for three different estimated population levels - 0%, 25%, and 50% - of contact reduction (through actions such as social distancing). Multiple national public and private datasets were linked and harmonized in order to calculate county-level critical care bed counts that included currently available beds and those that could be made available under four surge response scenarios - very low, low, medium, and high - as well as excess deaths stemming from inaccessible critical care.\n\nResultsSurge response scenarios ranged from a very low total supply 77,588 critical care beds to a high total of 278,850 critical care beds. Over the four week study period, excess deaths from inaccessible critical care ranged from 24,688 in the very low response scenario to 13,268 in the high response scenario. Northeastern and urban counties were projected to be most affected by excess deaths due to critical care shortages, and counties in New York, Colorado, and Virginia were projected to exceed their critical care bed limits despite high levels of COVID-19 contact reduction. Over the four week study period, an estimated 12,203-19,594 excess deaths stemming from inaccessible critical care could be averted through greater preventive actions such as travel restrictions, publicly imposed contact precautions, greater availability of rapid testing for COVID-19, social distancing, self-isolation when sick, and similar interventions. An estimated 4,029-11,420 excess deaths stemming from inaccessible critical care could be averted through aggressive critical care surge response and preparations, including high clearance of ICU and non-ICU critical care beds and extraordinary measures like using a single ventilator for multiple patients.\n\nConclusionsUnless the epidemic curve of COVID-19 cases is flattened over an extended period of time, the US COVID-19 epidemic will cause a shortage of critical care beds and drive up otherwise preventable deaths. The findings here support value of preventive actions to flatten the epidemic curve, as well as the value of exercising extraordinary surge capacity measures to increase access to hospital critical care for severely ill COVID-19 patients.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Charles C Branas", + "author_inst": "Gelman Professor of Epidemiology and Chair, Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, NY" + }, + { + "author_name": "Andrew Rundle", + "author_inst": "Associate Professor of Epidemiology, Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, NY" + }, + { + "author_name": "Sen Pei", + "author_inst": "Associate Research Scientist, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, NY, NY" + }, + { + "author_name": "Wan Yang", + "author_inst": "Assistant Professor of Epidemiology, Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, NY" + }, + { + "author_name": "Brendan G Carr", + "author_inst": "Chair, Department of Emergency Medicine, Icahn School of Medicine, Mount Sinai Health System, NY, NY; Senior Advisor and Director, Emergency Care Coordination C" + }, + { + "author_name": "Sarah Sims", + "author_inst": "CEO, Patient Insight, Santa Monica, CA; Research Contractor, Office of the Assistant Secretary for Preparedness and Response, US Department of Health and Human " + }, + { + "author_name": "Alexis Zebrowski", + "author_inst": "Assistant Professor of Emergency Medicine, Department of Emergency Medicine, Icahn School of Medicine, Mount Sinai Health System, NY, NY" + }, + { + "author_name": "Ronan Doorley", + "author_inst": "Research Contractor, Media Lab, Massachusetts Institute of Technology, Cambridge, MA" + }, + { + "author_name": "Neil Schluger", + "author_inst": "Chief, Division of Pulmonary, Allergy and Critical Care Medicine, Professor of Medicine, Epidemiology and Environmental Health Sciences, Columbia University Irv" + }, + { + "author_name": "James W Quinn", + "author_inst": "Staff Associate, Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, NY" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Professor, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, NY, NY" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.02.20051052", "rel_title": "Global epidemiology, pathogenesis, immune response, diagnosis, treatment, economic and psychological impact, challenges, and future prevention of COVID-19: A scoping review", @@ -1549119,33 +1545789,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.02.20051490", - "rel_title": "Forecast of the COVID-19 outbreak, collapse of medical facilities, and lockdown effects in Tokyo, Japan", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051490", - "rel_abs": "BackgroundThe number of patients of COVID-19 in Tokyo has been increasing gradually through the end of March, 2020.\n\nObjectSupport for policymaking requires forecasting of the entire course and outcome of the outbreak if a self-restraint in going out is not initiated. Moreover, the effects of a self-restraint in going out must be considered when choosing to initiate one. Method: Data of Tokyo patients with symptoms during January 14 - March 28, 2020 were used to formulate a susceptible-infected-recovered (SIR) model using three age classes and to estimate the basic reproduction number (R0). Based on the estimated R0, We inferred outbreak outcomes and medical burden if a self-restraint in going out were not enacted. Then we estimate the self-restraint in going out effects.\n\nResultsResults suggest R0 as 2.86, with a 95% confidence interval of [2.73, 2.97]. Exhaustion of medical resources can be expected to occur on April 26 if no self-restraint in going out occurs. If a self-restraint in going out were enacted from April 6, and if more than 60% of trips outside the home were restricted voluntarily, then medical care service could be maintained.\n\nDiscussion and ConclusionThe estimated R0 was similar to that found from other studies conducted in China and Japan. Results demonstrate that a self-restraint in going out with reasonable cooperation of residents is required to maintain medical care.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Department of Nursig, Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohkusa", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.01.20047373", "rel_title": "Frequency of testing for COVID 19 infection and the presence of higher number of available beds per country predict outcomes with the infection, not the GDP of the country - A descriptive statistical analysis", @@ -1549722,6 +1546365,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.03.003699", + "rel_title": "Coronavirus hemagglutinin-esterase and spike proteins co-evolve for functional balance and optimal virion avidity", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.03.003699", + "rel_abs": "Human coronaviruses OC43 and HKU1 are respiratory pathogen of zoonotic origin that have gained worldwide distribution. OC43 apparently emerged from a bovine coronavirus (BCoV) spill-over. All three viruses attach to 9-O-acetylated sialoglycans via spike protein S with hemagglutinin-esterase HE acting as a receptor-destroying enzyme. In BCoV, an HE lectin domain promotes esterase activity towards clustered substrates. OC43 and HKU1, however, lost HE lectin function as an adaptation to humans. Replaying OC43 evolution, we knocked-out BCoV HE lectin function and performed forced evolution-population dynamics analysis. Loss of HE receptor-binding selected for second-site mutations in S, decreasing S binding affinity by orders of magnitude. Irreversible HE mutations selected for cooperativity in virus swarms with low-affinity S minority variants sustaining propagation of high-affinity majority phenotypes. Salvageable HE mutations induced successive second-site substitutions in both S and HE. Apparently, S and HE are functionally interdependent and co-evolve to optimize the balance between attachment and release. This mechanism of glycan-based receptor usage, entailing a concerted, fine-tuned activity of two envelope protein species, is unique among CoVs, but reminiscent of that of influenza A viruses (IAVs). Apparently, general principles fundamental to virion-sialoglycan interactions prompted convergent evolution of two important groups of human and animal pathogens.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yifei Lang", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Wentao Li", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Zeshi Li", + "author_inst": "Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht Universit" + }, + { + "author_name": "Danielle Koerhuis", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Arthur C.S. van den Burg", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Erik Rozemuller", + "author_inst": "GenDx B.V., Yalelaan 48, 3584 CM Utrecht, the Netherlands" + }, + { + "author_name": "Berend-Jan Bosch", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Frank J.M. van Kuppeveld", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Geert-Jan P.H. Boons", + "author_inst": "Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht Universit" + }, + { + "author_name": "Eric G. Huizinga", + "author_inst": "Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands" + }, + { + "author_name": "Hilde M. van der Schaar", + "author_inst": "GenDx B.V., Yalelaan 48, 3584 CM Utrecht, the Netherlands" + }, + { + "author_name": "Raoul J. de Groot", + "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, the Netherlands" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.02.022194", "rel_title": "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein", @@ -1550497,45 +1547203,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.31.018556", - "rel_title": "Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice", - "rel_date": "2020-04-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.018556", - "rel_abs": "Guided by the principle of primum non nocere (first do no harm), we report a cautionary note on the potential fatal toxicity of chloroquine (CQ) or hydroxychloroquine (HCQ) in combination with anti-diabetic drug metformin. We observed that the combination of CQ or HCQ and metformin, which were used in our studies as potential anti-cancer drugs, killed 30-40% of mice. While our observations in mice may not translate to toxicity in humans, the reports that CQ or HCQ has anti-COVID-19 activity, the use of CQ resulting in toxicity and at least one death, and the recent Emergency Use Authorization (EUA) for CQ and HCQ by the US Food and Drug Administration (FDA) prompted our report. Here we report the lethality of CQ or HCQ in combination with metformin as a warning of its potential serious clinical toxicity. We hope that our report will be helpful to stimulate pharmacovigilance and monitoring of adverse drug reactions with the use of CQ or HCQ, particularly in combination with metformin.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "N.V Rajeshkumar", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Shinichi Yabuuchi", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Shweta G Pai", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Anirban Maitra", - "author_inst": "UT MD Anderson Cancer Center" - }, - { - "author_name": "Manuel Hidalgo", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Chi V Dang", - "author_inst": "Ludwig Institute for Cancer Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.03.31.20038935", "rel_title": "Angiotensin II Receptor Blockers and Angiotensin-Converting Enzyme Inhibitors Usage is Associated with Improved Inflammatory Status and Clinical Outcomes in COVID-19 Patients With Hypertension", @@ -1551220,6 +1547887,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.04.01.020966", + "rel_title": "Deducing the N- and O- glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2", + "rel_date": "2020-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.01.020966", + "rel_abs": "The current emergence of the novel coronavirus pandemic caused by SARS-CoV-2 demands the development of new therapeutic strategies to prevent rapid progress of mortalities. The coronavirus spike (S) protein, which facilitates viral attachment, entry and membrane fusion is heavily glycosylated and plays a critical role in the elicitation of the host immune response. The spike protein is comprised of two protein subunits (S1 and S2), which together possess 22 potential N-glycosylation sites. Herein, we report the glycosylation mapping on spike protein subunits S1 and S2 expressed on human cells through high resolution mass spectrometry. We have characterized the quantitative N-glycosylation profile on spike protein and interestingly, observed unexpected O-glycosylation modifications on the receptor binding domain (RBD) of spike protein subunit S1. Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1. Our data on the N- and O-glycosylation is strengthened by extensive manual interpretation of each glycopeptide spectra in addition to using bioinformatics tools to confirm the complexity of glycosylation in the spike protein. The elucidation of the glycan repertoire on the spike protein provides insights into the viral binding studies and more importantly, propels research towards the development of a suitable vaccine candidate.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Asif Shajahan", + "author_inst": "University of Georgia" + }, + { + "author_name": "Nitin T Supekar", + "author_inst": "University of Georgia" + }, + { + "author_name": "Anne S Gleinich", + "author_inst": "University of Georgia" + }, + { + "author_name": "Parastoo Azadi", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.01.019299", "rel_title": "Structural basis to design multi-epitope vaccines against Novel Coronavirus 19 (COVID19) infection, the ongoing pandemic emergency: an in silico approach", @@ -1551835,53 +1548533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.03.31.20049023", - "rel_title": "Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049023", - "rel_abs": "BackgroundTo mitigate and slow the spread of COVID-19, many countries have adopted unprecedented physical distancing policies, including the UK. We evaluate whether these measures might be sufficient to control the epidemic by estimating their impact on the reproduction number (R0, the average number of secondary cases generated per case).\n\nMethodsWe asked a representative sample of UK adults about their contact patterns on the previous day. The questionnaire documents the age and location of contacts and as well as a measure of their intimacy (whether physical contact was made or not). In addition, we asked about adherence to different physical distancing measures. The first surveys were sent on Tuesday 24th March, one day after a \" lockdown\" was implemented across the UK. We compared measured contact patterns during the \" lockdown\" to patterns of social contact made during a non-epidemic period. By comparing these, we estimated the change in reproduction number as a consequence of the physical distancing measures imposed. We used a meta-analysis of published estimates to inform our estimates of the reproduction number before interventions were put in place.\n\nFindingsWe found a 73% reduction in the average daily number of contacts observed per participant (from 10.2 to 2.9). This would be sufficient to reduce R0 from 2.6 prior to lockdown to 0.62 (95% confidence interval [CI] 0.37 - 0.89) after the lockdown, based on all types of contact and 0.37 (95% CI = 0.22 - 0.53) for physical contacts only.\n\nInterpretationThe physical distancing measures adopted by the UK public have substantially reduced contact levels and will likely lead to a substantial impact and a decline in cases in the coming weeks. However, this projected decline in incidence will not occur immediately as there are significant delays between infection, the onset of symptomatic disease and hospitalisation, as well as further delays to these events being reported. Tracking behavioural change can give a more rapid assessment of the impact of physical distancing measures than routine epidemiological surveillance.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSMany governments have adopted physical distancing measures to mitigate the impact of the COVID-19 pandemic. However, it is unclear to what extent these measures reduce the number of contacts and therefore transmission. We searched PubMed and medRxiv on March 28, 2020, with the terms \" (coronavirus OR COVID-19 OR influenza) AND ((school OR work) AND (closure OR holiday)) AND (contact OR mixing)\" and identified 59 and 17 results, respectively. Only one study conducted in China during the COVID-19 pandemic reported a reduction in daily contacts outside the home during the period of \" lockdown\". We found no other published articles that empirically quantify the impact of these measures on age- and location-specific mixing patterns.\n\nAdded value of this studyBy surveying adults behaviour in the UK during a period of stringent physical distancing (\" lockdown\") and comparing the results to previously collected data, we found a large reduction in daily contacts particularly outside the home, resulting in a marked reduction in the estimated reproduction number from 2.6 to 0.62 (95% bootstrapped confidence interval [CI] 0.37 - 0.89). This method allows for rapid assessment of changes in the reproduction number that is unaffected by reporting delays.\n\nImplications of all the available evidenceChanges in human contact behaviour drive respiratory infection rates. Understanding these changes at different stages of the COVID-19 pandemic allows us to rapidly quantify the impact of physical distancing measures on the transmission of pathogens.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christopher I Jarvis", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Kevin Van Zandvoort", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Amy Gimma", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "Kiesha Prem", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "- CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Petra Klepac", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - }, - { - "author_name": "G James Rubin", - "author_inst": "Department of Psychological Medicine, King's College London, Denmark Hill, London United Kingdom" - }, - { - "author_name": "W John Edmunds", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.31.20049312", "rel_title": "Projected ICU and Mortuary load due to COVID-19 in Sydney", @@ -1552374,6 +1549025,25 @@ "type": "contradictory results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.04.01.021196", + "rel_title": "SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation", + "rel_date": "2020-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.01.021196", + "rel_abs": "Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, and rapidly spread worldwide. Previous studies suggested cat could be a potential susceptible animal of SARS-CoV-2. Here, we investigated the infection of SARS-CoV-2 in cats by detecting specific serum antibodies. A cohort of serum samples were collected from cats in Wuhan, including 102 sampled after COVID-19 outbreak, and 39 prior to the outbreak. 15 of 102 (14.7%) cat sera collected after the outbreak were positive for the receptor binding domain (RBD) of SARS-CoV-2 by indirect enzyme linked immunosorbent assay (ELISA). Among the positive samples, 11 had SARS-CoV-2 neutralizing antibodies with a titer ranging from 1/20 to 1/1080. No serological cross-reactivity was detected between the SARS-CoV-2 and type I or II feline infectious peritonitis virus (FIPV). Our data demonstrates that SARS-CoV-2 has infected cat population in Wuhan during the outbreak.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Meilin Jin", + "author_inst": "State Key Laboratory of Agriculture Microbiology, Huazhong Agriculture University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.31.20048579", "rel_title": "Blood glucose levels in elderly subjects with type 2 diabetes during COVID-19 outbreak: a retrospective study in a single center", @@ -1552929,89 +1549599,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.03.31.015941", - "rel_title": "Identification of a common deletion in the spike protein of SARS-CoV-2", - "rel_date": "2020-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.015941", - "rel_abs": "Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Zhe Liu", - "author_inst": "Guangdong Provincial Institution of Public Health, Guangzhou, China" - }, - { - "author_name": "Huanying Zheng", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Runyu Yuan", - "author_inst": "Guangdong Provincial Institution of Public Health, Guangzhou" - }, - { - "author_name": "Mingyue Li", - "author_inst": "The Third Affilated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Huifang Lin", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Jingju Peng", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Qianlin Xiong", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Jiufeng Sun", - "author_inst": "Guangdong Provincial Institution of Public Health" - }, - { - "author_name": "Baisheng Li", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jie Wu", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Changwen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Ruben J.G. Hulswit", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Thomas A. Bowden", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "University of Edinburgh, UK" - }, - { - "author_name": "Oliver G Pybus", - "author_inst": "University of Oxford, Oxford, UK" - }, - { - "author_name": "Nick Loman", - "author_inst": "Institute of Microbiology and Infection, University of Birmingham, UK" - }, - { - "author_name": "Jing Lu", - "author_inst": "Guangdong Provincial Center for Diseases Control and prevention" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.03.31.017889", "rel_title": "Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia", @@ -1553548,6 +1550135,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.29.20046904", + "rel_title": "Global trends in air travel: implications for connectivity and resilience to infectious disease threats", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046904", + "rel_abs": "BackgroundIncreased connectivity via air travel can facilitate the geographic spread of infectious diseases. The number of travelers alone does not explain risk; passenger origin and destination will also influence risk of disease introduction and spread. We described trends in international air passenger numbers and connectivity between countries with different capacities to detect and respond to infectious disease threats.\n\nMethodsWe used the Fragile States Index (FSI) as an annual measure of country-level resilience and capacity to respond to infectious disease events. Countries are categorized as: Sustainable, Stable, Warning, or Alert, in order of increasing fragility. We included data for 177 sovereign states for the years 2007 to 2016. Annual inbound and outbound international air passengers for each country were obtained for the same time period. We examined trends in FSI score, trends in worldwide air travel, and the association between a states FSI score and air travel.\n\nResultsAmong countries included in the FSI rankings, the total number of passengers increased from 0.791 billion to 1.28 billion between 2007 and 2016. Increasing fragility was associated with a decrease in travel volumes, with a 2.9% (95% CI: 2.3-3.5%) reduction in passengers per 1-unit increase in FSI score. Overall, travel between countries of different FSI categories either increased or remained stable. The greatest increase was observed for travel to Warning countries from Warning countries, with an annual increase of 8,967,623 passengers (95%CI: 6,546,494 to 11,388,753) over the study period.\n\nConclusionsThe worlds connectivity via air travel has increased dramatically over the past decade. There has been notable growth in travel from Warning and Stable countries, which comprise more than three-quarters of international air travel passengers. These countries may have suboptimal capacity to detect and respond to infectious disease threats that emerge within their borders.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ashleigh R Tuite", + "author_inst": "University of Toronto" + }, + { + "author_name": "Deepit Bhatia", + "author_inst": "BlueDot" + }, + { + "author_name": "Rahim Moineddin", + "author_inst": "University of Toronto" + }, + { + "author_name": "Isaac Bogoch", + "author_inst": "University of Toronto" + }, + { + "author_name": "Alexander G Watts", + "author_inst": "BlueDot" + }, + { + "author_name": "Kamran Khan", + "author_inst": "BlueDot" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.30.20047019", "rel_title": "Early behavior of Madrid Covid-19 disease outbreak: A mathematical model", @@ -1554211,33 +1550837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.03.29.20046649", - "rel_title": "COVID-19, City Lockdown, and Air Pollution: Evidence from China", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046649", - "rel_abs": "The rapid spread of COVID-19 is a global public health challenge. To prevent the escalation of its transmission, China locked down one-third of its cities and strictly restricted personal mobility and economic activities. Using timely and comprehensive air quality data in China, we show that these counter-COVID-19 measures led to a remarkable improvement in air quality. Within weeks, the Air Quality Index and PM2.5 concentrations were brought down by 25%. The effects are larger in colder, richer, and more industrialized cities. We estimate that such improvement would avert 24,000 to 36,000 premature deaths from air pollution on a monthly basis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Guojun He", - "author_inst": "Division of Social Science, Division of Environment and Sustainability, and Department of Economics, Hong Kong University of Science and Technology" - }, - { - "author_name": "Yuhang Pan", - "author_inst": "Division of Environment and Sustainability, Hong Kong University of Science and Technology" - }, - { - "author_name": "Takanao Tanaka", - "author_inst": "Division of Social Science, Hong Kong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.03.30.20047308", "rel_title": "Predicting Mortality Risk in Patients with COVID-19 Using Artificial Intelligence to Help Medical Decision-Making", @@ -1554702,6 +1551301,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.03.26.20044636", + "rel_title": "Evaluation of the awareness level of Healthcare workers toward NCOVID-2019 in Pakistan", + "rel_date": "2020-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044636", + "rel_abs": "BackgroundNovel Coronavirus infection disease 2019 (NCOVID-19), caused by the corona virus, was first spotted in Wuhan, city of China, December 2019. The NCOVID-19 virus is spread among individuals through close communication in the form of droplets, not via airborne. Those individuals are at risk of infection who are in close contact with a NCOVID-19 patient or who take care of NCOVID-19 patients. Infection prevention and control measures are critical to prevent the possible spread of any infection in healthcare facilities. Therefore, healthcare workers should be aware of basic knowledge and all procedures concerning prevention and protection from NCOVID-19.\n\nObjectiveThe objective of this study was to evaluate the awareness level of healthcare workers toward NCOVID-2019 in Pakistan.\n\nMaterial and MethodsA questionnaire was generated according to WHO information that was circulated among the healthcare workers of different hospitals and medical institutes of Pakistan. Calculated sample size was 650.\n\nConclusionHealthcare workers have insufficient knowledge of preventive measures and infection control. The authorities must take initiatives on urgent basis to increase the awareness among the healthcare workers and general public also so that the drastic circumstances can be avoided in the developing country like Pakistan.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ambrina Qureshi", + "author_inst": "Dow University of Health Sciences" + }, + { + "author_name": "Bushra Imdad", + "author_inst": "Dow University of Health Sciences" + }, + { + "author_name": "Uzair Abbas", + "author_inst": "Dow University of Health Sciences" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.03.23.20041897", "rel_title": "Targeted adaptive isolation strategy for Covid-19 pandemic", @@ -1555433,20 +1552059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.29.20046706", - "rel_title": "No Evidence for Temperature-Dependence of the COVID-19 Epidemic", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046706", - "rel_abs": "1.The pandemic of the COVID-19 disease extended from China across the north-temperate zone, and more recently to the tropics and southern hemisphere. We find no evidence that spread rates decline with temperatures above 20 {degrees}C, suggesting that the COVID-19 disease is unlikely to behave as a seasonal respiratory virus.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.28.013672", "rel_title": "Cigarette smoke triggers the expansion of a subpopulation of respiratory epithelial cells that express the SARS-CoV-2 receptor ACE2", @@ -1555979,6 +1552591,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.29.014381", + "rel_title": "Computational Prediction of the Comprehensive SARS-CoV-2 vs. Human Interactome to Guide the Design of Therapeutics", + "rel_date": "2020-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.29.014381", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the disease pathogenesis of the novel coronavirus, denoted SARS-CoV-2, is critical to the development of anti-SARS-CoV-2 therapeutics. The global propagation of the viral disease, denoted COVID-19 (\"coronavirus disease 2019\"), has unified the scientific community in searching for possible inhibitory small molecules or polypeptides. Given the known interaction between the human ACE2 (\"Angiotensin-converting enzyme 2\") protein and the SARS-CoV virus (responsible for the coronavirus outbreak circa. 2003), considerable focus has been directed towards the putative interaction between the SARS-CoV-2 Spike protein and ACE2. However, a more holistic understanding of the SARS-CoV-2 vs. human inter-species interactome promises additional putative protein-protein interactions (PPI) that may be considered targets for the development of inhibitory therapeutics.\n\nTo that end, we leverage two state-of-the-art, sequence-based PPI predictors (PIPE4 & SPRINT) capable of generating the comprehensive SARS-CoV-2 vs. human interactome, comprising approximately 285,000 pairwise predictions. Of these, we identify the high-scoring subset of human proteins predicted to interact with each of the 14 SARS-CoV-2 proteins by both methods, comprising 279 high-confidence putative interactions involving 225 human proteins. Notably, the Spike-ACE2 interaction was the highest ranked for both the PIPE4 and SPRINT predictors, corroborating existing evidence for this PPI. Furthermore, the PIPE-Sites algorithm was used to predict the putative subsequence that might mediate each interaction and thereby inform the design of inhibitory polypeptides intended to disrupt the corresponding host-pathogen interactions.\n\nWe hereby publicly release the comprehensive set of PPI predictions and their corresponding PIPE-Sites landscapes in the following DataVerse repository: 10.5683/SP2/JZ77XA. All data and metadata are released under a CC-BY 4.0 licence. The information provided represents theoretical modeling only and caution should be exercised in its use. It is intended as a resource for the scientific community at large in furthering our understanding of SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kevin Dick", + "author_inst": "Carleton University" + }, + { + "author_name": "Kyle K Biggar", + "author_inst": "Carleton University" + }, + { + "author_name": "James R Green", + "author_inst": "Carleton University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.03.30.016832", "rel_title": "Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design", @@ -1557046,29 +1553685,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.27.20043752", - "rel_title": "Forecasting COVID-19 impact on hospital bed-days, ICU-days, ventilator-days and deaths by US state in the next 4 months", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043752", - "rel_abs": "ImportanceThis study presents the first set of estimates of predicted health service utilization and deaths due to COVID-19 by day for the next 4 months for each state in the US.\n\nObjectiveTo determine the extent and timing of deaths and excess demand for hospital services due to COVID-19 in the US.\n\nDesign, Setting, and ParticipantsThis study used data on confirmed COVID-19 deaths by day from WHO websites and local and national governments; data on hospital capacity and utilization for US states; and observed COVID-19 utilization data from select locations to develop a statistical model forecasting deaths and hospital utilization against capacity by state for the US over the next 4 months.\n\nExposure(s)COVID-19.\n\nMain outcome(s) and measure(s)Deaths, bed and ICU occupancy, and ventilator use.\n\nResultsCompared to licensed capacity and average annual occupancy rates, excess demand from COVID-19 at the peak of the pandemic in the second week of April is predicted to be 64,175 (95% UI 7,977 to 251,059) total beds and 17,380 (95% UI 2,432 to 57,955) ICU beds. At the peak of the pandemic, ventilator use is predicted to be 19,481 (95% UI 9,767 to 39,674). The date of peak excess demand by state varies from the second week of April through May. We estimate that there will be a total of 81,114 (95% UI 38,242 to 162,106) deaths from COVID-19 over the next 4 months in the US. Deaths from COVID-19 are estimated to drop below 10 deaths per day between May 31 and June 6.\n\nConclusions and RelevanceIn addition to a large number of deaths from COVID-19, the epidemic in the US will place a load well beyond the current capacity of hospitals to manage, especially for ICU care. These estimates can help inform the development and implementation of strategies to mitigate this gap, including reducing non-COVID-19 demand for services and temporarily increasing system capacity. These are urgently needed given that peak volumes are estimated to be only three weeks away. The estimated excess demand on hospital systems is predicated on the enactment of social distancing measures in all states that have not done so already within the next week and maintenance of these measures throughout the epidemic, emphasizing the importance of implementing, enforcing, and maintaining these measures to mitigate hospital system overload and prevent deaths.\n\nData availability statementA full list of data citations are available by contacting the corresponding author.\n\nFunding StatementBill & Melinda Gates Foundation and the State of Washington\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAssuming social distancing measures are maintained, what are the forecasted gaps in available health service resources and number of deaths from the COVID-19 pandemic for each state in the United States?\n\nFindingsUsing a statistical model, we predict excess demand will be 64,175 (95% UI 7,977 to 251,059) total beds and 17,380 (95% UI 2,432 to 57,955) ICU beds at the peak of COVID-19. Peak ventilator use is predicted to be 19,481 (95% UI 9,767 to 39,674) ventilators. Peak demand will be in the second week of April. We estimate 81,114 (95% UI 38,242 to 162,106) deaths in the United States from COVID-19 over the next 4 months.\n\nMeaningEven with social distancing measures enacted and sustained, the peak demand for hospital services due to the COVID-19 pandemic is likely going to exceed capacity substantially. Alongside the implementation and enforcement of social distancing measures, there is an urgent need to develop and implement plans to reduce non-COVID-19 demand for and temporarily increase capacity of health facilities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "IHME COVID-19 health service utilization forecasting team", - "author_inst": "" - }, - { - "author_name": "Christopher JL Murray", - "author_inst": "Institute for Health Metrics and Evaluation" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20045807", "rel_title": "The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: a web-based survey", @@ -1557577,6 +1554193,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.28.20040204", + "rel_title": "The time-series ages distribution of the reported COVID-2019 infected people suggests the undetected local spreading of COVID-2019 in Hubei and Guangdong provinces before 19th Jan 2020", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20040204", + "rel_abs": "COVID-2019 is broken out in China. It becomes a severe public health disaster in one month. Find the period in which the spreading of COVID-2019 was overlooked, and understand the epidemiological characteristics of COVID-2019 in the period will provide valuable information for the countries facing the threats of COVID-2019. The most extensive epidemiological analysis of COVID-2019 shows that older people have lower infection rates compared to middle-aged persons. Common sense is that older people prefer to report their illness and get treatment from the hospital compared to middle-aged persons. We propose a hypothesis that when the spreading of COVID-2019 was overlooked, we will find more older cases than the middle-aged cases.\n\nAt first, we tested the hypothesis with 4597 COVID-2019 infected samples reported from 26th Nov 2019 to 17th Feb 2020 across the mainland of China. We found that 19th Jan 2020 is a critical time point. Few samples were reported before that day, and most of them were older ones. Then samples were explosively increased after that day, and many of them were middle-aged people. We have demonstrated the hypothesis to this step.\n\nThen, we grouped samples by their residences(provinces). We found that, in the provinces of Hubei and Guangdong, the ages of samples reported before 19th Jan 2020 are significantly higher than the ages of samples reported after that day. It suggests the COVID-2019 may be spreading in Hubei and Guangdong provinces before 19th Jan 2020 while people were unconscious of it.\n\nAt last, we proposed that the ages distribution of each-day-reported samples could serve as a warning indicator of whether all potential COVID-2019 infected people are found.\n\nWe think the power of our analysis is limit because 1. the work is data-driven, and 2. only [~]5% of the COVID-2019 infected people in China are included in the study. However, we believe it still shows some value for its ability to estimate the possible unfound COVID-2019 infected people.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "CHAO WU", + "author_inst": "Zhe Jiang University, China" + }, + { + "author_name": "min zheng", + "author_inst": "zhe jiang university" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.29.20039529", "rel_title": "SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission", @@ -1558248,37 +1554887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.26.20041426", - "rel_title": "Clinical features and outcomes of 197 adult discharged patients with COIVD-19 in Yichang, Hubei", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20041426", - "rel_abs": "PurposeTo investigate the epidemiology and clinical features of discharged adult patients with coronavirus infection disease 2019 (COVID-19) in Yichang.\n\nMethodThe retrospective study recruited 197 cases of COVID-19 discharged from Yichang Central Peoples Hospital and Yichang Third Peoples Hospital from Jan 17 to Feb 26, 2020. All cases were confirmed by real-time RT-PCR or chest computer tomography (CT). The survivors were followed up until March 4,2020. Clinical data, including demographic characteristic, presentation, underlying illness, exposure history, laboratory examination, radiology and prognosis were enrolled and analyzed by SPSS 19.0 software.\n\nResultsThere were 197 adult discharged patients with COVID-19 in this study. Statistical analysis indicated that the average age was 55.94 years, and female patients were 99(50.3%).Those patients mainly resided in urban with exposure history in 2 weeks, while 7 medical staffs were infected. Fever (77.6%%), cough (43.6%) and weakness (14.7%) were the common symptoms. Leukocytes were mainly normal or decreased in 185 patients (92.9%), both lymphocytes and eosinophils were below normal range, the ratios were 56.9% and 50.3%, respectively. On the contrary, lactate dehydrogenases raised in 65 patients. C-reactive protein (72.4%) elevated in the most of patients. The sensitivity of RT-PCR was 63.5%. Chest CT indicated that bilateral patchy shadows (69.0%) were the most common imaging manifestations.169(85.8%) patients recovered and transferred to a designated hospital for observation, and the others (14.2%) turned worst and died of acute respiratory failure.\n\nConclusionCOVID-19 infection with highly contagious have become a life-threaten public healthy problem, the sensitivity of RT-PCR was limited. Chest CT scan was recommended for the suspected patients. Furthermore, lymphocytopenia and eosinophils declining without leukocytes increasing may be considered as a useful evidence for the diagnosis.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Fating Zhou", - "author_inst": "Yichang Central people's hospital" - }, - { - "author_name": "Xiaogang Yu", - "author_inst": "Yichang Central people's hospital" - }, - { - "author_name": "Xiaowei Tong", - "author_inst": "Yichang Third people's hospital" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Yichang Central people's hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.27.20045302", "rel_title": "Mobility traces and spreading of COVID-19", @@ -1558875,6 +1555483,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.28.20043059", + "rel_title": "Virus shedding patterns in nasopharyngeal and fecal specimens of COVID-19 patients", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20043059", + "rel_abs": "Diagnosis is the key point for confirmation and treatment of COVID-19. we focused on comparative analysis of virus dynamics between the upper respiratory and feces specimens in the COVID-19 patients. A total of 66 upper respiratory swabs, 51 feces, 56 urine and 56 plasma samples were sequentially collected from 23 patients in a designated hospital. The plasma and urine samples were all negative, except for urine samples from two severe cases at the latest available detection point. Conversely, virus was shed in respiratory swabs and feces samples during the diseased period. Ten of 12 (83.3%) cases were positive for feces samples, while 14 of 21 (66.7%) were positive for respiratory samples. In addition, the median duration of virus shedding was 10.0 days (IQR 8.0 to 17.0) in the upper respiratory swabs, but was 22.0 days (IQR 15.5 to 23.5) for the feces. Notably, at 26 days after discharge, case 3 (a 45-year-old) was detected positive again in the feces samples, but appears to be healthy and negative for respiratory swabs. These results indicated that beside respiratory samples, intestinal samples (e.g. feces) should be recommended for diagnosis of COVID-19, especially before a patient discharge and for monitoring the relapse of discharged patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ning Zhang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Acad" + }, + { + "author_name": "Yuhuan Gong", + "author_inst": "Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China" + }, + { + "author_name": "Fanping Meng", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + }, + { + "author_name": "Yuhai Bi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Acad" + }, + { + "author_name": "Penghui Yang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + }, + { + "author_name": "Fusheng Wang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.28.20045765", "rel_title": "The comparative superiority of IgM-IgG antibody test to real-time reverse transcriptase PCR detection for SARS-CoV-2 infection diagnosis", @@ -1559586,29 +1556233,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.03.26.20044420", - "rel_title": "Causal empirical estimates suggest COVID-19 transmission rates are highly seasonal", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044420", - "rel_abs": "Nearly every country is now combating the 2019 novel coronavirus (COVID-19). It has been hypothesized that if COVID-19 exhibits seasonality, changing temperatures in the coming months will shift transmission patterns around the world. Such projections, however, require an estimate of the relationship between COVID-19 and temperature at a global scale, and one that isolates the role of temperature from confounding factors, such as public health capacity. This paper provides the first plausibly causal estimates of the relationship between COVID-19 transmission and local temperature using a global sample comprising of 166,686 confirmed new COVID-19 cases from 134 countries from January 22, 2020 to March 15, 2020. We find robust statistical evidence that a 1{degrees}C increase in local temperature reduces transmission by 13% [-21%, -4%, 95%CI]. In contrast, we do not find that specific humidity or precipitation influence transmission. Our statistical approach separates effects of climate variation on COVID-19 transmission from other potentially correlated factors, such as differences in public health responses across countries and heterogeneous population densities. Using constructions of expected seasonal temperatures, we project that changing temperatures between March 2020 and July 2020 will cause COVID-19 transmission to fall by 43% on average for Northern Hemisphere countries and to rise by 71% on average for Southern Hemisphere countries. However, these patterns reverse as the boreal winter approaches, with seasonal temperatures in January 2021 increasing average COVID-19 transmission by 59% relative to March 2020 in northern countries and lowering transmission by 2% in southern countries. These findings suggest that Southern Hemisphere countries should expect greater transmission in the coming months. Moreover, Northern Hemisphere countries face a crucial window of opportunity: if contagion-containing policy interventions can dramatically reduce COVID-19 cases with the aid of the approaching warmer months, it may be possible to avoid a second wave of COVID-19 next winter.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Tamma Carleton", - "author_inst": "University of Chicago" - }, - { - "author_name": "Kyle C. Meng", - "author_inst": "University of California, Santa Barbara" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.29.014209", "rel_title": "Orthogonal genome-wide screenings in bat cells identify MTHFD1 as a target of broad antiviral therapy", @@ -1560201,6 +1556825,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044677", + "rel_title": "Suppression and Mitigation Strategies for Control of COVID-19 in New Zealand", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044677", + "rel_abs": "A standard SEIR-type compartment model, parameterised for New Zealand, was used to simulate the spread of Covid19 in New Zealand and to test the effectiveness of various control strategies. Control aims can be broadly categorised as either suppression or mitigation. Suppression aims to keep cases to an absolute minimum for as long as possible. Mitigation aims to allow a controlled outbreak to occur, with the aim of preventing significant overloads on healthcare systems and gradually allowing the population to develop herd immunity.\n\nBoth types of strategy are fraught with uncertainty. Suppression strategies can succeed in delaying an outbreak, but only for as long as such control measures can be sustained. Once controls are eased or restricted, an epidemic is likely to follow as no herd immunity has been acquired. The success or failure of mitigation strategies can depend sensitively on the timing and efficacy of control measures, and require the ability to bring rapidly growing outbreaks under immediate control when needed. This is as yet untested even for a combination of national interventions including case isolation, household quarantine, population-wide social distancing and closure of schools and universities.\n\nAlthough there are disadvantages to both types of approach, suppression has the advantage of buying time until a vaccine and/or treatment become available and allowing NZ to learn from rapidly unfolding events in other countries. A combination of successful suppression, strong border measures, and widespread contact tracing and testing resulting in containment could allow periods when control measures can be relaxed, but only if cases are reduced to a handful.\n\nExecutive SummaryO_LISuppression strategies aim to keep the number of cases to an absolute minimum for as long as possible. This requires early and effective control interventions.\nC_LIO_LISuppression can only delay an epidemic, not prevent it, but may buy enough time for a vaccine or treatment to become available.\nC_LIO_LIMitigation strategies aim to control an epidemic so that herd immunity is acquired by the population without overwhelming healthcare systems.\nC_LIO_LIMitigation strategies are likely to be very high risk: they are unproven internationally, potentially sensitive to uncertainty, and it may take years for herd immunity to be acquired.\nC_LIO_LIStrategy can be switched from suppression to mitigation. For example, once successful mitigation strategies have been tested in other countries. It is likely to be difficult or impossible to switch from a mitigation to a suppression strategy.\nC_LIO_LIA combination of successful suppression, strong border measures, and widespread contact tracing and testing resulting in containment could allow periods when control measures can be relaxed, but only if we can reduce cases to a handful.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Alex James", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Shaun C Hendy", + "author_inst": "University of Auckland" + }, + { + "author_name": "Michael J Plank", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Nicholas Steyn", + "author_inst": "University of Auckland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.26.20044529", "rel_title": "Temperature dependence of COVID-19 transmission", @@ -1560884,69 +1557539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.03.26.20044198", - "rel_title": "No SARS-CoV-2 in expressed prostatic secretion of patients with coronavirus disease 2019: a descriptive multicentre study in China", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044198", - "rel_abs": "PurposeThe aim of the present study was to assess whether SARS-CoV-2 can be detected in the expressed prostatic secretion (EPS) of patients with corona virus disease 2019 (COVID-19).\n\nMethods18 cases of COVID-19, and 5 suspected cases, were selected from three medical centers to detect the RNA expression of SARS-CoV-2 in their EPS with RT-PCR.\n\nResultsResults were negative in all EPS samples for SARS-CoV-2 of suspected and confirmed patients.\n\nConclusionsNo SARS-CoV-2 was expressed in EPS of patients with COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "weihe quan", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "qingyou zheng", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jinfei tian", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jun chen", - "author_inst": "Xiangyang Central Hospital" - }, - { - "author_name": "zhigang liu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "xiangqiu chen", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "tao wu", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "ziliang ji", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "jinqi tang", - "author_inst": "Shenzhen Hospital of Southern Medical University" - }, - { - "author_name": "hao chu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "haijia xu", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - }, - { - "author_name": "yong zhao", - "author_inst": "Wuhan Third Hospital (Hospital-Tongren) of Wuhan University Wuhan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "urology" - }, { "rel_doi": "10.1101/2020.03.28.20043471", "rel_title": "Disposable N95 Masks Pass Qualitative Fit-Test But Have Decreased Filtration Efficiency after Cobalt-60 Gamma Irradiation", @@ -1561471,6 +1558063,45 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.24.20042937", + "rel_title": "Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study", + "rel_date": "2020-03-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042937", + "rel_abs": "COVID-19 has spread to most countries in the world. Puzzlingly, the impact of the disease is different in different countries. These differences are attributed to differences in cultural norms, mitigation efforts, and health infrastructure. Here we propose that national differences in COVID- 19 impact could be partially explained by the different national policies respect to Bacillus Calmette-Guerin (BCG) childhood vaccination. BCG vaccination has been reported to offer broad protection to respiratory infections. We compared large number of countries BCG vaccination policies with the morbidity and mortality for COVID-19. We found that countries without universal policies of BCG vaccination (Italy, Nederland, USA) have been more severely affected compared to countries with universal and long-standing BCG policies. Countries that have a late start of universal BCG policy (Iran, 1984) had high mortality, consistent with the idea that BCG protects the vaccinated elderly population. We also found that BCG vaccination also reduced the number of reported COVID-19 cases in a country. The combination of reduced morbidity and mortality makes BCG vaccination a potential new tool in the fight against COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Aaron Miller", + "author_inst": "New York Institute of Technology, College of Osteopathic Medicine" + }, + { + "author_name": "Mac Josh Reandelar", + "author_inst": "New York Institute of Technology, College os Osteopathic Medicine" + }, + { + "author_name": "Kimberly Fasciglione", + "author_inst": "New York Institute of Technology, College of Osteopathic Medicine" + }, + { + "author_name": "Violeta Roumenova", + "author_inst": "New York Institute of Technology, College of Osteopathic Medicine" + }, + { + "author_name": "Yan Li", + "author_inst": "New York Institute of Technology, College of Osteopathic Medicine" + }, + { + "author_name": "Gonzalo H Otazu", + "author_inst": "New York Institute of Technology, College of Osteopathic Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.26.009233", "rel_title": "Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity", @@ -1562238,45 +1558869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.03.24.20041095", - "rel_title": "Modeling for Corona Virus Outbreak in IRAN", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20041095", - "rel_abs": "BackgroundAs the outbreak of coronavirus disease 2019 (COVID-19) is a worldwide pandemic, it is rapidly expanding in Iran, real-time analyses of epidemiological data are needed to increase situational awareness and inform interventions. In this study, we built a predictive model based on the cumulative trend of new cases and deaths for the top five provinces. we will also look at modeling the trends for confirmed cases, deaths and recovered for the whole country.\n\nMethodIn this study, we have chosen to apply the exponential smoothing model to iteratively forecast future values of a regular time seires from weighted averages of past daily values of the series. This method is exponential because the value of each level is influenced by every preceeding actual value to an exponentially decreasing degree - more recent values are given a greater weight. The available data is too small to identify seasonal patterns and make predictable variation in value, such as annual fluctuation in temperature relative to the season. Trend is a tendency in the data to increase or decrease over time.\n\nResultsIf no control measures are put in place, it is expected that over 40,000 would be infected in Tehran around the middle of June. However, if control measures were implemented with a high degree of success, one would expect the spread of the COV-19 virus would peak at the start of April with a downward trend dropping off by the end of May (70 days). In the scenario, that no further measures are implemented, one would expect the spread of COVID-19 to continue on a gentle incline, reaching 21,000 by mid-June. The same process has been applied to review the confirmed, deaths and recovered dataset. The forecast has been carried out for the next 30 days, a shorter timeframe has been selected as there is a high probability that the Iranian New Years celebration, Farvardin, first month of Spring (30th March in Western calendar) will have an impact on the infection rate following the event.\n\nThe best predictive model predicts the confirmed cases to be in the range of 35,000-70,000, with the number of reported COVDI-19 deaths to be between 3,000 - 5,000 and 5,000 - 30,000 of recovered cases.\n\nConclusionsModeling outbreak ofCovid-19 shows that the number of patients and deaths is still increasing. Contagious diseases follow an exponential model and the same be Haves this one. This is because, the virus can spread to others and finally each person turns into a carrier of the virus and transmit it to another person. Disease control depends on disconnection and social distancing. In addition, many factors are effective in stopping the disease. These include citizens participation in the prevention process, health education, the effectiveness of instructive traditions, environmental conditions, and so on.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Maryam Moghadami", - "author_inst": "Tehran university" - }, - { - "author_name": "Maryam Moghadami", - "author_inst": "Tehran University" - }, - { - "author_name": "Mohammad Hassanzadeh", - "author_inst": "Tarbiat Modare University" - }, - { - "author_name": "ka wa", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Aziz Hedayati", - "author_inst": "Shahid Madani Azarbayjan University" - }, - { - "author_name": "Mila Malekolkalami", - "author_inst": "Tarbiat Modares University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.24.20041087", "rel_title": "Hydrogen Peroxide Vapor sterilization of N95 respirators for reuse", @@ -1562981,6 +1559573,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.22.20041111", + "rel_title": "Exponential damping key to successful containment of COVID-19 outbreak", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20041111", + "rel_abs": "Due to its excessively high capacity for human-to-human transmission, the 2019 novel coronavirus disease (COVID-19), first reported in Wuhan in China, spread rapidly to the entire nation and beyond, and has now been declared a global public health emergency. Understanding the transmission pattern of the virus and the efficacy of transmission control measures is crucial to ensuring regional and global disease control. Here we propose a simple model based on exponential infectious growth, but with a time-varying, largely damping, transmission rate. This model provides an excellent fit to the existing data from the 102 countries and regions which have reported cases for more than 6 days, and, we think, has largely captured the transmission patterns of the COVID-19 outbreak under a variety of intervention and control measures. We found that the damping rate, defined as the rate of the exponential decline in transmission rate, ranged from -0.125 to 0.513 d-1 globally (a negative damping rate represents acceleration in spread). The estimated peak time (when the fastest spread occurs) and the final number of infections were found to be greatly affected by the damping rate. Successful control measures, such as those implemented in China and South Korea, have resulted in a clear pattern of exponential damping in the viral spread (also shown during the 2003 outbreak of Severe Acute Respiratory Syndrome, SARS). The damping rate, therefore, could be used as an indicator for the efficacy of implemented control measures. Our model suggests that the COVID-19 outbreak is currently accelerating worldwide, especially rapidly in certain countries (e.g. USA and Australia) where exponential damping is yet to emerge. Consistent with the message from the World Health Organisation (WHO), we thus strongly suggest all countries to take active measures to contain this global pandemic. Slight increments in the damping rate from additional control efforts, especially in countries showing weak or no exponential damping in COVID-19 transmission, could lead to a radically more positive outcome in the fight to contain the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Feng Zhang", + "author_inst": "Anhui University" + }, + { + "author_name": "Jinmei Zhang", + "author_inst": "Xiguan Community Health Center of Liangzhou" + }, + { + "author_name": "Menglan Cao", + "author_inst": "Anhui University" + }, + { + "author_name": "Yong Zhang", + "author_inst": "Anhui University" + }, + { + "author_name": "Cang Hui", + "author_inst": "Stellenbosch University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.23.20041517", "rel_title": "Spatio-temporal propagation of COVID-19 pandemics", @@ -1563832,113 +1560459,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.03.25.009084", - "rel_title": "Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients", - "rel_date": "2020-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.25.009084", - "rel_abs": "Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing and immunostaining demonstrated ACE2 expression in support cells, stem cells, and perivascular cells; in contrast, neurons in both the olfactory epithelium and bulb did not express ACE2 message or protein. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "David Brann", - "author_inst": "Harvard Medical School Department of Neurobiology" - }, - { - "author_name": "Tatsuya Tsukahara", - "author_inst": "Harvard Medical School Department of Neurobiology" - }, - { - "author_name": "Caleb Weinreb", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Koen Van den Berge", - "author_inst": "Department of Statistics, University of California, Berkeley; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgi" - }, - { - "author_name": "Boying Gong", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Rebecca Chance", - "author_inst": "Department of Molecular and Cell Biology, University of California," - }, - { - "author_name": "Iain C Macaulay", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Hsin-jung Chou", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Russell Fletcher", - "author_inst": "Department of Molecular and Cell Biology, University of California," - }, - { - "author_name": "Diya Das", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Kelly Street", - "author_inst": "Department of Data Sciences, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Hector Roux de Bezieux", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Yoon-Gi Choi", - "author_inst": "QB3 Functional Genomics Laboratory, University of California, Berkeley" - }, - { - "author_name": "Davide Risso", - "author_inst": "Department of Statistical Sciences, University of Padova" - }, - { - "author_name": "Sandrine Dudoit", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Elizabeth Purdom", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Jonathan C Mill", - "author_inst": "University of Exeter" - }, - { - "author_name": "Ralph Abi Hachem", - "author_inst": "Duke University" - }, - { - "author_name": "Hiroaki Matsunami", - "author_inst": "Duke University" - }, - { - "author_name": "Darren W. Logan", - "author_inst": "Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK" - }, - { - "author_name": "Bradley Goldstein", - "author_inst": "Duke University" - }, - { - "author_name": "John Ngai", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley; Helen Wills Neuroscience Institute; QB3 Functional Genomics Laboratory" - }, - { - "author_name": "Sandeep Robert Datta", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.03.25.20043893", "rel_title": "A Simple Mathematical Model for Estimating the Inflection Points of COVID-19 Outbreaks", @@ -1564483,6 +1561003,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.20.20039586", + "rel_title": "Anti-hypertensive Angiotensin II receptor blockers associated to mitigation of disease severity in elderly COVID-19 patients", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039586", + "rel_abs": "BackgroundThe novel coronavirus (CoV) severe acute respiratory syndrome (SARS)-CoV-2 outbreak started at the end of 2019 in Wuhan, China, and spread over 100 countries. SARS-CoV-2 uses the membrane protein Angiotensin I converting enzyme 2(ACE2) as a cell entry receptor. Indeed, it was reported that the balance of Renin-Angiotensin System (RAS), regulated by both ACE and ACE2, was altered in COVID-19 patients. It is controversial, however, whether commonly used anti-hypertensive drugs Angiotensin I converting enzyme inhibitor (ACEI) and Angiotensin II receptor blocker (ARB) shall be continued in the confirmed COVID-19 patients. This study was designed to investigate any difference in disease severity between COVID-19 patients with hypertension comorbidity. The included COVID-19 patients used ACEI, ARB, calcium channel blockers (CCB), beta blockers (BB), or thiazide to treat preexisting hypertension prior to the hospital were compared to patients who did not take any of those drugs.\n\nMethodsIn this multicentre retrospective study, clinical data of 511 COVID-19 patients were analyzed. Patients were categorized into six sub-groups of hypertension comorbidity based on treatment using one of anti-hypertension drugs (ACEI, ARB, CCB, BB, thiazide), or none. A meta-analysis was performed to evaluate the use of ACEI and ARB associated with pneumonia using published studies.\n\nFindingsAmong the elderly (age>65) COVID-19 patients with hypertension comorbidity, the risk of COVID-19-S (severe disease) was significantly decreased in patients who took ARB drugs prior to hospitalization compared to patients who took no drugs (OR=0{middle dot}343, 95% CI 0{middle dot}128-0{middle dot}916, p=0{middle dot}025). The meta-analysis showed that ARB use has positive effects associated with morbidity and mortality of pneumonia.\n\nInterpretationElderly (age>65) COVID-19 patients with hypertension comorbidity who are taking ARB anti-hypertension drugs may be less likely to develop severe lung disease compared to patients who take no anti-hypertension drugs.\n\nFundingNational Natural Science Foundation of China, Chinese Academy of Medical Sciences\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for articles published up to March 15, 2020 using keywords \"2019-nCoV\", \"SARS-CoV-2\", \"novel coronavirus\", and COVID-19 AND \"ARB\", and \"angiotensin II receptor blocker\" for papers published in both English and Chinese. We found three papers: one from our group, published in Science China Life Science that demonstrated an elevated Angiotensin II level in blood samples from COVID-19 patients; another a perspective article in Chinese recommending ACEI and ARBs as potential remedies for SARS-CoV-2 infections; the third a retrospective study in Chinese identifying no significant difference between ACEI/ARB associated with outcomes in 112 COVID-19 patients with CVD comorbidity. The International society of Hypertension stated on March 16th, 2020: \"there are no clinical data in human to show that ACE-inhibitors or ARBs either improve or worsen susceptibility to COVID-19 infection nor do they affect the outcomes of those infected\".\n\nAdded value of this studyWe retrospectively reviewed different types of anti-hypertensive drugs taken by COVID-19 patients with hypertension comorbidity prior to entering the hospital. We discovered that ARB hypertensive drugs were associated with a decreased risk of severe disease in elderly (age>65) COVID-19 patients (OR=0{middle dot}343, 95% CI 0{middle dot}128-0{middle dot}916, p=0{middle dot}025), the first evidence of ARBs association to COVID-19 infections in human. We conducted a meta-analysis in the literature and found that ARB has positive effects associated with morbidity and mortality of pneumonia.\n\nImplications of all the available evidenceARB drugs are widely used in the population with hypertension. Treatments with ACEI and ARBs should be continuous according to medical guidelines. RCT trials of ARB associated with morbidity and mortality of SARS-CoV-2 infection are recommended in the future.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yingxia Liu", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Fengming Huang", + "author_inst": "State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS-Oxford Institute, Chinese Academy of Medical Sciences, Department o" + }, + { + "author_name": "Jun Xu", + "author_inst": "Department of Emergency, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China." + }, + { + "author_name": "Penghui Yang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + }, + { + "author_name": "Yuhao Qin", + "author_inst": "State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS-Oxford Institute, Chinese Academy of Medical Sciences, Department o" + }, + { + "author_name": "Mengli Cao", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Zhaoqin Wang", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Xiaohe Li", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Shaogeng Zhang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + }, + { + "author_name": "Lu Ye", + "author_inst": "Emergency Department, Renmin Hospital of Wuhan University 430060" + }, + { + "author_name": "Jingjun Lv", + "author_inst": "Emergency Departmen, Renmin Hospital of Wuhan University 430060" + }, + { + "author_name": "Jie Wei", + "author_inst": "Emergency Department, Renmin Hospital of Wuhan University 430060" + }, + { + "author_name": "Tuxiu Xie", + "author_inst": "Department of General Medicine , Guang-gu hospital affiliated Renmin Hospital of Wuhan University 430200" + }, + { + "author_name": "Hong Gao", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Kai-Feng Xu", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China." + }, + { + "author_name": "Fusheng Wang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, P. R. China." + }, + { + "author_name": "Lei Liu", + "author_inst": "Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to So" + }, + { + "author_name": "Chengyu Jiang", + "author_inst": "Institute of Basic Medical Science Chinese Academy of Medical Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.24.20040162", "rel_title": "Lactate dehydrogenase, a Risk Factor of Severe COVID-19 Patients", @@ -1565250,125 +1561857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20042184", - "rel_title": "Serological diagnostic kit of SARS-CoV-2 antibodies using CHO-expressed full-length SARS-CoV-2 S1 proteins", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20042184", - "rel_abs": "WHO has declared COVID-19 a pandemic with more than 300,000 confirmed cases and more than 14,000 deaths. There is urgent need for accurate and rapid diagnostic kits. Here we report the development and validation of a COVID-19/SARS-CoV-2 S1 serology ELISA kit for the detection of total anti-virus antibody (IgG+IgM) titers in sera from either the general population or patients suspected to be infected. For indirect ELISA, CHO-expressed recombinant full length SARS-CoV-2-S1 protein with 6* His tag was used as the coating antigen to capture the SARS-CoV-2-S1 antibodies specifically. The specificity of the ELISA kit was determined to be 97.5%, as examined against total 412 normal human sera including 257 samples collected prior to the outbreak and 155 collected during the outbreak. The sensitivity of the ELISA kit was determined to be 97.5% by testing against 69 samples from hospitalized and/or recovered COVID-19 patients. The overall accuracy rate reached 97.3%. Most importantly, in one case study, the ELISA test kit was able to identify an infected person who had previously been quarantined for 14 days after coming into contact with a confirmed COVID-19 patient, and discharged after testing negative twice by nucleic acid test. With the assays developed here, we can screen millions of medical staffs in the hospitals and people in residential complex, schools, public transportations, and business parks in the epidemic centers of the outbreaks to fish out the \"innocent viral spreaders\", and help to stop the further spreading of the virus.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Rongqing Zhao", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Maohua Li", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Hao Song", - "author_inst": "Research Network of Immunity and Health (RNIH)" - }, - { - "author_name": "Jianxin Chen", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Wenlin Ren", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Yingmei Feng", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Jin-Wen Song", - "author_inst": "The Fifth Medical Center of PLA General Hospital" - }, - { - "author_name": "Ya Peng", - "author_inst": "Research Network of Immunity and Health (RNIH)" - }, - { - "author_name": "Bin Su", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Xianghua Guo", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Yanjun Wang", - "author_inst": "Beijing Institute of Hepatology" - }, - { - "author_name": "Jingong Chen", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Jianli Li", - "author_inst": "AbMax Biotechnology Co., LTD" - }, - { - "author_name": "Hunter Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Zhonghu Bai", - "author_inst": "School of Biotechnology, Jiangnan University" - }, - { - "author_name": "Wen Jing Cao", - "author_inst": "Bengbu Medical University" - }, - { - "author_name": "Jin Zhu", - "author_inst": "Quzhou People's Hospital" - }, - { - "author_name": "Qinlu Zhang", - "author_inst": "ShaanXi Provincial Engineering Research Center for Nano-BioMedical Detection" - }, - { - "author_name": "Yufei Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Sean Sun", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Xinkun Mao", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Junchi Su", - "author_inst": "AnyGo Technology Co., Ltd" - }, - { - "author_name": "Hui Chen", - "author_inst": "School of Biotechnology, Jiangnan Univ" - }, - { - "author_name": "Ailiang He", - "author_inst": "Zhenge Biotechnology Co., LTD" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing You an Hospital, Capital Medical University" - }, - { - "author_name": "Le Sun", - "author_inst": "AbMax Biotechnology Co., LTD" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.22.20040642", "rel_title": "The Effect of Large-Scale Anti-Contagion Policies on the Coronavirus (COVID-19) Pandemic", @@ -1565893,6 +1562381,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.03.25.20037721", + "rel_title": "Risk Factors Associated with Clinical Outcomes in 323 COVID-19 Patients in Wuhan, China", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20037721", + "rel_abs": "BackgroundWith evidence of sustained transmission in more than 190 countries, coronavirus disease 2019 (COVID-19) has been declared a global pandemic. As such, data are urgently needed about risk factors associated with clinical outcomes.\n\nMethodsA retrospective chart review of 323 hospitalized patients with COVID-19 in Wuhan was conducted. Patients were classified into three disease severity groups (non-severe, severe, and critical), based on their initial clinical presentation. Clinical outcomes were designated as favorable and unfavorable, based on disease progression and response to treatments. Logistic regression models were performed to identify factors associated with clinical outcomes, and log-rank test was conducted for the association with clinical progression.\n\nResultsCurrent standard treatments did not show significant improvement on patient outcomes in the study. By univariate logistic regression model, 27 risk factors were significantly associated with clinical outcomes. Further, multivariate regression indicated that age over 65 years, smoking, critical disease status, diabetes, high hypersensitive troponin I (>0.04 pg/mL), leukocytosis (>10 x 109/L) and neutrophilia (>75 x 109/L) predicted unfavorable clinical outcomes. By contrast, the use of hypnotics was significantly associated with favorable outcomes. Survival analysis also confirmed that patients receiving hypnotics had significantly better survival.\n\nConclusionsTo our knowledge, this is the first indication that hypnotics could be an effective ancillary treatment for COVID-19. We also found that novel risk factors, such as higher hypersensitive troponin I, predicted poor clinical outcomes. Overall, our study provides useful data to guide early clinical decision making to reduce mortality and improve clinical outcomes of COVID-19.\n\n(Funded by the Natural Science Foundation of Hubei Province ZRMS2019000029 and the Top Youth Talent Program in Hubei Province.)", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Ling Hu", + "author_inst": "Tianyou Hospital, Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Shaoqiu Chen", + "author_inst": "John A. Burns School of Medicine" + }, + { + "author_name": "Yuanyuan Fu", + "author_inst": "John A. Burns School of Medicine" + }, + { + "author_name": "Zitong Gao", + "author_inst": "John A. Burns School of Medicine" + }, + { + "author_name": "Hui Long", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Hong-wei Ren", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Yi Zuo", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Huan Li", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Jie Wang", + "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Qing-bang Xv", + "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Wen-xiong Yu", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Jia Liu", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Chen Shao", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Jun-jie Hao", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Chuan-zhen Wang", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Yao Ma", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Zhanwei Wang", + "author_inst": "University of Hawaii Cancer Center" + }, + { + "author_name": "Richard Yanagihara", + "author_inst": "John A. Burns School of Medicine" + }, + { + "author_name": "Jian-ming Wang", + "author_inst": "Tianyou Hospital Affiliated to Wuhan University of Science and Technology" + }, + { + "author_name": "Youping Deng", + "author_inst": "University of Hawaii John A. Burns School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.25.008805", "rel_title": "An artificial intelligence based first-line defence against COVID-19: digitally screeningcitizens for risks via a chatbot", @@ -1566852,65 +1563435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2020.03.21.20037127", - "rel_title": "A Multicentre Study of 2019 Novel Coronavirus Disease Outcomes of Cancer Patients in Wuhan, China", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20037127", - "rel_abs": "BackgroundAt present, there is a global pandemic of coronavirus disease 2019 (COVID-19) pneumonia. For COVID-19 patients, cancer is a coexisting disease that should not be Here, we conducted a multicenter retrospective study to show the clinical information and outcomes of cancer patients infected with COVID-19.\n\nMeasurementsMedical records of COVID-19 patients with cancer admitted to hospitals from Jan 5, 2020 to Feb 18, 2020 were collected.\n\nResultsOf the 67 patients (median age: 66 years), the median age of patients with severe illness was older than that of patients with mild symptoms (P<0.001). The proportion of severe patients had co-morbidities was higher than patients with mild disease (P=0.004). During the treatment of COVID-19 pneumonia, tumor progression and recurrence was not observed for those patients still at the anticancer treatment phase. Lymphocytopenia was the main laboratory finding accompanying increased C-reactive protein and procalcitonin in cancer patients, especially in severe cases. By Mar 10, 2020, 18 (26.9%) patients died from COVID-19. The median age of survivors was younger than that of deaths (P=0.014). Lung cancer (n=15, 22.4%) was the most common cancer type and accounted for the highest proportion COVID-19 resulted deaths (33.3%, 5/15). We observed a tendency that patients at the follow-up phase had a better prognosis than that at anticancer treatment phase (P=0.095).\n\nConclusionThis study showed COVID-19 patients with cancer seem to have a higher proportion of severe cases and poorer prognosis. We should pay more intensive attentions to cancer patients infected with COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hong-Yan Zhang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lin-Wei Wang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yuan-Yuan Chen", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Xiao-Kun Shen", - "author_inst": "Convalife (Shanghai) Co., Ltd." - }, - { - "author_name": "Qun Wang", - "author_inst": "the Fifth Hospital of Wuhan" - }, - { - "author_name": "You-Qin Yan", - "author_inst": "the Seventh Hospital of Wuhan" - }, - { - "author_name": "Yi Yu", - "author_inst": "Han Kou Hospital of Wuhan" - }, - { - "author_name": "Qiuji Wu", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Ya-Hua Zhong", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Melvin Chua Lee Kiang", - "author_inst": "National Cancer Centre Singapore" - }, - { - "author_name": "Cong-Hua Xie", - "author_inst": "Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.03.22.20040600", "rel_title": "Human leukocyte antigen susceptibility map for SARS-CoV-2", @@ -1567615,6 +1564139,57 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.22.20038919", + "rel_title": "The impact of temperature and absolute humidity on the coronavirus disease 2019 (COVID-19) outbreak - evidence from China", + "rel_date": "2020-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20038919", + "rel_abs": "OBJECTIVETo investigate the impact of temperature and absolute humidity on the coronavirus disease 2019 (COVID-19) outbreak.\n\nDESIGNEcological study.\n\nSETTING31 provincial-level regions in mainland China.\n\nMAIN OUTCOME MEASURESData on COVID-19 incidence and climate between Jan 20 and Feb 29, 2020.\n\nRESULTSThe number of new confirm COVID-19 cases in mainland China peaked on Feb 1, 2020. COVID-19 daily incidence were lowest at -10 {degrees}C and highest at 10 {degrees}C, while the maximum incidence was observed at the absolute humidity of approximately 7 g/m3. COVID-19 incidence changed with temperature as daily incidence decreased when the temperature rose. No significant association between COVID-19 incidence and absolute humidity was observed in distributed lag nonlinear models. Additionally, A modified susceptible-exposed-infectious-recovered (M-SEIR) model confirmed that transmission rate decreased with the increase of temperature, leading to further decrease of infection rate and outbreak scale.\n\nCONCLUSIONTemperature is an environmental driver of the COVID-19 outbreak in China. Lower and higher temperatures might be positive to decrease the COVID-19 incidence. M-SEIR models help to better evaluate environmental and social impacts on COVID-19.\n\nWhat is already known on this topicO_LIMany infectious diseases present an environmental pattern in their incidence.\nC_LIO_LIEnvironmental factors, such as climate and weather condition, could drive the space and time correlations of infectious diseases, including influenza.\nC_LIO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted through aerosols, large droplets, or direct contact with secretions (or fomites) as influenza virus can.\nC_LIO_LILittle is known about environmental pattern in COVID-19 incidence.\nC_LI\n\nWhat this study addsO_LIThe significant association between COVID-19 daily incidence and temperature was confirmed, using 3 methods, based on the data on COVID-19 and weather from 31 provincial-level regions in mainland China.\nC_LIO_LIEnvironmental factors were considered on the basis of SEIR model, and a modified susceptible-exposed-infectious-recovered (M-SEIR) model was developed.\nC_LIO_LISimulations of the COVID-19 outbreak in Wuhan presented similar effects of temperature on incidence as the incidence decrease with the increase of temperature.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Peng Shi", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Yinqiao Dong", + "author_inst": "Department of Occupational Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Huanchang Yan", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China" + }, + { + "author_name": "Xiaoyang Li", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Chenkai Zhao", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Wei Liu", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Miao He", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + }, + { + "author_name": "Shixing Tang", + "author_inst": "Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China" + }, + { + "author_name": "Shuhua Xi", + "author_inst": "Department of Environmental Health, School of Public Health, China Medical University, Shenyang, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.03.22.20040774", "rel_title": "Hypertension and Diabetes Delay the Viral Clearance in COVID-19 Patients", @@ -1568378,53 +1564953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.24.004655", - "rel_title": "SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems", - "rel_date": "2020-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.24.004655", - "rel_abs": "One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Daniel Blanco-Melo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin Nilsson-Payant", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Wen-Chun Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Rasmus Moeller", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Maryline Panis", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "David Sachs", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Randy Albrecht", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin R. tenOever", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.21.20040691", "rel_title": "Meplazumab treats COVID-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial", @@ -1569385,6 +1565913,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.20.20040055", + "rel_title": "The Effectiveness of Social Distancing in Mitigating COVID-19 Spread: a modelling analysis", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20040055", + "rel_abs": "BackgroundThe novel coronavirus COVID-19 has been classified by the World Health Organisation as a pandemic due to its worldwide spread. The ability of countries to contain and control transmission is critical in the absence of a vaccine. We evaluated a range of social distancing measures to determine which strategies are most effective in reducing the peak daily infection rate, and consequential pressure on the health care system.\n\nMethodsUsing COVID-19 transmission data from the outbreak source in Hubei Province, China, collected prior to activation of containment measures, we adapted an established individual based simulation model of the city of Newcastle, Australia, population 272,409. Simulation of virus transmission in this community model without interventions provided a baseline from which to compare alternative social distancing strategies. The infection history of each individual was determined, as was the time infected. From this model-generated data, the rate of growth in cases, the magnitude of the epidemic peak, and the outbreak duration were obtained.\n\nFindingsThe application of all four social distancing interventions: school closure, workplace non-attendance, increased case isolation, and community contact reduction is highly effective in flattening the epidemic curve, reducing the maximum daily case numbers, and lengthening outbreak duration. These were also found to be effective even after 10 weeks delay from index case arrivals. The most effective single intervention was found to be increasing case isolation, to 100% of children and 90% of adults.\n\nInterpretationAs strong social distancing intervention strategies had the most effect in reducing the epidemic peak, this strategy may be considered when weaker strategies are first tried and found to be less effective. Questions arise as to the duration of strong social distancing measures, given they are highly disruptive to society. Tradeoffs may need to be made between the effectiveness of social distancing strategies and population willingness to adhere to them.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "George J Milne", + "author_inst": "University of Western Australia" + }, + { + "author_name": "Simon Xie", + "author_inst": "the University of Western Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.19.20039057", "rel_title": "Forecasting ultra-early intensive care strain from COVID-19 in England", @@ -1570020,33 +1566571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.21.20040444", - "rel_title": "From a single host to global spread. The global mobility based modelling of the COVID-19 pandemic implies higher infection and lower detection rates than current estimates.", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040444", - "rel_abs": "BackgroundSince the outbreak of the COVID-19 pandemic, multiple efforts of modelling of the geo-temporal transmissibility of the virus have been undertaken, but none describes the pandemic spread at the global level. The aim of this research is to provide a high-resolution global model of the pandemic that overcomes the problem of biased country-level data on the number of infected cases. To achieve this we propose a novel SIR-type metapopulation transmission model and a set of analytically derived model parameters. We used them to perform a simulation of the disease spread with help of the Global Epidemic and Mobility (GLEAM) framework embedding actual population densities, commute patterns and long-range travel networks. The simulation starts on Nov 17th, 2019 with just a single pre-symptomatic, yet infectious, case in Wuhan, China, and results in an accurate prediction of the number of diagnosed cases after 154 days in multiple countries across five continents. In addition, the model outcome shows high compliance with the results of a random screening test conducted on pregnant women in the New York area.\n\nMethodsWe have built a modified SIR metapopulation transmission model and parameterized it analytically either by setting the values of the parameters based on the literature, or by assuming their plausible values. We compared our results with the number of diagnosed cases in twenty selected countries which provide reliable statistics but differ substantially in terms of strength and speed of undertaken Non-Drug Interventions. The obtained 95% confidence intervals for the predictions are in agreement with the empirical data.\n\nResultsThe parameters that successfully model the pandemic are: the basic reproduction number R0, 4.4; a latent non-infectious period of 1.1. days followed by 4.6 days of the presymptomatic infectious period; the probability of developing severe symptoms, 0.01; the probability of being diagnosed when presenting severe symptoms of 0.6; the probability of diagnosis for cases with mild symptoms or asymptomatic, 0.001.\n\nDiscussionParameters that successfully reproduce the observed number of cases indicate that both R0 and the prevalence of the virus might be underestimated. This is in concordance with the newest research on undocumented COVID-19 cases. Consequently, the actual mortality rate is putatively lower than estimated. Confirmation of the pandemic characteristic by further refinement of the model and screening tests is crucial for developing an effective strategy for the global epidemiological crisis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marlena M Siwiak", - "author_inst": "Data 3.0" - }, - { - "author_name": "Pawel Szczesny", - "author_inst": "Data 3.0" - }, - { - "author_name": "Marian P Siwiak", - "author_inst": "Data 3.0" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.20.20038422", "rel_title": "Estimating the reproduction number of COVID-19 in Iran using epidemic modeling", @@ -1570571,6 +1567095,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.20.20039834", + "rel_title": "Development and Evaluation of an AI System for COVID-19", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039834", + "rel_abs": "Early detection of COVID-19 based on chest CT will enable timely treatment of patients and help control the spread of the disease. With rapid spreading of COVID-19 in many countries, however, CT volumes of suspicious patients are increasing at a speed much faster than the availability of human experts. We proposed an artificial intelligence (AI) system for fast COVID-19 detection and performed extensive statistical analysis of CTs of COVID-19 based on the AI system. We developed and evaluated our system on a large dataset with more than 10 thousand CT volumes from COVID-19, influenza-A/B, non-viral community acquired pneumonia (CAP) and non-pneumonia subjects. In such a difficult multi-class diagnosis task, our deep convolutional neural network-based system is able to achieve an area under the receiver operating characteristic curve (AUC) of 97.17%, a sensitivity of 90.19%, and a specificity of 95.76% for COVID-19 on internal test cohort of 3,203 scans and AUC of 97.77% on the publicly available CC-CCII database with 1,943 test samples. In a reader study involving five radiologists, the AI system outperforms all of radiologists in more challenging tasks at a speed of two orders of magnitude above them. Diagnosis performance of chest x-ray (CXR) is compared. Detailed interpretation of deep network is also performed to relate AI results with CT findings. The code is available at https://github.com/ChenWWWeixiang/diagnosis_covid19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cheng Jin", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Weixiang Chen", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yukun Cao", + "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Zhanwei Xu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Zimeng Tan", + "author_inst": "Department of Automation, Tsinghua University, Beijing, China" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Lei Deng", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Chuansheng Zheng", + "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Heshui Shi", + "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jianjiang Feng", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.03.21.20040303", "rel_title": "Initial Simulation of SARS-CoV2 Spread and Intervention Effects in the Continental US", @@ -1571878,37 +1568461,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.21.001586", - "rel_title": "Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis", - "rel_date": "2020-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.21.001586", - "rel_abs": "The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein function and stability, using computational approach. To gain further insights into host responses to viral infection, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa-miR-27b is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rahila Sardar", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB) and Jamia Hamdard, India" - }, - { - "author_name": "Deepshikha Satish", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - }, - { - "author_name": "Shweta Birla", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - }, - { - "author_name": "Dinesh Gupta", - "author_inst": "International Centre for Genetic Engineering and Biotechnology (ICGEB), India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.03.19.998724", "rel_title": "All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus", @@ -1572521,6 +1569073,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.16.20035014", + "rel_title": "Evaluation of Nucleocapsid and Spike Protein-based ELISAs for detecting antibodies against SARS-CoV-2", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20035014", + "rel_abs": "BackgroundAt present, PCR-based nucleic acid detection cannot meet the demands for coronavirus infectious disease (COVID-19) diagnosis.\n\nMethods214 confirmed COVID-19 patients who were hospitalized in the General Hospital of Central Theater Command of the Peoples Liberation Army between January 18 and February 26, 2020, were recruited. Two Enzyme-Linked Immunosorbent Assay (ELISA) kits based on recombinant SARS-CoV-2 nucleocapsid protein (rN) and spike protein (rS) were used for detecting IgM and IgG antibodies, and their diagnostic feasibility was evaluated.\n\nResultsAmong the 214 patients, 146 (68.2%) and 150 (70.1%) were successfully diagnosed with the rN-based IgM and IgG ELISAs, respectively; 165 (77.1%) and 159 (74.3%) were successfully diagnosed with the rS-based IgM and IgG ELISAs, respectively. The positive rates of the rN-based and rS-based ELISAs for antibody (IgM and/or IgG) detection were 80.4% and 82.2%, respectively. The sensitivity of the rS-based ELISA for IgM detection was significantly higher than that of the rN-based ELISA. We observed an increase in the positive rate for IgM and IgG with an increasing number of days post-disease onset (d.p.o.), but the positive rate of IgM dropped after 35 d.p.o. The positive rate of rN-based and rS-based IgM and IgG ELISAs was less than 60% during the early stage of the illness 0-10 d.p.o., and that of IgM and IgG was obviously increased after 10 d.p.o.\n\nConclusionsELISA has a high sensitivity, especially for the detection of serum samples from patients after 10 d.p.o, it can be an important supplementary method for COVID-19 diagnosis.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wanbing Liu", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Lei Liu", + "author_inst": "Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China" + }, + { + "author_name": "Guomei Kou", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Yaqiong Zheng", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Yinjuan Ding", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Wenxu Ni", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Qiongshu Wang", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Li Tan", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Wanlei Wu", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Shi Tang", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Zhou Xiong", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + }, + { + "author_name": "Shangen Zheng", + "author_inst": "General Hospital of Central Theater Command of PLA, Wuhan, Hubei, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.03.15.20032870", "rel_title": "GENOMIC CHARACTERISATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 IN ITALY", @@ -1573228,77 +1569843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.17.20037432", - "rel_title": "Favipiravir versus Arbidol for COVID-19: A Randomized Clinical Trial", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037432", - "rel_abs": "BackgroundNo clinically proven effective antiviral strategy exists for the epidemic Coronavirus Disease 2019 (COVID-19).\n\nMethodsWe conducted a prospective, randomized, controlled, open-label multicenter trial involving adult patients with COVID-19. Patients were randomly assigned in a 1:1 ratio to receive conventional therapy plus Umifenovir (Arbidol) (200mg*3/day) or Favipiravir (1600mg*2/first day followed by 600mg*2/day) for 10 days. The primary outcome was clinical recovery rate of Day 7. Latency to relief for pyrexia and cough, the rate of auxiliary oxygen therapy (AOT) or noninvasive mechanical ventilation (NMV) were the secondary outcomes. Safety data were collected for 17 days.\n\nResults240 enrolled COVID-19 patients underwent randomization; 120 patients were assigned to receive Favipiravir (116 assessed), and 120 to receive Arbidol (120 assessed). Clinical recovery rate of Day 7 does not significantly differ between Favipiravir group (71/116) and Arbidol group (62/120) (P=0.1396, difference of recovery rate: 0.0954; 95% CI: -0.0305 to 0.2213). Favipiravir led to shorter latencies to relief for both pyrexia (difference: 1.70 days, P<0.0001) and cough (difference: 1.75 days, P<0.0001). No difference was observed of AOT or NMV rate (both P>0.05). The most frequently observed Favipiravir-associated adverse event was raised serum uric acid (16/116, OR: 5.52, P=0.0014).\n\nConclusionsAmong patients with COVID-19, Favipiravir, compared to Arbidol, did not significantly improve the clinically recovery rate at Day 7. Favipiravir significantly improved the latency to relief for pyrexia and cough. Adverse effects caused Favipiravir are mild and manageable. This trial is registered with Chictr.org.cn (ChiCTR2000030254).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Chang Chen", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Center for Life Sciences, Peking University" - }, - { - "author_name": "Jianying Huang", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Ping Yin", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Zhenshun Cheng", - "author_inst": "Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Jianyuan Wu", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Song Chen", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yongxi Zhang", - "author_inst": "Department of Infectious Diseases, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Bo Chen", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Mengxin Lu", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Yongwen Luo", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Lingao Ju", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Jingyi Zhang", - "author_inst": "Department of Cardiology, The Third People Hospital of Hubei Province" - }, - { - "author_name": "Xinghuan Wang", - "author_inst": "Clinical Trial Center, Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.17.20036640", "rel_title": "Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2", @@ -1573895,6 +1570439,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.19.20038729", + "rel_title": "Fear, Access, and the Real-Time Estimation of Etiological Parameters for Outbreaks of Novel Pathogens", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038729", + "rel_abs": "Early analysis of outbreaks of novel pathogens to evaluate their likely public health impact depends on fitting predictive models to data gathered and updated in real-time. Both transmission rates and the critical R0 threshold (i.e. the pathogens reproductive number) are inferred by finding the values that provide the best model fit to reported case incidence. These models and inferred results are then the basic tools used for public health planning: how many people expected to be infected, at what scales of time and space, and whether potential intervention strategies impact disease transmission and spread. An underlying assumption, however, is that the ability to observe new cases is either constant, or at least constant relative to diagnostic test availability.\n\nWe present a demonstration, discussion, and mathematical analysis of how this assumption of predictable observability in disease incidence can drastically impact model accuracy. We also demonstrate how to tailor estimations of these parameters to a few examples of different types of shifting influences acting on detection, depending on the likely sensitivity of surveillance systems to errors from sources such as clinical testing rates and differences in healthcare-seeking behavior from the public over time. Finally, we discuss the implications of these corrections for both historical and current outbreaks.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nina H Fefferman", + "author_inst": "University of Tennessee" + }, + { + "author_name": "Eric Lofgren", + "author_inst": "Washington State University" + }, + { + "author_name": "Nianpeng Li", + "author_inst": "Howard University" + }, + { + "author_name": "Pieter Blue", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "David Weber", + "author_inst": "University of North Carolina, Gillings School of Global Public Health" + }, + { + "author_name": "Abdul-Aziz Yakubu", + "author_inst": "Howard University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.18.20038448", "rel_title": "Response and role of palliative care during the COVID-19 pandemic: a national telephone survey of hospices in Italy", @@ -1574602,25 +1571185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.03.17.20037838", - "rel_title": "AAEDM: Theoretical Dynamic Epidemic Diffusion Model and Covid-19 Korea Pandemic Cases", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037838", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThis paper deals with an advanced analytical epidemic diffusion model which is capable to predict the status of epidemic impacts. This newly propose model well describes an epidemic growth and it could be widely applied into various topics including pathology, epidemiology, business and data sciences. The Advanced Analytical Epidemic Diffusion Model (AAEDM) is a dynamic diffusion prediction model which is theoretically intuitive and its tractable closed formula could be easily adapted into versatile Bigdata driven analytics including the machine learning system. This dynamic model is still an analytical model but the periods of prediction are segmented for adapting the values from the dataset when the data is available. The epidemiologically vital parameters which effect on the AAEDM are also introduced in this paper. The evaluation of this theoretical model based on the Covid-19 data in Korea has been accomplished with relative fair future prediction accuracies. Although this analytical model has been designed from a basic exponential growth model, the performance of the AAEDM is competitive with other Bigdata based simulation models. Since the AAEDM is relatively simple and handy, anyone can use this model into analyzing outbreak situations in his daily life.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Song-Kyoo Kim", - "author_inst": "Macao Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.17.20037788", "rel_title": "Intensive Care Unit Resource Planning During COVID-19 Emergency at the Regional Level: the Italian case.", @@ -1575341,6 +1571905,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.15.20036418", + "rel_title": "Understanding Epidemic Data and Statistics: A case study of COVID-19", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036418", + "rel_abs": "The 2019-Novel-Coronavirus (COVID-19) has affected 181 countries and out of about 1197405 confirmed cases (By April 5). Understanding the transmission dynamics of the infection in each country which affected on a daily basis and evaluating the effectiveness of control policies is critical for our further actions. To date, the statistics of COVID-19 reported cases show more than 80 percent of infected had a mild case of disease, while around 14 percent of infected experienced a severe one and about 5 percent are categorized as critical disease victims. Todays report (2020-04-05; daily updates in the prepared website) shows the confirmed cases of COVID-19 in US, Spain, Italy, and Germany are 308850, 126168, 124632 and 96092; respectively. Calculating the total Case Fatality Rate (CFR) of Italy (2020-04-04), about 13.3% of confirmed cases passed away. Compared to South Koreas rate of 1.8% (7 times lower than Italy) and Chinas 4% (69% lower than Italy), the CFR of Italy is too high. There are some effective policies that yield significant changes in the trend of cases. The lockdown policy in China, Italy and Spain (the effect observed after some days), Shutdown of all non-essential companies in Hubei (the effect observed after 5 days), combined policy in South Korea and reducing working hours in Iran.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Amirhoshang Hoseinpour Dehkordi", + "author_inst": "Institute for Research in Fundamental Sciences" + }, + { + "author_name": "Majid Alizadeh", + "author_inst": "University of Tehran" + }, + { + "author_name": "Pegah Derakhshan", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Peyman Babazadeh", + "author_inst": "Islamic Azad University Central Tehran Branch" + }, + { + "author_name": "Arash Jahandideh", + "author_inst": "Iran polymer and petrochemical institute IPPI" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.14.20036202", "rel_title": "Propagation analysis and prediction of the COVID-19", @@ -1576192,73 +1572791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.15.991844", - "rel_title": "RBD mutations from circulating SARS-CoV-2 strains enhance the structure stability and infectivity of the spike protein", - "rel_date": "2020-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.15.991844", - "rel_abs": "The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD during the early transmission phase have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Among 32,123 genomes of SARS-CoV-2 isolates (January through March, 2020), 302 non-synonymous RBD mutants were identified and clustered into 96 mutant types. The six dominant mutations were analyzed applying molecular dynamics simulations. The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The increased infectivity of V367 mutants was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G) which emerged later and formed a distinct sub-cluster. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of SARS-CoV-2 under negative selection pressure and supports the continuing surveillance of spike mutations to aid in the development of new COVID-19 drugs and vaccines.\n\nImportanceA novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the mutations in the RBD of the circulating SARS-CoV-2 isolates have altered the receptor binding affinity and caused them more infectious, should be paid more attentions to. Given that SARS-CoV-2 is a novel coronavirus, the significance of our research is in identifying and validating the RBD mutant types emerging during the early transmission phase that have increased human ACE2 receptor binding affinity and infectivity. The RBD mutation analysis provides insights into SARS-CoV-2 evolution. The continuous surveillance of RBD mutations with increased human ACE2 affinity in human or other animals is important and necessary, particularly when the direct correlation between the virus variations and vaccine effectiveness is underdetermined during the sustained COVID-19 pandemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Junxian Ou", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Zhonghua Zhou", - "author_inst": "Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Te" - }, - { - "author_name": "Ruixue Dai", - "author_inst": "Fudan University Department of Environmental Science and Engineering" - }, - { - "author_name": "Shan Zhao", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Xiaowei Wu", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University" - }, - { - "author_name": "Jing Zhang", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong 510632, China" - }, - { - "author_name": "Wendong Lan", - "author_inst": "Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China" - }, - { - "author_name": "Lilian Cui", - "author_inst": "Novoprotein Scientific Inc" - }, - { - "author_name": "Jianguo Wu", - "author_inst": "Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong 510632, China" - }, - { - "author_name": "Donald Seto", - "author_inst": "Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA" - }, - { - "author_name": "James Chodosh", - "author_inst": "Department of Ophthalmology, Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School" - }, - { - "author_name": "Gong Zhang", - "author_inst": "Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Te" - }, - { - "author_name": "Qiwei Zhang", - "author_inst": "Southern Medical University" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.12.20027185", "rel_title": "Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label", @@ -1577023,6 +1573555,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.14.20034884", + "rel_title": "Modelling the epidemic 2019-nCoV event in Italy: a preliminary note", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.14.20034884", + "rel_abs": "An analysis of the time evolution of the 2019-nCoV outbreak event in Italy is proposed and is based on the preliminary data at disposal (till March 11th, 2020) on one side, and on an epidemiological model recently used to describe the same epidemic event in the Wuhan region (February 2020) on the other side. The equations of the model include the description of compartments like Susceptible (S), exposed (E), infectious but not yet symptomatic (pre-symptomatic) (A), infectious with symptoms (I), hospitalized (H) and recovered (R). Further stratification includes quarantined susceptible (Sq), isolated exposed (Eq) and isolated infected (Iq) compartments. The equations are numerically solved for boundary (initial) conditions tuned on the Italian event. The role of quarantine is specifically emphasized and supports the strategies adopted providing a numerical description of the effects.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marco Claudio Traini", + "author_inst": "Physics Department - Trento University" + }, + { + "author_name": "Carla Caponi", + "author_inst": "Clinica Geriatrica, Azienda Ospedaliero-Universitaria\\\\Piazzale Gambuli 1, 06132, Perugia, Italy." + }, + { + "author_name": "Giuseppe Vittorio De Socio", + "author_inst": "Clinica Malattie Infettive, Azienda Ospedaliero-Universitaria\\\\Piazzale Gambuli 1, 06132, Perugia, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.16.994236", "rel_title": "The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2", @@ -1577934,45 +1574493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.13.20035642", - "rel_title": "Epidemiological Trends of Coronavirus Disease 2019 in China", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035642", - "rel_abs": "BackgroundThe Coronavirus Disease 2019 (COVID-19) epidemic broke out in Wuhan, China, and it spread rapidly. Since January 23, 2020, China has launched a series of unusual and strict measures, including the lockdown of Wuhan city to contain this highly contagious disease. We collected the epidemiological data to analyze the trend of this epidemic in China.\n\nMethodsWe closely tracked the Chinese and global official websites to collect the epidemiological information about COVID-19. The number of total and daily new confirmed cases of COVID-19 in China was presented to illustrate the trend of this epidemic.\n\nResultsOn January 23, 2020, 835 confirmed COVID-19 cases were reported in China. On February 6, 2020, there were 31211 cases. By February 20, 2020, the number reached as high as 75,993. Most cases were distributed in and around Wuhan, Hubei province. Since January 23, 2020, the number of daily new cases in China except Hubei province reached a peak of 890 on the eleventh day and then it declined to a low level of 34 within two full-length incubation periods (28 days), and the number of daily new cases in Hubei also started to decrease on the twelfth day, from 3156 on February 4, 2020 to 955 on February 15, 2020.\n\nConclusionThe COVID-19 epidemic has been primarily contained in China. The battle against this epidemic in China has provided valuable experiences for the rest of the world. Strict measures need to be taken as earlier as possible to prevent its spread.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bilin Chen", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Huanhuan Zhong", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Yueyan Ni", - "author_inst": "Jinling, Hospital, Nanjing Medical University" - }, - { - "author_name": "Lulu Liu", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Jinjin Zhong", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - }, - { - "author_name": "Xin Su", - "author_inst": "Jinling Hospital, Medical School of Nanjing University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.14.20035741", "rel_title": "Excess cases of Influenza like illnesses in France synchronous with COVID19 invasion.", @@ -1578505,6 +1575025,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.03.12.20034678", + "rel_title": "Ocular manifestations and clinical characteristics of 534 cases of COVID-19 in China: A cross-sectional study", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.12.20034678", + "rel_abs": "ObjectiveThe novel coronavirus disease (COVID-19) was first reported in Wuhan, China in December 2019 and is now pandemic all over the world. Previous study has reported several COVID-19 cases with conjunctivitis. However, the complete profiling of COVID-19 related ocular symptoms and diseases are still missing. We aim to investigate the ocular manifestations and clinical characteristics of COVID-19 patients.\n\nMethodsA total of five hundred and thirty-four patients were recruited at Mobile Cabin Hospital and Tongji Hospital. We collected information on demographic characteristics, exposure history, ocular symptoms, systemic concomitant symptoms, eye drop medication, eye protections, radiologic findings, and SARS-CoV-2 detection in nasopharyngeal swabs by RT-PCR from questionnaires and electronic medical records.\n\nResultsThe median age of patients was 40 and 50 years at Mobile Cabin Hospital and Tongji Hospital, respectively. Of 534 COVID-19 patients, 25 patients (4.68%) presented with conjunctival congestion and 3 patients had conjunctival congestion as the initial symptom. The average duration of conjunctival congestion was 4.9 {+/-} 2.6 days (mean [SD]), ranging from 2 to 10 days. Dry eye (112, 20.97%), blurred vision (68, 12.73%), and foreign body sensation (63, 11.80%) ranked as the top three COVID-19 related ocular symptoms. Notably, a total of 332 COVID-19 patients (62%) had a hand-eye contact history. We also found that some COVID-19 patients had a history of eye disease, including conjunctivitis (33, 6.18%), dry eye (24, 4.49%), keratitis (14, 2.62%), cataract (9, 1.69%), and diabetic retinopathy (5, 0.94%). In consistent with previous studies, the most common clinical symptoms were fever, cough, and fatigue. Patients, 60.5% in Mobile Cabin Hospital and 67.5% in Tongji Hospital, respectively were confirmed with positive SARS-CoV-2 detection.\n\nConclusionsConjunctival congestion was one of the COVID-19 related ocular symptoms, which may have clinical diagnostic significance. It is essential to provide eye-care equipment and strengthen education on eye protection, as dirty hand-eye contact might be a high risk factor of COVID-19. Further detailed and comprehensive ophthalmological guidance is needed for COVID-19 control.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Liwen Chen", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Chaohua Deng", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xuhui Chen", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xian Zhang", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Bo Chen", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Huimin Yu", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yuanjun Qin", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Ke Xiao", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hong Zhang", + "author_inst": "Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xufang Sun", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "ophthalmology" + }, { "rel_doi": "10.1101/2020.03.10.20033852", "rel_title": "Strongly heterogeneous transmission of COVID-19 in mainland China: local and regional variation", @@ -1579411,53 +1575986,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.03.13.991083", - "rel_title": "Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2", - "rel_date": "2020-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.991083", - "rel_abs": "17 years after the SARS-CoV epidemic, the world is facing the COVID-19 pandemic. COVID-19 is caused by a coronavirus named SARS-CoV-2. Given the most optimistic projections estimating that it will take over a year to develop a vaccine, the best short-term strategy may lie in identifying virus-specific targets for small molecule interventions. All coronaviruses utilize a molecular mechanism called -1 PRF to control the relative expression of their proteins. Prior analyses of SARS-CoV revealed that it employs a structurally unique three-stemmed mRNA pseudoknot to stimulate high rates of -1 PRF, and that it also harbors a -1 PRF attenuation element. Altering -1 PRF activity negatively impacts virus replication, suggesting that this molecular mechanism may be therapeutically targeted. Here we present a comparative analysis of the original SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar rates of -1 PRF and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablated -1 PRF activity. The upstream attenuator hairpin activity has also been functionally retained. Small-angle x-ray scattering indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 had the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit -1 PRF was similarly effective against -1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may provide promising lead compounds to counter the current pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jamie A. Kelly", - "author_inst": "University of Maryland" - }, - { - "author_name": "Alexandra N Olson", - "author_inst": "University of Maryland" - }, - { - "author_name": "Krishna Neupane", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sneha Munshi", - "author_inst": "University of Alberta" - }, - { - "author_name": "Josue San Emerterio", - "author_inst": "Cornell University" - }, - { - "author_name": "Lois Pollack", - "author_inst": "Cornell University" - }, - { - "author_name": "Michael T. Woodside", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jonathan D. Dinman", - "author_inst": "University of Maryland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.03.12.988246", "rel_title": "High sensitivity detection of SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method", @@ -1580318,6 +1576846,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.10.20033803", + "rel_title": "Prediction of the COVID-19 outbreak based on a realistic stochastic model", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033803", + "rel_abs": "The current outbreak of coronavirus disease 2019 (COVID-19) has become a global crisis due to its quick and wide spread over the world. A good understanding of the dynamic of the disease would greatly enhance the control and prevention of COVID-19. However, to the best of our knowledge, the unique features of the outbreak have limited the applications of all existing models. In this paper, a novel stochastic model is proposed which aims to account for the unique transmission dynamics of COVID-19 and capture the effects of intervention measures implemented in Mainland China. We find that, (1) instead of aberration, there is a remarkable amount of asymptomatic individuals, (2) an individual with symptoms is approximately twice more likely to pass the disease to others than that of an asymptomatic patient, (3) the transmission rate has reduced significantly since the implementation of control measures in Mainland China, (4) it is expected that the epidemic outbreak would be contained by early March in the the selected provinces and cities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yuan Zhang", + "author_inst": "Peking university" + }, + { + "author_name": "Chong You", + "author_inst": "Peking university" + }, + { + "author_name": "Zhenghao Cai", + "author_inst": "Peking university" + }, + { + "author_name": "Jiarui Sun", + "author_inst": "Peking university" + }, + { + "author_name": "Wenjie Hu", + "author_inst": "Peking university" + }, + { + "author_name": "Xiao-Hua Zhou", + "author_inst": "Peking university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.10.20033944", "rel_title": "Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site", @@ -1581163,37 +1577730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.10.20033613", - "rel_title": "Analysis clinical features of COVID-19 infection in secondary epidemic area and report potential biomarkers in evaluation", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033613", - "rel_abs": "ObjectiveBased on the clinical characteristics of infected patients with novel coronavirus in secondary epidemic areas, we aimed to identify potential biomarkers for the evaluation of novel coronavirus-infected patients, guide the diagnosis and treatment of this disease in secondary epidemic areas and provide a reference for the clinical prevention and control of this epidemic situation.\n\nMethodsThe clinical data of 33 patients with respiratory symptoms caused by the novel coronavirus in Wenzhou city from January 15 to February 12, 2020, were thoroughly reviewed. At the onset of the disease, we found that the primary symptoms were fever, cough, fatigue, chest tightness, chest pain and specific blood test results. According to the patients histories, the patients were divided into two groups: those who spent time in the main epidemic area and those who did not spend time in the main epidemic area. The differences in the clinical manifestations between these two groups were analyzed.\n\nResultsThe main clinical symptoms of patients infected with novel coronavirus in the secondary epidemic area were respiratory tract ailments and systemic symptoms. After grouping patients based on the presence or absence of residency in or travel history to the main epidemic area, there was no significant difference between the baseline data of these two groups, and there were no significant differences in symptoms and signs between the two groups (P>0.05). Some patients had abnormally increased serum amyloid protein A (SAA). There were statistically significant differences in the leukocyte count/C-reactive protein, monocyte ratio/C-reactive protein, neutrophil count/C-reactive protein, monocyte count/C-reactive protein and hemoglobin/C-reactive protein values between the two groups (P < 0.05).\n\nConclusionRespiratory tract ailments and systemic symptoms were the primary symptoms of novel coronavirus infection in the secondary epidemic area; these symptoms are not typical. The abnormal increase in serum amyloid protein (SAA) may be used as an auxiliary index for diagnosis and treatment. CRP changes before other blood parameters and thus may be an effective evaluation index for patients with COVID-19 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Weiping Ji", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Gautam Bishnu", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Zhenzhai Cai", - "author_inst": "wenzhou medical university" - }, - { - "author_name": "Xian Shen", - "author_inst": "wenzhou medical university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.10.20033605", "rel_title": "Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study", @@ -1581938,6 +1578474,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.11.987222", + "rel_title": "Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2", + "rel_date": "2020-03-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.11.987222", + "rel_abs": "To date, the SARS-CoV-2 genome has been considered genetically more stable than SARS-CoV or MERS-CoV. Here we report a 382-nt deletion covering almost the entire open reading frame 8 (ORF8) of SARS-CoV-2 obtained from eight hospitalized patients in Singapore. The deletion also removes the ORF8 transcription-regulatory sequence (TRS), which in turn enhances the downstream transcription of the N gene. We also found that viruses with the deletion have been circulating for at least four weeks. During the SARS-CoV outbreak in 2003, a number of genetic variants were observed in the human population [1], and similar variation has since been observed across SARS-related CoVs in humans and bats. Overwhelmingly these viruses had mutations or deletions in ORF8, that have been associated with reduced replicative fitness of the virus [2]. This is also consistent with the observation that towards the end of the outbreak sequences obtained from human SARS cases possessed an ORF8 deletion that may be associated with host adaptation [1]. We therefore hypothesise that the major deletion revealed in this study may lead to an attenuated phenotype of SARS-CoV-2.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Yvonne Su", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Danielle Anderson", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Barnaby Young", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Feng Zhu", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Martin Linster", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Shirin Kalimuddin", + "author_inst": "Singapore General Hospital, Singapore" + }, + { + "author_name": "Jenny Low", + "author_inst": "Singapore General Hospital, Singapore" + }, + { + "author_name": "Zhuang Yan", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Jayanthi Jayakumar", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Louisa Sun", + "author_inst": "Alexandra Hospital, Singapore" + }, + { + "author_name": "Gabriel Yan", + "author_inst": "National University Hospital, Singapore" + }, + { + "author_name": "Ian Mendenhall", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Yee-Sin Leo", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "David Lye", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Medical School, Singapore" + }, + { + "author_name": "Gavin Smith", + "author_inst": "Duke-NUS Medical School, Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.10.20032995", "rel_title": "Revealing the influence of national public health policies for the outbreak of the SARS-CoV-2 epidemic in Wuhan, China through status dynamic modeling", @@ -1583428,45 +1580043,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.06.20031377", - "rel_title": "Clinical Characteristics on 25 Discharged Patients with COVID-19 Virus Returning", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20031377", - "rel_abs": "Here we report the clinical features of 25 discharged patients with COVID-19 recovery. Our analysis indicated that there was a significant inverse correlation existed between serum D-Dimer level and the duration of antiviral treatment, while lymphocyte concentration significantly positively correlated with the duration of virus reversal.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jing Yuan", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Shanglong Kou", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Yanhua Liang", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Jianfeng Zeng", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Yanchao Pan", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - }, - { - "author_name": "Lei Liu", - "author_inst": "Diagnosis and Treatment of Infectious Diseases Research Laboratory, Shenzhen Third People's Hospital, Shenzhen 518112, China." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.07.20031393", "rel_title": "The epidemiological characteristics of 2019 novel coronavirus diseases (COVID-19) in Jingmen,Hubei,China", @@ -1583983,6 +1580559,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.07.20031575", + "rel_title": "Prognostic value of NT-proBNP in patients with severe COVID-19", + "rel_date": "2020-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.07.20031575", + "rel_abs": "The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China has been declared a public health emergency of international concern. The cardiac injury was dominate in the process. However, whether N terminal pro B type natriuretic peptide (NT-proBNP) predicted outcome of COVID-19 patients was unknown. The study initially enrolled 102 patients with severe COVID-19 pneumonia from a continuous sample. After screening out the ineligible cases, 54 patients were analyzed in this study. Results found that patients with higher NT-proBNP (above 88.64 pg/mL) level had more risks of in-hospital death. After adjusting for potential cofounders in separate modes, NT-proBNP presented as an independent risk factor of in-hospital death in patients with severe COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lei Gao", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Dan Jiang", + "author_inst": "Department of Cardiology, The First Branch of the First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Xuesong Wen", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Xiaocheng Cheng", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Min Sun", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Bin He", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Lin-na You", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Peng Lei", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Xiao-wei Tan", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Shu Qin", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Guoqiang Cai", + "author_inst": "Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University; Traditional Chinese Medicine hospital Dianjiang Chongqing" + }, + { + "author_name": "Dongying Zhang", + "author_inst": "The First Affiliated Hospital of Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.07.20032524", "rel_title": "Diagnosis of Acute Respiratory Syndrome Coronavirus 2 Infection by Detection of Nucleocapsid Protein", @@ -1584890,93 +1581529,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.05.20031849", - "rel_title": "A mathematical model for estimating the age-specific transmissibility of a novel coronavirus", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031849", - "rel_abs": "BackgroundA novel coronavirus named as \"SARS-CoV-2\" has spread widely in many countries since December 2019, especially in China. This study aimed to quantify the age-specific transmissibility by using a mathematical model.\n\nMethodsAn age-specific susceptible - exposed - symptomatic - asymptomatic - recovered - seafood market (SEIARW) model was developed based on two suspected transmission routes (from market to person and person to person). The susceptible people from Wuhan City were divided into different age groups. We used the subscript i and j to represent age group 1 to 4 (i = j; 1: [≤] 14 years; 2: 15-44 years; 3: 45-64 years; 4: [≥] 65 years) and 1 to 5 (i = j; 1: [≤] 5 years; 2: 6-14 years; 3: 15-24 years; 4: 25-59 years; 4: [≥] 60 years), respectively. Data of reported COVID-19 cases were collected from one published literature from 26 November to 22 December, 2019 in Wuhan City, China. The age-specific transmissibility of the virus was estimated accordingly secondary attack rate (SAR).\n\nResultsThe age-specific SEIARW model fitted with the reported data well by dividing the population into four age groups ({chi}2 = 4.99 x 10-6, P > 0.999), and five age groups ({chi}2 = 4.85 x 10-6, P > 0.999). Based on the four-age-group SEIARW model, the highest transmissibility occurred from age group 2 to 3 (SAR23 = 17.56 per 10 million persons), followed by from age group 3 to 2 (SAR32 = 10.17 per 10 million persons). The lowest transmissibility occurred from age group 1 to 2 (SAR12 = 0.002 per 10 million persons). Based on the five-age-group SEIARW model, the highest transmissibility occurred from age group 4 to 5 (SAR45 = 12.40 per 10 million persons), followed by from age group 5 to 4 (SAR54 = 6.61 per 10 million persons). The lowest transmissibility occurred from age group 3 to 4 (SAR34 = 0.0002 per 10 million persons).\n\nConclusionsSARS-CoV-2 has high transmissibility among adults and elder people but low transmissibility among children and young people.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Zeyu Zhao", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yuan-Zhao Zhu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jing-Wen Xu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Qing-Qing Hu", - "author_inst": "University of Utah" - }, - { - "author_name": "Zhao Lei", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jia Rui", - "author_inst": "Xiamen University" - }, - { - "author_name": "Xingchun Liu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yao Wang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Li Luo", - "author_inst": "Xiamen University" - }, - { - "author_name": "Shan-Shan Yu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Jia Li", - "author_inst": "Xiamen University" - }, - { - "author_name": "Ruo-Yun Liu", - "author_inst": "Xiamen University" - }, - { - "author_name": "Fang Xie", - "author_inst": "Xiamen University" - }, - { - "author_name": "Ying-Ying Su", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yi-Chen Chiang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yanhua Su", - "author_inst": "Xiamen University" - }, - { - "author_name": "Benhua Zhao", - "author_inst": "Xiamen University" - }, - { - "author_name": "Tianmu Chen", - "author_inst": "Xiamen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.06.20031880", "rel_title": "Estimating the scale of COVID-19 Epidemic in the United States: Simulations Based on Air Traffic directly from Wuhan, China", @@ -1585560,6 +1582112,41 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.03.05.20031476", + "rel_title": "Appealing for Efficient, Well Organized Clinical Trials on COVID-19", + "rel_date": "2020-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031476", + "rel_abs": "ABSTRATCThe rapid emergence of clinical trials on COVID-19 stimulated a wave of discussion in scientific community. We reviewed the characteristics of interventional trials from Chinese Clinical Trial Registration (ChiCTR) and ClinicalTrials.gov. A total of 171 COVID-19-related interventional trials were identified on Feb 22nd, 2020. These trials are classified into 4 categories based on treatment modalities, including chemical drugs, biological therapies, traditional Chinese medicine treatments and other therapies. Our analysis focused on the issues of stage, design, randomization, blinding, primary endpoints definition and sample size of these trials. We found some studies with potential defects including unreasonable design, inappropriate primary endpoint definition, insufficient sample size and ethical issue. Clinical trials on COVID-19 should be designed based on scientific rules, ethics and benefits for patients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yang Zhao", + "author_inst": "Department of Biostatistics, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Yongyue Wei", + "author_inst": "Department of Biostatistics, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Sipeng Shen", + "author_inst": "Department of Biostatistics, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Mingzhi Zhang", + "author_inst": "Department of Biostatistics, School of Public Health, Nanjing Medical University Corresponding Email: fengchen@njmu.edu.cn" + }, + { + "author_name": "Feng Chen", + "author_inst": "Department of Biostatistics, School of Public Health, Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.05.976167", "rel_title": "Direct RNA sequencing and early evolution of SARS-CoV-2", @@ -1586563,41 +1583150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.04.20030973", - "rel_title": "Study of the mental health status of medical personnel dealing with new coronavirus pneumonia", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20030973", - "rel_abs": "ObjectiveThis paper studied the relationship between personality traits and mental health conditions of medical personnel to provide a basis and reference for the implementation of targeted education on mental health.\n\nMethodsA self-report inventory, the Symptom Checklist-90 (SCL-90), was used to investigate the mental health status of 548 medical personnel dealing with the new coronavirus pneumonia in eight provinces and cities of China.\n\nResultsThe overall mean SCL-90 score and mean values of factors (somatization, obsessive-compulsive, anxiety, phobic anxiety, and psychoticism) of the medical personnel were significantly higher than in the norm group (p < 0.05), while their average interpersonal sensitivity score was significantly lower (p < 0.01). In addition, personal factors affecting the mental health status of medical personnel were identified. ( all p < 0.05).\n\nConclusionThe overall mental health status of medical personnel responding to new coronavirus pneumonia is generally higher than that of the norm group in China. The results of this study should contribute to measures to alleviate the psychological pressures on medical personnel dealing with the new coronavirus epidemic in China.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "ning sun", - "author_inst": "ningbo college of health sciences" - }, - { - "author_name": "jun xing", - "author_inst": "The Second Affiliated Hospital of Harbin Medical University" - }, - { - "author_name": "jun xu", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - }, - { - "author_name": "ling shu geng", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - }, - { - "author_name": "qian yu li", - "author_inst": "The Second Affiliated Hospital of Harbin Medical" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.03.20030775", "rel_title": "Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis", @@ -1587222,6 +1583774,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.03.20029843", + "rel_title": "Effect of non-pharmaceutical interventions for containing the COVID-19 outbreak: an observational and modelling study", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20029843", + "rel_abs": "BackgroundThe COVID-19 outbreak containment strategies in China based on non-pharmaceutical interventions (NPIs) appear to be effective. Quantitative research is still needed however to assess the efficacy of different candidate NPIs and their timings to guide ongoing and future responses to epidemics of this emerging disease across the World.\n\nMethodsWe built a travel network-based susceptible-exposed-infectious-removed (SEIR) model to simulate the outbreak across cities in mainland China. We used epidemiological parameters estimated for the early stage of outbreak in Wuhan to parameterise the transmission before NPIs were implemented. To quantify the relative effect of various NPIs, daily changes of delay from illness onset to the first reported case in each county were used as a proxy for the improvement of case identification and isolation across the outbreak. Historical and near-real time human movement data, obtained from Baidu location-based service, were used to derive the intensity of travel restrictions and contact reductions across China. The model and outputs were validated using daily reported case numbers, with a series of sensitivity analyses conducted.\n\nResultsWe estimated that there were a total of 114,325 COVID-19 cases (interquartile range [IQR] 76,776 - 164,576) in mainland China as of February 29, 2020, and these were highly correlated (p<0.001, R2=0.86) with reported incidence. Without NPIs, the number of COVID-19 cases would likely have shown a 67-fold increase (IQR: 44 - 94), with the effectiveness of different interventions varying. The early detection and isolation of cases was estimated to prevent more infections than travel restrictions and contact reductions, but integrated NPIs would achieve the strongest and most rapid effect. If NPIs could have been conducted one week, two weeks, or three weeks earlier in China, cases could have been reduced by 66%, 86%, and 95%, respectively, together with significantly reducing the number of affected areas. However, if NPIs were conducted one week, two weeks, or three weeks later, the number of cases could have shown a 3-fold, 7-fold, and 18-fold increase across China, respectively. Results also suggest that the social distancing intervention should be continued for the next few months in China to prevent case numbers increasing again after travel restrictions were lifted on February 17, 2020.\n\nConclusionThe NPIs deployed in China appear to be effectively containing the COVID-19 outbreak, but the efficacy of the different interventions varied, with the early case detection and contact reduction being the most effective. Moreover, deploying the NPIs early is also important to prevent further spread. Early and integrated NPI strategies should be prepared, adopted and adjusted to minimize health, social and economic impacts in affected regions around the World.\n\nFundingBill & Melinda Gates Foundation; EU Horizon 2020; National Natural Science Fund of China; Wellcome Trust.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe COVID-19 outbreak has spread widely across China since December 2019, with many other countries affected. The containment strategy of integrated nonpharmaceutical interventions (NPIs) including travel bans and restrictions, contact reductions and social distancing, early case identification and isolation have been rapidly deloyed across China to contain the outbreak, and the combination of these interventions appears to be effective. We searched PubMed, Wanfang Data, and preprint archives for articles in English and Chinese published up to February 29, 2020, that contained information about the intervention of the COVID-19 outbreak. We found 15 studies that have investigated or discussed the potential effects of traveller screening, Wuhans lockdown, travel restrictions, and contact tracing in China or other countries. However, none of them comprehensively and quantitatively compared the effectiveness of various NPIs and their timings for containing the COVID-19 outbreak.\n\nAdded value of this studyTo our knowledge, this is the most comprehensive study to date on quantifying the relative effect of different NPIs and their timings for COVID-19 outbreak containment, based on human movement and disease data. Our findings show that NPIs, inter-city travel restrictions, social distancing and contact reductions, as well as early case detection and isolations, have substantially reduced COVID-19 transmission across China, with the effectiveness of different interventions varying. The early detection and isolation of cases was estimated to prevent more infections than travel restrictions and contact reductions, but integrated NPIs would achieve the strongest and most rapid effect. Our findings contribute to improved understanding of integrated NPI measures on COVID-19 containment and can help in tailoring control strategies across contexts.\n\nImplications of all the available evidenceGiven that effective COVID-19-specific pharmaceutical interventions and vaccines are not expected to be available for months, NPIs are essential components of the public health response to the ongoing outbreaks.\n\nConsidering the narrowing window of opportunity around the World, early and integrated NPI strategies should be prepared, deployed and adjusted to maximise the benefits of these interventions for containing COVID-19 spread.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Shengjie Lai", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Nick W Ruktanonchai", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Liangcai Zhou", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China" + }, + { + "author_name": "Olivia Prosper", + "author_inst": "Department of Mathematics, University of Tennessee, Knoxville, TN, USA" + }, + { + "author_name": "Wei Luo", + "author_inst": "Department of Pediatrics, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Jessica R Floyd", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Amy Wesolowski", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Computational Health Informatics Program, Boston Children Hospital" + }, + { + "author_name": "Chi Zhang", + "author_inst": "School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Xiangjun Du", + "author_inst": "School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Andrew J Tatem", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.02.20030007", "rel_title": "The timing of one-shot interventions for epidemic control", @@ -1588197,97 +1584812,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.02.20026708", - "rel_title": "The effect of human mobility and control measures on the COVID-19 epidemic in China", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20026708", - "rel_abs": "The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Moritz U.G. Kraemer", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Chia-Hung Yang", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "Bernardo Gutierrez", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Chieh-Hsi Wu", - "author_inst": "Mathematical Sciences, University of Southampton, Southampton, United Kingdom" - }, - { - "author_name": "Brennan Klein", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "David M. Pigott", - "author_inst": "Institute for Health Metrics and Evaluation, Department of Health Metrics, University of Washington, Seattle, United States" - }, - { - "author_name": "- open COVID-19 data working group", - "author_inst": "see manuscript" - }, - { - "author_name": "Louis du Plessis", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Nuno R Faria", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Ruoran Li", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, United States" - }, - { - "author_name": "William P. Hanage", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, United States" - }, - { - "author_name": "John S Brownstein", - "author_inst": "Harvard Medical School, Harvard University, Boston, United States" - }, - { - "author_name": "Maylis Layan", - "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Network Science Institute, Northeastern University, Boston, United States" - }, - { - "author_name": "Huaiyu Tian", - "author_inst": "State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China" - }, - { - "author_name": "Christopher Dye", - "author_inst": "Department of Zoology, University of Oxford, United Kingdom" - }, - { - "author_name": "Simon Cauchemez", - "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Samuel V Scarpino", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.01.20029801", "rel_title": "Evaluation of the incidence of COVID-19 and of the efficacy of contention measures in Spain: a data-driven approach.", @@ -1588903,6 +1585427,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.20029306", + "rel_title": "Clinical Characteristics of Patients with Severe Pneumonia Caused by the 2019 Novel Coronavirus in Wuhan, China", + "rel_date": "2020-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20029306", + "rel_abs": "BackgroundA new virus broke out in Wuhan, Hubei, China, and was later named 2019 novel coronavirus (2019-nCoV). The clinical characteristics of severe pneumonia caused by 2019-nCoV are still not clear.\n\nObjectivesThe aim of this study was to explore the clinical characteristics and risk factors of the severe pneumonia caused by the 2019-nCoV in Wuhan, China.\n\nMethodThe study included patients hospitalized at the central hospital of Wuhan who had been diagnosed with a pneumonia caused by the novel coronavirus. Clinical features, chronic co-morbidities, demographic data, laboratory examinations, and chest computed tomography (CT) scans were reviewed through electronic medical records. SPSS was used for data analysis to explore the clinical characteristics and risk factors of the patients with the severe pneumonia.\n\nResultsA total of 110 patients diagnosed with 2019 novel coronavirus pneumonia were included in the study, including 38 with severe pneumonia and 72 with non-severe pneumonia. Statistical analysis showed that advanced age, an increase of D-dimer, and a decrease of lymphocytes were characteristics of the patients with severe pneumonia. Moreover, in the early stage of the disease, chest CT scans of patients with the severe pneumonia showed the illness can progress rapidly.\n\nConclusionsAdvanced age, lymphocyte decline, and D-dimer elevation are important characteristics of patients with severe pneumonia. Clinicians should focus on these characteristics to identify high-risk patients at an early stage.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yafei Wang", + "author_inst": "The central hospital of Wuhan" + }, + { + "author_name": "Ying Zhou", + "author_inst": "The central hospital of Wuhan" + }, + { + "author_name": "Zhen Yang", + "author_inst": "The central hospital of Wuhan" + }, + { + "author_name": "Dongping Xia", + "author_inst": "The central hospital of Wuhan" + }, + { + "author_name": "Shuang Geng", + "author_inst": "The central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.01.20029819", "rel_title": "COVID-19 Epidemic Outside China: 34 Founders and Exponential Growth", @@ -1590118,93 +1586677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.02.20027599", - "rel_title": "Effects of weather-related social distancing on city-scale transmission of respiratory viruses", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20027599", - "rel_abs": "BACKGROUNDUnusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses.\n\nMETHODSResidual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus, with disruption of contact rates and care-seeking informed by data on local traffic volumes and hospital admissions.\n\nRESULTSDisruption in contact patterns reduced effective contact rates during the intervention period by 16% to 95%, and cumulative disease incidence through the remainder of the season by 3% to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in early epidemic phase.\n\nCONCLUSIONHigh-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak.\n\nOne sentence summaryDisruptions of school and work due to heavy snowfall in the Seattle metro area reduced the total size of respiratory virus epidemics by up to 9%.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Michael L Jackson", - "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle WA" - }, - { - "author_name": "Gregory R Hart", - "author_inst": "Institute for Disease Modeling, Bellevue WA" - }, - { - "author_name": "Denise J McCulloch", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Amanda Adler", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Elisabeth Brandstetter", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Kairsten Fay", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Peter Han", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle WA" - }, - { - "author_name": "Kirsten Lacombe", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Jover Lee", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Thomas Sibley", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Deborah A Nickerson", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle WA" - }, - { - "author_name": "Mark Rieder", - "author_inst": "Brotman Baty Institute for Precision Medicine, Seattle WA" - }, - { - "author_name": "Lea Starita", - "author_inst": "Department of Genome Sciences, University of Washington, Seattle WA" - }, - { - "author_name": "Janet A Englund", - "author_inst": "Seattle Children's Research Institute, Seattle WA" - }, - { - "author_name": "Trevor Bedford", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA" - }, - { - "author_name": "Helen Chu", - "author_inst": "Department of Medicine, University of Washington School of Medicine, Seattle WA" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "the Seattle Flu Study Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.28.20029272", "rel_title": "Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19)", @@ -1590897,6 +1587369,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.27.967588", + "rel_title": "TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection", + "rel_date": "2020-03-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.27.967588", + "rel_abs": "Faced with the current large-scale public health emergency, collecting, sorting, and analyzing biomedical information related to the \"coronavirus\" should be done as quickly as possible to gain a global perspective, which is a basic requirement for strengthening epidemic control capacity. However, for human researchers studying the viruses and the hosts, the vast amount of information available cannot be processed effectively and in a timely manner, particularly when the scientific understanding may be limited, which can further lower the information processing efficiency. We present TWIRLS, a method that can automatically acquire, organize, and classify information. Additionally, independent functional data sources can be added to build an inference system using a machine-based approach, which can provide relevant knowledge to help human researchers quickly establish subject cognition and to make more effective decisions. TWIRLS can automatically analyze more than three million words in more than 14,000 literature articles in only 4 hours. Combining with generalized gene interaction databases creates a data interface that can help researchers to further analyze the information. Using the TWIRLS system, we found that an important regulatory factor angiotensin-converting enzyme 2 (ACE2) may be involved in the host pathological changes on binding to the coronavirus after infection. After triggering functional changes in ACE2/AT2R, an imbalance in the steady-state cytokine regulatory axis involving the Renin-Angiotensin System and IP-10 leads to a cytokine storm.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xiaoyang Ji", + "author_inst": "Joint Turing-Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Phil Rivers Te" + }, + { + "author_name": "Chunming Zhang", + "author_inst": "Joint Turing-Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Phil Rivers Te" + }, + { + "author_name": "Yubo Zhai", + "author_inst": "State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; West Institute of Computing Techn" + }, + { + "author_name": "Zhonghai Zhang", + "author_inst": "State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China" + }, + { + "author_name": "Chunli Zhang", + "author_inst": "Phil Rivers Technology, Beijing, China" + }, + { + "author_name": "Yiqing Xue", + "author_inst": "Joint Turing-Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Phil Rivers Te" + }, + { + "author_name": "Guangming Tan", + "author_inst": "State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; West Institute of Computing Techn" + }, + { + "author_name": "Gang Niu", + "author_inst": "Joint Turing-Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Phil Rivers Te" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.02.27.969006", "rel_title": "Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13", @@ -1591527,41 +1588046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.27.20028829", - "rel_title": "Transmission potential of COVID-19 in South Korea", - "rel_date": "2020-02-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20028829", - "rel_abs": "Since the first identified individual of 2019 novel coronavirus (COVID-19) infection on Jan 20, 2020 in South Korea, the number of confirmed cases rapidly increased. As of Feb 26, 2020, 1,261 cases of COVID-19 including 12 deaths were confirmed in South Korea. Using the incidence data of COVID-19, we estimate the reproduction number at 1.5 (95% CI: 1.4-1.6), which indicates sustained transmission and support the implementation of social distancing measures to rapidly control the outbreak.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eunha Shim", - "author_inst": "Soongsil University" - }, - { - "author_name": "Amna Tariq", - "author_inst": "Georgia State University" - }, - { - "author_name": "Wongyeong Choi", - "author_inst": "Soongsil University" - }, - { - "author_name": "Yiseul Lee", - "author_inst": "Georgia State University" - }, - { - "author_name": "Gerardo Chowell", - "author_inst": "Georgia State University School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.27.20028928", "rel_title": "A simple ecological model captures the transmission pattern of the coronavirus COVID-19 outbreak in China", @@ -1592226,6 +1588710,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.02.24.20027474", + "rel_title": "Estimate the incubation period of coronavirus 2019 (COVID-19)", + "rel_date": "2020-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027474", + "rel_abs": "MotivationWuhan pneumonia is an acute infectious disease caused by the 2019 novel coronavirus (COVID-19). It is being treated as a Class A infectious disease though it was classified as Class B according to the Infectious Disease Prevention Act of China. Accurate estimation of the incubation period of the coronavirus is essential to the prevention and control. However, it remains unclear about its exact incubation period though it is believed that symptoms of COVID-19 can appear in as few as 2 days or as long as 14 or even more after exposure. The accurate incubation period calculation requires original chain-of-infection data that may not be fully available in the Wuhan regions. In this study, we aim to accurately calculate the incubation period of COVID-19 by taking advantage of the chain-of-infection data, which is well-documented and epidemiologically informative, outside the Wuhan regions.\n\nMethodsWe acquired and collected officially reported COVID-19 data from 10 regions in China except for Hubei province. To achieve the accurate calculation of the incubation period, we only involved the officially confirmed cases with a clear history of exposure and time of onset. We excluded those without relevant epidemiological descriptions, working or living in Wuhan for a long time, or hard to determine the possible exposure time. We proposed a Monte Caro simulation approach to estimate the incubation of COVID-19 as well as employed nonparametric ways. We also employed manifold learning and related statistical analysis to decipher the incubation relationships between different age/gender groups.\n\nResultThe incubation period of COVID-19 did not follow general incubation distributions such as lognormal, Weibull, and Gamma distributions. We estimated that the mean and median of its incubation were 5.84 and 5.0 days via bootstrap and proposed Monte Carlo simulations. We found that the incubation periods of the groups with age>=40 years and age<40 years demonstrated a statistically significant difference. The former group had a longer incubation period and a larger variance than the latter. It further suggested that different quarantine time should be applied to the groups for their different incubation periods. Our machine learning analysis also showed that the two groups were linearly separable. incubation of COVID-19 along with previous statistical analysis. Our results further indicated that the incubation difference between males and females did not demonstrate a statistical significance.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Henry Han", + "author_inst": "Fordham University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.27.967885", "rel_title": "Prediction of receptorome for human-infecting virome", @@ -1593333,37 +1589836,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.25.20027433", - "rel_title": "An R package and a website with real-time data on the COVID-19 coronavirus outbreak", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20027433", - "rel_abs": "The COVID-19 outbreak originated at the end of 2019 from Wuhan [1, 2], a city in Hubei province in central China. According to the World Health Organization (WHO), there were 88,948 confirmed cases and 3,043 deaths from 65 countries as of March 2, 2020. In China, the outbreak has effectively confined over 1 billion people to their apartments and homes since the end of January 2020 and continues to disrupt healthcare, wellbeing, and the economy. As the situation in China appears to be stabilizing, sharp increases in confirmed cases are being reported in South Korea, Italy, Japan, and Iran.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tianzhi Wu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Xijin Ge", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Guangchuang Yu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Erqiang Hu", - "author_inst": "Southern Medical University, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.22.951178", "rel_title": "Spike protein binding prediction with neutralizing antibodies of SARS-CoV-2", @@ -1594012,6 +1590484,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.25.20021568", + "rel_title": "Deep learning-based model for detecting 2019 novel coronavirus pneumonia on high-resolution computed tomography: a prospective study in 27 patients", + "rel_date": "2020-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20021568", + "rel_abs": "BackgroundComputed tomography (CT) is the preferred imaging method for diagnosing 2019 novel coronavirus (COVID19) pneumonia. Our research aimed to construct a system based on deep learning for detecting COVID-19 pneumonia on high resolution CT, relieve working pressure of radiologists and contribute to the control of the epidemic.\n\nMethodsFor model development and validation, 46,096 anonymous images from 106 admitted patients, including 51 patients of laboratory confirmed COVID-19 pneumonia and 55 control patients of other diseases in Renmin Hospital of Wuhan University (Wuhan, Hubei province, China) were retrospectively collected and processed. Twenty-seven consecutive patients undergoing CT scans in Feb, 5, 2020 in Renmin Hospital of Wuhan University were prospectively collected to evaluate and compare the efficiency of radiologists against 2019-CoV pneumonia with that of the model.\n\nFindingsThe model achieved a per-patient sensitivity of 100%, specificity of 93.55%, accuracy of 95.24%, PPV of 84.62%, and NPV of 100%; a per-image sensitivity of 94.34%, specificity of 99.16%, accuracy of 98.85%, PPV of 88.37%, and NPV of 99.61% in retrospective dataset. For 27 prospective patients, the model achieved a comparable performance to that of expert radiologist. With the assistance of the model, the reading time of radiologists was greatly decreased by 65%.\n\nConclusionThe deep learning model showed a comparable performance with expert radiologist, and greatly improve the efficiency of radiologists in clinical practice. It holds great potential to relieve the pressure of frontline radiologists, improve early diagnosis, isolation and treatment, and thus contribute to the control of the epidemic.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jun Chen", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Lianlian Wu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Liang Zhang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Dexin Gong", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yilin Zhao", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Shan Hu", + "author_inst": "Wuhan EndoAngel Medical Technology Company" + }, + { + "author_name": "Yonggui Wang", + "author_inst": "China University of Geosciences" + }, + { + "author_name": "Xiao Hu", + "author_inst": "Wuhan EndoAngel Medical Technology Company" + }, + { + "author_name": "Biqing Zheng", + "author_inst": "Wuhan EndoAngel Medical Technology Company" + }, + { + "author_name": "Kuo Zhang", + "author_inst": "Wuhan EndoAngel Medical Technology Company" + }, + { + "author_name": "Huiling Wu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zehua Dong", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Youming Xu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yijie Zhu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Xi Chen", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Lilei Yu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Honggang Yu", + "author_inst": "Renmin Hospital of Wuhan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.23.20026690", "rel_title": "The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing", @@ -1594959,73 +1591518,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.21.20026559", - "rel_title": "Estimating the serial interval of the novel coronavirus disease (COVID-19): A statistical analysis using the public data in Hong Kong from January 16 to February 15, 2020", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026559", - "rel_abs": "BackgroundsThe emerging virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a large outbreak of novel coronavirus disease (COVID-19) in Wuhan, China since December 2019. Based on the publicly available surveillance data, we identified 21 transmission chains in Hong Kong and estimated the serial interval (SI) of COVID-19.\n\nMethodsIndex cases were identified and reported after symptoms onset, and contact tracing was conducted to collect the data of the associated secondary cases. An interval censored likelihood framework is adopted to fit a Gamma distribution function to govern the SI of COVID-19.\n\nFindingsAssuming a Gamma distributed model, we estimated the mean of SI at 4.4 days (95%CI: 2.9-6.7) and SD of SI at 3.0 days (95%CI: 1.8-5.8) by using the information of all 21 transmission chains in Hong Kong.\n\nConclusionThe SI of COVID-19 may be shorter than the preliminary estimates in previous works. Given the likelihood that SI could be shorter than the incubation period, pre-symptomatic transmission may occur, and extra efforts on timely contact tracing and quarantine are recommended in combating the COVID-19 outbreak.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Daozhou Gao", - "author_inst": "Shanghai Normal University" - }, - { - "author_name": "Zian Zhuang", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Marc Chong", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Yongli Cai", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Jinjun Ran", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Peihua Cao", - "author_inst": "Southern Medical University" - }, - { - "author_name": "Kai Wang", - "author_inst": "Xinjiang Medical University" - }, - { - "author_name": "Yijun Lou", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Weiming Wang", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Lin Yang", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Maggie Wang", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.23.20024802", "rel_title": "Intrinsic growth rules of patients infected, dead and cured with 2019 novel coronavirus in mainland China", @@ -1595570,6 +1592062,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025874", + "rel_title": "Rapid colorimetric detection of COVID-19 coronavirus using a reverse tran-scriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic plat-form: iLACO", + "rel_date": "2020-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025874", + "rel_abs": "The recent outbreak of a novel coronavirus SARS-CoV-2 (also known as 2019-nCoV) threatens global health, given serious cause for concern. SARS-CoV-2 is a human-to-human pathogen that caused fever, severe respiratory disease and pneumonia (known as COVID-19). By press time, more than 70,000 infected people had been confirmed worldwide. SARS-CoV-2 is very similar to the severe acute respiratory syndrome (SARS) coronavirus broke out 17 years ago. However, it has increased transmissibility as compared with the SARS-CoV, e.g. very often infected individuals without any symptoms could still transfer the virus to others. It is thus urgent to develop a rapid, accurate and onsite diagnosis methods in order to effectively identify these early infects, treat them on time and control the disease spreading. Here we developed an isothermal LAMP based method-iLACO (isothermal LAMP based method for COVID-19) to amplify a fragment of the ORF1ab gene using 6 primers. We assured the species-specificity of iLACO by comparing the sequences of 11 related viruses by BLAST (including 7 similar coronaviruses, 2 influenza viruses and 2 normal coronaviruses). The sensitivity is comparable to Taqman based qPCR detection method, detecting synthesized RNA equivalent to 10 copies of 2019-nCoV virus. Reaction time varied from 15-40 minutes, depending on the loading of virus in the collected samples. The accuracy, simplicity and versatility of the new developed method suggests that iLACO assays can be conveniently applied with for 2019-nCoV threat control, even in those cases where specialized molecular biology equipment is not available.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lin Yu", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + }, + { + "author_name": "Shanshan Wu", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + }, + { + "author_name": "Xiaowen Hao", + "author_inst": "Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, Ch" + }, + { + "author_name": "Xuelong Li", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + }, + { + "author_name": "Xiyang Liu", + "author_inst": "Biotech & Biomedicine Science Co. Ltd, Shenyang, 110000, China" + }, + { + "author_name": "Shenglong Ye", + "author_inst": "Biotech & Biomedicine Science Co. Ltd, Shenyang, 110000, China" + }, + { + "author_name": "Heng Han", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + }, + { + "author_name": "Xue Dong", + "author_inst": "Shenyang Center for Disease Control And Prevention, 110031, Shenyang, China" + }, + { + "author_name": "Xin Li", + "author_inst": "Shenyang Center for Disease Control And Prevention, 110031, Shenyang, Liaoning, China" + }, + { + "author_name": "Jiyao Li", + "author_inst": "Shenyang Center for Disease Control And Prevention, 110031, Shenyang, Liaoning, China" + }, + { + "author_name": "Jianmin Liu", + "author_inst": "Shenyang Center for Disease Control And Prevention, 110031, Shenyang, Liaoning, China" + }, + { + "author_name": "Na Liu", + "author_inst": "Shenyang Center for Disease Control And Prevention, 110031, Shenyang, Liaoning, China" + }, + { + "author_name": "Wanzhong Zhang", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + }, + { + "author_name": "Vicent Pelechano", + "author_inst": "MTC, Karolinska Institute, S-17177 Stockholm, Sweden" + }, + { + "author_name": "Wei-Hua Chen", + "author_inst": "Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, Ch" + }, + { + "author_name": "Xiushan Yin", + "author_inst": "Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.23.961912", "rel_title": "Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins and insights into coronavirus evolution", @@ -1596629,73 +1593200,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.20.20025841", - "rel_title": "Breadth of concomitant immune responses underpinning viral clearance and patient recovery in a non-severe case of COVID-19", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025841", - "rel_abs": "We report the kinetics of the immune response in relation to clinical and virological features of a patient with mild-to-moderate coronavirus disease-19 (COVID-19) requiring hospitalisation. Increased antibody-secreting cells, follicular T-helper cells, activated CD4+ and CD8+ T-cells and IgM/IgG SARS-CoV-2-binding antibodies were detected in blood, prior to symptomatic recovery. These immunological changes persisted for at least 7 days following full resolution of symptoms, indicating substantial anti-viral immunity in this non-severe COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Irani Thevarajan", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Thi HO Nguyen", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Marios Koutsakos", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Julian Druce", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Leon Caly", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Carolien E van de Sandt", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Xiaoxiao Jia", - "author_inst": "University of Melbourne/Doherty Institute" - }, - { - "author_name": "Suellen Nicholson", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Mike Catton", - "author_inst": "VIDRL/Doherty Institute" - }, - { - "author_name": "Benjamin Cowie", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Steven Tong", - "author_inst": "VIDS/Doherty Institute" - }, - { - "author_name": "Sharon Lewin", - "author_inst": "Doherty Institute" - }, - { - "author_name": "Katherine Kedzierska", - "author_inst": "University of Melbourne/Doherty Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.20.20025619", "rel_title": "Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China", @@ -1597315,6 +1593819,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.21.20026112", + "rel_title": "Epidemiological characteristics of 1212 COVID-19 patients in Henan, China", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026112", + "rel_abs": "Based on publicly released data for 1212 patients, we investigated the epidemiological characteristics of COVID-19 in Henan of China. The following findings are obtained: 1) COVID-19 patients in Henan show gender (55% vs 45%) and age (81% aged between 21 and 60) preferences, possible causes were explored; 2) Statistical analysis on 483 patients reveals that the estimated average, mode and median incubation periods are 7.4, 4 and 7 days; Incubation periods of 92% patients were no more than 14 days; 3) The epidemic of COVID-19 in Henan has undergone three stages and showed high correlations with the numbers of patients that recently return from Wuhan; 4) Network analysis on the aggregate outbreak phenomena of COVID-19 revealed that 208 cases were clustering infected, and various peoples Hospital are the main force in treating patients. The related investigations have potential implications for the prevention and control of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Pei Wang", + "author_inst": "Henan University" + }, + { + "author_name": "Junan Lu", + "author_inst": "Wuhan University" + }, + { + "author_name": "Yanyu Jin", + "author_inst": "Henan University" + }, + { + "author_name": "Mengfan Zhu", + "author_inst": "Zhongnan University of Economics and Law" + }, + { + "author_name": "Lingling Wang", + "author_inst": "Henan University" + }, + { + "author_name": "Shunjie Chen", + "author_inst": "Henan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.15.20023457", "rel_title": "Profiling ACE2 expression in colon tissue of healthy adults and colorectal cancer patients by single-cell transcriptome analysis", @@ -1598234,45 +1594777,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.02.19.956581", - "rel_title": "Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.19.956581", - "rel_abs": "The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike (S) glycoprotein trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2, establishing ACE2 as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Young-Jun Park", - "author_inst": "University of Washington" - }, - { - "author_name": "M. Alexandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Abigail Wall", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew T McGuire", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.02.19.957118", "rel_title": "Mucin 4 Protects Female Mice from Coronavirus Pathogenesis", @@ -1598845,6 +1595349,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.17.20024257", + "rel_title": "Tracking and Predicting COVID-19 Epidemic in China Mainland", + "rel_date": "2020-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.17.20024257", + "rel_abs": "By proposing a varying coefficient Susceptible-Infected-Removal model (vSIR), we track the epidemic of COVID-19 in 30 provinces in China and 15 cities in Hubei province, the epicenter of the outbreak. It is found that the spread of COVID-19 has been significantly slowing down within the two weeks from January 27 to February 10th with 87.0% and 84.3% reductions in the reproduction number R0 among the 30 provinces and 15 Hubei cities, respectively. This suggests the extreme control measures implemented since January 23, which include cutting off Wuhan and many other cities and towns, a great public awareness and high level of self isolation at home, have contributed to a substantial decline in the reproductivity of the COVID-19 in China. We predict that Hubei province will reach its peak between February 20 and 22, 2020, and if the removal rate can be increased to 0.1, the epidemic outside Hubei province will end in May 2020, and inside Hubei in early June.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Haoxuan Sun", + "author_inst": "Peking University" + }, + { + "author_name": "Yumou Qiu", + "author_inst": "Iowa State Univeristy" + }, + { + "author_name": "Han Yan", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yaxuan Huang", + "author_inst": "Peking University" + }, + { + "author_name": "Yuru Zhu", + "author_inst": "Peking University" + }, + { + "author_name": "Song Xi Chen", + "author_inst": "Guanghua School of Management and Center for Statistical Science, Peking University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.18.20023242", "rel_title": "Kidney impairment is associated with in-hospital death of COVID-19 patients", @@ -1599668,77 +1596211,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.02.13.945485", - "rel_title": "Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China", - "rel_date": "2020-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.13.945485", - "rel_abs": "The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, provisionally termed 2019-nCoV. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, the identity of any intermediate host facilitating transfer to humans is unknown. Here, we report the identification of 2019-nCoV related coronaviruses in pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin associated CoVs that belong to two sub-lineages of 2019-nCoV related coronaviruses, including one very closely related to 2019-nCoV in the receptor-binding domain. The discovery of multiple lineages of pangolin coronavirus and their similarity to 2019-nCoV suggests that pangolins should be considered as possible intermediate hosts for this novel human virus and should be removed from wet markets to prevent zoonotic transmission.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Tommy Tsan-Yuk Lam", - "author_inst": "The University of Hong Kong, Shantou University" - }, - { - "author_name": "Marcus Ho-Hin Shum", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hua-Chen Zhu", - "author_inst": "The University of Hong Kong, Shantou University" - }, - { - "author_name": "Yi-Gang Tong", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Xue-Bing Ni", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yun-Shi Liao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wei Wei", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "William Yiu-Man Cheung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wen-Juan Li", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Lian-Feng Li", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Gabriel M Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Yan-Ling Hu", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Yi Guan", - "author_inst": "The University of Hong Kong, Shantou University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.10.942748", "rel_title": "Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus", @@ -1600111,6 +1596583,213 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.16.20023671", + "rel_title": "Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients", + "rel_date": "2020-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.16.20023671", + "rel_abs": "BackgroundThe dynamic changes of lymphocyte subsets and cytokines profiles of patients with novel coronavirus disease (COVID-19) and their correlation with the disease severity remain unclear.\n\nMethodsPeripheral blood samples were longitudinally collected from 40 confirmed COVID-19 patients and examined for lymphocyte subsets by flow cytometry and cytokine profiles by specific immunoassays.\n\nResultsOf the 40 COVID-19 patients enrolled, 13 severe cases showed significant and sustained decreases in lymphocyte counts but increases in neutrophil counts than 27 mild cases. Further analysis demonstrated significant decreases in the counts of T cells, especially CD8 + T cells, as well as increases in IL-6, IL-10, IL-2 and IFN-{gamma} levels in the peripheral blood in the severe cases compared to those in the mild cases. T cell counts and cytokine levels in severe COVID-19 patients who survived the disease gradually recovered at later time points to levels that were comparable to those of the mild cases. Moreover, the neutrophil-to-CD8+ T cell ratio (N8R) were identified as the most powerful prognostic factor affecting the prognosis for severe COVID-19.\n\nConclusionsThe degree of lymphopenia and a proinflammatory cytokine storm is higher in severe COVID-19 patients than in mild cases, and is associated with the disease severity. N8R may serve as a useful prognostic factor for early identification of severe COVID-19 cases.\n\nSummaryLymphocyte subsets and cytokine profiles in the peripheral blood of COVID-19 patients were longitudinally characterized. The study revealed the kinetics features of immune parameters associated with the disease severity and identified N8R as a useful prognostic factor for predicting severe COVID-19 cases.", + "rel_num_authors": 48, + "rel_authors": [ + { + "author_name": "Jing Liu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Sumeng Li", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jia Liu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Boyun Liang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Xiaobei Wang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Hua Wang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Wei Li", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Qiaoxia Tong", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jianhua Yi", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Lei Zhao", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Lijuan Xiong", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Chunxia Guo", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jin Tian", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jinzhuo Luo", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jinghong Yao", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ran Pang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Hui Shen", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Cheng Peng", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ting Liu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Qian Zhang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jun Wu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ling Xu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Sihong Lu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Baoju Wang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Zhihong Weng", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Chunrong Han", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Huabing Zhu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ruxia Zhou", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Helong Zhou", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Xiliu Chen", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Pian Ye", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Bin Zhu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Shengsong He", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Yongwen He", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Shenghua Jie", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ping Wei", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jianao Zhang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Yinping Lu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Weixian Wang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Li Zhang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Ling Li", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Fengqin Zhou", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Jun Wang", + "author_inst": "University Hospital of Essen" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "University Hospital of Essen" + }, + { + "author_name": "Mengji Lu", + "author_inst": "University Hospital of Essen" + }, + { + "author_name": "Yu Hu", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Dongliang Yang", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Xin Zheng", + "author_inst": "Wuhan Union Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.16.20023838", "rel_title": "Risk map of the novel coronavirus (2019-nCoV) in China: proportionate control is needed", @@ -1600842,37 +1597521,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.13.20022707", - "rel_title": "Estimating underdetection of internationally imported COVID-19 cases", - "rel_date": "2020-02-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.13.20022707", - "rel_abs": "Risk of COVID-19 infection in Wuhan has been estimated using imported case counts of international travelers, often under the assumption that all cases in travelers are ascertained. Recent work indicates variation among countries in detection capacity for imported cases. Singapore has historically had very strong epidemiological surveillance and contact-tracing capacity and has shown in the COVID-19 epidemic evidence of a high sensitivity of case detection. We therefore used a Bayesian modeling approach to estimate the relative imported case detection capacity for other countries compared to that of Singapore.We estimate that the global ability to detect imported cases is 38% (95% HPDI 22% - 64%) of Singapores capacity. Equivalently, an estimate of 2.8 (95% HPDI 1.5 - 4.4) times the current number of imported cases, could have been detected, if all countries had had the same detection capacity as Singapore. Using the second component of the Global Health Security index to stratify likely case-detection capacities, we found that the ability to detect imported cases relative to Singapore among high surveillance locations is 40% (95% HPDI 22% - 67%), among intermediate surveillance locations it is 37% (95% HPDI 18% - 68%), and among low surveillance locations it is 11% (95% HPDI 0% - 42%). Using a simple mathematical model, we further find that treating all travelers as if they were residents (rather than accounting for the brief stay of some of these travelers in Wuhan) can modestly contribute to underestimation of prevalence as well. We conclude that estimates of case counts in Wuhan based on assumptions of perfect detection in travelers may be underestimated by several fold, and severity correspondingly overestimated by several fold. Undetected cases are likely in countries around the world, with greater risk in countries of low detection capacity and high connectivity to the epicenter of the outbreak.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rene Niehus", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Pablo M De Salazar", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Aimee Taylor", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.13.20022251", "rel_title": "Understanding the present status and forecasting of COVID-19 in Wuhan", @@ -1601297,6 +1597945,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.12.20022327", + "rel_title": "Clinical diagnosis of 8274 samples with 2019-novel coronavirus in Wuhan", + "rel_date": "2020-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.12.20022327", + "rel_abs": "Background2019-Novel coronavirus (2019-nCoV) outbreaks create challenges for hospital laboratories because thousands of samples must be evaluated each day. Sample types, interpretation methods, and corresponding laboratory standards must be established. The possibility of other infections should be assessed to provide a basis for clinical classification, isolation, and treatment. Accordingly, in the present study, we evaluated the testing methods for 2019-nCoV and co-infections.\n\nMethodsWe used a fluorescence-based quantitative PCR kit urgently distributed by the Chinese CDC to detect 8274 close contacts in the Wuhan region against two loci on the 2019-nCoV genome. We also analyzed 613 patients with fever who underwent multiple tests for 13 respiratory pathogens; 316 subjects were also tested for 2019-nCoV.\n\nFindingsAmong the 8274 subjects, 2745 (33.2%) had 2019-nCoV infection; 5277 (63.8%) subjects showed negative results in the 2019-nCoV nucleic acid test (non-2019-nCoV); and 252 cases (3.0%) because only one target was positive, the diagnosis was not definitive. Eleven patients who originally had only one positive target were re-examined a few days later; 9 patients (81.8%) were finally defined as 2019-nCoV-positive, and 2 (18.2%) were finally defined as negative. The positive rates of nCoV-NP and nCovORF1ab were 34.7% and 34.7%, respectively. nCoV-NP-positive only and nCovORF1ab-positive cases accounted for 1.5% and 1.5%, respectively. In the 316 patients with multiple respiratory pathogens, 104 were positive for 2019-nCov and 6/104 had co-infection with coronavirus (3/104), influenza A virus (2/104), rhinovirus (2/104), and influenza A H3N2 (1/104); the remaining 212 patients had influenza A virus (11/202), influenza A H3N2 (11/202), rhinovirus (10/202), respiratory syncytial virus (7/202), influenza B virus (6/202), metapneumovirus (4/202), and coronavirus (2/202).\n\nInterpretationClinical testing methods for 2019-nCoV require improvement. Importantly, 5.8% of 2019-nCoV infected and 18.4% of non-2019-nCoV-infected patients had other pathogen infections. It is important to treat combined infections and perform rapid screening to avoid cross-contamination of patients. A test that quickly and simultaneously screens as many pathogens as possible is needed.\n\nFundingNo founding was received\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for articles published up to January 31, 2020 using the keywords \"2019 novel coronavirus\" or \"2019-nCoV\". No published study on the characteristics of 2019-nCoV tests or 2019-nCoV co-infections was found. We only noted recent laboratory findings for other tests of patients infected with 2019-nCoV.\n\nAdded value of this studyPositive detection of nCoV-NP or nCovORF1ab is presented, and individuals with/without 2019-nCoV infections or with inconclusive results were identified. Patients with inconclusive results may be diagnosed with 2019-nCoV infection or found to be negative for the infection after resampling and retesting in the next few days. Approximately 5.8% of the subjects diagnosed with 2019-nCoV had co-infection.\n\nImplications of all the available evidenceManagement of the population showing inconclusive results should be given attention; additionally, such results can be minimized by improving the sampling, sample pretreatment, and testing methodologies. When diagnosing 2019-nCoV subjects, the possibility of co-infection should be considered. Finally, better clinical detection methods are needed to simultaneously screen as many pathogens as possible.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Ming Wang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Qing Wu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Wanzhou Xu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Bin Qiao", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Jingwei Wang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Hongyun Zheng", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Shupeng Jiang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Junchi Mei", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zegang Wu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yayun Deng", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Fangyuan Zhou", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Wei Wu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yan Zhang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zhihua Lv", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Jingtao Huang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Xiaoqian Guo", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Lina Feng", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zunen Xia", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Di Li", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zhiliang Xu", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Tiangang Liu", + "author_inst": "Wuhan University" + }, + { + "author_name": "Pingan Zhang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yongqing Tong", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yan Li", + "author_inst": "Renmin Hospital of Wuhan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.12.20022434", "rel_title": "Early epidemiological assessment of the transmission potential and virulence of 2019 Novel Coronavirus in Wuhan City: China, 2019-2020", @@ -1602096,121 +1598855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.08.20021212", - "rel_title": "Caution on Kidney Dysfunctions of 2019-nCoV Patients", - "rel_date": "2020-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.08.20021212", - "rel_abs": "BackgroundTo date, large amounts of epidemiological and case study data have been available for the Coronavirus Disease 2019 (COVID-19), which suggested that the mortality was related to not just respiratory complications. Here, we specifically analyzed kidney functions in COVID-19 patients and their relations to mortality.\n\nMethodIn this multi-centered, retrospective, observational study, we included 193 adult patients with laboratory-confirmed COVID-19 from 2 hospitals in Wuhan, 1 hospital in Huangshi (Hubei province, 83 km from Wuhan) and 1 hospital in Chongqing (754 km from Wuhan). Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected, including data regarding to kidney functions. Data were compared among three groups: non-severe COVID-19 patients (128), severe COVID-19 patients (65) and a control group of other pneumonia (28). For the data from computed tomographic (CT) scans, we also included a control group of healthy subjects (110 cases, without abnormalities in the lung and without kidney diseases). The primary outcome was a common presence of kidney dysfunctions in COVID-19 patients and the occurrence of acute kidney injury (AKI) in a fraction of COVID-19 patients. Secondary outcomes included a survival analysis of COVID-19 patients in conditions of AKI or comorbid chronic illnesses.\n\nFindingsWe included 193 COVID-19 patients (128 non-severe, 65 severe (including 32 non-survivors), between January 6th and February 21th,2020; the final date of follow-up was March 4th, 2020) and 28 patients of other pneumonia (15 of viral pneumonia, 13 of mycoplasma pneumonia) before the COVID-19 outbreak. On hospitaladmission, a remarkable fraction of patients had signs of kidney dysfunctions, including 59% with proteinuria, 44% with hematuria, 14% with increased levels of blood urea nitrogen, and 10% with increased levels of serum creatinine, although mild but worse than that in cases with other pneumonia. While these kidney dysfunctions might not be readily diagnosed as AKI at admission, over the progress during hospitalization they could be gradually worsened and diagnosed as AKI. A univariate Cox regression analysis showed that proteinuria, hematuria, and elevated levels of blood urea nitrogen, serum creatinine, uric acid as well as D-dimer were significantly associated with the death of COVID-19 patients respectively. Importantly, the Cox regression analysis also suggested that COVID-19 patients that developed AKI had a [~]5.3-times mortality risk of those without AKI, much higher than that of comorbid chronic illnesses ([~]1.5 times risk of those without comorbid chronic illnesses).\n\nInterpretationTo prevent fatality in such conditions, we suggested a high degree of caution in monitoring the kidney functions of severe COVID-19 patients regardless of the past disease history. In addition, upon day-by-day monitoring, clinicians should consider any potential interventions to protect kidney functions at the early stage of the disease and renal replacement therapies in severely ill patients, particularly for those with strong inflammatory reactions or a cytokine storm.\n\nFundingNone.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "- Anti-2019-nCoV Volunteers", - "author_inst": "-" - }, - { - "author_name": "Zhen Li", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China" - }, - { - "author_name": "Ming Wu", - "author_inst": "Department of Critical Care Medicine, the General Hospital of Central Theater Command and Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan " - }, - { - "author_name": "Jiwei Yao", - "author_inst": "Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Jie Guo", - "author_inst": "Department of Gastrointestinal Endoscopy, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi 43500" - }, - { - "author_name": "Xiang Liao", - "author_inst": "Center for Neurointelligence, Chongqing University, Chongqing 400030, China." - }, - { - "author_name": "Siji Song", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Jiali Li", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China." - }, - { - "author_name": "Guangjie Duan", - "author_inst": "Department of Pathology, Southwest Hospital, Third Military Medical University, Chongqing 400038,China." - }, - { - "author_name": "Yuanxiu Zhou", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Xiaojun Wu", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Zhansong Zhou", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Taojiao Wang", - "author_inst": "Department of Otolaryngology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi 435000, China." - }, - { - "author_name": "Ming Hu", - "author_inst": "Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan 430030, China." - }, - { - "author_name": "Xianxiang Chen", - "author_inst": "Department of Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan 430030, China." - }, - { - "author_name": "Yu Fu", - "author_inst": "Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597 and Singapore Bioimaging Consortium, Agency for Sc" - }, - { - "author_name": "Chong Lei", - "author_inst": "Department of Anesthesiology and Perioprative Medicine, Xijing Hospital, Fourth Military Medical University, Xi an 710032, China." - }, - { - "author_name": "Hailong Dong", - "author_inst": "Department of Anesthesiology and Perioprative Medicine, Xijing Hospital, Fourth Military Medical University, Xi an 710032, China." - }, - { - "author_name": "Chuou Xu", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan 430030, China" - }, - { - "author_name": "Yahua Hu", - "author_inst": "Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, 435000, China." - }, - { - "author_name": "Min Han", - "author_inst": "Division of Nephrology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China." - }, - { - "author_name": "Yi Zhou", - "author_inst": "Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Hongbo Jia", - "author_inst": "Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Xiaowei Chen", - "author_inst": "Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing 400038, China." - }, - { - "author_name": "Junan Yan", - "author_inst": "Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.05.20020107", "rel_title": "Tobacco-use disparity in gene expression of ACE2, the receptor of 2019-nCov", @@ -1602671,6 +1599315,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.09.20021444", + "rel_title": "EPIDEMIC TRENDS ANALYSIS AND RISK ESTIMATION OF 2019-NCOV OUTBREAK", + "rel_date": "2020-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.09.20021444", + "rel_abs": "Since December 1, 2019, the spread of COVID-19 is increasing every day. It is particularly important to predict the trend of the epidemic for the timely adjustment of the economy and industries. We proposed a Flow-SEHIR model in this paper to perform the trends of 2019-nCoV (COVID-19) in China.\n\nThe results show that the number of daily confirmed new cases reaches the inflection point on Feb. 6 - 10 outside Hubei. For the maximum of temporal infected cases number, the predicted peak value in China except Hubei was estimated to be 21721 (95% CI: 18764 - 24929). The peak arrival time is on March 3 - 9. The temporal number of patients in most areas of China outside Hubei will peak from March 12 to March 15. The peak values of more than 73.5% provinces or regions in China will be controlled within 1000. According to Flow-SEHIR model and estimations from the data of evacuation of nationals from Wuhan, the real peak cumulative number of patients in Hubei is estimated to be 403481 (95% CI: 143284 - 1166936).", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Deqiang Li", + "author_inst": "Southeast University" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.07.939124", "rel_title": "Exploring the coronavirus epidemic using the new WashU Virus Genome Browser", @@ -1603846,41 +1600533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.04.20020495", - "rel_title": "Using predicted imports of 2019-nCoV cases to determine locations that may not be identifying all imported cases", - "rel_date": "2020-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.04.20020495", - "rel_abs": "Cases from the ongoing outbreak of atypical pneumonia caused by the 2019 novel coronavirus (2019-nCoV) exported from mainland China can lead to self-sustained outbreaks in other populations. Internationally imported cases are currently being reported in several different locations. Early detection of imported cases is critical for containment of the virus. Based on air travel volume estimates from Wuhan to international destinations and using a generalized linear regression model we identify locations which may potentially have undetected internationally imported cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Pablo M De Salazar", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rene Niehus", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Aimee Taylor", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caroline O Buckee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.04.20020503", "rel_title": "Risk assessment of novel coronavirus 2019-nCoVoutbreaks outside China", @@ -1604445,6 +1601097,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.02.20020016", + "rel_title": "The incubation period of 2019-nCoV from publicly reported confirmed cases: estimation and application", + "rel_date": "2020-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.02.20020016", + "rel_abs": "A novel human coronavirus (2019-nCoV) was identified in China in December, 2019. There is limited support for many of its key epidemiologic features, including the incubation period, which has important implications for surveillance and control activities. Here, we use data from public reports of 101 confirmed cases in 38 provinces, regions, and countries outside of Wuhan (Hubei province, China) with identifiable exposure windows and known dates of symptom onset to estimate the incubation period of 2019-nCoV. We estimate the median incubation period of 2019-nCoV to be 5.2 days (95% CI: 4.4, 6.0), and 97.5% of those who develop symptoms will do so within 10.5 days (95% CI: 7.3, 15.3) of infection. These estimates imply that, under conservative assumptions, 64 out of every 10,000 cases will develop symptoms after 14 days of active monitoring or quarantine. Whether this risk is acceptable depends on the underlying risk of infection and consequences of missed cases. The estimates presented here can be used to inform policy in multiple contexts based on these judgments.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Stephen A Lauer", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Kyra H Grantz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Qifang Bi", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Forrest K Jones", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Qulu Zheng", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Hannah Meredith", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Andrew S Azman", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts, Amherst" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.02.931162", "rel_title": "Phylogenomic analysis of the 2019-nCoV coronavirus", @@ -1605132,49 +1601835,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.01.929976", - "rel_title": "Potent neutralization of 2019 novel coronavirus by recombinant ACE2-Ig", - "rel_date": "2020-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.01.929976", - "rel_abs": "2019-nCoV, which is a novel coronavirus emerged in Wuhan, China, at the end of 2019, has caused at least infected 11,844 as of Feb 1, 2020. However, there is no specific antiviral treatment or vaccine currently. Very recently report had suggested that novel CoV would use the same cell entry receptor, ACE2, as the SARS-CoV. In this report, we generated a novel recombinant protein by connecting the extracellular domain of human ACE2 to the Fc region of the human immunoglobulin IgG1. An ACE2 mutant with low catalytic activity was also used in the study. The fusion proteins were then characterized. Both fusion proteins has high affinity binding to the receptor-binding domain (RBD) of SARS-CoV and 2019-nCoV and exerted desired pharmacological properties. Moreover, fusion proteins potently neutralized SARS-CoV and 2019-nCoV in vitro. As these fusion proteins exhibit cross-reactivity against coronaviruses, they could have potential applications for diagnosis, prophylaxis, and treatment of 2019-nCoV.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Changhai Lei", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Wenyan Fu", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Kewen Qian", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Tian Li", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Sheng Zhang", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Min Ding", - "author_inst": "Pharchoice Therapeutics Inc" - }, - { - "author_name": "Shi Hu", - "author_inst": "Second Militarily Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.01.31.929497", "rel_title": "Highly Distinguished Amino Acid Sequences of 2019-nCoV (Wuhan Coronavirus)", @@ -1605635,6 +1602295,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.01.26.20018754", + "rel_title": "Epidemiological characteristics of novel coronavirus infection: A statistical analysis of publicly available case data", + "rel_date": "2020-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.26.20018754", + "rel_abs": "The geographic spread of 2019 novel coronavirus (COVID-19) infections from the epicenter of Wuhan, China, has provided an opportunity to study the natural history of the recently emerged virus. Using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of COVID-19 infections. Our results show that the incubation period falls within the range of 2-14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. The mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3-4 days without truncation and at 5-9 days when right truncated. Based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. The median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the COVID-19 case fatality risk.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Natalie M. Linton", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Tetsuro Kobayashi", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yichi Yang", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Katsuma Hayashi", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Andrei R. Akhmetzhanov", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Sung-mok Jung", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Baoyin Yuan", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Ryo Kinoshita", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hiroshi Nishiura", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.01.26.20018887", "rel_title": "Epidemiological identification of a novel infectious disease in real time: Analysis of the atypical pneumonia outbreak in Wuhan, China, 2019-20", @@ -1606357,65 +1603068,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.01.23.916395", - "rel_title": "Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak", - "rel_date": "2020-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.23.916395", - "rel_abs": "BackgroundsAn ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number, R0, of 2019-nCoV in the early phase of the outbreak.\n\nMethodsAccounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate ({gamma}), we estimated R0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI.\n\nFindingsThe early outbreak data largely follows the exponential growth. We estimated that the mean R0 ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R0.\n\nConclusionThe mean estimate of R0 for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Shi Zhao", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Qianying Lin", - "author_inst": "Michigan Institute for Data Science, University of Michigan, Ann Arbor, Michigan, USA" - }, - { - "author_name": "Jinjun Ran", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" - }, - { - "author_name": "Salihu Sabiu MUSA", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Guangpu Yang", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Weiming Wang", - "author_inst": "Huaiyin Normal University" - }, - { - "author_name": "Yijun Lou", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Daozhou Gao", - "author_inst": "Shanghai Normal University, Shanghai, China" - }, - { - "author_name": "Lin Yang", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Maggie H Wang", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2020.01.23.917351", "rel_title": "Pattern of early human-to-human transmission of Wuhan 2019-nCoV",